Protein : Qrob_P0708870.2 Q. robur
Protein Identifier  ? Qrob_P0708870.2 Organism . Name  Quercus robur
Score  100.0 Score Type  egn
Protein Description  (M=1) K03086 - RNA polymerase primary sigma factor Gene Prediction Quality  validated
Protein length 

Sequence

Length: 509  
Kegg Orthology  K03086
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0 Synonyms

5 GO Terms

Identifier Name Description
GO:0003700 sequence-specific DNA binding transcription factor activity Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
GO:0006355 regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0006352 DNA-templated transcription, initiation Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
GO:0016987 sigma factor activity A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.

40 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|rcu:RCOM_1517450 1 508 + 508 none 100.00 508 77.56 0.0 RNA polymerase sigma factor rpoD putative
blastp_kegg lcl|cit:102606892 1 508 + 508 Gaps:1 99.80 508 78.50 0.0 RNA polymerase sigma factor sigA-like
blastp_kegg lcl|cic:CICLE_v10031289mg 1 508 + 508 Gaps:1 99.80 508 78.11 0.0 hypothetical protein
blastp_kegg lcl|pmum:103333466 1 508 + 508 Gaps:3 99.80 512 78.08 0.0 RNA polymerase sigma factor sigA
blastp_kegg lcl|cmo:103501092 1 508 + 508 Gaps:2 99.80 509 76.57 0.0 RNA polymerase sigma factor sigA
blastp_kegg lcl|tcc:TCM_025640 1 508 + 508 Gaps:1 99.80 508 77.51 0.0 Sigma factor A isoform 1
blastp_kegg lcl|pper:PRUPE_ppa004393mg 1 508 + 508 Gaps:3 99.80 512 77.50 0.0 hypothetical protein
blastp_kegg lcl|csv:101225471 1 508 + 508 Gaps:3 99.80 508 75.74 0.0 RNA polymerase sigma factor sigA-like
blastp_kegg lcl|csv:101207786 1 508 + 508 Gaps:3 99.80 508 75.74 0.0 RNA polymerase sigma factor sigA-like
blastp_kegg lcl|pop:POPTR_0019s06020g 1 508 + 508 none 99.80 509 75.79 0.0 POPTRDRAFT_665539 RNA POLYMERASE SIGMA SUBUNIT 1 family protein
blastp_pdb 3iyd_F 265 497 + 233 Gaps:8 37.36 613 34.06 6e-36 mol:protein length:613 RNA polymerase sigma factor rpoD
blastp_pdb 1l9u_Q 261 505 + 245 Gaps:11 73.49 332 36.07 5e-35 mol:protein length:332 SIGMA FACTOR SIGA
blastp_pdb 1l9u_H 261 505 + 245 Gaps:11 73.49 332 36.07 5e-35 mol:protein length:332 SIGMA FACTOR SIGA
blastp_pdb 1l9z_H 261 505 + 245 Gaps:17 55.71 438 36.07 1e-34 mol:protein length:438 SIGMA FACTOR SIGA
blastp_pdb 3eql_P 261 505 + 245 Gaps:11 57.68 423 35.66 2e-34 mol:protein length:423 RNA polymerase sigma factor rpoD
blastp_pdb 3eql_F 261 505 + 245 Gaps:11 57.68 423 35.66 2e-34 mol:protein length:423 RNA polymerase sigma factor rpoD
blastp_pdb 3dxj_P 261 505 + 245 Gaps:11 57.68 423 35.66 2e-34 mol:protein length:423 RNA polymerase pricipal sigma factor (RpoD)
blastp_pdb 3dxj_F 261 505 + 245 Gaps:11 57.68 423 35.66 2e-34 mol:protein length:423 RNA polymerase pricipal sigma factor (RpoD)
blastp_pdb 2cw0_P 261 505 + 245 Gaps:11 57.68 423 35.66 2e-34 mol:protein length:423 RNA polymerase sigma factor rpoD
blastp_pdb 2cw0_F 261 505 + 245 Gaps:11 57.68 423 35.66 2e-34 mol:protein length:423 RNA polymerase sigma factor rpoD
blastp_uniprot_sprot sp|O24629|SIGA_ARATH 1 507 + 507 Gaps:26 99.80 502 72.46 0.0 RNA polymerase sigma factor sigA OS Arabidopsis thaliana GN SIGA PE 1 SV 1
blastp_uniprot_sprot sp|P26683|SIGA_NOSS1 206 497 + 292 Gaps:15 73.59 390 37.63 1e-49 RNA polymerase sigma factor SigA OS Nostoc sp. (strain PCC 7120 / UTEX 2576) GN sigA PE 3 SV 1
blastp_uniprot_sprot sp|P38023|SIGA1_SYNE7 212 497 + 286 Gaps:15 70.43 399 38.43 4e-47 RNA polymerase sigma factor SigA1 OS Synechococcus elongatus (strain PCC 7942) GN sigA1 PE 3 SV 2
blastp_uniprot_sprot sp|Q31QG5|SIGA3_SYNE7 206 495 + 290 Gaps:18 89.38 320 35.31 4e-46 RNA polymerase sigma factor SigA3 OS Synechococcus elongatus (strain PCC 7942) GN sigA3 PE 3 SV 1
blastp_uniprot_sprot sp|Q31ME3|SIGA2_SYNE7 185 498 + 314 Gaps:13 95.31 320 33.11 5e-46 RNA polymerase sigma factor SigA2 OS Synechococcus elongatus (strain PCC 7942) GN sigA2 PE 1 SV 1
blastp_uniprot_sprot sp|O33662|SIGA_STRMU 265 501 + 237 Gaps:10 62.80 371 38.20 1e-45 RNA polymerase sigma factor SigA OS Streptococcus mutans serotype c (strain ATCC 700610 / UA159) GN sigA PE 3 SV 1
blastp_uniprot_sprot sp|Q03065|RPSB_NOSS1 206 493 + 288 Gaps:11 85.24 332 34.63 2e-45 RNA polymerase sigma-B factor OS Nostoc sp. (strain PCC 7120 / UTEX 2576) GN sigB PE 3 SV 1
blastp_uniprot_sprot sp|P0A4J0|SIGA_STRR6 265 497 + 233 Gaps:10 62.06 369 38.43 1e-44 RNA polymerase sigma factor SigA OS Streptococcus pneumoniae (strain ATCC BAA-255 / R6) GN sigA PE 3 SV 1
blastp_uniprot_sprot sp|P0A4I9|SIGA_STRPN 265 497 + 233 Gaps:10 62.06 369 38.43 1e-44 RNA polymerase sigma factor SigA OS Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) GN sigA PE 3 SV 1
blastp_uniprot_sprot sp|O22056|SIGB_ARATH 214 506 + 293 Gaps:8 50.52 572 36.68 1e-44 RNA polymerase sigma factor sigB OS Arabidopsis thaliana GN SIGB PE 2 SV 2

19 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
Pfam 445 494 50 PF04545 none Sigma-70, region 4 IPR007630
PANTHER 18 508 491 PTHR30603 none none none
Pfam 272 339 68 PF04542 none Sigma-70 region 2 IPR007627
Gene3D 339 390 52 G3DSA:1.10.10.10 none none IPR011991
SUPERFAMILY 195 339 145 SSF88946 none none IPR013325
Pfam 348 419 72 PF04539 none Sigma-70 region 3 IPR007624
SUPERFAMILY 423 496 74 SSF88659 none none IPR013324
Gene3D 191 223 33 G3DSA:1.10.601.10 none none none
Gene3D 261 338 78 G3DSA:1.10.601.10 none none none
PRINTS 446 458 13 PR00046 none Major sigma-70 factor signature IPR000943
PRINTS 293 306 14 PR00046 none Major sigma-70 factor signature IPR000943
PRINTS 466 481 16 PR00046 none Major sigma-70 factor signature IPR000943
PRINTS 317 325 9 PR00046 none Major sigma-70 factor signature IPR000943
PRINTS 481 492 12 PR00046 none Major sigma-70 factor signature IPR000943
PANTHER 18 508 491 PTHR30603:SF5 none none none
TIGRFAM 265 495 231 TIGR02937 none sigma70-ECF: RNA polymerase sigma factor, sigma-70 family IPR014284
ProSitePatterns 293 306 14 PS00715 none Sigma-70 factors family signature 1. IPR000943
Gene3D 444 504 61 G3DSA:1.10.10.10 none none IPR011991
SUPERFAMILY 341 397 57 SSF88659 none none IPR013324

0 Localization

10 Qtllist

Qtl Name Chromosome Name Linkage Group Prox Marker Dist Marker Position QTL Pos One Pos Two Test Type Test Value R 2
Bourran1_2004_QTL4_peak_Bud_burst_A4 Qrob_Chr09 9 s_1BY6BQ_440 s_1AOIKO_756 16,45 0 27,45 lod 4,5 10,6
Bourran_2000_2002_QTL7_Delta.F Qrob_Chr09 9 v_5944_442 s_1BA1PC_866 23.51 10,96 35,74 lod 4.1466 0.041
Bourran2_2003_QTL11_peak_Bud_burst_3P Qrob_Chr09 9 s_1CGP2H_273 v_15801_330 27,16 4,16 48,16 lod 2,3 5,1
Bourran2_2004_QTL12_peak_Bud_burst_3P Qrob_Chr09 9 s_1BDO6G_250 s_1A83AM_496 34,31 9,31 44,31 lod 3,6 7,6
Bourran2_2004_QTL14_peak_Bud_burst_A4 Qrob_Chr09 9 s_1BY6BQ_440 s_1AOIKO_756 16,83 10,33 22,33 lod 3,8 9
Bourran2_2015_nEpis_A4 Qrob_Chr09 9 v_15847_485 v_8329_369 34,94 34,88 37,45 lod 3.1 7
Bourran2_2015_nSecLBD_A4 Qrob_Chr09 9 v_15847_485 v_8329_369 35,81 34,88 37,45 lod 4.4 10.4
PM_1999_QTL15_peak_Bud_burst_3P Qrob_Chr09 9 s_1CGP2H_273 v_15801_330 27,16 9,16 47,16 lod 3,6 6,5
Bourran1_2003_QTL5_peak_Bud_burst_3P Qrob_Chr09 9 s_1ATM17_504 s_1AYZFM_899 29,81 19,81 41,81 lod 3,3 8,9
NancyGreenhouseCO2_2001_ambient_elevated_leaf_cellulose_QTL8_d13Cf Qrob_Chr09 9 s_1C1GRV_1289 s_1BXT7R_864 29.91 0 47,18 lod 7.0997 0.044

0 Targeting