Citrus Sinensis ID: 001050
Local Sequence Feature Prediction
| Prediction and (Method) | Result |
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Close Homologs for Annotation Transfer
Close Homologs in SWISS-PROT Database Detected by BLAST 
Original result of BLAST against SWISS-PROT Database
| ID | Alignment graph | Length |
Definition |
RBH(Q2H) |
RBH(H2Q) |
Q cover |
H cover |
Identity |
E-value |
| Query | 1173 | 2.2.26 [Sep-21-2011] | |||||||
| Q9LK40 | 1172 | DNA-directed RNA polymera | yes | no | 0.976 | 0.976 | 0.692 | 0.0 | |
| Q9LV32 | 1119 | DNA-directed RNA polymera | no | no | 0.944 | 0.990 | 0.663 | 0.0 | |
| P38420 | 1188 | DNA-directed RNA polymera | no | no | 0.938 | 0.926 | 0.356 | 0.0 | |
| Q42877 | 1191 | DNA-directed RNA polymera | N/A | no | 0.952 | 0.937 | 0.349 | 0.0 | |
| Q753Q4 | 1222 | DNA-directed RNA polymera | yes | no | 0.941 | 0.903 | 0.345 | 0.0 | |
| P08518 | 1224 | DNA-directed RNA polymera | yes | no | 0.954 | 0.915 | 0.344 | 0.0 | |
| Q8SR75 | 1141 | DNA-directed RNA polymera | yes | no | 0.909 | 0.935 | 0.344 | 0.0 | |
| Q02061 | 1210 | DNA-directed RNA polymera | yes | no | 0.948 | 0.919 | 0.345 | 1e-180 | |
| Q54J75 | 1170 | DNA-directed RNA polymera | yes | no | 0.920 | 0.923 | 0.350 | 1e-180 | |
| Q6FLD5 | 1223 | DNA-directed RNA polymera | yes | no | 0.938 | 0.900 | 0.343 | 1e-180 |
| >sp|Q9LK40|RPD2A_ARATH DNA-directed RNA polymerase D subunit 2a OS=Arabidopsis thaliana GN=NRPD2a PE=1 SV=1 | Back alignment and function desciption |
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Score = 1693 bits (4385), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 814/1175 (69%), Positives = 970/1175 (82%), Gaps = 30/1175 (2%)
Query: 9 TDPTSLCDLGEEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVE 68
T +L +LGE FL++FC+KAA SFF++YGL+SHQ+NSYN FI++GLQ F SFGE +VE
Sbjct: 18 TGEINLSELGEGFLQSFCKKAATSFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEMLVE 77
Query: 69 PGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVK 128
P +D KK + +WRYA+++FG+VT++KP+FF+ + E + P HARLQNMTYS+R+KV
Sbjct: 78 PSFDVVKKKDNDWRYATVKFGEVTVEKPTFFSDD--KELEFLPWHARLQNMTYSARIKVN 135
Query: 129 VQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWM--KGVE-- 184
VQ +V+ V SDKFKTG++ Y++K++L + +I+IG IPVMVKS LC KG E
Sbjct: 136 VQVEVFKNTVVKSDKFKTGQDNYVEKKILDVKKQDILIGSIPVMVKSILCKTSEKGKENC 195
Query: 185 -KGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWVSNSMGWTVAYKSENKRNRLIVRLVD 243
KGDC FD GGYF+IKGAEKVF+AQEQ+C KRLW+SNS WTV+++SENKRNR IVRL +
Sbjct: 196 KKGDCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWISNS-PWTVSFRSENKRNRFIVRLSE 254
Query: 244 MSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFAS 303
K ED K EKVL+VYFLSTEIP+W+LFFALGVSSDKE ++LI F +D SI N L AS
Sbjct: 255 NEKAEDYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITNSLIAS 314
Query: 304 IHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLFPSLHGTKQKARFLGY 363
IH AD C+ FR G NAL YV++ IK T FPP ES +EC++ YLFP L K+KARFLGY
Sbjct: 315 IHVADAVCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLFPGLQSLKKKARFLGY 374
Query: 364 MVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDR 423
MVKCLL +Y+G+RKC+NRD FRNKR+ELAGELLERE++VH+AHAR++M +A+Q+ L GD
Sbjct: 375 MVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARRKMTRAMQKHLSGDG 434
Query: 424 TVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTR 483
++PIE+YLDAS++TNGLSRAFSTGAWSHPF++ ER+SG+VANLGRANPLQTL+DLRRTR
Sbjct: 435 DLKPIEHYLDASVITNGLSRAFSTGAWSHPFRKMERVSGVVANLGRANPLQTLIDLRRTR 494
Query: 484 QQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQLFN 543
QQV YTGKVGDARYPHPSHWG++CFLSTPDGENCGLVKN+ + GLVST LE + E+LF
Sbjct: 495 QQVLYTGKVGDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEKLFA 554
Query: 544 SGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDEL 603
GME+L DD L GK KV ++GDW+G+C DS SFV+EL+ +RR+ ELP ++EIKRD+
Sbjct: 555 CGMEELMDDTCTPLFGKHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKD 614
Query: 604 QSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAW 663
+EVRIF DAGR+LRPLLVVEN+ K+K + Y F LLDHGI+EL+G EEEEDC TAW
Sbjct: 615 DNEVRIFTDAGRLLRPLLVVENLQKLKQEKPSQYPFDHLLDHGILELIGIEEEEDCNTAW 674
Query: 664 GIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGF 723
GIK LLK+ P +THCELD+SFLLG+SC ++PFANHDH RRVLYQSQKH QAIGF
Sbjct: 675 GIKQLLKE-----PKIYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKHCQQAIGF 729
Query: 724 PTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNV 783
+TNP+IR DTLS QLFYPQ+PLF+T+ S+CL K L+NGQNAIVAVNV
Sbjct: 730 SSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKK-----------EVLFNGQNAIVAVNV 778
Query: 784 HLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIG 843
HLGYNQEDS+VMN+ASLERGMFRSE IRSYKAEVD K+ + KR+ D++V FGK SKIG
Sbjct: 779 HLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDAKDSE-KRKKMDELVQFGKTHSKIG 837
Query: 844 RVDSLDDDGFPFIGANLQSGDIVIGKYADSGADHSIKLKHTERGMVQKVVLSSNDDGKNF 903
+VDSL+DDGFPFIGAN+ +GDIVIG+ +SGADHSIKLKHTERG+VQKVVLSSND+GKNF
Sbjct: 838 KVDSLEDDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDEGKNF 897
Query: 904 SVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTP 963
+ VSLRQVRSPCLGDKFSSMHGQKGVLG+LE Q+NFPFTIQGIVPDIVINPHAFPSRQTP
Sbjct: 898 AAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTP 957
Query: 964 GQLLEAALGKGIAAL-----GKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERL 1018
GQLLEAAL KGIA + L R+ATPF+TP V ITEQLHRAGFS+WG ER+
Sbjct: 958 GQLLEAALSKGIACPIQKEGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERV 1017
Query: 1019 YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGE 1078
Y+GR+GEM+RS+IF+GPTFYQRL+HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGE
Sbjct: 1018 YNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGE 1077
Query: 1079 MERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICD 1138
MERDCLIAHGA+ANLHERLFTLSDS QMHICRKCK ANVI+R GRK+RGPYCR+C
Sbjct: 1078 MERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIERTPSSGRKIRGPYCRVCV 1137
Query: 1139 SGDDIVKANVPYGAKLLCQELFSMGITLKFDTEFC 1173
S D +V+ VPYGAKLLCQELFSMGITL FDT+ C
Sbjct: 1138 SSDHVVRVYVPYGAKLLCQELFSMGITLNFDTKLC 1172
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DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity). Second largest component of RNA polymerase IVa (Pol IV) and IVb (Pol V) which mediate short-interfering RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-dependent (RdDM) transcriptional gene silencing (TGS) of endogenous repeated sequences, including transposable elements. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Also required for full erasure of methylation when the RNA trigger is withdrawn. Required for intercellular RNA interference (RNAi) leading to systemic post-transcriptional gene silencing. Involved in the maintenance of post-transcriptional RNA silencing. During interphase, mediates siRNA-independent heterochromatin association and methylation into chromocenters and condensation and cytosine methylation at pericentromeric major repeats. Required for complete maintenance of the 35S promoter homology-dependent TGS in transgenic plants. Arabidopsis thaliana (taxid: 3702) EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6 |
| >sp|Q9LV32|RPD2B_ARATH DNA-directed RNA polymerase D subunit 2b OS=Arabidopsis thaliana GN=NRPD2b PE=2 SV=1 | Back alignment and function description |
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| >sp|P38420|RPB2_ARATH DNA-directed RNA polymerase II subunit RPB2 OS=Arabidopsis thaliana GN=RPB135 PE=2 SV=2 | Back alignment and function description |
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| >sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1 | Back alignment and function description |
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| >sp|Q753Q4|RPB2_ASHGO DNA-directed RNA polymerase II subunit RPB2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB2 PE=3 SV=1 | Back alignment and function description |
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| >sp|P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB2 PE=1 SV=2 | Back alignment and function description |
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| >sp|Q8SR75|RPB2_ENCCU DNA-directed RNA polymerase II subunit RPB2 OS=Encephalitozoon cuniculi (strain GB-M1) GN=RPB2 PE=3 SV=1 | Back alignment and function description |
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| >sp|Q02061|RPB2_SCHPO DNA-directed RNA polymerase II subunit RPB2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb2 PE=1 SV=2 | Back alignment and function description |
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| >sp|Q54J75|RPB2_DICDI DNA-directed RNA polymerase II subunit rpb2 OS=Dictyostelium discoideum GN=polr2b PE=3 SV=1 | Back alignment and function description |
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| >sp|Q6FLD5|RPB2_CANGA DNA-directed RNA polymerase II subunit RPB2 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=RPB2 PE=3 SV=1 | Back alignment and function description |
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Close Homologs in the Non-Redundant Database Detected by BLAST
Original result of BLAST against Nonredundant Database
| GI | Alignment Graph | Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1173 | ||||||
| 255548744 | 1203 | DNA-directed RNA polymerase subunit, put | 0.992 | 0.967 | 0.782 | 0.0 | |
| 224141967 | 1160 | predicted protein [Populus trichocarpa] | 0.975 | 0.986 | 0.780 | 0.0 | |
| 225430474 | 1198 | PREDICTED: DNA-directed RNA polymerase D | 0.992 | 0.971 | 0.760 | 0.0 | |
| 449455519 | 1197 | PREDICTED: DNA-directed RNA polymerase D | 0.986 | 0.966 | 0.756 | 0.0 | |
| 296082132 | 1220 | unnamed protein product [Vitis vinifera] | 0.982 | 0.944 | 0.754 | 0.0 | |
| 356518213 | 1205 | PREDICTED: DNA-directed RNA polymerase D | 0.986 | 0.960 | 0.735 | 0.0 | |
| 356509878 | 1205 | PREDICTED: DNA-directed RNA polymerase D | 0.987 | 0.960 | 0.730 | 0.0 | |
| 357466021 | 1237 | DNA-directed RNA polymerase subunit beta | 0.982 | 0.931 | 0.716 | 0.0 | |
| 297830452 | 1169 | NRPD2a [Arabidopsis lyrata subsp. lyrata | 0.982 | 0.986 | 0.686 | 0.0 | |
| 79416709 | 1172 | nuclear RNA polymerase D2A [Arabidopsis | 0.976 | 0.976 | 0.692 | 0.0 |
| >gi|255548744|ref|XP_002515428.1| DNA-directed RNA polymerase subunit, putative [Ricinus communis] gi|223545372|gb|EEF46877.1| DNA-directed RNA polymerase subunit, putative [Ricinus communis] | Back alignment and taxonomy information |
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Score = 1915 bits (4960), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 922/1179 (78%), Positives = 1037/1179 (87%), Gaps = 15/1179 (1%)
Query: 1 MDSD---DNGFTDP-TSLCDLGEEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQ 56
DSD D F D TSL D+GE LK FC KAA FFNEYGL+SHQINSYN+FI NG+Q
Sbjct: 34 FDSDSGSDCDFMDSSTSLTDIGEAKLKDFCNKAATLFFNEYGLISHQINSYNDFINNGIQ 93
Query: 57 KAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARL 116
KAFDSFGE +VEPGYDPSKKGE EWRYAS++FG+V L+KP+F++G DEH M PRHARL
Sbjct: 94 KAFDSFGELVVEPGYDPSKKGENEWRYASVKFGKVALEKPTFWSG--ADEHKMLPRHARL 151
Query: 117 QNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSD 176
QNMTYSS+MKV V +VYT+K V SDKFKTG++QY+ KEVL+ + NI IG +PVMVKSD
Sbjct: 152 QNMTYSSKMKVNVSVEVYTRKVVRSDKFKTGKDQYVDKEVLNTDNRNITIGSLPVMVKSD 211
Query: 177 LCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWVSNSMGWTVAYKSENKRNR 236
LCWMK EKGDCDFDHGGYF+IKGAEKVF+AQEQICLKRLW+SN GWTV+YKSE KRNR
Sbjct: 212 LCWMKTAEKGDCDFDHGGYFLIKGAEKVFIAQEQICLKRLWISNIQGWTVSYKSEIKRNR 271
Query: 237 LIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSI 296
LIVRLV +S ED+K +K L+VYFLSTEIP+WILFFALGV+SDKE+++LI + D I
Sbjct: 272 LIVRLVGLSALEDVKAEKKCLTVYFLSTEIPLWILFFALGVTSDKEVIDLIGYGSNDARI 331
Query: 297 LNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLFPSLHGTKQ 356
+NI FASIHDAD K + FR+G+ AL+YV + I+GT FPPGE+ E+ YLFP+LH +Q
Sbjct: 332 VNIFFASIHDADEKTEGFRRGKEALEYVVRQIRGTRFPPGEN-EDFFLLYLFPTLHSLRQ 390
Query: 357 KARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQ 416
KARFLGYMVKCLLQAY+G+RKC+N D FRNKR ELA ELLERELKVHIAHAR+RMAKALQ
Sbjct: 391 KARFLGYMVKCLLQAYNGQRKCNNWDSFRNKRFELAKELLERELKVHIAHARRRMAKALQ 450
Query: 417 RDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTL 476
+DLYGDR VRPIE+YLDASI+TNGLSRAFSTGAWSHP+KR ERISG+VANLGRANPLQT+
Sbjct: 451 KDLYGDRDVRPIEHYLDASIVTNGLSRAFSTGAWSHPYKRMERISGVVANLGRANPLQTM 510
Query: 477 VDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILEP 536
VDLR+TR VQYTGKVGDAR+PHPSHWG++CFLSTPDGENCGLVKNL TGLVS +ILEP
Sbjct: 511 VDLRKTRYHVQYTGKVGDARFPHPSHWGRVCFLSTPDGENCGLVKNLATTGLVSVNILEP 570
Query: 537 IFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQV 596
+ ++L GMEK+ +D+ L K KVF++G+W+GVC+DS FV+ELRR RRRK+LP QV
Sbjct: 571 LIDKLIARGMEKVPEDSHSDLDEKDKVFLNGEWVGVCEDSRLFVAELRRLRRRKKLPQQV 630
Query: 597 EIKRDELQSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEE 656
EIKRDE Q EVRIF DAGRILRPLLVV+N+ KI++ +G N TFQ+LLD GIIE VGTEEE
Sbjct: 631 EIKRDEQQQEVRIFSDAGRILRPLLVVQNLHKIEAFKGGNCTFQSLLDKGIIEFVGTEEE 690
Query: 657 EDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKH 716
EDC TAWGIK+LL ++ K+ +K+THCELDMSFLLGLSCGIIPFANHDHARRVLYQ+QKH
Sbjct: 691 EDCSTAWGIKFLLSGVDGKQSLKYTHCELDMSFLLGLSCGIIPFANHDHARRVLYQAQKH 750
Query: 717 SSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPG--YGHNHILPRPELYNG 774
S QAIGFPTTNP+IRVDTLSHQL+YPQRPLFRT+ SDCLGKPG GHN I+P+PELYNG
Sbjct: 751 SQQAIGFPTTNPNIRVDTLSHQLYYPQRPLFRTVTSDCLGKPGDTRGHNGIVPKPELYNG 810
Query: 775 QNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVN 834
QNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKA+VDNKE+ KRR DD VN
Sbjct: 811 QNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKADVDNKELLDKRRKYDDNVN 870
Query: 835 FGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGADHSIKLKHTERGMVQKVVL 894
FGKI SKIGRVDSLDDDGFPFIGANLQSGDIVIG+ A+SG DHSIKLKHTERGMVQKVVL
Sbjct: 871 FGKIPSKIGRVDSLDDDGFPFIGANLQSGDIVIGRCAESGPDHSIKLKHTERGMVQKVVL 930
Query: 895 SSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINP 954
SSND+GKNF+VVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFT QGIVPDIVINP
Sbjct: 931 SSNDEGKNFAVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTRQGIVPDIVINP 990
Query: 955 HAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWG 1014
H+FPSRQTPGQLLEAALGKGIA C G +YATPF+T SV+AIT QLHRAGFS+WG
Sbjct: 991 HSFPSRQTPGQLLEAALGKGIA------CGGSMKYATPFSTLSVEAITNQLHRAGFSRWG 1044
Query: 1015 TERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGI 1074
ER+Y+GRTGEMVRSLIF+GPTFYQRLIHM+EDKVKFRNTGPVHPLTRQPVADRKRFGGI
Sbjct: 1045 NERVYNGRTGEMVRSLIFMGPTFYQRLIHMAEDKVKFRNTGPVHPLTRQPVADRKRFGGI 1104
Query: 1075 KFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYC 1134
KFGEMERDCLIAHGA+ANLHERLFTLSDS QMHIC+KCKNVANVIQR V GGRK+RGPYC
Sbjct: 1105 KFGEMERDCLIAHGASANLHERLFTLSDSSQMHICQKCKNVANVIQRAVPGGRKIRGPYC 1164
Query: 1135 RICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTEFC 1173
R+C+S D+IVK NVPYGAKLLCQELFSMGI+LKF+T C
Sbjct: 1165 RVCESVDEIVKVNVPYGAKLLCQELFSMGISLKFETRLC 1203
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Source: Ricinus communis Species: Ricinus communis Genus: Ricinus Family: Euphorbiaceae Order: Malpighiales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|224141967|ref|XP_002324332.1| predicted protein [Populus trichocarpa] gi|222865766|gb|EEF02897.1| predicted protein [Populus trichocarpa] | Back alignment and taxonomy information |
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| >gi|225430474|ref|XP_002283296.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|449455519|ref|XP_004145500.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|296082132|emb|CBI21137.3| unnamed protein product [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|356518213|ref|XP_003527775.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|356509878|ref|XP_003523670.1| PREDICTED: DNA-directed RNA polymerase D subunit 2a-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|357466021|ref|XP_003603295.1| DNA-directed RNA polymerase subunit beta [Medicago truncatula] gi|355492343|gb|AES73546.1| DNA-directed RNA polymerase subunit beta [Medicago truncatula] | Back alignment and taxonomy information |
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| >gi|297830452|ref|XP_002883108.1| NRPD2a [Arabidopsis lyrata subsp. lyrata] gi|297328948|gb|EFH59367.1| NRPD2a [Arabidopsis lyrata subsp. lyrata] | Back alignment and taxonomy information |
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| >gi|79416709|ref|NP_189020.2| nuclear RNA polymerase D2A [Arabidopsis thaliana] gi|334185578|ref|NP_001189957.1| nuclear RNA polymerase D2A [Arabidopsis thaliana] gi|75335101|sp|Q9LK40.1|RPD2A_ARATH RecName: Full=DNA-directed RNA polymerase D subunit 2a; Short=AtNRPD2a; Short=Nuclear RNA polymerase D 2a; AltName: Full=Nuclear RNA polymerase E 2; AltName: Full=Protein DEFECTIVE IN MERISTEM SILENCING 2; AltName: Full=Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 2; AltName: Full=RNA polymerase IV subunit 2a; Short=POL IV 2a gi|9293951|dbj|BAB01854.1| DNA-directed RNA polymerase, subunit B [Arabidopsis thaliana] gi|57791156|gb|AAW56422.1| polymerase IV second largest subunit [Arabidopsis thaliana] gi|62183738|gb|AAX73261.1| RNA polymerase IV second-largest subunit [Arabidopsis thaliana] gi|332643291|gb|AEE76812.1| nuclear RNA polymerase D2A [Arabidopsis thaliana] gi|332643292|gb|AEE76813.1| nuclear RNA polymerase D2A [Arabidopsis thaliana] | Back alignment and taxonomy information |
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Prediction of Gene Ontology (GO) Terms
Close Homologs with Gene Ontology terms Detected by BLAST
Original result of BLAST against Gene Ontology (AMIGO)
| ID |
Alignment graph |
Length |
Definition |
Q cover |
H cover |
Identity |
E-value |
| Query | 1173 | ||||||
| TAIR|locus:2095233 | 1172 | NRPD2A "nuclear RNA polymerase | 0.976 | 0.976 | 0.664 | 0.0 | |
| GENEDB_PFALCIPARUM|PFB0715w | 1340 | PFB0715w "DNA-directed RNA pol | 0.744 | 0.651 | 0.304 | 3e-159 | |
| UNIPROTKB|O96236 | 1340 | PFB0715w "DNA-directed RNA pol | 0.744 | 0.651 | 0.304 | 3e-159 | |
| CGD|CAL0004145 | 1234 | orf19.3349 [Candida albicans ( | 0.398 | 0.378 | 0.398 | 4.7e-159 | |
| UNIPROTKB|Q5A8Y5 | 1234 | RPB140 "DNA-directed RNA polym | 0.398 | 0.378 | 0.398 | 4.7e-159 | |
| POMBASE|SPAC23G3.01 | 1210 | rpb2 "RNA polymerase II comple | 0.397 | 0.385 | 0.400 | 7.6e-158 | |
| SGD|S000005677 | 1224 | RPB2 "RNA polymerase II second | 0.467 | 0.447 | 0.374 | 3.9e-155 | |
| ASPGD|ASPL0000039770 | 1252 | AN9120 [Emericella nidulans (t | 0.406 | 0.380 | 0.382 | 3.9e-155 | |
| DICTYBASE|DDB_G0288257 | 1170 | rpb2 "RNA polymerase II core s | 0.934 | 0.936 | 0.335 | 2e-152 | |
| TAIR|locus:2119013 | 1188 | NRPB2 [Arabidopsis thaliana (t | 0.941 | 0.929 | 0.327 | 1e-148 |
| TAIR|locus:2095233 NRPD2A "nuclear RNA polymerase D2A" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 4120 (1455.4 bits), Expect = 0., P = 0.
Identities = 781/1175 (66%), Positives = 931/1175 (79%)
Query: 9 TDPTSLCDLGEEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVE 68
T +L +LGE FL++FC+KAA SFF++YGL+SHQ+NSYN FI++GLQ F SFGE +VE
Sbjct: 18 TGEINLSELGEGFLQSFCKKAATSFFDKYGLISHQLNSYNYFIEHGLQNVFQSFGEMLVE 77
Query: 69 PGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVK 128
P +D KK + +WRYA+++FG+VT++KP+FF+ + E + P HARLQNMTYS+R+KV
Sbjct: 78 PSFDVVKKKDNDWRYATVKFGEVTVEKPTFFSDD--KELEFLPWHARLQNMTYSARIKVN 135
Query: 129 VQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWM--KGVE-- 184
VQ +V+ V SDKFKTG++ Y++K++L + +I+IG IPVMVKS LC KG E
Sbjct: 136 VQVEVFKNTVVKSDKFKTGQDNYVEKKILDVKKQDILIGSIPVMVKSILCKTSEKGKENC 195
Query: 185 -KGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWVSNSMGWTVAYKSENKRNRLIVRLVD 243
KGDC FD GGYF+IKGAEKVF+AQEQ+C KRLW+SNS WTV+++SENKRNR IVRL +
Sbjct: 196 KKGDCAFDQGGYFVIKGAEKVFIAQEQMCTKRLWISNSP-WTVSFRSENKRNRFIVRLSE 254
Query: 244 MSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFAS 303
K ED K EKVL+VYFLSTEIP+W+LFFALGVSSDKE ++LI F +D SI N L AS
Sbjct: 255 NEKAEDYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITNSLIAS 314
Query: 304 IHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTEECMNTYLFPSLHGTKQKARFLGY 363
IH AD C+ FR G NAL YV++ IK T FPP ES +EC++ YLFP L K+KARFLGY
Sbjct: 315 IHVADAVCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLFPGLQSLKKKARFLGY 374
Query: 364 MVKCLLQAYSGRRKCDNRDDFRNKXXXXXXXXXXXXXKVHIAHARKRMAKALQRDLYGDR 423
MVKCLL +Y+G+RKC+NRD FRNK +VH+AHAR++M +A+Q+ L GD
Sbjct: 375 MVKCLLNSYAGKRKCENRDSFRNKRIELAGELLEREIRVHLAHARRKMTRAMQKHLSGDG 434
Query: 424 TVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTR 483
++PIE+YLDAS++TNGLSRAFSTGAWSHPF++ ER+SG+VANLGRANPLQTL+DLRRTR
Sbjct: 435 DLKPIEHYLDASVITNGLSRAFSTGAWSHPFRKMERVSGVVANLGRANPLQTLIDLRRTR 494
Query: 484 QQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQLFN 543
QQV YTGKVGDARYPHPSHWG++CFLSTPDGENCGLVKN+ + GLVST LE + E+LF
Sbjct: 495 QQVLYTGKVGDARYPHPSHWGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEKLFA 554
Query: 544 SGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSXXXXXXXXXXXPTQVEIKRDEL 603
GME+L DD L GK KV ++GDW+G+C DS SFV+ P ++EIKRD+
Sbjct: 555 CGMEELMDDTCTPLFGKHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDKD 614
Query: 604 QSEVRIFMDAGRILRPLLVVENMGKIKSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAW 663
+EVRIF DAGR+LRPLLVVEN+ K+K + Y F LLDHGI+EL+G EEEEDC TAW
Sbjct: 615 DNEVRIFTDAGRLLRPLLVVENLQKLKQEKPSQYPFDHLLDHGILELIGIEEEEDCNTAW 674
Query: 664 GIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGF 723
GIK LLK+ P +THCELD+SFLLG+SC ++PFANHDH RRVLYQSQKH QAIGF
Sbjct: 675 GIKQLLKE-----PKIYTHCELDLSFLLGVSCAVVPFANHDHGRRVLYQSQKHCQQAIGF 729
Query: 724 PTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNV 783
+TNP+IR DTLS QLFYPQ+PLF+T+ S+CL K L+NGQNAIVAVNV
Sbjct: 730 SSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKKE-----------VLFNGQNAIVAVNV 778
Query: 784 HLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIG 843
HLGYNQEDS+VMN+ASLERGMFRSE IRSYKAEVD K+ + KR+ D++V FGK SKIG
Sbjct: 779 HLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVDAKDSE-KRKKMDELVQFGKTHSKIG 837
Query: 844 RVDSLDDDGFPFIGANLQSGDIVIGKYADSGADHSIKLKHTERGMVQKVVLSSNDDGKNF 903
+VDSL+DDGFPFIGAN+ +GDIVIG+ +SGADHSIKLKHTERG+VQKVVLSSND+GKNF
Sbjct: 838 KVDSLEDDGFPFIGANMSTGDIVIGRCTESGADHSIKLKHTERGIVQKVVLSSNDEGKNF 897
Query: 904 SVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTP 963
+ VSLRQVRSPCLGDKFSSMHGQKGVLG+LE Q+NFPFTIQGIVPDIVINPHAFPSRQTP
Sbjct: 898 AAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQGIVPDIVINPHAFPSRQTP 957
Query: 964 GQXXXXXXXXXXX-----XXXXXXCSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERL 1018
GQ + L R+ATPF+TP V ITEQLHRAGFS+WG ER+
Sbjct: 958 GQLLEAALSKGIACPIQKEGSSAAYTKLTRHATPFSTPGVTEITEQLHRAGFSRWGNERV 1017
Query: 1019 YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGE 1078
Y+GR+GEM+RS+IF+GPTFYQRL+HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGE
Sbjct: 1018 YNGRSGEMMRSMIFMGPTFYQRLVHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGE 1077
Query: 1079 MERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQXXXXXXXXXXXPYCRICD 1138
MERDCLIAHGA+ANLHERLFTLSDS QMHICRKCK ANVI+ PYCR+C
Sbjct: 1078 MERDCLIAHGASANLHERLFTLSDSSQMHICRKCKTYANVIERTPSSGRKIRGPYCRVCV 1137
Query: 1139 SGDDIVKANVPYGAKLLCQELFSMGITLKFDTEFC 1173
S D +V+ VPYGAKLLCQELFSMGITL FDT+ C
Sbjct: 1138 SSDHVVRVYVPYGAKLLCQELFSMGITLNFDTKLC 1172
|
|
| GENEDB_PFALCIPARUM|PFB0715w PFB0715w "DNA-directed RNA polymerase II second largest subunit, putative" [Plasmodium falciparum (taxid:5833)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|O96236 PFB0715w "DNA-directed RNA polymerase" [Plasmodium falciparum 3D7 (taxid:36329)] | Back alignment and assigned GO terms |
|---|
| CGD|CAL0004145 orf19.3349 [Candida albicans (taxid:5476)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|Q5A8Y5 RPB140 "DNA-directed RNA polymerase" [Candida albicans SC5314 (taxid:237561)] | Back alignment and assigned GO terms |
|---|
| POMBASE|SPAC23G3.01 rpb2 "RNA polymerase II complex subunit Rpb2" [Schizosaccharomyces pombe (taxid:4896)] | Back alignment and assigned GO terms |
|---|
| SGD|S000005677 RPB2 "RNA polymerase II second largest subunit B150" [Saccharomyces cerevisiae (taxid:4932)] | Back alignment and assigned GO terms |
|---|
| ASPGD|ASPL0000039770 AN9120 [Emericella nidulans (taxid:162425)] | Back alignment and assigned GO terms |
|---|
| DICTYBASE|DDB_G0288257 rpb2 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)] | Back alignment and assigned GO terms |
|---|
| TAIR|locus:2119013 NRPB2 [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Prediction of Enzyme Commission (EC) Number
EC Number Prediction by Annotation Transfer from SWISS-PROT Entries
Original result of BLAST against SWISS-PROT
| ID | Name | Annotated EC number | Identity | Query coverage | Hit coverage | RBH(Q2H) | RBH(H2Q) |
| Q8SR75 | RPB2_ENCCU | 2, ., 7, ., 7, ., 6 | 0.3447 | 0.9096 | 0.9351 | yes | no |
| Q8CFI7 | RPB2_MOUSE | 2, ., 7, ., 7, ., 6 | 0.3448 | 0.9215 | 0.9207 | yes | no |
| P08518 | RPB2_YEAST | 2, ., 7, ., 7, ., 6 | 0.3441 | 0.9548 | 0.9150 | yes | no |
| Q10578 | RPB2_CAEEL | 2, ., 7, ., 7, ., 6 | 0.3292 | 0.9386 | 0.9228 | yes | no |
| P08266 | RPB2_DROME | 2, ., 7, ., 7, ., 6 | 0.3398 | 0.9266 | 0.9243 | yes | no |
| P30876 | RPB2_HUMAN | 2, ., 7, ., 7, ., 6 | 0.3456 | 0.9215 | 0.9207 | yes | no |
| Q02061 | RPB2_SCHPO | 2, ., 7, ., 7, ., 6 | 0.3459 | 0.9488 | 0.9198 | yes | no |
| Q54J75 | RPB2_DICDI | 2, ., 7, ., 7, ., 6 | 0.3505 | 0.9207 | 0.9230 | yes | no |
| Q6FLD5 | RPB2_CANGA | 2, ., 7, ., 7, ., 6 | 0.3439 | 0.9386 | 0.9002 | yes | no |
| Q9LK40 | RPD2A_ARATH | 2, ., 7, ., 7, ., 6 | 0.6927 | 0.9761 | 0.9769 | yes | no |
| Q03587 | RPOB_THEAC | 2, ., 7, ., 7, ., 6 | 0.3054 | 0.8976 | 0.8811 | yes | no |
| Q753Q4 | RPB2_ASHGO | 2, ., 7, ., 7, ., 6 | 0.3453 | 0.9411 | 0.9034 | yes | no |
| P11513 | RPOB_SULAC | 2, ., 7, ., 7, ., 6 | 0.3239 | 0.8976 | 0.9351 | yes | no |
EC Number Prediction by Ezypred Server
Original result from Ezypred Server
Fail to connect to Ezypred Server
EC Number Prediction by EFICAz Software
| Prediction Level | EC number | Confidence of Prediction |
| 3rd Layer | 2.7.7 | 0.766 |
| 4th Layer | 2.7.7.6 | 0.824 |
Prediction of Functionally Associated Proteins
Functionally Associated Proteins Detected by STRING
Original result from the STRING server
Fail to connect to STRING server
Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
| ID | Alignment Graph | Length |
Definition |
E-value |
| Query | 1173 | |||
| PRK08565 | 1103 | PRK08565, PRK08565, DNA-directed RNA polymerase su | 0.0 | |
| COG0085 | 1060 | COG0085, RpoB, DNA-directed RNA polymerase, beta s | 0.0 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 0.0 | |
| TIGR03670 | 599 | TIGR03670, rpoB_arch, DNA-directed RNA polymerase | 1e-167 | |
| PRK07225 | 605 | PRK07225, PRK07225, DNA-directed RNA polymerase su | 1e-162 | |
| pfam00562 | 373 | pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do | 1e-137 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 6e-83 | |
| PRK09606 | 494 | PRK09606, PRK09606, DNA-directed RNA polymerase su | 2e-66 | |
| pfam04563 | 394 | pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub | 3e-47 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 2e-46 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 4e-39 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 6e-34 | |
| pfam04560 | 78 | pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do | 2e-26 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 2e-24 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 3e-23 | |
| pfam04566 | 63 | pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, do | 2e-17 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 3e-14 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 1e-13 | |
| pfam04561 | 185 | pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do | 1e-13 | |
| pfam04565 | 68 | pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do | 1e-11 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 3e-09 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 6e-08 | |
| pfam04567 | 46 | pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, do | 1e-07 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 9e-07 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 2e-06 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 6e-06 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 3e-05 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 0.001 |
| >gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Score = 744 bits (1924), Expect = 0.0
Identities = 407/1207 (33%), Positives = 587/1207 (48%), Gaps = 194/1207 (16%)
Query: 32 SFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVE-PGYDPSKKGEGEWRYASMRFGQ 90
++F E GLV ++SYN+FI+ GLQ+ D FGE E PG + G+
Sbjct: 7 AYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLK-------------IVLGK 53
Query: 91 VTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQ 150
+ + +P +G + + P ARL+N+TY++ + + + G E
Sbjct: 54 IRVGEPEIKEADGSERP-ITPMEARLRNLTYAAPLYLTMIPVE------------NGIEY 100
Query: 151 YIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDHGGYFIIKGAEKV 204
E + IG +P+MVKS +C + G +E G+ D GGYFII G+E+V
Sbjct: 101 ---------EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERV 151
Query: 205 FVAQEQICLKRLWVSNSMGWTVAYKSE-----------NKRNRLIVRLVDMSKFEDIKGG 253
V+QE + R+ V A S R ++ V E K G
Sbjct: 152 IVSQEDLAPNRVLV----DKGEAGSSITHTAKVISSRAGYRAQVTV--------ERRKDG 199
Query: 254 EKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDE 313
+S + +IP IL ALG+ +D++IV + D I L S+ A
Sbjct: 200 TIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSL---DPEIQQELLPSLEQAS---SI 253
Query: 314 FRKGRNALKYVDKLIKGTTFPPG-------ESTEECMNTYLFPSLHGT-----KQKARFL 361
+AL Y+ K + G E E+ ++ YL P L GT +KA FL
Sbjct: 254 AATVEDALDYIGKRVA-----IGQPREYRIERAEQILDKYLLPHL-GTSPEDRIKKAYFL 307
Query: 362 GYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYG 421
G M LL+ Y GRR+ D++D + NKRL LAG+LL +V K + L++
Sbjct: 308 GQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEK--SY 365
Query: 422 DRTVRP-IEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLR 480
R + + + I+T + A +TG W RT G+ L R N L TL LR
Sbjct: 366 ARGRKLDLRAIVRPDIITERIRHALATGNW--VGGRT----GVSQLLDRTNYLSTLSHLR 419
Query: 481 R-----TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILE 535
R +R Q + +AR H + WG+IC TP+G NCGLVKNL + +S + E
Sbjct: 420 RVVSPLSRGQPHF-----EARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDE 474
Query: 536 -PIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPT 594
+ E L+ G+ + + +V+++G IG D ++R RR ++
Sbjct: 475 EEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISD 534
Query: 595 QVEIK--RDELQSEVRIFMDAGRILRPLLVVENMGKIK-------SLEGKNYTFQALLDH 645
+V + +EV + D+GR+ RPL+VVEN GK K L+ TF L+
Sbjct: 535 EVNVAYIETGEINEVYVNCDSGRVRRPLIVVEN-GKPKLTREHVEKLKKGELTFDDLVKM 593
Query: 646 GIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDH 705
G+IE + EEEE+ Y+ D ED P + TH E+ +LG++ IIP+ H+
Sbjct: 594 GVIEYLDAEEEENA-------YVALDPEDLTP-EHTHLEIWPPAILGITASIIPYPEHNQ 645
Query: 706 ARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHI 765
+ R YQ+ + Q++G N IR DT H L YPQRPL +T + +G Y
Sbjct: 646 SPRNTYQAAM-AKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIG---YND--- 698
Query: 766 LPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVK 825
RP GQNA+VAV + GYN ED+++MN+AS+ERG+ RS R+Y+ E + K
Sbjct: 699 --RPA---GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETE-ERKYP--- 749
Query: 826 RRSSDDMVNFGKIQSKIGRVDS-------------LDDDGFPFIGANLQSGDIVIGK--- 869
G + KI + LD+DG ++ GD++IGK
Sbjct: 750 ----------GGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSP 799
Query: 870 ------YADSGA------DHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLG 917
+ D S+ ++H E+G+V V+++ + +G V +R +R P LG
Sbjct: 800 PRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELG 859
Query: 918 DKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAA 977
DKF+S HGQKGV+G L QE+ PFT GIVPD++INPHA PSR T GQLLE+ GK A
Sbjct: 860 DKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAAL 919
Query: 978 LGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTF 1037
G+ + ATPF + + ++L + G+ GTE +YDGRTGE +++ IFIG +
Sbjct: 920 EGRFV------DATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVY 973
Query: 1038 YQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERL 1097
YQ+L HM DK+ R GPV LTRQP R R GG++FGEMERDCLI HGAA L ERL
Sbjct: 974 YQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERL 1033
Query: 1098 FTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQ 1157
SD +++C C ++A R+ C I +I V Y KLL Q
Sbjct: 1034 LDSSDKTTIYVCELCGHIAWY-------DRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQ 1086
Query: 1158 ELFSMGI 1164
EL SMGI
Sbjct: 1087 ELMSMGI 1093
|
Length = 1103 |
| >gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B | Back alignment and domain information |
|---|
| >gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6 | Back alignment and domain information |
|---|
| >gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B''; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7 | Back alignment and domain information |
|---|
| >gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4 | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, domain 2 | Back alignment and domain information |
|---|
| >gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, domain 3 | Back alignment and domain information |
|---|
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5 | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | Back alignment and domain information |
|---|
| >gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1173 | |||
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 100.0 | |
| PRK08565 | 1103 | DNA-directed RNA polymerase subunit B; Provisional | 100.0 | |
| KOG0216 | 1111 | consensus RNA polymerase I, second largest subunit | 100.0 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 100.0 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 100.0 | |
| TIGR02013 | 1065 | rpoB DNA-directed RNA polymerase, beta subunit. Th | 100.0 | |
| cd00653 | 866 | RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po | 100.0 | |
| PRK00405 | 1112 | rpoB DNA-directed RNA polymerase subunit beta; Rev | 100.0 | |
| CHL00001 | 1070 | rpoB RNA polymerase beta subunit | 100.0 | |
| CHL00207 | 1077 | rpoB RNA polymerase beta subunit; Provisional | 100.0 | |
| PRK09603 | 2890 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| PRK14844 | 2836 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| PRK07225 | 605 | DNA-directed RNA polymerase subunit B'; Validated | 100.0 | |
| TIGR03670 | 599 | rpoB_arch DNA-directed RNA polymerase subunit B. T | 100.0 | |
| PF00562 | 386 | RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; Int | 100.0 | |
| PRK09606 | 494 | DNA-directed RNA polymerase subunit B''; Validated | 100.0 | |
| PF04563 | 203 | RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter | 100.0 | |
| PF04560 | 81 | RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; Int | 99.96 | |
| PF04565 | 68 | RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int | 99.93 | |
| PF04561 | 190 | RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; Int | 99.82 | |
| PF04566 | 63 | RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; Int | 99.68 | |
| PF04567 | 48 | RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int | 98.96 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 98.91 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 98.76 | |
| PF06883 | 58 | RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do | 97.71 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 97.1 | |
| PHA03394 | 865 | lef-8 DNA-directed RNA polymerase subunit beta-lik | 94.59 |
| >KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=4.4e-274 Score=2355.32 Aligned_cols=1091 Identities=42% Similarity=0.675 Sum_probs=1020.1
Q ss_pred hhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCccccCC
Q 001050 23 KTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGN 102 (1173)
Q Consensus 23 ~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~~e~~ 102 (1173)
+|++|.+|++||..+||+++|++||+.|++.++++|+++.++|+.....++. .....++.|.|+++++.+|+..|.|
T Consensus 2 qe~~w~vis~~f~ekglvrqQldsFdeFiq~~~qeiv~~~p~i~l~~~~qh~---~~~~~r~~l~f~qiylskP~~~e~d 78 (1141)
T KOG0214|consen 2 QEDCWDVISAYFEEKGLVRQQLDSFDEFIQQTLQEIVADSPKIELQDEAQHT---QENPARYQLFFEQIYLSKPTHTESD 78 (1141)
T ss_pred hhHHHHHHHhhhcccchHHHHHHHHHHHHHHHHHHHHhcCCCceehhhhhhh---ccCccceEEEeeeEEEecccccccC
Confidence 7899999999999999999999999999999999999999999876544443 1234568999999999999999999
Q ss_pred CCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCccccCC
Q 001050 103 GGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKG 182 (1173)
Q Consensus 103 ~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C~L~~ 182 (1173)
|....++|+|||+|++|||+||||+++..+... ..+ ..+.+.++|+||+||||+||.+|.|++
T Consensus 79 -g~~~~m~p~eARlrnLTYSspLyVd~~k~~~~~------~~~----------~~~~~~qkvfIGkIPiMlrS~~C~l~~ 141 (1141)
T KOG0214|consen 79 -GSTSTMFPNEARLRNLTYSSPLYVDATKIVKTS------RDE----------VEDMQEQKVFIGKIPIMLRSSYCLLSG 141 (1141)
T ss_pred -CCccccCchhhHhhhcccccceEEEeEEEEeec------ccc----------ccccccceeeEeccceeeehhhhhhcc
Confidence 999999999999999999999999999877431 000 122346789999999999999999999
Q ss_pred ------CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCC----ceEEEEEeecCC-----ceEEEEEEecCc
Q 001050 183 ------VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSM----GWTVAYKSENKR-----NRLIVRLVDMSK 246 (1173)
Q Consensus 183 ------~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~----~~~a~irS~~~~-----~~~~i~~~~~~~ 246 (1173)
.+.||||+|+||||||||+|||+|+||++|+|++|+ .+.. .|++++||..++ ++.|+++.....
T Consensus 142 ~~d~dl~~l~eCp~DqgGyfIINGseKVlIAQe~matn~vyvf~k~~p~~~ay~~EirS~le~~sR~~stl~v~~~ar~~ 221 (1141)
T KOG0214|consen 142 LTDKDLTELGECPYDQGGYFIINGSEKVLIAQEKMATNIVYVFKKAHPGTYAYTGEIRSCLERSSRFISTLSVNMDARAG 221 (1141)
T ss_pred cchhhhhhccCCCcCCCceEEEcCceeeeeehhhccCceEEEEecCCCCceeEeeeeehhhhccCCCcceeeeeeccccC
Confidence 789999999999999999999999999999999999 4322 679999987665 777888764321
Q ss_pred cccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHHHHHh
Q 001050 247 FEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDK 326 (1173)
Q Consensus 247 ~~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~yig~ 326 (1173)
+.-.|.++++|++++||+++||||||+.+|+||+++|+|+.+|.+|.+++.++++++ +-+..+..||+|||+
T Consensus 222 ----~gq~i~~tlpyikqeIPI~ilfrALG~v~dreILehIcYd~~D~em~e~lkpsieea----fviq~qn~ALdfig~ 293 (1141)
T KOG0214|consen 222 ----KGQEIIATLPYIKQEIPILILFRALGFVSDREILEHICYDFDDAEMFESLKPSIEEA----FVIQEQNVALDFIGQ 293 (1141)
T ss_pred ----CCceEEEEeeeecccCcEEEEehhhcCCccHHHHHhhcCCCCcHHHHHHhhhhhhhh----hhhhhhHHHHHHHHh
Confidence 123788999999999999999999999999999999999999999999999999998 558889999999998
Q ss_pred h---ccCCCCCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhhHHHH
Q 001050 327 L---IKGTTFPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLERE 399 (1173)
Q Consensus 327 ~---~~~~~~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~Ll~~l 399 (1173)
+ .+..++.++++|+++|.+++|||++..+ +|++||+|||++|+.++.|++.+||+|||+|||++++|+||..+
T Consensus 294 rga~~Gvtkekri~yakdiLqKe~lPhi~~~e~~etkKA~fLGYmi~rlll~aLgRr~~ddRDHfG~KRLDlaGpLLa~l 373 (1141)
T KOG0214|consen 294 RGACIGVTKEKRIKYAKEILQKELLPHVGLGEICETKKAYFLGYMVHRLLLAALGRRELDDRDHFGNKRLDLAGPLLAKL 373 (1141)
T ss_pred cCCCCCCCcchhhHHHHHHHHHHhccccccchhhhhhHHHHHHhhHHHHHHHHcCCCCccchhhccccchhhchhHHHHH
Confidence 7 5667888999999999999999999887 89999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhhhccc
Q 001050 400 LKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDL 479 (1173)
Q Consensus 400 fr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~lSh~ 479 (1173)
||..|+++++++...+++++++..++ ++..+++++.||++++|+||||||+.++..|+.++||||||+|+||+++|||+
T Consensus 374 fR~lf~~l~rd~~~~mQk~le~~~df-ni~~aika~iIt~gl~yslaTgnwgdq~ka~~~ragVsQVLnR~t~~sTLsHl 452 (1141)
T KOG0214|consen 374 FRSLFAKLLRDVTRYMQKCLENGVDF-NIELAIKAKIITNGLNYALATGNWGDQKKAMQGRAGVSQVLNRLNPLSTLSHL 452 (1141)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCccc-eEEEEEEeeeecccceeeeccCCccchhHHhhccccHHHHhccccHHHHHHHH
Confidence 99999999999999999999998889 89999999999999999999999999988899999999999999999999999
Q ss_pred cccccccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceecccccCccCC
Q 001050 480 RRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKLADDASYSLG 558 (1173)
Q Consensus 480 Rrv~s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~~~~~~~~~~ 558 (1173)
||+|+|.++++|.+.||+|||||||++||+|||||++||||||||+||.|+.|. ++|++++|+++||+.++++++....
T Consensus 453 RR~n~Pigr~GKlAkpRqlHnthwGmvCPaeTPEGqacGLVKNLSLmayIsvGS~~sPi~EfLeewgmE~le~~~ps~~~ 532 (1141)
T KOG0214|consen 453 RRTNSPIGRTGKLAKPRQLHNSHWGMVCPAETPEGQACGLVKNLSLMAYISVGSLESPIVEFLEEWGMENLEEISPSPSP 532 (1141)
T ss_pred hhcCCccccccccCCccccCcccceeeccccCCCcceeeccccceEEEEEecCCCccHHHHHHHHhchhhHhhcCCCcCC
Confidence 999999999999999999999999999999999999999999999999999998 9999999999999999999999888
Q ss_pred CcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeeccc------c---c
Q 001050 559 GKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMG------K---I 629 (1173)
Q Consensus 559 ~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~------~---~ 629 (1173)
+.++||+||.|+|++++|+.++..||.+||+..++.++++++|...++++||||+||++||||+|+|++ + +
T Consensus 533 datkvfvNG~wvGlhrdp~~l~~tlr~lRR~~di~~Evs~vRDIr~kE~ri~tDaGR~~rPLliven~~l~~~k~hi~~L 612 (1141)
T KOG0214|consen 533 DATKVFVNGVWVGLHRDPEELVATLKRLRRQFDIIAEVSMVRDIRDKEIRIFTDAGRSLRPLLIVENAKLLIKKRHIRAL 612 (1141)
T ss_pred CceEEEEcccEEEecCCHHHHHHHHHHHHHhhccchhhhhhccccccceeeeeccCccccceEEEechhhhhhhHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999995 2 3
Q ss_pred ccccCCcchhHhhhhcCceeeecccccceeEEeecccccccccCCCCCceeeeecccccccccceeecccccCCCccchh
Q 001050 630 KSLEGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRV 709 (1173)
Q Consensus 630 ~~~~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn 709 (1173)
+.......+|..|+.+|.+||||++||+..+||+.++++.+. ..+..||||||||+.|||++||.||||||||||||
T Consensus 613 ~~~~~~~~~w~~lv~~G~ie~idteeEEtvmiam~~~dL~~~---~~~~~~THCEiHpsmILgv~asiIpFpdh~qspr~ 689 (1141)
T KOG0214|consen 613 KQSKPNEYRWAHLLSSGEVEYIDTEEEETVMIAMGPKDLAES---AYPKTYTHCEIHPSMILGVCASIIPFPDHNQSPRN 689 (1141)
T ss_pred hhCchhhcchhhhccccceeeeccchhhhHHHhcCHHHHhhc---cCCcccccccccHHHhhhhceeeeecCCCCCchHH
Confidence 333345789999999999999999999999999999999742 23678999999999999999999999999999999
Q ss_pred hhhhcccccccccccccCCeeeeeccccccccCCcceEeccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCC
Q 001050 710 LYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQ 789 (1173)
Q Consensus 710 ~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~ 789 (1173)
+||++ |+|||||++.+|+..|+||..|.|+|||+|+|+|+++++. .+.++|+|+|++||++||+||||
T Consensus 690 tYQsa-~~kqamg~y~tn~~vR~dtl~~~l~ypqkpl~tt~~~e~l-----------~~~eL~aG~NaiVAi~~~~GYNq 757 (1141)
T KOG0214|consen 690 TYQSA-MGKQAMGVYHTNPQVRMDTLAKVLYYPQKPLVTTRAMEYL-----------RFRELPAGQNAIVAIACYSGYNQ 757 (1141)
T ss_pred HHHHH-HhhhcceeeeecchhhhhhhhhcccccccchhhHHHHhhh-----------hhhhcccccceEEEEecccCccH
Confidence 99999 9999999999999999999999999999999999999999 89999999999999999999999
Q ss_pred CCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccccccccccccccccccCCCCCCCCcccCcEEccCCeEEEE
Q 001050 790 EDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGK 869 (1173)
Q Consensus 790 EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k 869 (1173)
|||||+|+++++||+|+|++|++|+.+...... +..+.|+.|........+.+.|++||+||++.+|++|..|||+|||
T Consensus 758 EDsvimn~s~v~rg~FrS~~~RsYk~q~~~~~~-~~ee~~~~~~~~~~~~mr~~~~dkLdddG~i~~G~~vs~~Dv~iGk 836 (1141)
T KOG0214|consen 758 EDSVIMNQSSVDRGLFRSFFIRSYKDQEHKKDQ-GPEEIFEEPPRGEGRGMRNGKYDKLDDDGIIMPGSRVSGGDVLIGK 836 (1141)
T ss_pred HHHHHHHhhhhhcchhhhhhhhHHHhhhhhccc-ccccccccccccccccccccccccccccCCccccceeecCCEEecc
Confidence 999999999999999999999999988765432 3445678888777777888889999999999999999999999999
Q ss_pred ecCC---------------CceeeEEccCCCceEEEEEEEEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeee
Q 001050 870 YADS---------------GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLE 934 (1173)
Q Consensus 870 ~~~~---------------~~~~s~~~~~~~~g~v~~v~~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~ 934 (1173)
.+|. .+|.|++++++|.|+||+|.++++.+|.++++|++|+.|.|++|||||||||||||||.++
T Consensus 837 ~t~~~~~~~~~~~~~~~~t~~d~s~~Lr~~e~Givd~V~vt~n~~G~kF~kv~vr~~ripqiGDKfasrHgqKG~ig~~~ 916 (1141)
T KOG0214|consen 837 TTPQPAKEDESGPEDRLYTKRDHSTKLRHTERGIVDQVWVTKNSEGPKFVKVRVRQVRIPQIGDKFASRHGQKGTIGITY 916 (1141)
T ss_pred ccCCcccchhccccccccccccceeecccCCcceEEEEEEecCCCCCceeEEEEeecccccccchhccccccCcccccee
Confidence 9974 5899999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCC
Q 001050 935 SQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWG 1014 (1173)
Q Consensus 935 ~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G 1014 (1173)
++||||||.+|++|||||||||||||||||||+||++||.++ +.|...|+|||++..+..+...|.++||..+|
T Consensus 917 ~qedmpft~eGi~pDiiiNPhaiPSRmtig~liEc~lgk~~a------~~~e~~~atpFs~v~v~~is~~l~~~g~~~~G 990 (1141)
T KOG0214|consen 917 RQEDMPFTIEGIVPDIIINPHAIPSRMTIGQLIECLLGKVAA------YEGEEGDATPFSDVTVSKISANLHVYGYQYRG 990 (1141)
T ss_pred ecCCCCccccCCCcceEECcccCccccchhhhHHHhhhhhhh------cccccccCCCCCccchhcccchHHHhccccCC
Confidence 999999999999999999999999999999999999999999 99999999999999999999999999999999
Q ss_pred ceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHH
Q 001050 1015 TERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLH 1094 (1173)
Q Consensus 1015 ~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~ 1094 (1173)
+|.||+|+||++|.++||+||.|||||+|||+||+|+|++||++.+||||++||||+||||||||||||+||||||++|+
T Consensus 991 ~e~~ynGrtG~~~~~~if~GptyyqrL~Hmvd~kih~R~~Gp~q~ltRQP~~gRsr~GGlRfGEMErdc~iahGaa~~L~ 1070 (1141)
T KOG0214|consen 991 NERMYNGRTGRKLRAQIFIGPTYYQRLKHMVDDKIHSRARGPVQILTRQPVEGRSRDGGLRFGEMERDCLIAHGAAAFLK 1070 (1141)
T ss_pred CEEEecCCCCceeeeeeecCchHHHHHHHhhhheeeecccCCceeeeccccccccccCCeeeehhHHHHHHHhhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCCCccceecccccCCccchheeeecCCcccCCccccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1095 ERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1095 erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
|||+..||.|.+|+|..||..+ ..+.+.+.+.|+.|.+.+.+..+.+|||||||+|||+||||.+++.++
T Consensus 1071 ERL~~~SD~~~~~~c~~c~l~~-------i~~~~~n~~~ck~c~n~~~v~~v~ipya~kLl~qelmsmni~pr~~~~ 1140 (1141)
T KOG0214|consen 1071 ERLFEKSDAYRVHICVLCGLTA-------IAGLIPNSFECRGCENKTLVVRVYIPYAAKLLFQELMSMNIAPRRKTK 1140 (1141)
T ss_pred HHhhccCccceEEEeccchhhh-------hhccCCCccccccccCccceEEEechhHHHHHHHHHHhccCccccccC
Confidence 9999999999999999999544 556666678999999999999999999999999999999999998764
|
|
| >PRK08565 DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
| >KOG0216 consensus RNA polymerase I, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit | Back alignment and domain information |
|---|
| >cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >PRK00405 rpoB DNA-directed RNA polymerase subunit beta; Reviewed | Back alignment and domain information |
|---|
| >CHL00001 rpoB RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >CHL00207 rpoB RNA polymerase beta subunit; Provisional | Back alignment and domain information |
|---|
| >PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >PRK07225 DNA-directed RNA polymerase subunit B'; Validated | Back alignment and domain information |
|---|
| >TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B | Back alignment and domain information |
|---|
| >PF00562 RNA_pol_Rpb2_6: RNA polymerase Rpb2, domain 6; InterPro: IPR007120 DNA-directed RNA polymerases 2 | Back alignment and domain information |
|---|
| >PRK09606 DNA-directed RNA polymerase subunit B''; Validated | Back alignment and domain information |
|---|
| >PF04563 RNA_pol_Rpb2_1: RNA polymerase beta subunit; InterPro: IPR007644 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04560 RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; InterPro: IPR007641 RNA polymerases catalyse the DNA-dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04565 RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; InterPro: IPR007645 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PF04567 RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; InterPro: IPR007647 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0215 consensus RNA polymerase III, second largest subunit [Transcription] | Back alignment and domain information |
|---|
| >PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2 | Back alignment and domain information |
|---|
| >COG0085 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional | Back alignment and domain information |
|---|
Homologous Structure Templates
Structure Templates Detected by BLAST
Original result of BLAST against Protein Data Bank
| ID | Alignment Graph | Length |
Definition |
E-value | |
| Query | 1173 | ||||
| 1i3q_B | 1224 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 1e-171 | ||
| 3h0g_B | 1210 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 1e-169 | ||
| 2pmz_B | 1124 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 1e-136 | ||
| 2waq_B | 1131 | The Complete Structure Of The Archaeal 13-Subunit D | 1e-135 | ||
| 1iw7_C | 1119 | Crystal Structure Of The Rna Polymerase Holoenzyme | 2e-32 | ||
| 1l9u_C | 1118 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 4e-31 | ||
| 1ynj_C | 1119 | Taq Rna Polymerase-Sorangicin Complex Length = 1119 | 4e-31 | ||
| 1hqm_C | 1119 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 5e-31 | ||
| 1i6v_C | 1118 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 5e-31 | ||
| 3lu0_C | 1342 | Molecular Model Of Escherichia Coli Core Rna Polyme | 7e-17 | ||
| 3iyd_C | 1342 | Three-Dimensional Em Structure Of An Intact Activat | 7e-17 |
| >pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 | Back alignment and structure |
|
| >pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 | Back alignment and structure |
| >pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 | Back alignment and structure |
| >pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 1131 | Back alignment and structure |
| >pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1119 | Back alignment and structure |
| >pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1118 | Back alignment and structure |
| >pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex Length = 1119 | Back alignment and structure |
| >pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 1119 | Back alignment and structure |
| >pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1118 | Back alignment and structure |
| >pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1342 | Back alignment and structure |
| >pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1342 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... Length = 1224 | Back alignment and structure |
|---|
Score = 1198 bits (3102), Expect = 0.0
Identities = 406/1248 (32%), Positives = 614/1248 (49%), Gaps = 110/1248 (8%)
Query: 1 MDSDDNGFTDPTSLCDLGEEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFD 60
+S+ DP D +FF E GLVS Q++S+N+F+ LQ
Sbjct: 5 ANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIIC 64
Query: 61 SFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQNMT 120
I+E + + + R + FG++ + KP +G H ++P+ ARL+N+T
Sbjct: 65 EDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGV-THALYPQEARLRNLT 123
Query: 121 YSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWM 180
YSS + V V+ + Y + E ++ E+ + IGR+P+M++S C++
Sbjct: 124 YSSGLFVDVKKRTYEAID--VPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYL 181
Query: 181 KG------VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-----SNSMGWTVAYK 229
+ +C FD GGYFII G+EKV +AQE+ + V + + +
Sbjct: 182 SEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIR 241
Query: 230 S--ENKRNRLIVRLVDMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLI 287
S E + V + E ++ ++ +IPI I+F ALG+ D EI+ I
Sbjct: 242 SALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHI 301
Query: 288 DFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTE---ECMN 344
+ D +L +L + D D AL ++ + + + + +
Sbjct: 302 CYDVNDWQMLEMLKPCVEDGFVIQDR----ETALDFIGRRGTALGIKKEKRIQYAKDILQ 357
Query: 345 TYLFPSLHGT----KQKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGELLEREL 400
P + +KA FLGYM+ LL R+ D+RD F KRL+LAG LL +
Sbjct: 358 KEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF 417
Query: 401 KVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERI 460
K K + + +QR + ++ ++A +T+GL A +TG W K
Sbjct: 418 KTLFKKLTKDIFRYMQRTVEEAHDFN-MKLAINAKTITSGLKYALATGNWGEQKKAMSSR 476
Query: 461 SGIVANLGRANPLQTLVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLV 520
+G+ L R TL LRRT + GK+ R H +HWG +C TP+G+ CGLV
Sbjct: 477 AGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLV 536
Query: 521 KNLGVTGLVST-SILEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSF 579
KNL + +S + PI L GME L D + +VFV+G W GV ++
Sbjct: 537 KNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARL 596
Query: 580 VSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVEN------------MG 627
+ LR RR+ ++ +V + RD + E++IF DAGR+ RPL +VE+ G
Sbjct: 597 METLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKG 656
Query: 628 KIKSL-------------EGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIED 674
I L + + YT+ +LL+ G++E + EEEE A + L +
Sbjct: 657 HIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEAN 716
Query: 675 K----------------KPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSS 718
+ FTHCE+ S +LG++ IIPF +H+ + R YQS
Sbjct: 717 EENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQS-AMGK 775
Query: 719 QAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAI 778
QA+G TN ++R+DT+++ L+YPQ+PL T + L EL GQNAI
Sbjct: 776 QAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFR-----------ELPAGQNAI 824
Query: 779 VAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKI 838
VA+ + GYNQEDS++MN++S++RG+FRS RSY + M + +
Sbjct: 825 VAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQ-RTNTL 883
Query: 839 QSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYA---------------DSGADHSIKLKH 883
+ K G D LDDDG G + D++IGK S D S L+
Sbjct: 884 RMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRS 943
Query: 884 TERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTI 943
TE G+V +V++++N DG F V +R + P +GDKF+S HGQKG +G +E+ PFT
Sbjct: 944 TENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA 1003
Query: 944 QGIVPDIVINPHAFPSRQTPGQLLEAALGKGIAALGKGICSGLKRYATPFATPSVDAITE 1003
+GIVPD++INPHA PSR T L+E L K SG + A+PF +V+ I++
Sbjct: 1004 EGIVPDLIINPHAIPSRMTVAHLIECLLSKV------AALSGNEGDASPFTDITVEGISK 1057
Query: 1004 QLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQ 1063
L G+ G E +Y+G TG+ + + IF GPT+YQRL HM +DK+ R GP+ LTRQ
Sbjct: 1058 LLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ 1117
Query: 1064 PVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVV 1123
PV R R GG++FGEMERDC+IAHGAA+ L ERL SD++++HIC C + +
Sbjct: 1118 PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVI----- 1172
Query: 1124 GGGRKVRGPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171
C+ CD+ DI + ++PY AKLL QEL +M IT + T+
Sbjct: 1173 -AKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTD 1219
|
| >3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1210 | Back alignment and structure |
|---|
| >4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B Length = 1131 | Back alignment and structure |
|---|
| >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 | Back alignment and structure |
|---|
| >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... Length = 1119 | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 | Back alignment and structure |
|---|
| >3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} Length = 188 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1173 | |||
| 3h0g_B | 1210 | DNA-directed RNA polymerase II subunit RPB2; trans | 100.0 | |
| 1twf_B | 1224 | DNA-directed RNA polymerase II 140 kDa polypeptid; | 100.0 | |
| 4ayb_B | 1131 | DNA-directed RNA polymerase; transferase, multi-su | 100.0 | |
| 2a6h_C | 1119 | DNA-directed RNA polymerase beta chain; RNA polyme | 100.0 | |
| 3lu0_C | 1342 | DNA-directed RNA polymerase subunit beta; E. coli | 100.0 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 99.96 | |
| 3tbi_B | 228 | DNA-directed RNA polymerase subunit beta; transcri | 99.25 | |
| 3qqc_A | 436 | DNA-directed RNA polymerase subunit B, DNA-direct | 99.06 | |
| 3lti_A | 296 | DNA-directed RNA polymerase subunit beta; BBM2, nu | 98.75 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 96.22 |
| >3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} | Back alignment and structure |
|---|
Probab=100.00 E-value=4.3e-291 Score=2725.30 Aligned_cols=1115 Identities=37% Similarity=0.607 Sum_probs=994.7
Q ss_pred cccchhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEEccCcc
Q 001050 19 EEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSF 98 (1173)
Q Consensus 19 ~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i~~P~~ 98 (1173)
++++++|+|.+|++||+.+||++|||||||+|+++||++|++++++|+++.+.++...+......+.|+|++++|++|++
T Consensus 10 ~~~~~ed~w~li~aff~~~gLV~qHIdSFN~FI~~~Lq~IV~~~~~I~~~~~~~~~~~~~~~~~~~~l~f~~i~v~kP~~ 89 (1210)
T 3h0g_B 10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPTM 89 (1210)
T ss_dssp CCCCHHHHHHHHHHHHHHTCTTCSSSSSSSSSTTTTHHHHSSTTCCCC-------------------CEEEEEECCCCCC
T ss_pred ccCCHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHHhccCcEEecCccCcccccccCCceEEEEEEEEEEcCCce
Confidence 45899999999999999999999999999999999999999999999876543221111122346889999999999999
Q ss_pred ccCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEecCCcc
Q 001050 99 FAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLC 178 (1173)
Q Consensus 99 ~e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMvkS~~C 178 (1173)
.+.+ +..++|||+|||+|++||+|||+|+|++++.+.. ++..++...............++.||+|||||||++|
T Consensus 90 ~e~d-~~~~~l~P~EcRlR~lTYsapl~Vdi~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~v~IG~iPIMlrS~~C 164 (1210)
T 3h0g_B 90 TEAD-GSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAA----DSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFC 164 (1210)
T ss_dssp BCTT-SCBCCCCTTTTTTTCCCCEEEEEEEEEC-------------------------CCSSCCCEEEEEEECCSSSTTS
T ss_pred ecCC-CcccccCHHHHHhcCCccceeEEEEEEEEEcCcc----ccccccccccccccccccccceEEEecCCEEeCCCcc
Confidence 9887 7889999999999999999999999999874310 0000000000000000122467999999999999999
Q ss_pred ccCC------CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCC----ceEEEEEeecCC-c----eEEEEEE
Q 001050 179 WMKG------VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSM----GWTVAYKSENKR-N----RLIVRLV 242 (1173)
Q Consensus 179 ~L~~------~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~----~~~a~irS~~~~-~----~~~i~~~ 242 (1173)
||++ ++.||||+||||||||||+|||||+||++|+|++++ .+++ .|.|++||..++ + .+.+++.
T Consensus 165 ~L~g~s~~eL~~~gEcp~D~GGYFIING~EKVII~qerla~N~~iv~~~~~~~~~~~~a~irS~~~~~~~~~s~~~v~~~ 244 (1210)
T 3h0g_B 165 ILNGVSDSELYDLNECPYDQGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLM 244 (1210)
T ss_dssp SSSSCCHHHHHHTTCCTTCCCCCBCGGGSCBCCCBCBCCCCSCCCCCCCCCSSSCCCCCCCCCCCCSSSCCCCCCCCCCC
T ss_pred cCCCCCHHHHHhcCCCCCCCCCEEEEeCEEEEEEechhhccceEEEEeecCCCCceEEEEEEEEecCCccceeEEEEEEE
Confidence 9999 789999999999999999999999999999999998 4332 578999988875 2 2233332
Q ss_pred ecCccccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCHHHHHH
Q 001050 243 DMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRNALK 322 (1173)
Q Consensus 243 ~~~~~~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~e~al~ 322 (1173)
.... . .+++.+++++++++.+||+++||||||.+||+||++.|+++.+|.++.++|+.+++++ ..++||++||+
T Consensus 245 ~~~~-~-~~~~~i~~~~~~~~~~IPi~ivlkALg~~sD~EI~~~I~~~~~d~~~~~~l~~slee~----~~i~tq~~aL~ 318 (1210)
T 3h0g_B 245 ARNT-E-NSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEA----FVIQDKDIALD 318 (1210)
T ss_dssp CCCT-T-SCSCCCCCCCTTSCSCCCSHHHHTTTTCCSTTHHHHHHCCSSCCHHHHHTHHHHHHTT----SSCCSSHHHHH
T ss_pred eccc-c-CCCceEEEEEeccccCCcHHHHHHHcCCCCHHHHHHHHhCCCCcHHHHHHHHHHHHHh----hhcCCHHHHHH
Confidence 1100 0 1257899999999999999999999999999999999998878889999999999987 34899999999
Q ss_pred HHHhhccCC---CCCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEeehhhh
Q 001050 323 YVDKLIKGT---TFPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLELAGEL 395 (1173)
Q Consensus 323 yig~~~~~~---~~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~l~G~L 395 (1173)
|||++|+.. +..+.++|+++|++++||||+... +|+.||++|+||||+++.|.+.+||+|||+||||+++|+|
T Consensus 319 yIG~r~~~~~~~~~~~~~~a~~iL~~~lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~L 398 (1210)
T 3h0g_B 319 YIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPL 398 (1210)
T ss_dssp TTCCCSSSCCCCHHHHHHHHHHHHTTTSSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHH
T ss_pred HHHHhccccCCCchhHHHHHHHHHHhhEEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHH
Confidence 999999642 334578999999999999999876 8999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCCChhhh
Q 001050 396 LERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQT 475 (1173)
Q Consensus 396 l~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRlN~ls~ 475 (1173)
|+.+||+.|+++++.+++.+++.+.+.+.+ ++..+++++.||++|+||||||||+.++..+++++||||+|+|+||+|+
T Consensus 399 l~~lfr~~~~~~~~~i~~~l~k~~~~~~~~-~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~ 477 (1210)
T 3h0g_B 399 LASLFRMLFRKMTRDVYKYMQKCVETNREF-NLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFAST 477 (1210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTCCSC-CCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCcc-CHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHH
Confidence 999999999999999999999988777777 7888899999999999999999999988888899999999999999999
Q ss_pred hccccccccccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceecccccC
Q 001050 476 LVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKLADDAS 554 (1173)
Q Consensus 476 lSh~Rrv~s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~~~~~~ 554 (1173)
|||||||++|+++++|+++||+||||||||+||+|||||++||||||||++|.||++. ++|+.++|.++||++++++.+
T Consensus 478 lShlRrv~~p~~~~~K~~~~R~Lhpt~WG~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le~~~~ 557 (1210)
T 3h0g_B 478 LSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNP 557 (1210)
T ss_dssp HHHTTBBCCSCCSSCCSSSSSSCCGGGTTTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCSCCCS
T ss_pred HHHHHhccCchhhccccccccccChhhheeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchhhcCc
Confidence 9999999999999999999999999999999999999999999999999999999988 999999999999999998877
Q ss_pred ccCCCcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeecc-------c
Q 001050 555 YSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENM-------G 627 (1173)
Q Consensus 555 ~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~-------~ 627 (1173)
...++.++|||||+|+|++++|..|++.||.+||+|.|+.++||++|...++++||||+||+||||++|+|+ +
T Consensus 558 ~~~~~~tkVfvNG~wVGvh~dp~~Lv~~lR~lRR~g~Is~eVSIvrdir~rE~~IfTDaGRv~RPLfvVen~~~~~~~g~ 637 (1210)
T 3h0g_B 558 SASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGE 637 (1210)
T ss_dssp SSSSSSCCCCSTTCCCCCCSCHHHHHHHHHHHHTTTSSCTTCCCCCCTTTCCCCCCCSSCCBCCEEEECCCSSCSSSSCC
T ss_pred ccCCCceEEEECCEEEEEeCCHHHHHHHHHHHhhcCCCCCceEEEecCCCCeEEEecCCCcccceEEEEccCCccccccc
Confidence 777788999999999999999999999999999999999999999999999999999999999999999985 2
Q ss_pred ------cccccc----------CCcchhHhhhhcCceeeecccccceeEEeeccccccccc-------------------
Q 001050 628 ------KIKSLE----------GKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDI------------------- 672 (1173)
Q Consensus 628 ------~~~~~~----------~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~------------------- 672 (1173)
++..+. ...++|++|++.|+|||||++||++++||++++|+..+.
T Consensus 638 L~l~k~hi~~L~~~~~~~~~~~~~~~~w~~Lv~~GvIEylDaeEEet~mIamtpeDL~~~r~~~~g~~~~~~~d~~~r~k 717 (1210)
T 3h0g_B 638 LCIRKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVK 717 (1210)
T ss_dssp CSSCHHHHHHHHHHHTCCCSCTTCCCSSTTTTTTTSEEECCTTTGGGCCEESCHHHHHHHHHHTTCCCCCCSSCCSSCCC
T ss_pred ccccHHHHHHHhcccccccccccccCCHHHHHhCCCEEEecHhhhhceeEEecHHHhhhhhhhhccccccccccchhhcc
Confidence 111111 234799999999999999999999999999999985411
Q ss_pred --CCCCCceeeeecccccccccceeecccccCCCccchhhhhhcccccccccccccCCeeeeeccccccccCCcceEecc
Q 001050 673 --EDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTM 750 (1173)
Q Consensus 673 --~~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~t~ 750 (1173)
.+.....||||||||++|||+|||+||||||||||||||||| |||||||++++|+..|+||++|+|+|||+|||+|+
T Consensus 718 ~~~~~~~~~~THcEIhPsmILGIcASiIPFpdHNQSPRNtYQ~a-MgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~ 796 (1210)
T 3h0g_B 718 PAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSA-MGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTR 796 (1210)
T ss_dssp CCSCCSCCSCSEECSCGGGSSCSSSTTSSSSTTSCSHHHHHHHH-HHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCT
T ss_pred ccCCCcccccccccccchhhhhheeecccCccccccchhhhhhh-hhcccccccccccccccCccccEeecCcCccccch
Confidence 011245799999999999999999999999999999999999 99999999999999999999999999999999999
Q ss_pred ccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccccc
Q 001050 751 ISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD 830 (1173)
Q Consensus 751 ~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~~~ 830 (1173)
.++++ +++|+|+|+||+||||||+||||||||||||+|+|||||||+||++|+.++++++. +..+.|+
T Consensus 797 ~~e~~-----------~~~elp~G~NaiVAvmsy~GYn~EDAiIink~sv~rg~~~s~~~~~y~~~~~~~~~-~~~~~~~ 864 (1210)
T 3h0g_B 797 SMEYL-----------KFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGM-TVMEEFE 864 (1210)
T ss_dssp TSTTT-----------TCTTSCSCCEECBEECCCSSSSCSSCEEEEHHHHTTTTTCEEEEEEEEECCCCCSS-SCCCCCC
T ss_pred hHHHh-----------CCCcccCccceEEEEeccCCCChhhheeeehhheecCceEEEEEEEEEEEeeecCC-CceeEEc
Confidence 99999 99999999999999999999999999999999999999999999999999887653 3467788
Q ss_pred cccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC---------------CceeeEEccCCCceEEEEEEEE
Q 001050 831 DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS---------------GADHSIKLKHTERGMVQKVVLS 895 (1173)
Q Consensus 831 ~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~---------------~~~~s~~~~~~~~g~v~~v~~~ 895 (1173)
.|........+.+.|++||+||||+||++|++|||||||++|. .+|+|++++++|.|+||+|.++
T Consensus 865 ~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gDiligK~~p~~~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~ 944 (1210)
T 3h0g_B 865 RPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVT 944 (1210)
T ss_dssp CCCTTSCCSCCSCCGGGCCTTSSCCTTCCCCTTCCCCCCCCCC-----------CCCCCCCCCCCCCTTCCCCCCEEEEE
T ss_pred CCCcchhcccchhhHhhcCCCCCcCCCCEecCCCEEEEEecCCCCCchhhcccccccccceeeEEecCCCCeEEEEEEEE
Confidence 7776544334456799999999999999999999999999874 4789999999999999999999
Q ss_pred eCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHHHH
Q 001050 896 SNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKGI 975 (1173)
Q Consensus 896 ~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk~~ 975 (1173)
.+++|.+.|||++|+.|+|++|||||||||||||||+|||+|||||++||++|||||||||||||||||||+|+++||||
T Consensus 945 ~~~~g~~~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~i~~~edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~ 1024 (1210)
T 3h0g_B 945 TNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVS 1024 (1210)
T ss_dssp ECSSSSEEEEEEECCCBCCCTTCEEECTTCCCEEEEEEECTTTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHS
T ss_pred EecCCCeEEEEEEEEecCCCchhhhhcccCCCceeeEEeccccCCcCCCCCCCeEEECCCcCCCCccchhhhHhHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeeecC
Q 001050 976 AALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTG 1055 (1173)
Q Consensus 976 ~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~~G 1055 (1173)
+ +.|.+.|+|||++...+++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+||||+|
T Consensus 1025 ~------~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~g~tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~g 1098 (1210)
T 3h0g_B 1025 A------LSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARG 1098 (1210)
T ss_dssp S------SSCCCCBCCSSCSCCHHHHHHHHHTTTSCTTSCBCCBCSSSCCBCSSCBEECCEECEECSCCSTTTCEECSSC
T ss_pred H------hcCCceeeccCCCCcHHHHHHHHHHcCcCCCCCEEEEcCCCCCCccccEEEEehHhhcchhhcccCcEEeccC
Confidence 9 8999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCcccc
Q 001050 1056 PVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCR 1135 (1173)
Q Consensus 1056 p~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~c~ 1135 (1173)
||+.|||||++||+|+|||||||||||||+|||||++|||||+.+||+|+++||+.||+++ +.+...+.++|+
T Consensus 1099 p~~~~t~QP~~gr~~~GG~r~GEME~~~l~a~Gaa~~l~e~l~~~SD~~~~~vC~~cg~~~-------~~~~~~~~~~c~ 1171 (1210)
T 3h0g_B 1099 PVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIA-------IASYKKDSYECR 1171 (1210)
T ss_dssp CBCSSSCSBCCSSTTCCCCCCCHHHHHHHHHHTBHHHHHHHHHTTTTCCEEEEESSSCCBC-------CCCSSSCCCCCT
T ss_pred CCchhccCCcccccccCCeeeehhhhhhhhhccHHHHHHHHhhcCCCcceeEeecCCCCee-------eecccCCceEcC
Confidence 9999999999999999999999999999999999999999999999999999999999997 445556678999
Q ss_pred ccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1136 ICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1136 ~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
.|+++.+|.++.||||||||+|||+||||++||.++
T Consensus 1172 ~c~~~~~i~~~~~p~~~k~l~~El~~~~i~~rl~~~ 1207 (1210)
T 3h0g_B 1172 SCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTK 1207 (1210)
T ss_dssp TTCCSSCEEEEECCHHHHHHHHHHHTTTCCEECCCS
T ss_pred ccCCCCccceecCCHHHHHHHHHHHhCCCceEEEec
Confidence 999999999999999999999999999999999765
|
| >1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B 1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B* 1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B* 1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ... | Back alignment and structure |
|---|
| >4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B 2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B | Back alignment and structure |
|---|
| >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ... | Back alignment and structure |
|---|
| >3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* | Back alignment and structure |
|---|
| >3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} | Back alignment and structure |
|---|
| >3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli} | Back alignment and structure |
|---|
| >3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase subunit A', DNA-directed...; transcription, fusion protein, chimera protein, multiprotein; 3.30A {Pyrococcus furiosus} | Back alignment and structure |
|---|
| >3lti_A DNA-directed RNA polymerase subunit beta; BBM2, nucleotidyltransferase, transcription, transferase; HET: MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A | Back alignment and structure |
|---|
| >3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus} | Back alignment and structure |
|---|
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
E-value |
| 1173 | ||||
| d1twfb_ | 1207 | e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces c | 0.0 | |
| d1smyc_ | 1119 | e.29.1.1 (C:) RNA-polymerase beta {Thermus thermop | 1e-158 |
| >d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1207 | Back information, alignment and structure |
|---|
class: Multi-domain proteins (alpha and beta) fold: beta and beta-prime subunits of DNA dependent RNA-polymerase superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase family: RNA-polymerase beta domain: RBP2 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Score = 787 bits (2032), Expect = 0.0
Identities = 400/1217 (32%), Positives = 610/1217 (50%), Gaps = 110/1217 (9%)
Query: 32 SFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQV 91
+FF E GLVS Q++S+N+F+ LQ I+E + + + R + FG++
Sbjct: 19 AFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKI 78
Query: 92 TLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQY 151
+ KP +G H ++P+ ARL+N+TYSS + V V+ + Y V + K E
Sbjct: 79 YVTKPMVNESDG-VTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKY--ELI 135
Query: 152 IQKEVLSDETTNIIIGRIPVMVKSDLCWMKG------VEKGDCDFDHGGYFIIKGAEKVF 205
++ E+ + IGR+P+M++S C++ + +C FD GGYFII G+EKV
Sbjct: 136 AEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVL 195
Query: 206 VAQEQICLKRLWV-----SNSMGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKVL--S 258
+AQE+ + V + + +S ++ + + + + + + +
Sbjct: 196 IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKAT 255
Query: 259 VYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGR 318
+ ++ +IPI I+F ALG+ D EI+ I + D +L +L + D D
Sbjct: 256 LPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDR----E 311
Query: 319 NALKYVDKLIKGTTFPPG---ESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQA 371
AL ++ + + ++ + P + + +KA FLGYM+ LL
Sbjct: 312 TALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLC 371
Query: 372 YSGRRKCDNRDDFRNKRLELAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYY 431
R+ D+RD F KRL+LAG LL + K K + + +QR +
Sbjct: 372 ALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAI 431
Query: 432 LDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQYTGK 491
+A +T+GL A +TG W K +G+ L R TL LRRT + GK
Sbjct: 432 -NAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGK 490
Query: 492 VGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVST-SILEPIFEQLFNSGMEKLA 550
+ R H +HWG +C TP+G+ CGLVKNL + +S + PI L GME L
Sbjct: 491 LAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLE 550
Query: 551 DDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIF 610
D + +VFV+G W GV ++ + LR RR+ ++ +V + RD + E++IF
Sbjct: 551 DYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIF 610
Query: 611 MDAGRILRPLLVVENM------------GKIKSL-------------EGKNYTFQALLDH 645
DAGR+ RPL +VE+ G I L + + YT+ +LL+
Sbjct: 611 TDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNE 670
Query: 646 GIIELVGTEEEEDCCTAWGIKYL----------------LKDIEDKKPIKFTHCELDMSF 689
G++E + EEEE A + L + FTHCE+ S
Sbjct: 671 GLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSM 730
Query: 690 LLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRT 749
+LG++ IIPF +H+ + R YQS QA+G TN ++R+DT+++ L+YPQ+PL T
Sbjct: 731 ILGVAASIIPFPDHNQSPRNTYQSA-MGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTT 789
Query: 750 MISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEH 809
+ L LP GQNAIVA+ + GYNQEDS++MN++S++RG+FRS
Sbjct: 790 RAMEYL------KFRELP-----AGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLF 838
Query: 810 IRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGK 869
RSY + M + + ++ K G D LDDDG G + D++IGK
Sbjct: 839 FRSYMDQEKKYGMSITETF-EKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGK 897
Query: 870 YADSGADH---------------SIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSP 914
D S L+ TE G+V +V++++N DG F V +R + P
Sbjct: 898 TTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIP 957
Query: 915 CLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGKG 974
+GDKF+S HGQKG +G +E+ PFT +GIVPD++INPHA PSR T L+E L K
Sbjct: 958 QIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKV 1017
Query: 975 IAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIG 1034
A G + A+PF +V+ I++ L G+ G E +Y+G TG+ + + IF G
Sbjct: 1018 AALSGN------EGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFG 1071
Query: 1035 PTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLH 1094
PT+YQRL HM +DK+ R GP+ LTRQPV R R GG++FGEMERDC+IAHGAA+ L
Sbjct: 1072 PTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLK 1131
Query: 1095 ERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPYCRICDSGDDIVKANVPYGAKL 1154
ERL SD++++HIC C + + C+ CD+ DI + ++PY AKL
Sbjct: 1132 ERLMEASDAFRVHICGICGLMTVI------AKLNHNQFECKGCDNKIDIYQIHIPYAAKL 1185
Query: 1155 LCQELFSMGITLKFDTE 1171
L QEL +M IT + T+
Sbjct: 1186 LFQELMAMNITPRLYTD 1202
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} Length = 1119 | Back information, alignment and structure |
|---|
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1173 | |||
| d1twfb_ | 1207 | RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta | 100.0 | |
| d1smyc_ | 1119 | RNA-polymerase beta {Thermus thermophilus [TaxId: | 100.0 |
| >d1twfb_ e.29.1.1 (B:) RBP2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} | Back information, alignment and structure |
|---|
class: Multi-domain proteins (alpha and beta) fold: beta and beta-prime subunits of DNA dependent RNA-polymerase superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase family: RNA-polymerase beta domain: RBP2 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=100.00 E-value=4.3e-261 Score=2529.28 Aligned_cols=1122 Identities=36% Similarity=0.589 Sum_probs=952.2
Q ss_pred cccCCcccchhhhhhhcccccCcCCchHHHHHHHHHHHHhHHHHHhcccCceEeCCCCCCCCCCCCcceeEEEEEceEEE
Q 001050 14 LCDLGEEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVTL 93 (1173)
Q Consensus 14 ~~~~~~~~~~~~~~~~i~~~f~~~~Lv~~qi~SFN~Fi~~gL~~ii~~~~pI~~~~~~~~~~~~~~~~~~~~l~f~~i~i 93 (1173)
++|.+++++++|+|++|++||+.+||++|||+|||+||++||++|+++.+||+++...+......+....+.|+|++++|
T Consensus 1 ~~~~~~~~~~~d~w~~i~~~f~~~~Lv~~qidSFn~Fi~~gi~~Ii~~~~pi~~~~~~~~~~~~~~~~~~~~l~f~~i~i 80 (1207)
T d1twfb_ 1 FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYV 80 (1207)
T ss_dssp CCCTTCCCCTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHTHHHHHHHTTCBCC------------------CCEECCCEE
T ss_pred CCccCCCCCHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHCHHHHHHhcCCeEeeccccccccccCCCceEEEEEEEEEE
Confidence 46789999999999999999999999999999999999999999999999997654333222112223468899999999
Q ss_pred ccCccccCCCCCcCCCChhhHHhcCCcccceEEEEEEEEEeeccccccccccccccceeeccccccceeEEEecccceEe
Q 001050 94 DKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMV 173 (1173)
Q Consensus 94 ~~P~~~e~~~~~~~~l~P~ecR~r~~TYsa~l~v~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~lG~IPIMv 173 (1173)
++|++.+.+ +..++|||+|||+|++||+|||+|+|++.+.+. .+..+ ..........+.......++|+||+|||||
T Consensus 81 ~kP~~~e~~-g~~~~l~P~EcR~r~lTYs~~l~v~i~~~~~~~-~~~~~-~~~k~~~~~~~~~~~~~~~~v~iG~IPIMv 157 (1207)
T d1twfb_ 81 TKPMVNESD-GVTHALYPQEARLRNLTYSSGLFVDVKKRTYEA-IDVPG-RELKYELIAEESEDDSESGKVFIGRLPIML 157 (1207)
T ss_dssp EEEEECCSS-SCCEECCHHHHHHTTCCCEEEEECCEECCCCC---------------------------CCEEEEEECCT
T ss_pred cCCeEEcCC-CcccccCHHHHHhcCCccceEEEEEEEEEEEec-ccccc-cccceeecccccccceeeeeEEEEECCEEe
Confidence 999998877 788999999999999999999999998765321 00000 000000000001122345689999999999
Q ss_pred cCCccccCC------CcCCCCcCCCCcEEEEeCcEEEeEeeeeeccceEEE-ecCC----ceEEEEEeecCC-----ceE
Q 001050 174 KSDLCWMKG------VEKGDCDFDHGGYFIIKGAEKVFVAQEQICLKRLWV-SNSM----GWTVAYKSENKR-----NRL 237 (1173)
Q Consensus 174 kS~~C~L~~------~~~gE~~~D~GGYFIING~ERVIi~Qe~~spnr~~i-~~~~----~~~a~irS~~~~-----~~~ 237 (1173)
+|++|||++ ++.||||+|+||||||||+|||||+||+.++|++++ .++. .|.|++||..++ ..+
T Consensus 158 ~S~~C~L~~~~~~~l~~~gEc~~D~GGYFIING~EKVIi~Q~r~~~n~~~v~~~~~~~~~~~~~~irS~~~~~~~~~~~~ 237 (1207)
T d1twfb_ 158 RSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTL 237 (1207)
T ss_dssp TSTTSGGGTCCHHHHHHTTCCTTCCCCSEEETTEEEEECEEEEECSSCCEEEECCTTSSEEEEEEEECCCSSSCCCCCEE
T ss_pred CCCcccCCCcCHHHHHHcCCCCCCCCcEEEECCEEEEEEEEEecCCCeEEEEEcCCCCceEEEEEEEEEeCCCCceeEEE
Confidence 999999999 889999999999999999999999999999999998 4332 578999998765 334
Q ss_pred EEEEEecCccccccCCEEEEEEeeccccccHhhHHHHhcCCChHHHHHHhcCCCCchHHHHHHHHhhHhhhccCCcCCCH
Q 001050 238 IVRLVDMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKG 317 (1173)
Q Consensus 238 ~i~~~~~~~~~~~~~~~i~v~i~~~k~~IPl~illrALG~~sD~eI~~~i~~~~~d~~~~~~l~~~l~~~~~~~~~i~t~ 317 (1173)
.+++...+ ......+.+.+++++.+||+++||||||..||+||++.++.+..+.++.+.+..++++. ..+.|+
T Consensus 238 ~~~~~~~~---~~~~~~i~~~~~~~~~~IPl~illrALG~~sD~eI~~~i~~~~~~~~~~~~l~~~~~~~----~~~~t~ 310 (1207)
T d1twfb_ 238 QVKLYGRE---GSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDG----FVIQDR 310 (1207)
T ss_dssp EEEEESCS---SCSSCCEEEECTTCSSCEEHHHHHHHTTCCSHHHHHHHHCCCTTCHHHHHHHHHHHHHT----TTCCSH
T ss_pred EEEEEEcC---CccceEEEEEeehhcccchHHHHHHHhCCcchhhhhhhcccCchhhHHHHHHHHHHhhc----cchhhH
Confidence 44443111 11234688999999989999999999999999999999998877778888888888876 458899
Q ss_pred HHHHHHHHhhccCC---CCCChhhHHHHHhhcccCcCCCcc----cccchHHHHHHHHHhhccCCCCCCCcccccCcEEe
Q 001050 318 RNALKYVDKLIKGT---TFPPGESTEECMNTYLFPSLHGTK----QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKRLE 390 (1173)
Q Consensus 318 e~al~yig~~~~~~---~~~~~e~~~~~L~~~llpHl~~~~----~K~~~L~~Mi~kLl~~~~g~~~~DD~D~l~nkRv~ 390 (1173)
++|+.|||+++... .....+.++++|++.+|||++... .|+.+|++|++||+.+..|.+.+||+|||+||||+
T Consensus 311 e~al~yig~~~~~~~~~~~~~~~~~~~iL~~~llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~ 390 (1207)
T d1twfb_ 311 ETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLD 390 (1207)
T ss_dssp HHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHTSSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEE
T ss_pred HHHHHHHHhhccccCCCccchHHHHHHHHHhhhccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhh
Confidence 99999999987643 233578999999999999998543 79999999999999999999999999999999999
Q ss_pred ehhhhHHHHHHHHHHHHHHHHHHHhhhcccCCcccccccccccccchhhccccccccccccccCccccccccceeecCCC
Q 001050 391 LAGELLERELKVHIAHARKRMAKALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRA 470 (1173)
Q Consensus 391 l~G~Ll~~lfr~~l~~~~~~i~~~l~~~~~~~~~~~~~~~~i~~~~It~~i~~~~sTGnw~~~~~~~~q~sGvSQvldRl 470 (1173)
++|+||+.+||+.|+++++.+++.+.+...+.+.+ ++..+++++.||++|++||+||||+.+.+.+.|++|+||+|+|+
T Consensus 391 ~~G~Ll~~~fr~~~~~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~ 469 (1207)
T d1twfb_ 391 LAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDF-NMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRY 469 (1207)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHSCCC---------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCS
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhcccccccccc-ChhhhhccCcHHHHHHHHHhcCcccccccccccccchhhhhhhc
Confidence 99999999999999999999999998876555556 67778888999999999999999999888878899999999999
Q ss_pred ChhhhhccccccccccccCCcccccCCCCCCCcceeeecCCCCCcccccccccceeeeeecCc-chhHHHHHHhcCceec
Q 001050 471 NPLQTLVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKL 549 (1173)
Q Consensus 471 N~ls~lSh~Rrv~s~~~~~~k~t~vR~Lhps~wG~iCPveTPEG~~cGLvk~LA~~a~It~~~-~~~i~~~l~~~g~~~~ 549 (1173)
||+|+|||+|||++++++++|+++||+||||||||+||+|||||+|||||||||++|+|+.+. +.++.++|..+|+..+
T Consensus 470 n~l~~lSh~Rrv~~~~~~~~k~~~~R~Lhps~~G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~~~~~~l~~~g~~~~ 549 (1207)
T d1twfb_ 470 TYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPL 549 (1207)
T ss_dssp SHHHHHHHHTEEECCC------CCTTSCCGGGTTTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEG
T ss_pred CHHHHHHhhhcccCCcccccccchhhhcchhhccceeeeeCCCCCcccceeccceeeeeccccccceeeEEeeccCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999987 8999999999999998
Q ss_pred ccccCccCCCcceeeeccEEEEEecChhHHHHHHHHHHhcCCCCceEEEEEeccCCeEEEeecCCeeeeeEEEeeccc--
Q 001050 550 ADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSELRRKRRRKELPTQVEIKRDELQSEVRIFMDAGRILRPLLVVENMG-- 627 (1173)
Q Consensus 550 ~~~~~~~~~~~~~VflnG~~iG~~~~~~~~~~~lR~~rr~~~i~~~~~i~~~~~~~~i~I~sd~GRl~RP~l~v~~~~-- 627 (1173)
.........+..+||+||.|+|+++++..|++.||.+|+.|.++.+++++++....+++|+||+||++|||+.++|+.
T Consensus 550 ~~~~~~~~~~~~~V~~nG~~~G~~~~~~~l~~~lr~~R~~g~i~~~~s~~~~~~~~~i~i~td~Gr~~rPlfi~~nd~~~ 629 (1207)
T d1twfb_ 550 EDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESL 629 (1207)
T ss_dssp GGCCGGGCTTCEEEEETTEEEEEESCHHHHHHHHHHHHHHTSSCTTCEEEEETTTTEEEEECCSCCEEEEEEEEECCCTT
T ss_pred eeeeeccccccceeeeeeeEEEEEcchheeehheeeeeeccCccceeeeeeeccccceEEEecCccccCCceeecchhhh
Confidence 777666667889999999999999999999999999999999999999999999999999999999999988887754
Q ss_pred ccccc-----------------------cCCcchhHhhhhcCceeeecccccceeEEeecccccccccC-----------
Q 001050 628 KIKSL-----------------------EGKNYTFQALLDHGIIELVGTEEEEDCCTAWGIKYLLKDIE----------- 673 (1173)
Q Consensus 628 ~~~~~-----------------------~~~~~~~~~l~~~g~iE~id~~Eq~~~~Ia~~~~~~~~~~~----------- 673 (1173)
.++.+ .....+|.+++..|.|||||++|++++.||+.++++...+.
T Consensus 630 ~~~~~~mqrq~v~~l~~~e~~~v~~~~e~~~~~~~~~~~~~g~ieyid~~E~~~~~Ia~~~~~i~~~~~~~~~~~~~~~~ 709 (1207)
T d1twfb_ 630 GHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPA 709 (1207)
T ss_dssp SSCEESCCHHHHHHHHHHHHCC---------CCCHHHHHHTTSEEEEEHHHHTTCCEESSGGGGCC---------CCCTT
T ss_pred cccceeeeHhhHhhhhccccccccccccchhhccccccccCCceeeecchhcceEEEEecccccccccccccccccccch
Confidence 22211 11345899999999999999999999999999999854321
Q ss_pred -----CCCCceeeeecccccccccceeecccccCCCccchhhhhhcccccccccccccCCeeeeeccccccccCCcceEe
Q 001050 674 -----DKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFR 748 (1173)
Q Consensus 674 -----~~~~~~~th~Ei~p~~ilgv~aslIPF~~hNqspRn~yqc~~M~KQaig~~~~n~~~r~D~~~~~l~ypQ~Plv~ 748 (1173)
......+||+||+|+.|||++|++|||+||||||||+|||| |+|||||++.+|+..|.|+++|+|+|||+|||+
T Consensus 710 ~~~~~~~~~~~~th~Ei~p~~ilg~~as~iPf~~hNqSpRn~yq~q-m~KQa~G~~~~~~~~r~D~~~~~l~~pQ~Plv~ 788 (1207)
T d1twfb_ 710 KRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSA-MGKQAMGVFLTNYNVRMDTMANILYYPQKPLGT 788 (1207)
T ss_dssp SCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSGGGSCHHHHHHHHH-HGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEE
T ss_pred hheeeecccccccccccccceEEeeecceEEecccccccceeeccc-CCcccCCccccccceeccccceeEecCCCceee
Confidence 01234689999999999999999999999999999999999 999999999999999999999999999999999
Q ss_pred ccccccccCCcccCCCCCCCCCccCCcccEEEEEecCCCCCCCeEEEecceeecCceEEEEEEEEEEEeeeccccccccc
Q 001050 749 TMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRS 828 (1173)
Q Consensus 749 t~~~~~~~~~~~~~~~~~~~~~~~~G~N~~VAv~~~~Gyn~EDaiiin~~~~~rg~f~s~~~~~~~~~~~~~~~~~~~e~ 828 (1173)
|+.++.+ +++++|+|+||+||||||+||||||||||||+|++||+|||+||++|+.++++.+. +..+.
T Consensus 789 t~~~~~~-----------~~~e~p~G~N~iVAvmsy~GYN~EDAiIiNk~si~rG~f~s~~~k~~~~~~~~~~~-~~~~~ 856 (1207)
T d1twfb_ 789 TRAMEYL-----------KFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGM-SITET 856 (1207)
T ss_dssp CTTHHHH-----------TTTTSCCCEEEEEEECBSSSTTTTTEEEEEHHHHHTTTTCEEEEEEEEECCCCSCT-TCCCE
T ss_pred ccchhhh-----------hhhcccchhceEEEEEeccCcccccccccchhhhhhcccceeeeEEEEEEeccccc-ccccc
Confidence 9999999 89999999999999999999999999999999999999999999999999887553 34455
Q ss_pred cccccccccccccccccCCCCCCCCcccCcEEccCCeEEEEecCC---------------CceeeEEccCCCceEEEEEE
Q 001050 829 SDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADS---------------GADHSIKLKHTERGMVQKVV 893 (1173)
Q Consensus 829 ~~~~~~~~~~~~~~~~~~~Ld~dGi~~~g~~v~~gdili~k~~~~---------------~~~~s~~~~~~~~g~v~~v~ 893 (1173)
+..|........+...|++||+||+|++|++|++||+||||++|. .+|.|++++.++.|+|++|.
T Consensus 857 ~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~~~g~V~~v~ 936 (1207)
T d1twfb_ 857 FEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVL 936 (1207)
T ss_dssp ESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC-------------CCBBCCEECCTTCCEEEEEEE
T ss_pred ccccccccccccchhhhhcccccccccccccccCCceeeeeeeccCCchhhhhhccccccccceeEEccCCCCeEEEEEE
Confidence 666655444445566799999999999999999999999999986 47889999999999999999
Q ss_pred EEeCCCCCeEEEEEEeeccCCCccccccccCCCceEEeeeecCCCcCCCCCCCcCcEEeCCCCCCCCCChHHHHHHHHHH
Q 001050 894 LSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQLLEAALGK 973 (1173)
Q Consensus 894 ~~~~~~~~~~~~v~~r~~R~~~iGDK~ssRhGqKGvvs~i~~~~dmPf~~~G~~pDiI~NPh~~PSRMtiGql~E~~~gk 973 (1173)
++.+.++.+.++|++|+.|+|+||||||||||||||||+|||+||||||+||++|||||||||||||||||||+|+++||
T Consensus 937 ~~~~~~~~~~~kv~i~~~R~p~iGDKfasRhGqKGv~s~i~p~eDMPf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk 1016 (1207)
T d1twfb_ 937 VTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSK 1016 (1207)
T ss_dssp EEECSSSCEEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTSCEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHH
T ss_pred EeecccccceeeEEEEEEeccchhhhhhhccCCcceeeeeechhhCCcCCCCCCccEEECCCcCcccCcHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCccccCCCEEEecCCCCCCHHHHHHHHHHcCCCCCCceEeeeCCCCcEEEeeEeEeeeehhccccccCccceeee
Q 001050 974 GIAALGKGICSGLKRYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRN 1053 (1173)
Q Consensus 974 ~~~~~~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~i~~G~~yy~rL~Hmv~dK~~~R~ 1053 (1173)
||+ +.|.+.|+|||++...+++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||+||+||||
T Consensus 1017 ~~~------~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~ly~G~tG~~~~~~i~~G~~yy~rL~HmV~DK~~~Rs 1090 (1207)
T d1twfb_ 1017 VAA------LSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARA 1090 (1207)
T ss_dssp HHH------HHCSCEECCSSSSCCHHHHHHHHHTTTSCTTSEECEECTTTCCBCSSCEEEEEEEEEEBSSCGGGTCEEEC
T ss_pred HHH------hcCCccccCCCCCccHHHHHHHHHHcCCCCCCCEEEECCCCCCCccceEEEehhHhhhhhhhhccccEeec
Confidence 999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccccCCcccccccCceeeeehhhhHHHHhhhHHHHHHhhhcCCCccceecccccCCccchheeeecCCcccCCcc
Q 001050 1054 TGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQRVVGGGRKVRGPY 1133 (1173)
Q Consensus 1054 ~Gp~~~lT~QP~~Gr~~~GG~R~GEME~d~l~a~Ga~~~l~erl~~~SD~~~~~vc~~cg~~~~~~~~~~~~~~~~~~~~ 1133 (1173)
+|||++|||||++|||++|||||||||||||+|||||++|||||+++||.++++||.+||+++. ..+.+...++
T Consensus 1091 ~Gp~~~lT~QP~~Gr~~~GG~R~GEME~dal~a~Gaa~~L~e~l~~~SD~~~~~vc~~cg~~~~------~~~~~~~~~~ 1164 (1207)
T d1twfb_ 1091 RGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTV------IAKLNHNQFE 1164 (1207)
T ss_dssp CCC----------------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCEEEEESSSCSSCC------EEETTTTEEE
T ss_pred cCCCCccccCCCCccccCCCcceehHHHHHHHHHhHHHHHHHHhhccCCccceeccccCCceEE------Eeccccccee
Confidence 9999999999999999999999999999999999999999999999999999999999999974 2223445688
Q ss_pred ccccCCCCCcccccchHhHHHHHHHHHhcCCcEEEEEe
Q 001050 1134 CRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171 (1173)
Q Consensus 1134 c~~c~~~~~~~~~~iPy~~k~L~~EL~sm~i~~~l~~~ 1171 (1173)
|+.|+++.++.++.+|||||||+|||+||||+++|.++
T Consensus 1165 c~~c~~~~~i~~~~iPy~fk~l~~EL~sm~i~~~l~~~ 1202 (1207)
T d1twfb_ 1165 CKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTD 1202 (1207)
T ss_dssp BTTTTBSSSEEEEECCHHHHHHHHHHHHTTBCCEEESC
T ss_pred ecCCCCCCCccccCCCHHHHHHHHHHHHCCCceEEEec
Confidence 99999999999999999999999999999999999875
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|