-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathmobio-base.owl
3265 lines (2312 loc) · 178 KB
/
mobio-base.owl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/mobio/mobio-base.owl#"
xml:base="http://purl.obolibrary.org/obo/mobio/mobio-base.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mobio/mobio-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mobio/releases/2023-04-13/mobio-base.owl"/>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:description>None</terms:description>
<terms:license rdf:resource="https://creativecommons.org/licenses/unspecified"/>
<terms:title>Mobilome Ontology</terms:title>
<owl:versionInfo>2023-04-13</owl:versionInfo>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<rdfs:label>definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/type -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
<!-- http://purl.org/dc/terms/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description"/>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
<!-- http://purl.org/dc/terms/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label>database_cross_reference</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
<rdfs:label>has_exact_synonym</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#id -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
<!-- http://www.w3.org/2000/01/rdf-schema#label -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<!-- http://xmlns.com/foaf/0.1/mbox -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/mbox"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<oboInOwl:hasDbXref>RO:part_of</oboInOwl:hasDbXref>
<rdfs:label>part_of</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000056 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000056">
<oboInOwl:hasDbXref>RO:participates_in</oboInOwl:hasDbXref>
<rdfs:label>participates_in</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0002211 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002211">
<oboInOwl:hasDbXref>RO:regulates</oboInOwl:hasDbXref>
<rdfs:label>regulates</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
<!-- http://purl.obolibrary.org/obo/BFO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000030"/>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000030"/>
<obo:IAO_0000115>Mobile genetic elements (MGEs) are a type of genetic material, a segment of DNA or RNA, that is capable of movement around a genome or that can be transferred from one species or replicon to another. These include transposons, plasmids, bacteriophages, and genomic islands. The mechanism of movement may be self-encoded or may rely on other enzymes and structures, such as a pilus. In bacteria, MGEs are often associated with the movement of antibiotic resistance genes and virulence factors from one species to another, for example by plasmid-mediated transfer.</obo:IAO_0000115>
<rdfs:label>mobile genetic element</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000001"/>
<obo:IAO_0000115>A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. Plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance. Plasmids have a wide range of lengths, from roughly one thousand DNA base pairs to hundreds of thousands of base pairs.</obo:IAO_0000115>
<rdfs:label>plasmid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000001"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the same genetic material. Transposons were originally discovered as "jumping genes" by Barbara McClintock.</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>transposon</oboInOwl:hasExactSynonym>
<rdfs:label>transposable element</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000001"/>
<obo:IAO_0000115>Bacteriophage are viral infectious agents with bacterial host organisms. Bacteriophage infect and replicate inside bacterial host cells, causing cell lysis as viral particles replicate. Bacteriophage are involved in DNA transfer between host organisms at low frequency through transduction: when segments of host DNA is accidentally packaged with the viral DNA, then integrated into a new host genome and later inherited.</obo:IAO_0000115>
<rdfs:label>bacteriophage</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000006 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000006">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
<obo:IAO_0000115>These plasmids contain genes that code for bacteriocins, proteins that can kill other bacteria.</obo:IAO_0000115>
<rdfs:label>Col Plasmids</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
<obo:IAO_0000115>Fertility F-plasmids contain tra genes and are capable of conjugation resulting in the expression of sex pilli.</obo:IAO_0000115>
<rdfs:label>Fertility F-Plasmids</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000008 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000008">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
<obo:IAO_0000115>These plasmids contain genes that provide resistance against antibiotics or poisons. Historically known as R-factors, before the nature of plasmids was understood.</obo:IAO_0000115>
<rdfs:label>Resistance Plasmids</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000009">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
<obo:IAO_0000115>These plasmids enable the digestion of unusual substances, e.g. toluene and salicylic acid.</obo:IAO_0000115>
<rdfs:label>Degradative Plasmids</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
<obo:IAO_0000115>which turn the bacterium into a pathogen</obo:IAO_0000115>
<rdfs:label>Virulence Plasmids</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>The set of specific processes that needed for plasmid partition, stability, replication, and mobility. These are all processes that allow for the plasmid to move between organisms.</obo:IAO_0000115>
<rdfs:label>mechanism of plasmid maintenance</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000012 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000012">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000011"/>
<obo:IAO_0000115>Any process or set of processes through which plasmid replication is initiated.</obo:IAO_0000115>
<rdfs:label>mechanism of replication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000012"/>
<obo:IAO_0000115>Replication by the Theta Mechanism - opening of the strands followed by RNA priming</obo:IAO_0000115>
<rdfs:label>theta type</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000014">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000012"/>
<obo:IAO_0000115>strand displacement replication. Opening of the strands followed by RNA priming</obo:IAO_0000115>
<rdfs:label>strand displacement</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000012"/>
<obo:IAO_0000115>A mechanism of plasmid replication in which the two strands are asynchronously copied, with one strand initially forming a single-stranded circle.</obo:IAO_0000115>
<rdfs:label>rolling circle replication</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>Molecular mechanisms involved in the intracellular and intercellular transfer, integration, stabilization and recombination of mobile genetic elements.</obo:IAO_0000115>
<rdfs:label>process or mechanism of genetic mobility</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000196"/>
<obo:IAO_0000115>Conjugation is the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient.</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>Conjugation</oboInOwl:hasExactSynonym>
<rdfs:label>conjugative transfer</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000011"/>
<obo:IAO_0000115>Stabilization mechanisms facilitate and promote the survival of plasmids in their host cells. This includes mechanisms that allow for the survival of the host cell itself in harsh conditions.</obo:IAO_0000115>
<rdfs:label>mechanism of stabilization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000016"/>
<obo:IAO_0000115>Transformation refers to process of free DNA uptake by competent cells and subsequent integration and functional expression of genes. Extracellular DNA continually enters the environment upon release from decomposing cells, disrupted cells, viral particles or excretion from living cells.</obo:IAO_0000115>
<rdfs:label>transformation</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000021 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000021">
<obo:IAO_0000115>A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable anti-toxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).</obo:IAO_0000115>
<rdfs:label>Toxin-antitoxin system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000021"/>
<obo:IAO_0000115>Type I toxin-antitoxin systems rely on the base-pairing of complementary antitoxin RNA with the toxin's mRNA. Translation of the mRNA is then inhibited either by degradation via RNase III or by occluding the Shine-Dalgarno sequence or ribosome binding site.</obo:IAO_0000115>
<rdfs:label>Type I TA System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000021"/>
<obo:IAO_0000115>In this system a labile protein antitoxin tightly binds and inhibits the activity of a stable toxin. Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression.</obo:IAO_0000115>
<rdfs:label>Type II TA System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000024 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000021"/>
<obo:IAO_0000115>Type III toxin-antitoxin systems rely on direct interaction between a toxic protein and an RNA antitoxin. The toxic effects of the protein are neutralised by the RNA gene.</obo:IAO_0000115>
<rdfs:label>Type III TA System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000025 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000025">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000185"/>
<obo:IAO_0000115>The process of conjugation requires several different types of subunits and complexes.</obo:IAO_0000115>
<rdfs:label>conjugal transfer subunit or complex</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000025"/>
<obo:IAO_0000115>Protein involved in the conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.</obo:IAO_0000115>
<rdfs:label>pilX7</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000026"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Protein involved in the conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:19717626</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000025"/>
<obo:IAO_0000115>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.</obo:IAO_0000115>
<rdfs:label>pilX8</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000027"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:19717626</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000028 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000028">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000188"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000006"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Colicin immunity proteins are plasmid encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress</obo:IAO_0000115>
<rdfs:label>colicin immunity protein</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000025"/>
<obo:IAO_0000115>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.
</obo:IAO_0000115>
<rdfs:label>pilX9</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000029"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli.
</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:19717626</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000025"/>
<obo:IAO_0000115>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to type IV secretory pathway VirB10 protein</obo:IAO_0000115>
<rdfs:label>pilX10</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000030"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to type IV secretory pathway VirB10 protein</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:19717626</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000025"/>
<obo:IAO_0000115>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to P-type DNA transfer ATPase VirB11.</obo:IAO_0000115>
<rdfs:label>pilX11</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000031"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Protein involved in conjugal transfer of DNA. First identified in conjugative plasmid R6K of E. coli. It is homologous to P-type DNA transfer ATPase VirB11.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:19717626</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000032">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000181"/>
<obo:IAO_0000115>conjugal transfer protein - conjugal transfer protein TraG</obo:IAO_0000115>
<rdfs:label>taxB</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000032"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>conjugal transfer protein - conjugal transfer protein TraG</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000051"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000123"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits. In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon. Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability. Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity.</obo:IAO_0000115>
<rdfs:label>RelE</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000033"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific, ribosome-dependent mRNA endoribonuclease that inhibits translation during amino acid starvation (the stringent response). In vitro acts by cleaving mRNA with high codon specificity in the ribosomal A site between positions 2 and 3. The stop codon UAG is cleaved at a fast rate while UAA and UGA are cleaved with intermediate and slow rates. In vitro mRNA cleavage can also occur in the ribosomal E site after peptide release from peptidyl-tRNA in the P site as well as on free 30S subunits. In vivo cuts frequently in the first 100 codons, most frequently after the second and third base and rarely near the stop codon. Overexpression of RelE results in the inhibition of bacterial growth and a sharp decrease in colony-forming ability which is neutralized by the labile cognate antitoxin RelB. Overexpression also sharply increases persisters (cells that neither grow nor die in the presence of bactericidal agents and are largely responsible for high levels of biofilm tolerance to antimicrobials). Plays a role in dormancy when expressed in high-density cells in the absence of antitoxin RelB; amino acid starvation and an unidentified extracellular factor promote dormancy, while expression of antitoxin RelB restores cell culturability. Acts with RelB as a corepressor of relBE transcription, considerably increasing the repression of RelB alone. 2 RelB dimers bind to 2 operator sequences; DNA-binding and repression is stronger when complexed with toxin/corepressor RelE by conditional cooperativity.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:12526800</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:15576765</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:21324908</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:22210768</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:9767574</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000187"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000014"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000015"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Topoisomerases are enzymes that participate in the overwinding or underwinding of DNA. They bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA strands. </obo:IAO_0000115>
<rdfs:label>DNA topoisomerase</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000035 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000034"/>
<obo:IAO_0000115>The traE gene, first identified in plasmid RP4, is a homologue of E. coli DNA topoisomerase III.</obo:IAO_0000115>
<rdfs:label>traE</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000035"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>The traE gene, first identified in plasmid RP4, is a homologue of E. coli DNA topoisomerase III.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000187"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000015"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Molecular chaperones are proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures. Chaperones are present when the macromolecules perform their normal biological functions and have correctly completed the processes of folding and/or assembly. The chaperones are concerned primarily with protein folding. One major function of chaperones is to prevent both newly synthesized polypeptide chains and assembled subunits from aggregating into nonfunctional structures. Many chaperones are heat shock proteins because the tendency to aggregate increases as proteins are denatured by stress.
Molecular chaperones have been shown to be involved in both the assembly and disassembly of DNA replication complexes.</obo:IAO_0000115>
<rdfs:label>Molecular Chaperone</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000037 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000037">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000036"/>
<obo:IAO_0000115>Chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. The J domain of DnaJ interacts with Hsp70 heat shock proteins. DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins.</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>Hsp40</oboInOwl:hasExactSynonym>
<rdfs:label>DnaJ</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000037"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. The J domain of DnaJ interacts with Hsp70 heat shock proteins. DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18375554</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000038 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000038">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000190"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000003"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Class 2 transposons encode transposase, which is an enzyme that binds to the end of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism.
</obo:IAO_0000115>
<rdfs:label>transposase</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000039 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000039">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000046"/>
<obo:IAO_0000115>This protein is a specific topoisomerase involved in initiating replication. This protein is specifically required and may be rate-limiting for replication of the plasmid in vivo.
</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>repC</oboInOwl:hasExactSynonym>
<rdfs:label>replication initiation protein RepC</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000188"/>
<obo:IAO_0000115>These proteins reduce chromate accumulation and are essential for chromate resistance. They are composed of one or two copies of this region. The short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm, while the long chain CHR proteins appear to have arisen from a gene fusion event of two short chain transporters</obo:IAO_0000115>
<rdfs:label>Chromate transport protein</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000041 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000041">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000187"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000014"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000015"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Dihydrofolate reductase converts dihydrofolate into tetrahydrofolate, a methyl group shuttle required for the de novo synthesis of purines, thymidylic acid, and certain amino acids.</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>DfrA</oboInOwl:hasExactSynonym>
<rdfs:label>Dihydrofolate reductase</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000042 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000042">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000104"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000043"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Class 1 Integrase is a site-specific recombination enzyme that is part of the class 1 integron system. It recognizes the recombination site, attI1, which is where it will catalyze the insertion of gene casettes.</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>Intl1</oboInOwl:hasExactSynonym>
<rdfs:label>Class 1 Integrase</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000042"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Class 1 Integrase is a site-specific recombination enzyme that is part of the class 1 integron system. It recognizes the recombination site, attI1, which is where it will catalyze the insertion of gene casettes.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:18193080</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>PMID:8574395</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000043 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000043">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000001"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000002"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000003"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Integrons are genetic mechanisms that allow bacteria to adapt and evolve rapidly through the acquisition, stockpiling and differential expression of new genes. Additionally, an integron will usually contain one or more gene cassettes that have been incorporated into it.</obo:IAO_0000115>
<rdfs:label>integron</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000044 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000044">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000045"/>
<obo:IAO_0000115>DNA-binding transcriptional regulator. Protein that is involved in negative regulation of phenolic acid metabolism.</obo:IAO_0000115>
<rdfs:label>PadR family transcriptional regulator</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000045 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000045">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000190"/>
<obo:IAO_0000115>transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity.</obo:IAO_0000115>
<rdfs:label>transcriptional regulator of operons found in MGEs</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000046 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000046">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000187"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000013"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000014"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000015"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>protein required for initiation of replication</obo:IAO_0000115>
<rdfs:label>replication initiation protein</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000047 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000047">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000046"/>
<obo:IAO_0000115>This protein is essential for plasmid replication; it is involved in copy control functions</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>RepA</oboInOwl:hasExactSynonym>
<rdfs:label>replication initiation protein RepA</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000048 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000048">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000025"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000017"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>papB may act as both positive and negative regulator of the pyelonephritis-associated pili (pap) pilin gene transcription. It is found in the pap operon.</obo:IAO_0000115>
<rdfs:label>Major pili subunit operon regulatory protein papB</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000049 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000023"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. </obo:IAO_0000115>
<oboInOwl:hasExactSynonym>antitoxin</oboInOwl:hasExactSynonym>
<rdfs:label>Type II post-segregation antitoxin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000050 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000050">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000045"/>
<obo:IAO_0000115>transcriptional regulator</obo:IAO_0000115>
<rdfs:label>C protein</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000051 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000051">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000191"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000023"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin. The antitoxin inhibits the toxin by downregulating its expression. </obo:IAO_0000115>
<rdfs:label>Type II toxin</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000052 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000052">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000049"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000079"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Labile antitoxin with a half-life of about 1 hour in the presence of CcdB. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. The N-terminal 36 residues are not required for rejuventation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB.</obo:IAO_0000115>
<rdfs:label>CcdA</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000052"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Labile antitoxin with a half-life of about 1 hour in the presence of CcdB. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. The N-terminal 36 residues are not required for rejuventation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB.</owl:annotatedTarget>
<oboInOwl:hasDbXref>PMID:27357537</oboInOwl:hasDbXref>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000053 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000053">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000051"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000079"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.</obo:IAO_0000115>
<rdfs:label>CcdB</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000054 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000054">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000046"/>
<obo:IAO_0000115>Replication initiator in the monomeric form, and autogenous repressor in the dimeric form.</obo:IAO_0000115>
<oboInOwl:hasExactSynonym>RepE</oboInOwl:hasExactSynonym>
<rdfs:label>replication initiation protein RepE</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000055 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000055">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000011"/>
<obo:IAO_0000115>A plasmid partition system is the mechanism that assures the stable transmission of plasmids during bacterial cell division. Each plasmid has its independent replication system which control the number of copy of a plasmid in a cell.</obo:IAO_0000115>
<rdfs:label>plasmid partition system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000056 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000056">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000055"/>
<obo:IAO_0000115>This system is also used by most bacteria for chromosome segregation. Type I partition system are composed of an ATPase which contains Walker motifs and a CBP which is structurally distinct in type Ia and Ib. ATPases and CBP from type Ia are longer than the one from type Ib, but both CBPs contain an arginine finger in their N-terminal part. ParA proteins from different plasmids and bacterial species show 25 to 30% of sequence identity to the protein ParA of the plasmid P1. The partition of type I system uses a "diffusion-ratchet" mechanism. </obo:IAO_0000115>
<oboInOwl:hasExactSynonym>Type 1 Partition System</oboInOwl:hasExactSynonym>
<rdfs:label>Type I Partition System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000057 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000057">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000056"/>
<obo:IAO_0000115>def</obo:IAO_0000115>
<rdfs:label>Type Ia Partition System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000058 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000058">
<obo:IAO_0000115>partition system</obo:IAO_0000115>
<rdfs:label>Type Ib partition system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000059 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000059">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000055"/>
<obo:IAO_0000115>This system is composed of an actin-like ATPase, ParM, and a CBP called ParR. The centromere-like site, parC contains two sets of five 11 base pair direct repeats separated by the parMR promoter. The amino-acid sequence identity can go down to 15% between ParM and other actin-like ATPase.</obo:IAO_0000115>
<rdfs:label>Type II Partition System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000060 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000060">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000055"/>
<obo:IAO_0000115>This mechanism is composed of tubulin-like GTPase termed TubZ, and the CBP is termed TubR. Amino-acid sequence identity can go down to 21% for TubZ proteins</obo:IAO_0000115>
<rdfs:label>Type III Partition System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000061 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000061">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000055"/>
<obo:IAO_0000115>The partition system of the plasmid R388 has been found within the stb operon. This operon is composed of three genes, stbA, stbB and stbC</obo:IAO_0000115>
<rdfs:label>R388 Partition System</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000062 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000062">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000055"/>
<obo:IAO_0000115>pSK1 is plasmid from Staphylococcus aureus. This plasmid has a partition system determined by a single gene, par, previously known as orf245. This gene has effect neither on the plasmid copy number nor on the growth rate (excluding its implication in a post-segregational killing system). A centromere-like binding sequence is present upstream the par gene, and is composed of seven direct repeats and one inverted repeat.</obo:IAO_0000115>
<rdfs:label>pSK1 partition system</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/MOBIO_0000063 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MOBIO_0000063">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000186"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MOBIO_0000058"/>
</owl:Restriction>