Family GP000726


Family ID GP000726  add to my list RDF
Family name RNA polymerase sigma factor, plastid SigB/SigC/SigD types family   suggest a name
Synonym(s) Sigma70-like transcription factor
Cross-reference(s) PMID:
Plastidic RNA polymerase sigma factors in Arabidopsis.
10555304
Family Ontology
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N/A
Curation status ?
Found in No specificity
Phylogenetic analyzes Phylogeny done




Clustering level Family ID (number of sequences)
1
RNA polymerase sigma factor, plastid SigB/SigC/SigD types family
GP000726 (430)
2 GP015847 (350) ,
(plant-specificity: 11%)
GP019656 (74) , GP115978 (3) , GP116150 (3)
3 GP040790 (259) , GP044725 (91) , GP044550 (74) , GP128510 (3) , GP128809 (3)
4 GP070970 (182) , GP074536 (91) , GP074118 (74) , GP075678 (70) , GP137115 (7) , GP144825 (3) , GP145311 (3)
Table 1: This table displays which relationship has the selected family with other families in GreenPhyl clustering ?.




Legend:
  • Families (clustering)
    • Sequences are clustered and classified at 4 levels (from less to more stringent).
    • The number between parenthesis indicates the number of sequences in the cluster.
    • Selected family is highlighted like this.
    • Annotated gene families are underlined and gene family name pops up when you move your mouse cursor over.
    • Gene families are coloured in this color when the phylogenetic analyses are available.


Sequence total: 430
Species Count (w/o splice) Count (w/ splice)
4 4
2 2
17 17
8 9
4 4
12 12
8 8
9 9
10 10
13 13
6 6
6 12
6 6
6 6
5 5
11 19
8 12
7 7
9 9
8 8
6 6
6 7
6 6
44 44
8 30
5 5
9 36
8 8
10 10
6 8
13 13
7 7
12 14
8 8
8 15
19 28
7 7


Information to display




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Close InterPro family
IPR Annotation Type % Occurence Specificity
RNA polymerase sigma factor, FliA/WhiG
IPR012845
RNA polymerase sigma factor, FliA/WhiG Family 1 (1) Yes
RNA polymerase sigma factor, SigB/SigC/SigD, plastid
IPR016262
RNA polymerase sigma factor, SigB/SigC/SigD, plastid Family 17 (71) Yes
RNA polymerase sigma factor, RpoD-like, cyanobacteria
IPR017848
RNA polymerase sigma factor, RpoD-like, cyanobacteria Family 1 (1) Yes

Close Other InterPro signatures
IPR Annotation Type % Occurence Specificity
RNA polymerase sigma-70
IPR000943
RNA polymerase sigma-70 Domain 76 (327) No
RNA polymerase sigma-70 region 3
IPR007624
RNA polymerase sigma-70 region 3 Domain 72 (311) No
RNA polymerase sigma-70 region 2
IPR007627
RNA polymerase sigma-70 region 2 Domain 82 (354) No
RNA polymerase sigma-70 region 4
IPR007630
RNA polymerase sigma-70 region 4 Domain 69 (295) No
Winged helix-turn-helix DNA-binding domain
IPR011991
Winged helix-turn-helix DNA-binding domain Domain 81 (350) No
RNA polymerase sigma factor, region 3/4
IPR013324
RNA polymerase sigma factor, region 3/4 Domain 78 (337) No
RNA polymerase sigma factor, region 2
IPR013325
RNA polymerase sigma factor, region 2 Domain 88 (380) No
RNA polymerase sigma-70 like domain
IPR014284
RNA polymerase sigma-70 like domain Domain 81 (348) No

Close Domain architecture
Clustering
 



Close Representative InterPro domains - Consensus schema
IPR011991 IPR000943 IPR014284 IPR013325 IPR007627 IPR007624 IPR013324 IPR007630


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Species
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[Masking step 1 details] [Masking step 2 details] [Filtration details] [Global HMM file]

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Alignment and filtration statistics:

Overall family sequences Sequences used for alignment (w/o splice) Sequences kept after filtration [min; median; max] ~average sequence length Alignment length Masked alignment length
430 341 (79%) 300 (70%) [69; 501; 788] ~452 2293 232




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