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Tribe List
 

TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. TribeMCL uses a novel clustering method (Markov Clustering or MCL) which solves problems which normally hinder protein sequence clustering. These problems include: multi-domain proteins, peptide fragments and proteins which possess domains which are very widespread (promiscuous domains).

More on clustering using MCL algorithm

Reference: Enright A.J., Van Dongen S., Ouzounis C.A; Nucleic Acids Res. 30(7):1575-1584 (2002) [PDF]

Gene names and Tribe names:
The nomenclature of chloroplast genes has gone through considerable revision in the years since the first chloroplast genomes were sequenced (Stoebe et al, 1998). The accelerated pace of chloroplast genome sequencing in recent years assures that new chloroplast genes will continue to be discovered and nomenclature will need to reflect those discoveries. Chloroplast DB does not override annotated gene names, and so orthologous annotated genes may have different names in Chloroplast DB. An example is cysA. As of September 1, 2005, this gene is annotated as cysA in four genomes, mbpX in one genome, and ycf85 in two other genomes. The Tribe function of chloroplast DB can help identify potentially orthologous genes that have been assigned different names by different investigators. A simple rule was used to assign valid chloroplast gene names to Tribes based on the names of valid chloroplast genes found in that tribe. Valid names were determined from the current version of Uniprot Database's "List of chloroplast and cyanelle encoded proteins." If Tribes contained exactly one valid name, that name was assigned to the tribe. If a tribe contained more than one Uniprot name, then all valid names were assigned seperated by a '/'. In two cases (ccsA and ycf32), the name was both a Uniprot name and a synonym for another Uniprot name (chlI and psbY, respectively). If it tribe contains only genes that have an ambiguous name, or no Uniprot name at all, it is marked by 'ambig[ | ]'. If other genes in the tribe are unambiguously named, the tribe will be named with that gene. If a tribe included no gene with a valid Uniprot name, the tribe was left unnamed. Multiple tribes may have a particular name, and multiple valid names may be found in a tribe. The tribe number and the genes that are contained within them are always unique.

References

Uniprot list chloroplast and cyanelle proteins: 47.6, 2 August 2005

Stoebe B., Martin W., Kowallik K.V.
Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes.
Plant Mol. Biol. Report. 16:243(1998).

                Select tribe(s) to download its sequence in FASTA format

               

  Genes Name
0 104 psaA/psaB
1 77 rps7
2 74 rpl2/rpl12
3 72 ycf2/ftsH
4 71 rpl23
5 66 rps12
6 54 ndhB
7 59 rps19
8 59 rps4
9 56 rps3
10 55 rpl16/rps12
11 56 rpoB
12 56 rps11
13 55 rps2
14 55 rpoC1
15 55 rpl14
16 54 rps8
17 52 psbA
18 54 rbcL
19 53 rps18
20 53 rps14
21 53 rpoC2
22 53 rpl20
23 53 psbK
24 52 atpE
25 51 psbD
26 52 atpH
27 52 atpA
28 52 psbF
29 52 psbE
30 52 psaC
31 52 psbH
32 52 psbB/psbT
33 52 petB
34 51 atpF
35 51 rpl36
36 51 atpB
37 51 psaJ
38 51 psbC
39 51 psbJ
40 51 psbI
41 51 psbN
42 50 petD
43 51 petA
44 51 petG
45 50 rpoA
46 50 atpI
47 50 psbZ
48 50 ycf4
49 50 ccsA
50 50 psbT
51 47 ycf3
52 49 psbL
53 48 psaI
54 47 rpl33
55 46 rpl22
56 46 clpP
57 45 petN
58 45 cemA
59 44 rps15
60 43 psbM
61 42 rpl32
62 41 ycf1
63 40 rps16
64 40 ndhH
65 39 accD
66 38 ndhK
67 38 ndhF
68 38 ndhI
69 37 ndhC
70 37 petL
71 37 ndhE
72 37 ndhA/ndhH
73 36 ndhJ
74 36 matK
75 36 ndhG
76 35 ndhD
77 31 infA
78 30 cpcB/apcA/apcF/apcB/apcD/cpeB/cpeA
79 26 ycf12
80 19 psaM
81 19 chlL
82 18 tufA
83 18 rpl21
84 18 chlB
85 18 chlN
86 17 ycf15/ycf2
87 17 rpl5
88 16 chlI
89 15 rps9
90 13 ycf68
91 13 ycf27/ycf29
92 12 rpl19
93 12 rpl12
94 12 tilS
95 12
96 11
97 11
98 11
99 10 rpl6
100 10 ftsH/ycf2
101 10 clpC
102 10 ycf24
103 10
104 10
105 9 dnaK
106 8 psbY
107 9 rpl11
108 9 groL
109 9 cysA
110 8 rpl3
111 8 rpl4
112 8 rps17
113 8 rps5
114 8 secY
115 8 rps13
116 8 rps10
117 8 psaF
118 8 psbV
119 8 atpG
120 8 atpD
121 8 ycf39
122 8 ycf30
123 8 rps6
124 8 rbcS
125 8 pdhB
126 8
127 8
128 8
129 8 ycf66
130 8 cysT/cysW
131 7 rpl18
132 7 rpl31
133 7 petF
134 7 psbX
135 7 psaL
136 7 rpl27
137 7 ycf20
138 7 secA
139 7 ycf44
140 7 acpP
141 7 psaE
142 7 rpl1
143 7 psbW
144 7 ycf65
145 7 cfxQ
146 7 ycf16
147 7 ycf43
148 7 rpl35
149 7 psaD
150 6
151 7 rpl32
152 7
153 7 minD
154 4
155 6 rpl24
156 6 rpl13
157 6 rps20
158 6 ycf19
159 6 thiG
160 6 dnaB
161 6 ycf40
162 6 ycf80
163 6 preA/crtE
164 6 rpl34
165 6 ycf35
166 6
167 6
168 6
169 5 tsf
170 5 ftrB
171 5 psaK
172 5 ycf23
173 5 rpoZ
174 5 cpcA
175 5 trpG
176 5
177 5 ycf45
178 5 ilvB
179 5 ycf17
180 5 rpl28
181 5 ilvH
182 5 ycf37
183 5 rpl29
184 5 apcE
185 5 petM
186 5 ycf33
187 5
188 5 ycf46
189 5 ycf47
190 5 ycf1
191 5
192 4 ycf38
193 4 petJ
194 4 carA
195 4 ycf53
196 4 ycf55
197 4 ycf54
198 4 cpcG
199 4 ycf18
200 4 accA
201 4 gltB
202 4 accB
203 4 chlN
204 4 ycf28
205 4 trxA
206 4 infC
207 4 trpA
208 4 argB
209 4 ycf26
210 4 pdhA
211 4
212 4 ycf36
213 4 ftsW
214 4
215 4 rne
216 4 infB
217 4
218 4
219 4
220 4
221 3
222 4
223 3 ycf52
224 3
225 3 hisH
226 3 ycf34
227 3 ycf21
228 3 petL
229 3 pbsA
230 3 ycf81
231 3
232 3 ycf42
233 3
234 3
235 3
236 3
237 3 ycf22
238 2
239 2 hup
240 2 glnB
241 2 ycf49
242 2 cobA
243 2
244 2 lipB
245 2 glmS
246 2
247 2 roaA
248 2 ycf83
249 2
250 2
251 2
252 2 menB
253 2
254 2
255 2
256 2 trmE
257 2 lpxA
258 2 lpxC
259 2
260 2
261 2
262 2
263 2
264 2
265 2
266 2 mat1
267 2
268 2
269 2 rpl36
270 2 ftsI
271 2
272 2
273 2
274 2
275 2
276 2
277 2
278 2
279 2
280 2
281 2
282 2
283 2
284 2
285 2
286 2
287 2
288 2
289 2
290 2
291 2
292 2
293 2
294 2
295 2
296 2
297 2
298 2
299 1
300 2
301 2
302 1
303 2
304 2
305 2
306 2
307 2
308 2
309 2
310 2
311 2
312 2
313 2
314 2
315 2
316 2
317 2
318 2
319 2
320 2 rpl36
321 2
322 1 ycf3
323 2
324 2
325 2
326 2 psaM
327 2
328 2
329 2 fabH
330 2 ycf56
331 2
332 2
333 2
334 2
335 2
336 2 rpl9
337 2 rps1
338 2
339 2 hisS
340 2
341 2
342 2 pgmA
343 2
344 2 rps7
345 2
346 2
347 2
348 2
349 2
350 2
351 2
352 2
353 2
354 2
355 2
356 2
357 2
358 2
359 2 ycf20
360 2
361 2
362 2
363 2
364 1 rpl29
365 1
366 1 ycf49
367 1 petL
368 1
369 1
370 1
371 1
372 1
373 1
374 1
375 1 rpl34
376 1
377 1
378 1
379 1
380 1
381 1
382 1
383 1 hemA
384 1
385 1
386 1
387 1 nadA
388 1
389 1
390 1 petL
391 1
392 1
393 1
394 1
395 1
396 1
397 1
398 1
399 1
400 1
401 1
402 1
403 1 psbD
404 1 psaM
405 1
406 1
407 1
408 1
409 1
410 1
411 1
412 1
413 1
414 1
415 1
416 1
417 1
418 1
419 1
420 1
421 1 minE
422 1
423 1
424 1
425 1
426 1
427 1
428 1
429 1
430 1
431 1 petL
432 1
433 1
434 1
435 1
436 1
437 1
438 1
439 1
440 1
441 1
442 1
443 1
444 1
445 1 ambig[psbY | ycf32]
446 1
447 1
448 1
449 1 ycf41
450 1 petL
451 1
452 1
453 1
454 1
455 1
456 1
457 1
460 1
462 1
467 1
469 1
470 1
471 1 rps12
472 1
473 1
474 1
475 1
476 1
477 1
478 1
479 1
480 1
481 1
482 1
483 1
484 1
485 1
486 1
487 1
488 1
489 1
490 1
491 1
492 1
493 1
494 1
495 1 rps12
496 1
497 1
498 1
499 1
500 1
501 1
502 1
503 1
504 1
505 1
506 1
507 1
508 1
509 1
510 1
511 1
512 1
513 1
514 1
515 1
516 1
517 1
518 1
519 1
520 1
521 1
522 1
523 1
524 1
525 1
526 1
527 1
528 1
529 1
530 1
531 1
532 1
533 1
534 1
535 1
536 1
537 1
538 1
539 1
540 1
541 1
542 1
543 1
544 1
545 1
546 1
547 1
548 1
549 1
550 1
551 1
552 1
553 1
554 1
555 1
556 1
557 1
558 1
559 1
560 1
561 1
562 1
563 1
564 1
565 1
566 1
567 1
568 1
569 1
570 1
571 1
572 1
573 1
574 1
575 1
577 1 petD
578 1
579 1
580 1
581 1
582 1
583 1
584 1
585 1
586 1
587 1
588 1
589 1
590 1
591 1
592 1
593 1
594 1
595 1
596 1
597 1
598 1
599 1
600 1
601 1
602 1
603 1
604 1
605 1
606 1
607 1
608 1
609 1 ycf3
610 1
611 1
612 1
613 1
614 1
615 1
616 1
617 1
618 1
619 1
620 1
621 1
622 1
623 1
624 1
625 1
626 1
627 1
628 1
629 1
630 1
631 1
632 1 petL
633 1 psbA
634 1
635 1
636 1
637 1
638 1
639 1
640 1
641 1
642 1
643 1
644 1
645 1
646 1
647 1
648 1
649 1
650 1
651 1
652 1
653 1
654 1
655 1
656 1
657 1
658 1
659 1
660 1
661 1
662 1
663 1
664 1
665 1
666 1
667 1
668 1
669 1
670 1
671 1
672 1
673 1
674 1
675 1
676 1
677 1
678 1
679 1
680 1
681 1
682 1
683 1
684 1
685 1
686 1
687 1
688 1 rpl16
689 1 psbM
690 1 psbN
691 1
692 1
693 1
694 1
695 1
696 1
697 1
698 1 infA
699 1
700 1
701 1
702 1
703 1
704 1
705 1
706 1
707 1
708 1
709 1
710 1
711 1
712 1
713 1
714 1
715 1
716 1
717 1
718 1
719 1
720 1
721 1
722 1
723 1
724 1
725 1
726 1
727 1
728 1
729 1
730 1
731 1 ftsH
732 1 psaI
733 1
734 1
735 1
736 1
737 1
738 1
739 1
740 1
741 1
742 1
743 1
744 1
745 1
746 1
747 1
748 1
749 1
750 1
751 1 minE
752 1
753 1
754 1
755 1
756 1
757 1
758 1
759 1
760 1
761 1
762 1
763 1
764 1
765 1
766 1
767 1
768 1
769 1
770 1
771 1
772 1
773 1 ycf55
774 1
775 1 rpoZ
776 1
777 1
778 1
779 1
780 1
781 1
782 1 rpl34
783 1 rps1
784 1
785 1
786 1 ycf33
787 1
788 1
789 1 petM