Citrus Sinensis ID: 003180
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 | 842 | 2.2.26 [Sep-21-2011] | |||||||
| Q42877 | 1191 | DNA-directed RNA polymera | N/A | no | 0.998 | 0.706 | 0.961 | 0.0 | |
| P38420 | 1188 | DNA-directed RNA polymera | yes | no | 0.983 | 0.696 | 0.957 | 0.0 | |
| Q54J75 | 1170 | DNA-directed RNA polymera | yes | no | 0.976 | 0.702 | 0.717 | 0.0 | |
| P30876 | 1174 | DNA-directed RNA polymera | yes | no | 0.976 | 0.700 | 0.703 | 0.0 | |
| Q8CFI7 | 1174 | DNA-directed RNA polymera | yes | no | 0.976 | 0.700 | 0.701 | 0.0 | |
| P08266 | 1176 | DNA-directed RNA polymera | yes | no | 0.977 | 0.699 | 0.683 | 0.0 | |
| Q02061 | 1210 | DNA-directed RNA polymera | yes | no | 0.983 | 0.684 | 0.651 | 0.0 | |
| P08518 | 1224 | DNA-directed RNA polymera | yes | no | 0.982 | 0.675 | 0.651 | 0.0 | |
| Q6FLD5 | 1223 | DNA-directed RNA polymera | yes | no | 0.982 | 0.676 | 0.646 | 0.0 | |
| Q10578 | 1193 | DNA-directed RNA polymera | yes | no | 0.991 | 0.699 | 0.652 | 0.0 |
| >sp|Q42877|RPB2_SOLLC DNA-directed RNA polymerase II subunit RPB2 OS=Solanum lycopersicum GN=RPB2 PE=2 SV=1 | Back alignment and function desciption |
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Score = 1681 bits (4352), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 810/842 (96%), Positives = 830/842 (98%), Gaps = 1/842 (0%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
MLPHVG G++CETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM
Sbjct: 351 MLPHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 410
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
LFRKLTRDVR YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS
Sbjct: 411 LFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 470
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA
Sbjct: 471 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 530
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTL 240
LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNG WVGIHRDP+MLV+TL
Sbjct: 531 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGTWVGIHRDPDMLVRTL 590
Query: 241 RRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRES 300
RRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRL+IKK+DI LQQRES
Sbjct: 591 RRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLMIKKKDIQTLQQRES 650
Query: 301 PEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLI 360
P++GGWHDLVAKG+IEYIDTEEEETTMISMTINDLVQARL+P +AY+DTYTHCEIHPSLI
Sbjct: 651 PDEGGWHDLVAKGYIEYIDTEEEETTMISMTINDLVQARLNPGDAYSDTYTHCEIHPSLI 710
Query: 361 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA 420
LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA
Sbjct: 711 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA 770
Query: 421 MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 480
MEHLHFRQLPAGINAIVAI+CYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT
Sbjct: 771 MEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 830
Query: 481 LVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQAS 540
LVKEDFGRPDR++TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD+AQGQAS
Sbjct: 831 LVKEDFGRPDRASTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDDAQGQAS 890
Query: 541 RYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 600
RYTR+DHS SLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV
Sbjct: 891 RYTRKDHSTSLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 950
Query: 601 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 660
GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV
Sbjct: 951 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 1010
Query: 661 TVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 720
TVDNISKALHKCGYQMRGFETMYNGHTGRRL+AMIFLGPTYYQRLKHMVDDKIHSRGRGP
Sbjct: 1011 TVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRGRGP 1070
Query: 721 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIA 780
VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGA+HFLKERLFDQSDAYRVHVCE CGLIA
Sbjct: 1071 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCERCGLIA 1130
Query: 781 IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDTKQSKDHKKK 840
IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK D K +KD KKK
Sbjct: 1131 IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK-DVKLAKDQKKK 1189
Query: 841 GA 842
GA
Sbjct: 1190 GA 1191
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DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. Solanum lycopersicum (taxid: 4081) EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6 |
| >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|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|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1 | Back alignment and function description |
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| >sp|Q8CFI7|RPB2_MOUSE DNA-directed RNA polymerase II subunit RPB2 OS=Mus musculus GN=Polr2b PE=2 SV=2 | Back alignment and function description |
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| >sp|P08266|RPB2_DROME DNA-directed RNA polymerase II subunit RPB2 OS=Drosophila melanogaster GN=RpII140 PE=2 SV=2 | 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|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|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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| >sp|Q10578|RPB2_CAEEL DNA-directed RNA polymerase II subunit RPB2 OS=Caenorhabditis elegans GN=rpb-2 PE=2 SV=2 | 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 | 842 | ||||||
| 356558375 | 1193 | PREDICTED: DNA-directed RNA polymerase I | 0.997 | 0.704 | 0.960 | 0.0 | |
| 356530409 | 1192 | PREDICTED: DNA-directed RNA polymerase I | 0.996 | 0.703 | 0.958 | 0.0 | |
| 255556051 | 1194 | DNA-directed RNA polymerase II subunit, | 0.998 | 0.704 | 0.969 | 0.0 | |
| 357438193 | 1213 | DNA-directed RNA polymerase [Medicago tr | 0.998 | 0.693 | 0.940 | 0.0 | |
| 225446351 | 1193 | PREDICTED: DNA-directed RNA polymerase I | 0.998 | 0.704 | 0.953 | 0.0 | |
| 449433841 | 1199 | PREDICTED: DNA-directed RNA polymerase I | 0.998 | 0.701 | 0.965 | 0.0 | |
| 68300814 | 1200 | RNA polymerase II second largest subunit | 0.998 | 0.700 | 0.951 | 0.0 | |
| 350534526 | 1191 | DNA-directed RNA polymerase II subunit R | 0.998 | 0.706 | 0.961 | 0.0 | |
| 68300812 | 1195 | RNA polymerase II second largest subunit | 0.998 | 0.703 | 0.956 | 0.0 | |
| 70794966 | 1191 | RNA polymerase II second largest subunit | 0.982 | 0.694 | 0.967 | 0.0 |
| >gi|356558375|ref|XP_003547482.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Glycine max] | Back alignment and taxonomy information |
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Score = 1707 bits (4422), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 809/842 (96%), Positives = 830/842 (98%), Gaps = 2/842 (0%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
MLPHVG G++CETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM
Sbjct: 354 MLPHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 413
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
LFRKLTRDVR YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS
Sbjct: 414 LFRKLTRDVRGYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 473
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA
Sbjct: 474 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 533
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTL 240
LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCW+GIHRDP+MLV+TL
Sbjct: 534 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWMGIHRDPDMLVRTL 593
Query: 241 RRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRES 300
R+LRRRVDVNTEVGVVRDI LKELRIYTDYGRCSRPLFIV+KQRLLIKK+DI ALQQRES
Sbjct: 594 RKLRRRVDVNTEVGVVRDIILKELRIYTDYGRCSRPLFIVDKQRLLIKKKDIHALQQRES 653
Query: 301 PEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLI 360
PEDGGWHDLV+KGFIEYIDTEEEETTMISMTINDLVQAR++PE+AYA TYTHCEIHPSLI
Sbjct: 654 PEDGGWHDLVSKGFIEYIDTEEEETTMISMTINDLVQARINPEDAYAGTYTHCEIHPSLI 713
Query: 361 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA 420
LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA
Sbjct: 714 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA 773
Query: 421 MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 480
MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT
Sbjct: 774 MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 833
Query: 481 LVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQAS 540
LVKEDFGRPDR+NTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ+EAQGQA
Sbjct: 834 LVKEDFGRPDRANTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQEEAQGQAL 893
Query: 541 RYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 600
RYTRRDHSISLRHSETG+VDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV
Sbjct: 894 RYTRRDHSISLRHSETGIVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 953
Query: 601 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 660
GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV
Sbjct: 954 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 1013
Query: 661 TVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 720
TVDNISKALHKCGYQMRGFETMYNGHTGRRL+AMIFLGPTYYQRLKHMVDDKIHSRGRGP
Sbjct: 1014 TVDNISKALHKCGYQMRGFETMYNGHTGRRLSAMIFLGPTYYQRLKHMVDDKIHSRGRGP 1073
Query: 721 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIA 780
VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGA+HFLKERLFDQSDAYRVHVCE CGLIA
Sbjct: 1074 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCERCGLIA 1133
Query: 781 IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDTKQSKDHKKK 840
IANLKKNSFECRGCKNKTDIVQV+IPYACKLLFQELMAMAIAPRMLTKE ++ + KKK
Sbjct: 1134 IANLKKNSFECRGCKNKTDIVQVYIPYACKLLFQELMAMAIAPRMLTKE--VKTTNQKKK 1191
Query: 841 GA 842
GA
Sbjct: 1192 GA 1193
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Source: Glycine max Species: Glycine max Genus: Glycine Family: Fabaceae Order: Fabales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|356530409|ref|XP_003533774.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|255556051|ref|XP_002519060.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis] gi|223541723|gb|EEF43271.1| DNA-directed RNA polymerase II subunit, putative [Ricinus communis] | Back alignment and taxonomy information |
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| >gi|357438193|ref|XP_003589372.1| DNA-directed RNA polymerase [Medicago truncatula] gi|355478420|gb|AES59623.1| DNA-directed RNA polymerase [Medicago truncatula] | Back alignment and taxonomy information |
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| >gi|225446351|ref|XP_002274051.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2 [Vitis vinifera] gi|147841183|emb|CAN72948.1| hypothetical protein VITISV_033708 [Vitis vinifera] gi|302143287|emb|CBI21848.3| unnamed protein product [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|449433841|ref|XP_004134705.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Cucumis sativus] gi|449479313|ref|XP_004155566.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB2-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|68300814|gb|AAY89348.1| RNA polymerase II second largest subunit [Antirrhinum majus] | Back alignment and taxonomy information |
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| >gi|350534526|ref|NP_001233889.1| DNA-directed RNA polymerase II subunit RPB2 [Solanum lycopersicum] gi|11134656|sp|Q42877.1|RPB2_SOLLC RecName: Full=DNA-directed RNA polymerase II subunit RPB2; Short=RNA polymerase II subunit 2; Short=RNA polymerase II subunit B2; AltName: Full=DNA-directed RNA polymerase II 135 kDa polypeptide gi|1049068|gb|AAC49273.1| RNA polymerase II subunit 2 [Solanum lycopersicum] | Back alignment and taxonomy information |
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| >gi|68300812|gb|AAY89347.1| RNA polymerase II second largest subunit [Petunia x hybrida] | Back alignment and taxonomy information |
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| >gi|70794966|gb|AAZ08457.1| RNA polymerase II second largest subunit [Rhododendron macrophyllum] | 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 | 842 | ||||||
| TAIR|locus:2119013 | 1188 | NRPB2 [Arabidopsis thaliana (t | 0.990 | 0.702 | 0.922 | 0.0 | |
| DICTYBASE|DDB_G0288257 | 1170 | rpb2 "RNA polymerase II core s | 0.976 | 0.702 | 0.696 | 0.0 | |
| UNIPROTKB|A5PJW8 | 1174 | POLR2B "DNA-directed RNA polym | 0.976 | 0.700 | 0.683 | 8.3e-312 | |
| UNIPROTKB|E2RNN5 | 1174 | POLR2B "DNA-directed RNA polym | 0.976 | 0.700 | 0.683 | 8.3e-312 | |
| UNIPROTKB|I3LGP4 | 1167 | POLR2B "DNA-directed RNA polym | 0.976 | 0.704 | 0.683 | 8.3e-312 | |
| UNIPROTKB|C9J2Y9 | 1167 | POLR2B "DNA-directed RNA polym | 0.976 | 0.704 | 0.682 | 3.6e-311 | |
| UNIPROTKB|C9J4M6 | 1099 | POLR2B "DNA-directed RNA polym | 0.976 | 0.747 | 0.682 | 3.6e-311 | |
| UNIPROTKB|P30876 | 1174 | POLR2B "DNA-directed RNA polym | 0.976 | 0.700 | 0.682 | 3.6e-311 | |
| RGD|1309477 | 1174 | Polr2b "polymerase (RNA) II (D | 0.976 | 0.700 | 0.682 | 3.6e-311 | |
| MGI|MGI:2388280 | 1174 | Polr2b "polymerase (RNA) II (D | 0.976 | 0.700 | 0.681 | 9.5e-311 |
| TAIR|locus:2119013 NRPB2 [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 4062 (1435.0 bits), Expect = 0., P = 0.
Identities = 770/835 (92%), Positives = 790/835 (94%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
MLPHVG G+ CETKKAYYFGYIIHRLLLCALGRR EDDRDHYGNKRLDLAGPLLGGLFRM
Sbjct: 352 MLPHVGIGEHCETKKAYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLDLAGPLLGGLFRM 411
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
LFRKLTRDVR+YVQKCVDNGK+VNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS
Sbjct: 412 LFRKLTRDVRSYVQKCVDNGKEVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 471
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA
Sbjct: 472 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 531
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTX 240
LMVYITVGSAAYPILEFLEEWGTENFEEISP+VIPQATKIFVNG WVG+HRDP+MLVKT
Sbjct: 532 LMVYITVGSAAYPILEFLEEWGTENFEEISPSVIPQATKIFVNGMWVGVHRDPDMLVKTL 591
Query: 241 XXXXXXVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRES 300
VDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIV+ Q+LLIKKRDI ALQQRES
Sbjct: 592 RRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVDNQKLLIKKRDIYALQQRES 651
Query: 301 PEDGGWHDLVAKGFXXXXXXXXXXXXXXXXXXNDLVQARLHPEEAYADTYTHCEIHPSLI 360
E+ GWH LVAKGF +DLVQARL PEEAY + YTHCEIHPSLI
Sbjct: 652 AEEDGWHHLVAKGFIEYIDTEEEETTMISMTISDLVQARLRPEEAYTENYTHCEIHPSLI 711
Query: 361 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA 420
LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA
Sbjct: 712 LGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRA 771
Query: 421 MEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 480
MEHLHFRQLPAGINAIVAI+CYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT
Sbjct: 772 MEHLHFRQLPAGINAIVAISCYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGT 831
Query: 481 LVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQAS 540
LVKEDFGRPDR +TMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQ+S
Sbjct: 832 LVKEDFGRPDRGSTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQSS 891
Query: 541 RYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 600
RYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV
Sbjct: 892 RYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTV 951
Query: 601 GMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 660
GMTYTQEDMPWT+EG+TPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV
Sbjct: 952 GMTYTQEDMPWTIEGVTPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDV 1011
Query: 661 TVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 720
TVDNISKALHKCGYQMRGFE MYNGHTGR LTAMIFLGPTYYQRLKHMVDDKIHSRGRGP
Sbjct: 1012 TVDNISKALHKCGYQMRGFERMYNGHTGRPLTAMIFLGPTYYQRLKHMVDDKIHSRGRGP 1071
Query: 721 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIA 780
VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGA+HFLKERLFDQSDAYRVHVCE CGLIA
Sbjct: 1072 VQILTRQPAEGRSRDGGLRFGEMERDCMIAHGAAHFLKERLFDQSDAYRVHVCEVCGLIA 1131
Query: 781 IANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDTKQSK 835
IANLKKNSFECRGCKNKTDIVQV+IPYACKLLFQELM+MAIAPRMLTK K +K
Sbjct: 1132 IANLKKNSFECRGCKNKTDIVQVYIPYACKLLFQELMSMAIAPRMLTKH-LKSAK 1185
|
|
| DICTYBASE|DDB_G0288257 rpb2 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|A5PJW8 POLR2B "DNA-directed RNA polymerase" [Bos taurus (taxid:9913)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|E2RNN5 POLR2B "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|I3LGP4 POLR2B "DNA-directed RNA polymerase" [Sus scrofa (taxid:9823)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|C9J2Y9 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|C9J4M6 POLR2B "DNA-directed RNA polymerase" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|P30876 POLR2B "DNA-directed RNA polymerase II subunit RPB2" [Homo sapiens (taxid:9606)] | Back alignment and assigned GO terms |
|---|
| RGD|1309477 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Rattus norvegicus (taxid:10116)] | Back alignment and assigned GO terms |
|---|
| MGI|MGI:2388280 Polr2b "polymerase (RNA) II (DNA directed) polypeptide B" [Mus musculus (taxid:10090)] | 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) |
| Q42877 | RPB2_SOLLC | 2, ., 7, ., 7, ., 6 | 0.9619 | 0.9988 | 0.7061 | N/A | no |
| Q8SR75 | RPB2_ENCCU | 2, ., 7, ., 7, ., 6 | 0.6293 | 0.9750 | 0.7195 | yes | no |
| Q8CFI7 | RPB2_MOUSE | 2, ., 7, ., 7, ., 6 | 0.7019 | 0.9762 | 0.7001 | yes | no |
| P08518 | RPB2_YEAST | 2, ., 7, ., 7, ., 6 | 0.6519 | 0.9821 | 0.6756 | yes | no |
| Q10578 | RPB2_CAEEL | 2, ., 7, ., 7, ., 6 | 0.6528 | 0.9916 | 0.6999 | yes | no |
| P08266 | RPB2_DROME | 2, ., 7, ., 7, ., 6 | 0.6838 | 0.9774 | 0.6998 | yes | no |
| P30876 | RPB2_HUMAN | 2, ., 7, ., 7, ., 6 | 0.7031 | 0.9762 | 0.7001 | yes | no |
| P38420 | RPB2_ARATH | 2, ., 7, ., 7, ., 6 | 0.9577 | 0.9833 | 0.6969 | yes | no |
| Q02061 | RPB2_SCHPO | 2, ., 7, ., 7, ., 6 | 0.6519 | 0.9833 | 0.6842 | yes | no |
| Q54J75 | RPB2_DICDI | 2, ., 7, ., 7, ., 6 | 0.7172 | 0.9762 | 0.7025 | yes | no |
| Q6FLD5 | RPB2_CANGA | 2, ., 7, ., 7, ., 6 | 0.6465 | 0.9821 | 0.6762 | yes | no |
| Q753Q4 | RPB2_ASHGO | 2, ., 7, ., 7, ., 6 | 0.6426 | 0.9821 | 0.6767 | 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 | 0.976 |
| 4th Layer | 2.7.7.6 | 0.991 |
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 | 842 | |||
| 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 | 0.0 | |
| PRK07225 | 605 | PRK07225, PRK07225, DNA-directed RNA polymerase su | 0.0 | |
| pfam00562 | 373 | pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, do | 0.0 | |
| cd00653 | 866 | cd00653, RNA_pol_B_RPB2, RNA polymerase beta subun | 2e-72 | |
| PRK09606 | 494 | PRK09606, PRK09606, DNA-directed RNA polymerase su | 3e-58 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 2e-54 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 4e-49 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 6e-43 | |
| pfam04563 | 394 | pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta sub | 1e-42 | |
| pfam04560 | 78 | pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, do | 6e-37 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 5e-33 | |
| pfam04566 | 63 | pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, do | 5e-29 | |
| pfam04565 | 68 | pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, do | 1e-26 | |
| pfam04567 | 46 | pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, do | 7e-19 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 3e-17 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 6e-16 | |
| pfam04561 | 185 | pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, do | 6e-15 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 2e-13 | |
| CHL00207 | 1077 | CHL00207, rpoB, RNA polymerase beta subunit; Provi | 7e-12 | |
| TIGR02013 | 1065 | TIGR02013, rpoB, DNA-directed RNA polymerase, beta | 6e-11 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 7e-11 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 2e-10 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 6e-10 | |
| CHL00001 | 1070 | CHL00001, rpoB, RNA polymerase beta subunit | 6e-07 | |
| PRK00405 | 1112 | PRK00405, rpoB, DNA-directed RNA polymerase subuni | 6e-06 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 3e-04 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 0.003 |
| >gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Score = 1024 bits (2651), Expect = 0.0
Identities = 402/833 (48%), Positives = 540/833 (64%), Gaps = 26/833 (3%)
Query: 2 LPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRML 61
LPH+GT KKAY+ G + +LL LGRR DD+DHY NKRL LAG LL LFR+
Sbjct: 290 LPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVA 349
Query: 62 FRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQ 121
F++L +D++ ++K G+ ++L+ ++ IT ++++LATGNW G R GVSQ
Sbjct: 350 FKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV-----GGRTGVSQ 404
Query: 122 VLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 181
+L+R Y STLSHLRR+ SP+ R + R LH +QWG +CP ETPEG CGLVKNLAL
Sbjct: 405 LLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLAL 464
Query: 182 MVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLR 241
M I+VG + E L E G EE +++++NG +G H D E L + +R
Sbjct: 465 MAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIR 524
Query: 242 RLRRRVDVNTEVGV--VRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 299
LRR ++ EV V + + E+ + D GR RPL +VE + + + + L++ E
Sbjct: 525 ELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE 584
Query: 300 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSL 359
+ DLV G IEY+D EEEE +++ DL PE +TH EI P
Sbjct: 585 LT----FDDLVKMGVIEYLDAEEEENAYVALDPEDLT-----PE------HTHLEIWPPA 629
Query: 360 ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTR 419
ILG+ ASIIP+P+HNQSPRNTYQ+AM KQ++G+Y N++ R DT ++L+YPQ+PLV TR
Sbjct: 630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTR 689
Query: 420 AMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMG 479
A+E + + PAG NA+VA+ Y+GYN ED++IMN++SI+RG RS FFR+Y EE+K
Sbjct: 690 ALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYP 749
Query: 480 TLVKEDFGRPDRSNTMGMR-HGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQ 538
++ P+ N G R Y KLD+DG+ P V G DV+IGKT+P E +
Sbjct: 750 GGQEDKIEIPE-PNVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEE 808
Query: 539 ASRYT--RRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQ 596
S RRD S+++RH E G+VD VL+T + +G + VKVRVR +RIP++GDKF+SRHGQ
Sbjct: 809 LSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQ 868
Query: 597 KGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATP 656
KG +GM QEDMP+T +GI PD+I+NPHAIPSRMT+GQL+E I GKVAA G+ DATP
Sbjct: 869 KGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATP 928
Query: 657 FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSR 716
F + + K L K GY+ G E MY+G TG ++ A IF+G YYQ+L HMV DKIH+R
Sbjct: 929 FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHAR 988
Query: 717 GRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHC 776
RGPVQILTRQP EGR+R+GGLRFGEMERDC+I HGA+ LKERL D SD ++VCE C
Sbjct: 989 ARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELC 1048
Query: 777 GLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829
G IA + +KN + C +K +I V + YA KLL QELM+M I+PR+ +
Sbjct: 1049 GHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101
|
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|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|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit | 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|113341 pfam04566, RNA_pol_Rpb2_4, RNA polymerase Rpb2, domain 4 | 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|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, domain 5 | 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|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | 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|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|233685 TIGR02013, rpoB, DNA-directed 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 |
|---|
| >gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | 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|214330 CHL00001, rpoB, RNA polymerase beta subunit | Back alignment and domain information |
|---|
| >gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed | 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|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 842 | |||
| PRK08565 | 1103 | DNA-directed RNA polymerase subunit B; Provisional | 100.0 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 100.0 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 100.0 | |
| KOG0216 | 1111 | consensus RNA polymerase I, second largest subunit | 100.0 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 100.0 | |
| cd00653 | 866 | RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA po | 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 | |
| TIGR02013 | 1065 | rpoB DNA-directed RNA polymerase, beta subunit. Th | 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 | |
| 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 | |
| PF04560 | 81 | RNA_pol_Rpb2_7: RNA polymerase Rpb2, domain 7; Int | 99.97 | |
| PF04565 | 68 | RNA_pol_Rpb2_3: RNA polymerase Rpb2, domain 3; Int | 99.93 | |
| PF04566 | 63 | RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; Int | 99.81 | |
| KOG0214 | 1141 | consensus RNA polymerase II, second largest subuni | 99.27 | |
| PF04567 | 48 | RNA_pol_Rpb2_5: RNA polymerase Rpb2, domain 5; Int | 99.21 | |
| PF06883 | 58 | RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific do | 97.63 | |
| KOG0215 | 1153 | consensus RNA polymerase III, second largest subun | 97.47 | |
| COG0085 | 1060 | RpoB DNA-directed RNA polymerase, beta subunit/140 | 97.41 | |
| PHA03394 | 865 | lef-8 DNA-directed RNA polymerase subunit beta-lik | 96.64 | |
| PF04563 | 203 | RNA_pol_Rpb2_1: RNA polymerase beta subunit; Inter | 96.59 |
| >PRK08565 DNA-directed RNA polymerase subunit B; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=1.1e-229 Score=2095.95 Aligned_cols=809 Identities=49% Similarity=0.821 Sum_probs=757.4
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
||||++.+..++.+|+.||++|++||+++..|.+.+||+|||+||||+++|+||+.+||+.|+++++.+++.+.+.+.+.
T Consensus 289 ll~Hig~~~~~~~~K~~~L~~Mi~kLl~l~~g~~~~DD~D~l~NKRv~l~G~Ll~~~fr~~l~~~~~~ik~~l~~~~~~~ 368 (1103)
T PRK08565 289 LLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARG 368 (1103)
T ss_pred CcccCCCcccchhHHHHHHHHHHHHHHhhhcCCCCCCCccccCCcEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 68999987766778999999999999999999999999999999999999999999999999999999999998876666
Q ss_pred CCCchhccccccchhhhhhhhhccCccccccccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCcc
Q 003180 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWG 160 (842)
Q Consensus 81 ~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~wG 160 (842)
+.+++..+++++.||++|++|||||||.+ |++||||+|+|+||+++|||||||++++.+++|.++||+|||||||
T Consensus 369 ~~~~~~~~i~~~~It~~i~~~~sTGnw~~-----~~sGvSq~ldr~N~l~~lSh~Rrv~s~~~r~~~~~~vR~Lhps~wG 443 (1103)
T PRK08565 369 RKLDLRAIVRPDIITERIRHALATGNWVG-----GRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWG 443 (1103)
T ss_pred ccCCHHHhcccchhhHHHHHHHhcCcccc-----CCcceEEecccCCHHHHHHHHhhccCCcccCCCCccccccChhhcc
Confidence 67788888888899999999999999995 6899999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHHH
Q 003180 161 MMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTL 240 (842)
Q Consensus 161 fiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~l 240 (842)
|+||+|||||++||||||||++|+|+++.+.++|.++|.++||.++.++.+...+..++|||||+|||++++|..|++.|
T Consensus 444 ~iCPveTPEG~~cGLv~~LA~~a~It~~~~~~~i~~~l~~~G~~~~~~~~~~~~~~~~~V~lnG~~iG~~~~~~~l~~~l 523 (1103)
T PRK08565 444 RICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKI 523 (1103)
T ss_pred ccCCCCCCCccccchhhhhhcccccccCCChHHHHHHHHHcCCCchhhcCcccCCCceEEEECCEEEEEECCHHHHHHHH
Confidence 99999999999999999999999999998999999999999999987666555667799999999999999999999999
Q ss_pred HHhhhcCCCCCcEEEEEec--cCCeEEEecCCCeeeeeEEEeecccccccHHHHHHHhcCCCCCCCCchhccccCcEEEe
Q 003180 241 RRLRRRVDVNTEVGVVRDI--RLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYI 318 (842)
Q Consensus 241 R~lRr~~~i~~~vsi~~~~--~~~~i~I~td~GRl~RPl~vv~n~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g~IE~I 318 (842)
|.+||+|.|+.++||++++ ..++|+|+||+||++|||++|+++++.+++++++.++.+. .+|++|+++|.||||
T Consensus 524 R~~Rr~g~i~~~v~I~~~~~~~~~~i~I~sd~GRl~RP~~~v~~g~~~~~~~~~~~l~~~~----~~~~~l~~~g~iEyi 599 (1103)
T PRK08565 524 RELRRSGKISDEVNVAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE----LTFDDLVKMGVIEYL 599 (1103)
T ss_pred HHHhhcCCCCCeEEEEEccccccceEEEecCCceeeeeEEEEecCceeccHHHHHHhhccc----cchhhHhhcCcEEee
Confidence 9999999999999999998 8899999999999999999999999999999999886543 489999999999999
Q ss_pred ccccccceeEeecccccccccCCCCcCCCCceeeeeccCCccccccccccCCCCCCCCccchhhhcccccccccccceeE
Q 003180 319 DTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQ 398 (842)
Q Consensus 319 d~~Eq~~~~Ia~~~~~l~~~~~~~k~~~~~~~TH~EI~Ps~ilgv~AslIPF~~HNqSpRn~yq~~M~KQaig~~~~n~~ 398 (842)
|++||++++||++++++.. .+||+||+|++|||++||+|||+||||||||||||||+|||||++.+|+.
T Consensus 600 d~~Ee~~~~Ia~~~~~l~~-----------~~th~Ei~p~~ilsv~asliPF~~hNqspRn~yq~~M~KQa~g~~~~n~~ 668 (1103)
T PRK08565 600 DAEEEENAYVALDPEDLTP-----------EHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668 (1103)
T ss_pred CHHHhcCcEEeccccccCc-----------ceeccccCCccccceeeeccCCcccCcccchhhhhhhhhcccccccccce
Confidence 9999999999999998843 47999999999999999999999999999999999999999999999999
Q ss_pred EecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCceeeeccccccCceeEEEEEEEEeeehhc
Q 003180 399 FRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKM 478 (842)
Q Consensus 399 ~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAiIiNk~si~rG~f~s~~~~~~~~~~~~~ 478 (842)
+|+|++.|+|+|||+|||+|++++.++++++|+|+||+||||||+||||||||||||+|+|||||||+||++|++++++.
T Consensus 669 ~r~d~~~~~l~~pQ~Plv~t~~~~~~~~~~~p~G~N~iVAv~sy~GYn~EDaiIink~s~~rG~~~s~~~~~~~~~~~~~ 748 (1103)
T PRK08565 669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748 (1103)
T ss_pred EeecCCcceeecCceeEEEeccccccccccCCCCeeEEEEEEcccCcchHHhhhhhhhhhhcCCceEEEEEEEEEEeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988765
Q ss_pred CCccccccccCCCCCCCCCCC-CCccCCCCCCCcCCCcEEcCCCEEEEeeCCCCc--cccccccCCCccceeeEEeeccc
Q 003180 479 GTLVKEDFGRPDRSNTMGMRH-GSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQ--DEAQGQASRYTRRDHSISLRHSE 555 (842)
Q Consensus 479 ~~~~~e~~~~p~~~~~~~~k~-~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~~--~~~~~~~~~~~~~d~s~~~~~~e 555 (842)
..+..+.|+.|.. +..+.+. ..|++||+||||++|++|++|||||||++|... +...........+|+|++++.+|
T Consensus 749 ~~~~~~~~~~~~~-~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdili~k~~p~~~~~~~~~~~~~~~~~~~~s~~~~~~e 827 (1103)
T PRK08565 749 PGGQEDKIEIPEP-NVRGYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGE 827 (1103)
T ss_pred CCCCceEEecCCC-cccccCchhhhhcCCCCCCcCCCcEEcCCCEEEEEecCCCCCcchhhccccCCccccceEEecCCC
Confidence 4444467877743 2223333 358999999999999999999999999998541 11011111124789999999999
Q ss_pred cceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCCCCCCCCCCceEEeCCCCCCCCCcHHH
Q 003180 556 TGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQ 635 (842)
Q Consensus 556 ~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dmPft~~G~~pDiIiNPh~~PSRMtiGq 635 (842)
+|+||+|.++.+.++.+.|||++|+.|+|+||||||||||||||||+|||+||||||+||++||||||||||||||||||
T Consensus 828 ~g~V~~V~~~~~~~~~~~vkv~ir~~R~p~iGDKfssRhGqKGv~s~i~~~edmPf~~~G~~pDiI~NPh~~PSRMtiG~ 907 (1103)
T PRK08565 828 KGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQ 907 (1103)
T ss_pred ceEEEEEEEEecCCCcEEEEEEEEEEecCchhhhhhhhccCcceeeeecccccCCcCCCCCCccEEECCCCCcccccHHH
Confidence 99999999999888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCcEEeeeEeEeeehhhhccCccCcceEE
Q 003180 636 LIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHS 715 (842)
Q Consensus 636 l~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~~~~~~if~G~~yy~rL~Hmv~DK~~~ 715 (842)
|+|+++|||+++.|.+.|+|||++...+++++.|+++||+++|+|.||||+||++|+++||+|++|||||+|||.||+||
T Consensus 908 l~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~l~~G~tG~~~~~~if~G~~yy~rL~HmV~DK~~~ 987 (1103)
T PRK08565 908 LLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHA 987 (1103)
T ss_pred HHHHHHHHHHHhcCceeeecCcCCchHHHHHHHHHHcCCCCCCcEEEEcCCCCCCcccceEEeehhheechhhhchhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCceeeeeccccCcceeecccCCceeeccCC
Q 003180 716 RGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCK 795 (842)
Q Consensus 716 R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~~~vC~~cG~~~~~~~~~~~~~C~~C~ 795 (842)
|++||++.|||||++||+|+|||||||||||||+|||||++|+|||+++||.+.++||.+||++++.+.+++.++|+.|+
T Consensus 988 R~~Gp~~~lt~QP~~Gr~~~GG~R~GEME~d~l~a~Gas~~L~erL~~~SD~~~~~vC~~Cg~~~~~~~~~~~~~C~~c~ 1067 (1103)
T PRK08565 988 RARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHG 1067 (1103)
T ss_pred ccCCCcchhhhCCccccccCCCeeeecchHHHHHhcccHHHHHHHhhccccceeeeeecccccccccccccCceeccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999877667788999999
Q ss_pred CCCCceeecchHhHHHHHHHHHhCCCceEEEEccC
Q 003180 796 NKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 830 (842)
Q Consensus 796 ~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~ 830 (842)
++..+.++.||||||||+|||+||||+++|.+++.
T Consensus 1068 ~~~~~~~v~iPy~~k~l~~EL~sm~i~~~l~~~~~ 1102 (1103)
T PRK08565 1068 DKGNISPVEVSYAFKLLLQELMSMGISPRLKLGDK 1102 (1103)
T ss_pred CCCcceeccCChhHHHHHHHHHhCCCceEEEeeec
Confidence 98899999999999999999999999999999753
|
|
| >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 |
|---|
| >KOG0216 consensus RNA polymerase I, 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 |
|---|
| >cd00653 RNA_pol_B_RPB2 RNA polymerase beta subunit | 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 |
|---|
| >TIGR02013 rpoB DNA-directed 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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >KOG0214 consensus RNA polymerase II, second largest subunit [Transcription] | 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 |
|---|
| >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 |
|---|
| >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 |
|---|
| >PHA03394 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional | 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 |
|---|
Homologous Structure Templates
Structure Templates Detected by BLAST
Original result of BLAST against Protein Data Bank
| ID | Alignment Graph | Length |
Definition |
E-value | |
| Query | 842 | ||||
| 3h0g_B | 1210 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 0.0 | ||
| 1i3q_B | 1224 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 0.0 | ||
| 2waq_B | 1131 | The Complete Structure Of The Archaeal 13-Subunit D | 0.0 | ||
| 2pmz_B | 1124 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 0.0 | ||
| 1l9u_C | 1118 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 5e-40 | ||
| 1ynj_C | 1119 | Taq Rna Polymerase-Sorangicin Complex Length = 1119 | 5e-40 | ||
| 1hqm_C | 1119 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 6e-40 | ||
| 1i6v_C | 1118 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 6e-40 | ||
| 1iw7_C | 1119 | Crystal Structure Of The Rna Polymerase Holoenzyme | 1e-39 | ||
| 3lu0_C | 1342 | Molecular Model Of Escherichia Coli Core Rna Polyme | 1e-25 | ||
| 3iyd_C | 1342 | Three-Dimensional Em Structure Of An Intact Activat | 1e-25 | ||
| 3qqc_A | 436 | Crystal Structure Of Archaeal Spt45 BOUND TO THE RN | 1e-05 |
| >pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1210 | Back alignment and structure |
|
| >pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1224 | 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|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 1124 | 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|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|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 |
| >pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP DOMAIN Length = 436 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >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 |
|---|
Score = 1329 bits (3440), Expect = 0.0
Identities = 556/863 (64%), Positives = 675/863 (78%), Gaps = 34/863 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
+LPH+ T + ET+KA++ GY+IHR+LLCAL RR DDRDH+G KRLDLAGPLL LFRM
Sbjct: 346 LLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRM 405
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGV 119
LFRK+TRDV Y+QKCV+ ++ NL A+K+ IT+GL+YSLATGNWG Q + R GV
Sbjct: 406 LFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGV 465
Query: 120 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 179
SQVLNR T+ASTLSHLRR N+PIGR+GKLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL
Sbjct: 466 SQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNL 525
Query: 180 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239
+LM Y++VGS + PI+EFLEEWG E E+ +P+ P ATK+FVNG W+G+HRDP L +T
Sbjct: 526 SLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTET 585
Query: 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVE-------KQRLLIKKRDI 292
LR LRRR+D++ EV +VRDIR KELR++TD GR RPLFIV+ + L I+K I
Sbjct: 586 LRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHI 645
Query: 293 IALQQRESPEDG------GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLH----- 341
L + + D GW LV+ G IEY+D EEEET MI+M+ DL +R
Sbjct: 646 QQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYE 705
Query: 342 -------------PEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 388
+ +THCEIHP++ILG+ ASIIPFPDHNQSPRNTYQSAMGKQ
Sbjct: 706 VKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQ 765
Query: 389 AMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 448
AMG+Y+TNYQ RMDT+A +LYYPQKPL TTR+ME+L FR+LPAG NAIVAI CYSGYNQE
Sbjct: 766 AMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 825
Query: 449 DSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDD 508
DS+IMNQ+SIDRG FRS+F+R+Y D+EKK+G V E+F RP RS T+ M+HG+YDKL+DD
Sbjct: 826 DSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDD 885
Query: 509 GLAPPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTT 566
GL PGTRVSGED+IIGKT PI D + + + +RD S LR +E+G+VDQV++TT
Sbjct: 886 GLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTT 945
Query: 567 NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 626
N +GL+FVKVR+RS RIPQIGDKF+SRHGQKGT+GMTY EDMP++ +GI PDII+NPHA
Sbjct: 946 NQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHA 1005
Query: 627 IPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGH 686
IPSRMT+ L+EC + KV+A G EGDATPFTDVTV+ +SK L G+Q RGFE MY+GH
Sbjct: 1006 IPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Query: 687 TGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERD 746
TGR+L A +FLGPTYYQRLKH+VDDKIH+R RGPVQILTRQP EGRSRDGGLRFGEMERD
Sbjct: 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERD 1125
Query: 747 CMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP 806
C I+HG S L+ERLFD SDAYRV VC+ CGLIAIA+ KK+S+ECR C+N+T QV++P
Sbjct: 1126 CQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLP 1185
Query: 807 YACKLLFQELMAMAIAPRMLTKE 829
YA KLLFQELM+M IAPR+ TK
Sbjct: 1186 YAAKLLFQELMSMNIAPRLFTKN 1208
|
| >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 |
|---|
| >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 |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 842 | |||
| 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 | |
| 3qqc_A | 436 | DNA-directed RNA polymerase subunit B, DNA-direct | 99.29 | |
| 3tbi_B | 228 | DNA-directed RNA polymerase subunit beta; transcri | 99.14 | |
| 3mlq_A | 188 | DNA-directed RNA polymerase subunit beta; tudor, t | 93.2 |
| >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=1.8e-248 Score=2251.06 Aligned_cols=830 Identities=67% Similarity=1.136 Sum_probs=784.1
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
||||++....++.+||+||++|+||||+++.|.+.+||+|||+||||+++|+||+.+||+.|+++++.+++++++.+++.
T Consensus 346 lLpHl~~~~~~~~~Ka~fL~~MvrkLl~~~~G~~~~Dd~D~~~nkrl~l~G~Ll~~lfr~~~~~~~~~i~~~l~k~~~~~ 425 (1210)
T 3h0g_B 346 LLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETN 425 (1210)
T ss_dssp SSCSSCCSSSCCSSHHHHHHHHHHHHHHHHTTSSCCCCTTCSSSCCBCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred EEeCcCCCccchhHHHHHHHHHHHHHHHHhCCCCCCCCCccccCeEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 69999998888899999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred CCCchhccccccchhhhhhhhhccCcccccc-ccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCc
Q 003180 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQAN-AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQW 159 (842)
Q Consensus 81 ~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~-~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~w 159 (842)
+.+++..+++++.||++|++|||||||+.++ +.++++||||+|+|+||+|+|||||||++|+++++|+++||+||||||
T Consensus 426 ~~~~~~~~i~~~~It~~l~~~laTGNW~~~kk~~~~~sGvsqvl~R~n~~s~lShlRrv~~p~~~~~K~~~~R~Lhpt~W 505 (1210)
T 3h0g_B 426 REFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHW 505 (1210)
T ss_dssp CSCCCTTSSCSTTTSHHHHHHHSSSCSSTTSSCCSCCCCSCCBCCCSSHHHHHHHTTBBCCSCCSSCCSSSSSSCCGGGT
T ss_pred CccCHHHhcchhhhHHHHHHHhhcCCcccccccccCcCCEEEEcccCCHHHHHHHHHhccCchhhccccccccccChhhh
Confidence 8889999999999999999999999999776 778999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHH
Q 003180 160 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239 (842)
Q Consensus 160 GfiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~ 239 (842)
||+||+|||||++||||||||++|+||++++.+||.++|.++||++++++.+...++.++|||||+|||+|++|..|+++
T Consensus 506 G~iCP~eTPEG~~cGLvknLal~~~Isvg~~~~pI~~~l~~~gme~le~~~~~~~~~~tkVfvNG~wVGvh~dp~~Lv~~ 585 (1210)
T 3h0g_B 506 GMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTET 585 (1210)
T ss_dssp TTCCCSCCCSSSSTTTSCBCCSSCCBCCCCCSSHHHHHHHSSSCCCCSCCCSSSSSSSCCCCSTTCCCCCCSCHHHHHHH
T ss_pred eeeccccCCCCCcccccccccceeeeECCCCcHHHHHHHHHhCCcchhhcCcccCCCceEEEECCEEEEEeCCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998888888999999999999999999999999
Q ss_pred HHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeecc-------cccccHHHHHHHhcCCC------CCCCCc
Q 003180 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQ-------RLLIKKRDIIALQQRES------PEDGGW 306 (842)
Q Consensus 240 lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~-------~~~~~~~~~~~l~~~~~------~~~~~~ 306 (842)
||.|||+|.|+.+|||++|.+++||+||||+||+|||||+|+|+ ++.++++|+++|+.+.. .+..+|
T Consensus 586 lR~lRR~g~Is~eVSIvrdir~rE~~IfTDaGRv~RPLfvVen~~~~~~~g~L~l~k~hi~~L~~~~~~~~~~~~~~~~w 665 (1210)
T 3h0g_B 586 LRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGW 665 (1210)
T ss_dssp HHHHHTTTSSCTTCCCCCCTTTCCCCCCCSSCCBCCEEEECCCSSCSSSSCCCSSCHHHHHHHHHHHTCCCSCTTCCCSS
T ss_pred HHHHhhcCCCCCceEEEecCCCCeEEEecCCCcccceEEEEccCCcccccccccccHHHHHHHhcccccccccccccCCH
Confidence 99999999999999999999999999999999999999999986 89999999999974321 124699
Q ss_pred hhccccCcEEEeccccccceeEeecccccccccCCC---------------Cc---CCCCceeeeeccCCcccccccccc
Q 003180 307 HDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHP---------------EE---AYADTYTHCEIHPSLILGVCASII 368 (842)
Q Consensus 307 ~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~---------------k~---~~~~~~TH~EI~Ps~ilgv~AslI 368 (842)
++|+++|+|||||++||++++|||+++||++++..+ +. ...+.||||||||++|||||||+|
T Consensus 666 ~~Lv~~GvIEylDaeEEet~mIamtpeDL~~~r~~~~g~~~~~~~d~~~r~k~~~~~~~~~~THcEIhPsmILGIcASiI 745 (1210)
T 3h0g_B 666 TALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASII 745 (1210)
T ss_dssp TTTTTTTSEEECCTTTGGGCCEESCHHHHHHHHHHTTCCCCCCSSCCSSCCCCCSCCSCCSCSEECSCGGGSSCSSSTTS
T ss_pred HHHHhCCCEEEecHhhhhceeEEecHHHhhhhhhhhccccccccccchhhccccCCCcccccccccccchhhhhheeecc
Confidence 999999999999999999999999999996532110 00 124679999999999999999999
Q ss_pred CCCCCCCCccchhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCC
Q 003180 369 PFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 448 (842)
Q Consensus 369 PF~~HNqSpRn~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~E 448 (842)
|||||||||||||||||+|||||++.+|++.|+||++|+|+|||+|||+|+++|+++++++|+|+||+||||||+|||||
T Consensus 746 PFpdHNQSPRNtYQ~aMgKQamG~~~~n~~~R~Dt~~~~L~yPQkPlv~T~~~e~~~~~elp~G~NaiVAvmsy~GYn~E 825 (1210)
T 3h0g_B 746 PFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 825 (1210)
T ss_dssp SSSTTSCSHHHHHHHHHHTTCCSCCCTTTTTSCCSSEEEESSCBCCSSBCTTSTTTTCTTSCSCCEECBEECCCSSSSCS
T ss_pred cCccccccchhhhhhhhhcccccccccccccccCccccEeecCcCccccchhHHHhCCCcccCccceEEEEeccCCCChh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeeccccccCceeEEEEEEEEeeehhcCCccccccccCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeC
Q 003180 449 DSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTT 528 (842)
Q Consensus 449 DAiIiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~ 528 (842)
|||||||+|+|||||||+||++|++++++.+.+..+.|++|+.+...++|.+.|++||+||||+||++|++|||||||++
T Consensus 826 DAiIink~sv~rg~~~s~~~~~y~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~LD~dGi~~~G~~v~~gDiligK~~ 905 (1210)
T 3h0g_B 826 DSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTA 905 (1210)
T ss_dssp SCEEEEHHHHTTTTTCEEEEEEEEECCCCCSSSCCCCCCCCCTTSCCSCCSCCGGGCCTTSSCCTTCCCCTTCCCCCCCC
T ss_pred hheeeehhheecCceEEEEEEEEEEEeeecCCCceeEEcCCCcchhcccchhhHhhcCCCCCcCCCCEecCCCEEEEEec
Confidence 99999999999999999999999999988776667899999876665677788999999999999999999999999999
Q ss_pred CCCcc--ccccccCCCccceeeEEeeccccceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecc
Q 003180 529 PISQD--EAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQ 606 (842)
Q Consensus 529 ~~~~~--~~~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~ 606 (842)
|+..+ +++...+....+|+|++++++|.|+||+|.++++++|.+.|||++|+.|+|++|||||||||||||||+|||+
T Consensus 906 p~~~~~~~~~~~~~~~~~rd~s~~~~~~e~g~Vd~V~~~~~~~g~~~vkv~~~~~R~~~~GDK~a~RhGqKGvi~~i~~~ 985 (1210)
T 3h0g_B 906 PIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRH 985 (1210)
T ss_dssp CC-----------CCCCCCCCCCCCCTTCCCCCCEEEEEECSSSSEEEEEEECCCBCCCTTCEEECTTCCCEEEEEEECT
T ss_pred CCCCCchhhcccccccccceeeEEecCCCCeEEEEEEEEEecCCCeEEEEEEEEecCCCchhhhhcccCCCceeeEEecc
Confidence 98642 2333333456799999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCC
Q 003180 607 EDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGH 686 (842)
Q Consensus 607 ~dmPft~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~ 686 (842)
|||||++||++|||||||||||||||||||+|+++|||+++.|.+.|+|||++..++++++.|+++||+++|+|.||||+
T Consensus 986 edmPf~~~G~~pDii~NP~~~PSRMtigq~~E~~~g~~~~~~g~~~~~tpF~~~~~~~~~~~l~~~g~~~~G~~~l~~g~ 1065 (1210)
T 3h0g_B 986 EDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065 (1210)
T ss_dssp TTSCCBTTTBCCSEECCGGGSTTSCCHHHHHHHHHHHHSSSSCCCCBCCSSCSCCHHHHHHHHHTTTSCTTSCBCCBCSS
T ss_pred ccCCcCCCCCCCeEEECCCcCCCCccchhhhHhHHHHHHHhcCCceeeccCCCCcHHHHHHHHHHcCcCCCCCEEEEcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcEEeeeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCC
Q 003180 687 TGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 766 (842)
Q Consensus 687 tG~~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD 766 (842)
||++|+++||+|++|||||+|||+||+|||++|||+.|||||++||+|+|||||||||||||+|||||++|+|||+++||
T Consensus 1066 tg~~~~~~i~~G~~yy~kL~Hmv~dK~h~r~~gp~~~~t~QP~~gr~~~GG~r~GEME~~~l~a~Gaa~~l~e~l~~~SD 1145 (1210)
T 3h0g_B 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSD 1145 (1210)
T ss_dssp SCCBCSSCBEECCEECEECSCCSTTTCEECSSCCBCSSSCSBCCSSTTCCCCCCCHHHHHHHHHHTBHHHHHHHHHTTTT
T ss_pred CCCCccccEEEEehHhhcchhhcccCcEEeccCCCchhccCCcccccccCCeeeehhhhhhhhhccHHHHHHHHhhcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeeccccCcceeecccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEccC
Q 003180 767 AYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 830 (842)
Q Consensus 767 ~~~~~vC~~cG~~~~~~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~ 830 (842)
.++++||+.||++++.+..++.++|+.|.++.+|.++.||||||||+|||+||||.+||.++++
T Consensus 1146 ~~~~~vC~~cg~~~~~~~~~~~~~c~~c~~~~~i~~~~~p~~~k~l~~El~~~~i~~rl~~~~~ 1209 (1210)
T 3h0g_B 1146 AYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTKNH 1209 (1210)
T ss_dssp CCEEEEESSSCCBCCCCSSSCCCCCTTTCCSSCEEEEECCHHHHHHHHHHHTTTCCEECCCSTT
T ss_pred cceeEeecCCCCeeeecccCCceEcCccCCCCccceecCCHHHHHHHHHHHhCCCceEEEecCC
Confidence 9999999999999987777778899999999999999999999999999999999999998653
|
| >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 |
|---|
| >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 |
|---|
| >3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory protein, transcription; 3.00A {Escherichia coli} | 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 |
| 842 | ||||
| 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 | 0.0 |
| >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 = 838 bits (2166), Expect = 0.0
Identities = 555/863 (64%), Positives = 669/863 (77%), Gaps = 32/863 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
LPH+ + E++KA++ GY+I+RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+
Sbjct: 343 FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKT 402
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA-NAAGTRAGV 119
LF+KLT+D+ Y+Q+ V+ D N++ AI AKTITSGLKY+LATGNWG+ A +RAGV
Sbjct: 403 LFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGV 462
Query: 120 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 179
SQVLNR TY+STLSHLRR N+PIGR+GKLAKPRQLHN+ WG++CPAETPEGQACGLVKNL
Sbjct: 463 SQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 522
Query: 180 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239
+LM I+VG+ PI+ FL EWG E E+ P P AT++FVNG W G+HR+P L++T
Sbjct: 523 SLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET 582
Query: 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVE------KQRLLIKKRDII 293
LR LRR+ D+N EV ++RDIR KEL+I+TD GR RPLFIVE + L ++K I
Sbjct: 583 LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIA 642
Query: 294 ALQQRESPEDGG---------WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEE 344
L E + G W L+ +G +EYID EEEE+ +I+M DL A + E
Sbjct: 643 KLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEN 702
Query: 345 -------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 391
+A T+THCEIHPS+ILGV ASIIPFPDHNQSPRNTYQSAMGKQAMG
Sbjct: 703 DLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMG 762
Query: 392 IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSV 451
+++TNY RMDT+A +LYYPQKPL TTRAME+L FR+LPAG NAIVAIACYSGYNQEDS+
Sbjct: 763 VFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSM 822
Query: 452 IMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLA 511
IMNQSSIDRG FRSLFFRSY D+EKK G + E F +P R+NT+ M+HG+YDKLDDDGL
Sbjct: 823 IMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI 882
Query: 512 PPGTRVSGEDVIIGKTTPISQD--EAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNAD 569
PG RVSGEDVIIGKTTPIS D E + + +++RD S LR +E G+VDQVL+TTN D
Sbjct: 883 APGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQD 942
Query: 570 GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPS 629
GL+FVKVRVR+ +IPQIGDKF+SRHGQKGT+G+TY +EDMP+T EGI PD+I+NPHAIPS
Sbjct: 943 GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPS 1002
Query: 630 RMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 689
RMT+ LIEC++ KVAA G EGDA+PFTD+TV+ ISK L + GYQ RGFE MYNGHTG+
Sbjct: 1003 RMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGK 1062
Query: 690 RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMI 749
+L A IF GPTYYQRL+HMVDDKIH+R RGP+Q+LTRQP EGRSRDGGLRFGEMERDCMI
Sbjct: 1063 KLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMI 1122
Query: 750 AHGASHFLKERLFDQSDAYRVHVCEHCGLIA-IANLKKNSFECRGCKNKTDIVQVHIPYA 808
AHGA+ FLKERL + SDA+RVH+C CGL+ IA L N FEC+GC NK DI Q+HIPYA
Sbjct: 1123 AHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYA 1182
Query: 809 CKLLFQELMAMAIAPRMLTKEDT 831
KLLFQELMAM I PR+ T
Sbjct: 1183 AKLLFQELMAMNITPRLYTDRSR 1205
|
| >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 | 842 | |||
| d1twfb_ | 1207 | RBP2 {Baker's yeast (Saccharomyces cerevisiae) [Ta | 100.0 | |
| d1smyc_ | 1119 | RNA-polymerase beta {Thermus thermophilus [TaxId: | 100.0 | |
| d1smyc_ | 1119 | RNA-polymerase beta {Thermus thermophilus [TaxId: | 84.5 |
| >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=3.2e-216 Score=2017.65 Aligned_cols=830 Identities=67% Similarity=1.128 Sum_probs=730.9
Q ss_pred CccccCCCCCCcchHHHHHHHHHHHHHhhcCCCCCCCCCCccCCcEECchhHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 003180 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNG 80 (842)
Q Consensus 1 llpHl~~~~~~~~~K~~~L~~Mi~kLl~~~~g~~~~Dd~D~~~nkRv~~~G~Ll~~lf~~~~~~~~~~~~~~~~~~~~~~ 80 (842)
+|||++...+++..|+.||++|++||+.+..|.+.+||+|||+||||+++|+||+.+||+.|+++++.+++.+.+...+.
T Consensus 343 llpHl~~~~~~~~~K~~~L~~mi~kll~~~~g~~~~dd~D~~~nkrv~~~G~Ll~~~fr~~~~~~~~~i~~~~~~~~~~~ 422 (1207)
T d1twfb_ 343 FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEA 422 (1207)
T ss_dssp SSTTTCCSSSCHHHHHHHHHHHHHHHHHHHTTSSCCCCTTCGGGEEEECHHHHHHHHHHHHHHHHHHHHHHHHHSCCC--
T ss_pred hccccccccchhhhHHHHHHHHHHHHHHhhhcccCCcchhhhccchhhhHHHHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence 69999988878889999999999999999999999999999999999999999999999999999999999998876666
Q ss_pred CCCchhccccccchhhhhhhhhccCcccccc-ccccccceeEeccccChhhhhcccccccCCcccCCCcCCcccccCCCc
Q 003180 81 KDVNLQFAIKAKTITSGLKYSLATGNWGQAN-AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQW 159 (842)
Q Consensus 81 ~~~~~~~~~~~~~it~~i~~~~sTGnw~~~~-~~~~~~G~sq~l~r~N~l~~lShlRrv~~~~~~~~K~t~~R~LhpS~w 159 (842)
+.+++..+++++.||++|++||+||||++.. ...+++|+||+|+|+||+++|||+||||+++++++|+++||+||||||
T Consensus 423 ~~~~~~~~~~~~~it~~i~~~~~TGn~~~~~~~~~~~~G~sq~l~r~n~l~~lSh~Rrv~~~~~~~~k~~~~R~Lhps~~ 502 (1207)
T d1twfb_ 423 HDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHW 502 (1207)
T ss_dssp ------CCCCTHHHHHHHHHHHHHCCCC---------CCCEEECCCSSHHHHHHHHTEEECCC------CCTTSCCGGGT
T ss_pred cccChhhhhccCcHHHHHHHHHhcCcccccccccccccchhhhhhhcCHHHHHHhhhcccCCcccccccchhhhcchhhc
Confidence 6788888888999999999999999999876 667899999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCcchhhhhcccceEEecCCCchhHHHHHHHhCCccccccCCCCCCCcEEEEECCEEEEEEcChHHHHHH
Q 003180 160 GMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239 (842)
Q Consensus 160 GfiCPveTPEG~~cGLvknLA~~a~Is~~~~~~~i~~~L~~~g~~~~~~~~~~~~~~~~~VflnG~~iG~~~~~~~lv~~ 239 (842)
||+||+|||||++||||||||++|+|+.+.++.++.++|..+|+..+.........+..+||+||.|+|+++++..|++.
T Consensus 503 G~iCPveTPEG~~~GLv~~La~~a~i~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~V~~nG~~~G~~~~~~~l~~~ 582 (1207)
T d1twfb_ 503 GLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET 582 (1207)
T ss_dssp TTBCSSCCCSGGGBTTEEEBCTTCEECCCCCCHHHHHHHHHTTCEEGGGCCGGGCTTCEEEEETTEEEEEESCHHHHHHH
T ss_pred cceeeeeCCCCCcccceeccceeeeeccccccceeeEEeeccCcccceeeeeccccccceeeeeeeEEEEEcchheeehh
Confidence 99999999999999999999999999999999999999999999988877666677889999999999999999999999
Q ss_pred HHHhhhcCCCCCcEEEEEeccCCeEEEecCCCeeeeeEEEeeccc------ccccHHHHHHHhcCC---------CCCCC
Q 003180 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQR------LLIKKRDIIALQQRE---------SPEDG 304 (842)
Q Consensus 240 lR~lRr~~~i~~~vsi~~~~~~~~i~I~td~GRl~RPl~vv~n~~------~~~~~~~~~~l~~~~---------~~~~~ 304 (842)
+|.+||.|.++.+++++++....+++|+||+||++||||+++|+. +.+.+.++..+...+ .....
T Consensus 583 lr~~R~~g~i~~~~s~~~~~~~~~i~i~td~Gr~~rPlfi~~nd~~~~~~~~~mqrq~v~~l~~~e~~~v~~~~e~~~~~ 662 (1207)
T d1twfb_ 583 LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEY 662 (1207)
T ss_dssp HHHHHHHTSSCTTCEEEEETTTTEEEEECCSCCEEEEEEEEECCCTTSSCEESCCHHHHHHHHHHHHCC---------CC
T ss_pred eeeeeeccCccceeeeeeeccccceEEEecCccccCCceeecchhhhcccceeeeHhhHhhhhccccccccccccchhhc
Confidence 999999999999999999999999999999999999999999853 456666666543211 01245
Q ss_pred CchhccccCcEEEeccccccceeEeecccccccccCCC-------------CcCCCCceeeeeccCCccccccccccCCC
Q 003180 305 GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHP-------------EEAYADTYTHCEIHPSLILGVCASIIPFP 371 (842)
Q Consensus 305 ~~~~l~~~g~IE~Id~~Eq~~~~Ia~~~~~l~~~~~~~-------------k~~~~~~~TH~EI~Ps~ilgv~AslIPF~ 371 (842)
.|.+++.+|.|||||++|++++.||+++++++...... ....+..+||+||+|+.|||++|++|||+
T Consensus 663 ~~~~~~~~g~ieyid~~E~~~~~Ia~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~th~Ei~p~~ilg~~as~iPf~ 742 (1207)
T d1twfb_ 663 TWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFP 742 (1207)
T ss_dssp CHHHHHHTTSEEEEEHHHHTTCCEESSGGGGCC---------CCCTTSCCCCCCCCSCCCEECSCGGGGSCTTGGGSSSG
T ss_pred cccccccCCceeeecchhcceEEEEecccccccccccccccccccchhheeeecccccccccccccceEEeeecceEEec
Confidence 89999999999999999999999999999986532110 00113568999999999999999999999
Q ss_pred CCCCCccchhhhcccccccccccceeEEecccCcceeccCCcceeeccccccccCCCCCCCceeeEEeeeccCCCCCCce
Q 003180 372 DHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSV 451 (842)
Q Consensus 372 ~HNqSpRn~yq~~M~KQaig~~~~n~~~R~Dt~~~~L~ypQ~PlV~t~~~~~~~~~e~p~G~N~iVAvmsy~GYn~EDAi 451 (842)
||||||||+|||||+|||||++.+|++.|.|+++|+|+|||+|||+|+.++.++++++|+|+||+||||||+||||||||
T Consensus 743 ~hNqSpRn~yq~qm~KQa~G~~~~~~~~r~D~~~~~l~~pQ~Plv~t~~~~~~~~~e~p~G~N~iVAvmsy~GYN~EDAi 822 (1207)
T d1twfb_ 743 DHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSM 822 (1207)
T ss_dssp GGSCHHHHHHHHHHGGGBCBCSCTTTTTCCCSEEEEESSCBCCSEECTTHHHHTTTTSCCCEEEEEEECBSSSTTTTTEE
T ss_pred ccccccceeecccCCcccCCccccccceeccccceeEecCCCceeeccchhhhhhhcccchhceEEEEEeccCccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccccccCceeEEEEEEEEeeehhcCCccccccccCCCCCCCCCCCCCccCCCCCCCcCCCcEEcCCCEEEEeeCCCC
Q 003180 452 IMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPIS 531 (842)
Q Consensus 452 IiNk~si~rG~f~s~~~~~~~~~~~~~~~~~~e~~~~p~~~~~~~~k~~~~~~Ld~dGl~~~G~~v~~gdvli~k~~~~~ 531 (842)
||||+|+|||||||+||++|++++++.+.+..+.+..|...+....+...|++||+||+|++|++|++||+||||++|..
T Consensus 823 IiNk~si~rG~f~s~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ld~dGi~~~G~~v~~gdilvgk~~p~~ 902 (1207)
T d1twfb_ 823 IMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPIS 902 (1207)
T ss_dssp EEEHHHHHTTTTCEEEEEEEEECCCCSCTTCCCEESCCCCSSSCBCCSSCGGGCCTTSBCCTTCEECTTCEEECEECCCC
T ss_pred ccchhhhhhcccceeeeEEEEEEeccccccccccccccccccccccchhhhhcccccccccccccccCCceeeeeeeccC
Confidence 99999999999999999999999988776677778777665555566778999999999999999999999999999986
Q ss_pred cccc--ccccCCCccceeeEEeeccccceEEeEEEeecCCCceEEEEEEeeecCCcccccccccCCCcceeeeeecccCC
Q 003180 532 QDEA--QGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDM 609 (842)
Q Consensus 532 ~~~~--~~~~~~~~~~d~s~~~~~~e~g~Vd~V~~~~~~~~~~~v~v~~r~~R~p~iGDKfssRhGqKGvvs~i~~~~dm 609 (842)
+++. .........+|.|++++.++.|+||+|.++.+.++.+.|+|++|+.|+|+||||||||||||||||+|||+|||
T Consensus 903 ~~~~~~~~~~~~~~~~~~s~~~~~~~~g~V~~v~~~~~~~~~~~~kv~i~~~R~p~iGDKfasRhGqKGv~s~i~p~eDM 982 (1207)
T d1twfb_ 903 PDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDM 982 (1207)
T ss_dssp -------------CCBBCCEECCTTCCEEEEEEEEEECSSSCEEEEEEEEEEECCCTTCEEECTTSCEEEEEEEECTTTS
T ss_pred CchhhhhhccccccccceeEEccCCCCeEEEEEEEeecccccceeeEEEEEEeccchhhhhhhccCCcceeeeeechhhC
Confidence 4321 11222345789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCceEEeCCCCCCCCCcHHHHHHHHhhhhhhccCCcceecCCCCCCHHHHHHHHHHcCCCCCCeEEEeeCCCCc
Q 003180 610 PWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 689 (842)
Q Consensus 610 Pft~~G~~pDiIiNPh~~PSRMtiGql~E~~~gk~~~~~g~~~d~tpF~~~~~~~~~~~l~~~g~~~~G~e~ly~g~tG~ 689 (842)
|||+||++|||||||||||||||||||+|+++||||++.|.+.|+|||++..++++++.|+++||+++|+|.||||+||+
T Consensus 983 Pf~~dG~~pDiI~NP~g~PSRMtiGql~E~~~gk~~~~~g~~~d~t~F~~~~~~~~~~~L~~~g~~~~G~e~ly~G~tG~ 1062 (1207)
T d1twfb_ 983 PFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGK 1062 (1207)
T ss_dssp CEETTSCCCSEEECGGGSTTTTCHHHHHHHHHHHHHHHHCSCEECCSSSSCCHHHHHHHHHTTTSCTTSEECEECTTTCC
T ss_pred CcCCCCCCccEEECCCcCcccCcHHHHHHHHHHHHHHhcCCccccCCCCCccHHHHHHHHHHcCCCCCCCEEEECCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeEeEeeehhhhccCccCcceEEeccCCccccccCCCCcccCCCcceeeehhhHHHHhhccHHHHHHhhhcCCCcee
Q 003180 690 RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYR 769 (842)
Q Consensus 690 ~~~~~if~G~~yy~rL~Hmv~DK~~~R~~Gp~~~lT~QP~~Gr~~~GG~R~GEMErd~l~a~Gas~~l~erl~~~SD~~~ 769 (842)
+|+++||+|++|||||+|||+||+|||++||+++|||||++||+|+|||||||||||||+|||||++|+|||+++||.+.
T Consensus 1063 ~~~~~i~~G~~yy~rL~HmV~DK~~~Rs~Gp~~~lT~QP~~Gr~~~GG~R~GEME~dal~a~Gaa~~L~e~l~~~SD~~~ 1142 (1207)
T d1twfb_ 1063 KLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFR 1142 (1207)
T ss_dssp BCSSCEEEEEEEEEEBSSCGGGTCEEECCCC----------------CCCCCHHHHHHHHHHTCHHHHHHHHCCSSCCCE
T ss_pred CccceEEEehhHhhhhhhhhccccEeeccCCCCccccCCCCccccCCCcceehHHHHHHHHHhHHHHHHHHhhccCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeccccCcceee-cccCCceeeccCCCCCCceeecchHhHHHHHHHHHhCCCceEEEEccC
Q 003180 770 VHVCEHCGLIAIA-NLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKED 830 (842)
Q Consensus 770 ~~vC~~cG~~~~~-~~~~~~~~C~~C~~~~~i~~v~iPy~~kll~~EL~sm~I~~~l~~~~~ 830 (842)
++||.+||+++.. +.+...++|+.|+++.++.++.||||||||+|||+||||++||.+++.
T Consensus 1143 ~~vc~~cg~~~~~~~~~~~~~~c~~c~~~~~i~~~~iPy~fk~l~~EL~sm~i~~~l~~~~~ 1204 (1207)
T d1twfb_ 1143 VHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRS 1204 (1207)
T ss_dssp EEEESSSCSSCCEEETTTTEEEBTTTTBSSSEEEEECCHHHHHHHHHHHHTTBCCEEESCSS
T ss_pred eeccccCCceEEEecccccceeecCCCCCCCccccCCCHHHHHHHHHHHHCCCceEEEecCc
Confidence 9999999999853 445667899999999999999999999999999999999999999764
|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|
| >d1smyc_ e.29.1.1 (C:) RNA-polymerase beta {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|