Citrus Sinensis ID: 000291
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 | 1714 | 2.2.26 [Sep-21-2011] | |||||||
| Q5D869 | 1976 | DNA-directed RNA polymera | yes | no | 0.562 | 0.487 | 0.602 | 0.0 | |
| Q9LQ02 | 1453 | DNA-directed RNA polymera | no | no | 0.539 | 0.636 | 0.255 | 3e-68 | |
| P17545 | 1766 | DNA-directed RNA polymera | N/A | no | 0.357 | 0.346 | 0.275 | 7e-50 | |
| P17546 | 1766 | DNA-directed RNA polymera | N/A | no | 0.357 | 0.346 | 0.275 | 1e-49 | |
| P36594 | 1752 | DNA-directed RNA polymera | yes | no | 0.330 | 0.323 | 0.268 | 3e-47 | |
| Q75A34 | 1745 | DNA-directed RNA polymera | yes | no | 0.323 | 0.317 | 0.275 | 2e-45 | |
| O94666 | 1405 | DNA-directed RNA polymera | no | no | 0.335 | 0.409 | 0.273 | 5e-44 | |
| P04050 | 1733 | DNA-directed RNA polymera | yes | no | 0.327 | 0.323 | 0.259 | 4e-43 | |
| P18616 | 1839 | DNA-directed RNA polymera | no | no | 0.356 | 0.332 | 0.256 | 4e-42 | |
| P35084 | 1727 | DNA-directed RNA polymera | yes | no | 0.365 | 0.362 | 0.249 | 8e-41 |
| >sp|Q5D869|NRPE1_ARATH DNA-directed RNA polymerase E subunit 1 OS=Arabidopsis thaliana GN=NRPE1 PE=1 SV=1 | Back alignment and function desciption |
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Score = 1233 bits (3190), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 631/1047 (60%), Positives = 770/1047 (73%), Gaps = 83/1047 (7%)
Query: 1 MEENTSSTILEGQIVGIRFGLATQKEICTASISDCSISHASQLANPFLGLPLEFGKCESC 60
MEE ++S IL+G+IVGI F LA+ EIC SIS+ +I+H SQL N FLGLPLEFGKCESC
Sbjct: 1 MEEESTSEILDGEIVGITFALASHHEICIQSISESAINHPSQLTNAFLGLPLEFGKCESC 60
Query: 61 GTSEPGKCEGHFGYIELPIPIYHPSHISELK---LTMYAFQLQIK-----NDGVAQRLLS 112
G +EP KCEGHFGYI+LP+PIYHP+H++ELK + L+IK + G+A RLL
Sbjct: 61 GATEPDKCEGHFGYIQLPVPIYHPAHVNELKQMLSLLCLKCLKIKKAKGTSGGLADRLLG 120
Query: 113 SCCE-----------------------------------------------VKEMLKR-- 123
CCE + +L R
Sbjct: 121 VCCEEASQISIKDRASDGASYLELKLPSRSRLQPGCWNFLERYGYRYGSDYTRPLLAREV 180
Query: 124 ------IPEETRKKLAGKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLK 177
IPEE+RKKL KG+ PQ+GYILEYLPVPPNCLSVP+ SDG STMS D S LK
Sbjct: 181 KEILRRIPEESRKKLTAKGHIPQEGYILEYLPVPPNCLSVPEASDGFSTMSVDPSRIELK 240
Query: 178 KVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGV-SQDP 236
VLK+V I+SSRSG NFES + E++++ V YL+VRGTAK++R++D R+GV
Sbjct: 241 DVLKKVIAIKSSRSGETNFESHKAEASEMFRVVDTYLQVRGTAKAARNIDMRYGVSKISD 300
Query: 237 NSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNI 296
+S++KAW EKMRTLFIRKGSGFSSRSVITGDAY+ VNE+G+P EIAQRITFEERV+VHN
Sbjct: 301 SSSSKAWTEKMRTLFIRKGSGFSSRSVITGDAYRHVNEVGIPIEIAQRITFEERVSVHNR 360
Query: 297 NYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHK 356
YLQ+LVD+KLCL+Y+ GS++YSLR+GSKGHT L+PGQVVHRR+MDGD VFINRPPTTHK
Sbjct: 361 GYLQKLVDDKLCLSYTQGSTTYSLRDGSKGHTELKPGQVVHRRVMDGDVVFINRPPTTHK 420
Query: 357 HSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLL 416
HSLQAL VYVH+D+TVKINPL+C PLSADFDGDC+HLFYPQSL+AKAEV+ELFSVEKQLL
Sbjct: 421 HSLQALRVYVHEDNTVKINPLMCSPLSADFDGDCVHLFYPQSLSAKAEVMELFSVEKQLL 480
Query: 417 SSHNGNLNLQLATDALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSK-ARCSARWT 475
SSH G L LQ+ +D+LLSL+VM ++ FLDKA QQLAM+ LP PAL K ++ WT
Sbjct: 481 SSHTGQLILQMGSDSLLSLRVMLERVFLDKATAQQLAMYGSLSLPPPALRKSSKSGPAWT 540
Query: 476 ALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEF 535
QILQ P GDR+L+ S++LK DF D + S+INEIVTSIF EKGP+E L F
Sbjct: 541 VFQILQLAFPERLSCKGDRFLVDGSDLLKFDFGVDAMGSIINEIVTSIFLEKGPKETLGF 600
Query: 536 FDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQ----KEIQALYSLLYHRMSTQNELV 591
FDSLQPLLME+LFA+GFS+SLED S+S+A + I +EI + S L R+S ++E
Sbjct: 601 FDSLQPLLMESLFAEGFSLSLEDLSMSRADMDVIHNLIIREISPMVSRL--RLSYRDE-- 656
Query: 592 DLQIENHIRHVKMLVAKFILKSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSK 651
LQ+EN I VK + A F+LKS ++ LID KS+SA++K+VQQ GFLGLQLSD+ KFY+K
Sbjct: 657 -LQLENSIHKVKEVAANFMLKSYSIRNLIDIKSNSAITKLVQQTGFLGLQLSDKKKFYTK 715
Query: 652 TLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLS 711
TLVED+A +R Y + + +G++KGCFFHGLDPYEEM HSI+ REVIVRSSRGL+
Sbjct: 716 TLVEDMAIFCKRKYGRISS--SGDFGIVKGCFFHGLDPYEEMAHSIAAREVIVRSSRGLA 773
Query: 712 EPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHS-LFPAGEPVGVLAA 770
EPGTLFKNLMAVLRD+VI DGTVRN CSNS+IQF Y V++ + H LF AGEPVGVLAA
Sbjct: 774 EPGTLFKNLMAVLRDIVITNDGTVRNTCSNSVIQFKYGVDSERGHQGLFEAGEPVGVLAA 833
Query: 771 TAMSNPAYKAVLDSSPSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQE 830
TAMSNPAYKAVLDSSP+SN+SWELMKE+LLC+V+F N DRRVILYLN+C CG+++CQE
Sbjct: 834 TAMSNPAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNECHCGKRFCQE 893
Query: 831 RAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISD----DEGLVGHIHLNKILLEDLRISM 886
AA V+N+L +VSLKD AVEFL+EY+K IS+ D L GHIHLNK LL+D ISM
Sbjct: 894 NAACTVRNKLNKVSLKDTAVEFLVEYRKQPTISEIFGIDSCLHGHIHLNKTLLQDWNISM 953
Query: 887 HDILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRG 946
DI KC++ + S +KKK KK FK TSLS+SECCSF+ C K S+MPCL F
Sbjct: 954 QDIHQKCEDVINSLGQKKK-KKATDDFKRTSLSVSECCSFRDPCGSKGSDMPCLTFSY-N 1011
Query: 947 ASDSYLDKLSGVLANMIYPVLLETIIK 973
A+D L++ VL N +YPVLLE +IK
Sbjct: 1012 ATDPDLERTLDVLCNTVYPVLLEIVIK 1038
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DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity). Largest and catalytic component of RNA polymerase IVb involved in RNA-directed DNA methylation-dependent (RdDM) silencing of endogenous repeated sequences, including transposable elements. Also required for full erasure of methylation when the RNA trigger is withdrawn. Seems also involved in the synthesis of short-interfering RNAs (siRNA). Essential component of a self-reinforcing loop coupling de novo DNA methylation to siRNA production. Involved in the maintenance of post-transcriptional RNA silencing. Arabidopsis thaliana (taxid: 3702) EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6 |
| >sp|Q9LQ02|NRPD1_ARATH DNA-directed RNA polymerase D subunit 1 OS=Arabidopsis thaliana GN=NRPD1 PE=1 SV=1 | Back alignment and function description |
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| >sp|P17545|RPB1B_TRYBB DNA-directed RNA polymerase II subunit RPB1-B OS=Trypanosoma brucei brucei GN=TRP5.9 PE=1 SV=1 | Back alignment and function description |
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| >sp|P17546|RPB1A_TRYBB DNA-directed RNA polymerase II subunit RPB1-A OS=Trypanosoma brucei brucei GN=TRP4.8 PE=1 SV=1 | Back alignment and function description |
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| >sp|P36594|RPB1_SCHPO DNA-directed RNA polymerase II subunit rpb1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb1 PE=1 SV=1 | Back alignment and function description |
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| >sp|Q75A34|RPB1_ASHGO DNA-directed RNA polymerase II subunit RPB1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=RPB1 PE=3 SV=2 | Back alignment and function description |
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| >sp|O94666|RPC1_SCHPO DNA-directed RNA polymerase III subunit rpc1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc1 PE=2 SV=1 | Back alignment and function description |
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| >sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPO21 PE=1 SV=2 | Back alignment and function description |
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| >sp|P18616|RPB1_ARATH DNA-directed RNA polymerase II subunit RPB1 OS=Arabidopsis thaliana GN=RPB205 PE=1 SV=3 | Back alignment and function description |
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| >sp|P35084|RPB1_DICDI DNA-directed RNA polymerase II subunit rpb1 OS=Dictyostelium discoideum GN=polr2a 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 | 1714 | ||||||
| 225465870 | 1830 | PREDICTED: DNA-directed RNA polymerase E | 0.565 | 0.529 | 0.688 | 0.0 | |
| 449479984 | 1959 | PREDICTED: DNA-directed RNA polymerase E | 0.571 | 0.500 | 0.661 | 0.0 | |
| 449445170 | 2019 | PREDICTED: LOW QUALITY PROTEIN: DNA-dire | 0.571 | 0.485 | 0.643 | 0.0 | |
| 255543995 | 991 | DNA-directed RNA polymerase, putative [R | 0.526 | 0.910 | 0.697 | 0.0 | |
| 224072881 | 924 | RNA polymerase IV subunit [Populus trich | 0.498 | 0.925 | 0.706 | 0.0 | |
| 356546354 | 2020 | PREDICTED: DNA-directed RNA polymerase E | 0.561 | 0.476 | 0.634 | 0.0 | |
| 296090333 | 1890 | unnamed protein product [Vitis vinifera] | 0.498 | 0.452 | 0.736 | 0.0 | |
| 356555019 | 2098 | PREDICTED: DNA-directed RNA polymerase E | 0.582 | 0.476 | 0.600 | 0.0 | |
| 297823913 | 1947 | NRPD1b [Arabidopsis lyrata subsp. lyrata | 0.554 | 0.488 | 0.605 | 0.0 | |
| 79571777 | 1976 | nuclear RNA polymerase D1B [Arabidopsis | 0.562 | 0.487 | 0.602 | 0.0 |
| >gi|225465870|ref|XP_002265533.1| PREDICTED: DNA-directed RNA polymerase E subunit 1 [Vitis vinifera] | Back alignment and taxonomy information |
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Score = 1427 bits (3694), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 719/1045 (68%), Positives = 829/1045 (79%), Gaps = 76/1045 (7%)
Query: 1 MEENTSSTILEGQIVGIRFGLATQKEICTASISDCSISHASQLANPFLGLPLEFGKCESC 60
MEE+ SSTIL+G+I GIRFGLAT++EIC AS+SDC ISHASQL NPFLGLPLEFGKCESC
Sbjct: 1 MEED-SSTILDGEISGIRFGLATRQEICIASVSDCPISHASQLTNPFLGLPLEFGKCESC 59
Query: 61 GTSEPGKCEGHFGYIELPIPIYHPSHISELKLTMYAF--------QLQIKNDGVAQRLLS 112
GT+EPG+CEGHFGYIELPIPIYHP H+SELK + + ++ N+G+ ++LL+
Sbjct: 60 GTAEPGQCEGHFGYIELPIPIYHPGHVSELKRMLSLLCLKCLKIRKSKVTNNGITEQLLA 119
Query: 113 SCCE------VKEM-------------------------------------LKRI----- 124
CC+ V+E L RI
Sbjct: 120 PCCQDSPQVSVREFRPTEGACFLELKIPSRSRPKDGFWDFLARYGYRYGHNLSRILLPSE 179
Query: 125 --------PEETRKKLAGKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAML 176
PE+TRKKL KGYFPQDGYIL+YLPVPPNCLSVPDISDGVS MSSDLS++ML
Sbjct: 180 VMEILRRIPEDTRKKLVRKGYFPQDGYILQYLPVPPNCLSVPDISDGVSIMSSDLSVSML 239
Query: 177 KKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDP 236
KKVLKQ+E+I+ SRSG PNFES ++E+N+LQ ++ QYLEVRGTAK+SR +D RFG S++P
Sbjct: 240 KKVLKQIEVIKGSRSGEPNFESHKIEANNLQSSIEQYLEVRGTAKTSRSLDTRFGSSKEP 299
Query: 237 N-STTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHN 295
N S+TKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIG+PFEIAQRITFEERVNVHN
Sbjct: 300 NESSTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGLPFEIAQRITFEERVNVHN 359
Query: 296 INYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTH 355
+ +LQ LVD KLCLTY DG S+YSLREGSKGHTFLRPGQVVHRRIMDGD VFINRPPTTH
Sbjct: 360 MKHLQNLVDEKLCLTYRDGLSTYSLREGSKGHTFLRPGQVVHRRIMDGDIVFINRPPTTH 419
Query: 356 KHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQL 415
KHSLQALSVYVHDDHTVKINPLICGPLSADFDGDC+HLFYPQSL AKAEVLELFSVEKQL
Sbjct: 420 KHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCVHLFYPQSLGAKAEVLELFSVEKQL 479
Query: 416 LSSHNGNLNLQLATDALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSKARCSAR-W 474
LSSH+GNLNLQLATD+LLSLKV+F++YFL+KA QQL MF LPRPAL K+ CS W
Sbjct: 480 LSSHSGNLNLQLATDSLLSLKVLFERYFLNKAAAQQLVMFVSMSLPRPALLKSPCSGPCW 539
Query: 475 TALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLE 534
TALQILQ+ LP FD G+R+ I KS +LK D++RD + S++NEIVTSIF EKGP EVL+
Sbjct: 540 TALQILQTALPSYFDCIGERHWISKSAILKVDYNRDVLQSLVNEIVTSIFSEKGPNEVLK 599
Query: 535 FFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMSTQNELVDLQ 594
FFDSLQPLLMENLF++GFSVSLEDFS+ NIQK ++ + SLLY+ S NEL+ LQ
Sbjct: 600 FFDSLQPLLMENLFSEGFSVSLEDFSIPSEVTQNIQKNVEDISSLLYNLRSMYNELLQLQ 659
Query: 595 IENHIRHVKMLVAKFILKSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLV 654
ENH+R K+ VA FIL SS LG LIDSKSDSA++KVVQQ GFLG QLS++GKFYS+TLV
Sbjct: 660 AENHLRLTKVPVANFILNSSALGNLIDSKSDSAINKVVQQIGFLGQQLSEKGKFYSRTLV 719
Query: 655 EDIASHFERIYPMD-LNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEP 713
E +A F+ YP +YP+ ++GLI+ CFFHGLDPYEEM HSISTRE+IVRSSRGLSEP
Sbjct: 720 EGMAYLFKSKYPFHGADYPSGEFGLIRSCFFHGLDPYEEMVHSISTREIIVRSSRGLSEP 779
Query: 714 GTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNAR-KSHSLFPAGEPVGVLAATA 772
GTLFKNLMA+LRDVVICYDGTVRNVCSNSIIQF+Y V AR K FPAGEPVGVLAATA
Sbjct: 780 GTLFKNLMAILRDVVICYDGTVRNVCSNSIIQFEYGVKARTKPQHFFPAGEPVGVLAATA 839
Query: 773 MSNPAYKAVLDSSPSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERA 832
MSNPAYKAVLDSSPSSN+SWELMKEILLC+V+F ND IDRRVILYLNDC CGRKYC+E A
Sbjct: 840 MSNPAYKAVLDSSPSSNSSWELMKEILLCQVNFKNDLIDRRVILYLNDCDCGRKYCRENA 899
Query: 833 AYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDE----GLVGHIHLNKILLEDLRISMHD 888
AY+VKNQLK+ SLKD AVEF+IEY K +S GLVGHIHLNK+LL+DL +SM +
Sbjct: 900 AYLVKNQLKKASLKDTAVEFMIEYVKQHAVSGSSEPGTGLVGHIHLNKLLLQDLNVSMQE 959
Query: 889 ILPKCQETLKSFCKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGAS 948
+ KC+ET+ SF KK K V FFK LS ECC+FQ SC K S+MPCL+F +G
Sbjct: 960 VCQKCEETINSFRKK---KNVGPFFKKIILSFRECCTFQHSCQSKGSDMPCLLFFWQGNR 1016
Query: 949 DSYLDKLSGVLANMIYPVLLETIIK 973
D L+++ +LA+ I PVLL+TIIK
Sbjct: 1017 DDNLEQILHILAHKICPVLLQTIIK 1041
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Source: Vitis vinifera Species: Vitis vinifera Genus: Vitis Family: Vitaceae Order: Vitales Class: Phylum: Streptophyta Superkingdom: Eukaryota |
| >gi|449479984|ref|XP_004155767.1| PREDICTED: DNA-directed RNA polymerase E subunit 1-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|449445170|ref|XP_004140346.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase E subunit 1-like [Cucumis sativus] | Back alignment and taxonomy information |
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| >gi|255543995|ref|XP_002513060.1| DNA-directed RNA polymerase, putative [Ricinus communis] gi|223548071|gb|EEF49563.1| DNA-directed RNA polymerase, putative [Ricinus communis] | Back alignment and taxonomy information |
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| >gi|224072881|ref|XP_002303925.1| RNA polymerase IV subunit [Populus trichocarpa] gi|222841357|gb|EEE78904.1| RNA polymerase IV subunit [Populus trichocarpa] | Back alignment and taxonomy information |
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| >gi|356546354|ref|XP_003541591.1| PREDICTED: DNA-directed RNA polymerase E subunit 1-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|296090333|emb|CBI40152.3| unnamed protein product [Vitis vinifera] | Back alignment and taxonomy information |
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| >gi|356555019|ref|XP_003545837.1| PREDICTED: DNA-directed RNA polymerase E subunit 1-like [Glycine max] | Back alignment and taxonomy information |
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| >gi|297823913|ref|XP_002879839.1| NRPD1b [Arabidopsis lyrata subsp. lyrata] gi|297325678|gb|EFH56098.1| NRPD1b [Arabidopsis lyrata subsp. lyrata] | Back alignment and taxonomy information |
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| >gi|79571777|ref|NP_181532.2| nuclear RNA polymerase D1B [Arabidopsis thaliana] gi|75320513|sp|Q5D869.1|NRPE1_ARATH RecName: Full=DNA-directed RNA polymerase E subunit 1; Short=Nuclear RNA polymerase E 1; AltName: Full=DNA-directed RNA polymerase D subunit 1b; Short=AtNRPD1b; Short=Nuclear RNA polymerase D 1b; AltName: Full=Protein DEFECTIVE IN MERISTEM SILENCING 5; AltName: Full=Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 3; AltName: Full=Protein RNA-DIRECTED DNA METHYLATION DEFECTIVE 1; AltName: Full=RNA polymerase IV subunit 1; Short=POL IV 1 gi|59939210|gb|AAX12373.1| DNA-directed RNA polymerase alpha subunit [Arabidopsis thaliana] gi|62822917|gb|AAY15198.1| DNA-dependent RNA polymerase large subunit [Arabidopsis thaliana] gi|330254673|gb|AEC09767.1| nuclear RNA polymerase D1B [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 | 1714 | ||||||
| TAIR|locus:2061151 | 1976 | NRPD1B "nuclear RNA polymerase | 0.495 | 0.429 | 0.629 | 0.0 | |
| TAIR|locus:2015163 | 1453 | NRPD1A "nuclear RNA polymerase | 0.212 | 0.250 | 0.330 | 3.9e-87 | |
| POMBASE|SPBC28F2.12 | 1752 | rpb1 "RNA polymerase II large | 0.259 | 0.253 | 0.301 | 4.7e-54 | |
| POMBASE|SPBC651.08c | 1405 | rpc1 "DNA-directed RNA polymer | 0.196 | 0.239 | 0.299 | 1.2e-48 | |
| SGD|S000002299 | 1733 | RPO21 "RNA polymerase II large | 0.257 | 0.255 | 0.285 | 1.3e-45 | |
| DICTYBASE|DDB_G0279193 | 1727 | rpb1 "RNA polymerase II core s | 0.225 | 0.223 | 0.285 | 7e-42 | |
| FB|FBgn0030687 | 1383 | CG17209 [Drosophila melanogast | 0.245 | 0.304 | 0.286 | 2.3e-41 | |
| ASPGD|ASPL0000054301 | 1745 | AN0809 [Emericella nidulans (t | 0.207 | 0.204 | 0.303 | 4.5e-40 | |
| UNIPROTKB|G4MT89 | 1757 | MGG_04652 "DNA-directed RNA po | 0.282 | 0.275 | 0.280 | 2.8e-39 | |
| ASPGD|ASPL0000047704 | 1445 | AN10316 [Emericella nidulans ( | 0.222 | 0.263 | 0.278 | 6.1e-39 |
| TAIR|locus:2061151 NRPD1B "nuclear RNA polymerase D1B" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
Score = 2710 (959.0 bits), Expect = 0., Sum P(3) = 0.
Identities = 547/869 (62%), Positives = 663/869 (76%)
Query: 116 EVKEMLKRIPEETRKKLAGKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAM 175
EVKE+L+RIPEE+RKKL KG+ PQ+GYILEYLPVPPNCLSVP+ SDG STMS D S
Sbjct: 179 EVKEILRRIPEESRKKLTAKGHIPQEGYILEYLPVPPNCLSVPEASDGFSTMSVDPSRIE 238
Query: 176 LKKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQ- 234
LK VLK+V I+SSRSG NFES + E++++ V YL+VRGTAK++R++D R+GVS+
Sbjct: 239 LKDVLKKVIAIKSSRSGETNFESHKAEASEMFRVVDTYLQVRGTAKAARNIDMRYGVSKI 298
Query: 235 DPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVH 294
+S++KAW EKMRTLFIRKGSGFSSRSVITGDAY+ VNE+G+P EIAQRITFEERV+VH
Sbjct: 299 SDSSSSKAWTEKMRTLFIRKGSGFSSRSVITGDAYRHVNEVGIPIEIAQRITFEERVSVH 358
Query: 295 NINYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTT 354
N YLQ+LVD+KLCL+Y+ GS++YSLR+GSKGHT L+PGQVVHRR+MDGD VFINRPPTT
Sbjct: 359 NRGYLQKLVDDKLCLSYTQGSTTYSLRDGSKGHTELKPGQVVHRRVMDGDVVFINRPPTT 418
Query: 355 HKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQ 414
HKHSLQAL VYVH+D+TVKINPL+C PLSADFDGDC+HLFYPQSL+AKAEV+ELFSVEKQ
Sbjct: 419 HKHSLQALRVYVHEDNTVKINPLMCSPLSADFDGDCVHLFYPQSLSAKAEVMELFSVEKQ 478
Query: 415 LLSSHNGNLNLQLATDALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSKARCSA-R 473
LLSSH G L LQ+ +D+LLSL+VM ++ FLDKA QQLAM+ LP PAL K+ S
Sbjct: 479 LLSSHTGQLILQMGSDSLLSLRVMLERVFLDKATAQQLAMYGSLSLPPPALRKSSKSGPA 538
Query: 474 WTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVL 533
WT QILQ P GDR+L+ S++LK DF D + S+INEIVTSIF EKGP+E L
Sbjct: 539 WTVFQILQLAFPERLSCKGDRFLVDGSDLLKFDFGVDAMGSIINEIVTSIFLEKGPKETL 598
Query: 534 EFFDSLQPLLMENLFADGFSVSLEDFSLSKA---ALWN-IQKEIQALYSLLYHRMSTQNE 589
FFDSLQPLLME+LFA+GFS+SLED S+S+A + N I +EI + S L R+S ++E
Sbjct: 599 GFFDSLQPLLMESLFAEGFSLSLEDLSMSRADMDVIHNLIIREISPMVSRL--RLSYRDE 656
Query: 590 LVDLQIENHIRHVKMLVAKFILKSSTLGYLIXXXXXXXXXXXXXXXGFLGLQLSDRGKFY 649
L Q+EN I VK + A F+LKS ++ LI GFLGLQLSD+ KFY
Sbjct: 657 L---QLENSIHKVKEVAANFMLKSYSIRNLIDIKSNSAITKLVQQTGFLGLQLSDKKKFY 713
Query: 650 SKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRG 709
+KTLVED+A +R Y + + +G++KGCFFHGLDPYEEM HSI+ REVIVRSSRG
Sbjct: 714 TKTLVEDMAIFCKRKYGRISS--SGDFGIVKGCFFHGLDPYEEMAHSIAAREVIVRSSRG 771
Query: 710 LSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHS-LFPAGEPVGVL 768
L+EPGTLFKNLMAVLRD+VI DGTVRN CSNS+IQF Y V++ + H LF AGEPVGVL
Sbjct: 772 LAEPGTLFKNLMAVLRDIVITNDGTVRNTCSNSVIQFKYGVDSERGHQGLFEAGEPVGVL 831
Query: 769 AATAMSNPAYKAVLDSSPSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYC 828
AATAMSNPAYKAVLDSSP+SN+SWELMKE+LLC+V+F N DRRVILYLN+C CG+++C
Sbjct: 832 AATAMSNPAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNECHCGKRFC 891
Query: 829 QERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISD----DEGLVGHIHLNKILLEDLRI 884
QE AA V+N+L +VSLKD AVEFL+EY+K IS+ D L GHIHLNK LL+D I
Sbjct: 892 QENAACTVRNKLNKVSLKDTAVEFLVEYRKQPTISEIFGIDSCLHGHIHLNKTLLQDWNI 951
Query: 885 SMHDILPKCQETLXXXXXXXXXXXXXXXXXNTSLSISECCSFQQSCADKRSNMPCLMFVL 944
SM DI KC++ + TSLS+SECCSF+ C K S+MPCL F
Sbjct: 952 SMQDIHQKCEDVINSLGQKKKKKATDDFK-RTSLSVSECCSFRDPCGSKGSDMPCLTFSY 1010
Query: 945 RGASDSYLDKLSGVLANMIYPVLLETIIK 973
A+D L++ VL N +YPVLLE +IK
Sbjct: 1011 N-ATDPDLERTLDVLCNTVYPVLLEIVIK 1038
|
|
| TAIR|locus:2015163 NRPD1A "nuclear RNA polymerase D1A" [Arabidopsis thaliana (taxid:3702)] | Back alignment and assigned GO terms |
|---|
| POMBASE|SPBC28F2.12 rpb1 "RNA polymerase II large subunit Rpb1" [Schizosaccharomyces pombe (taxid:4896)] | Back alignment and assigned GO terms |
|---|
| POMBASE|SPBC651.08c rpc1 "DNA-directed RNA polymerase III complex large subunit Rpc1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] | Back alignment and assigned GO terms |
|---|
| SGD|S000002299 RPO21 "RNA polymerase II largest subunit B220" [Saccharomyces cerevisiae (taxid:4932)] | Back alignment and assigned GO terms |
|---|
| DICTYBASE|DDB_G0279193 rpb1 "RNA polymerase II core subunit" [Dictyostelium discoideum (taxid:44689)] | Back alignment and assigned GO terms |
|---|
| FB|FBgn0030687 CG17209 [Drosophila melanogaster (taxid:7227)] | Back alignment and assigned GO terms |
|---|
| ASPGD|ASPL0000054301 AN0809 [Emericella nidulans (taxid:162425)] | Back alignment and assigned GO terms |
|---|
| UNIPROTKB|G4MT89 MGG_04652 "DNA-directed RNA polymerase" [Magnaporthe oryzae 70-15 (taxid:242507)] | Back alignment and assigned GO terms |
|---|
| ASPGD|ASPL0000047704 AN10316 [Emericella nidulans (taxid:162425)] | 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
No confident hit for EC number transfering in SWISSPROT detected by BLAST
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 | LOW CONFIDENCE prediction! |
| 4th Layer | 2.7.7.6 | 0.737 |
Prediction of Functionally Associated Proteins
Functionally Associated Proteins Detected by STRING
Original result from the STRING server
 |
 |
 |
 |
 |
 |
 |
 |
 |
|||
 | GSVIVG00030927001 | RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1830 aa) | |||||||||
(Vitis vinifera) | |||||||||||
 | GSVIVG00037254001 | • | • | 0.470 | |||||||
 | GSVIVG00032775001 | • | 0.441 |
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 | 1714 | |||
| smart00663 | 295 | smart00663, RPOLA_N, RNA polymerase I subunit A N- | 4e-71 | |
| TIGR02390 | 867 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer | 6e-51 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase su | 3e-50 | |
| cd02737 | 381 | cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) | 2e-49 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 3e-49 | |
| cd02737 | 381 | cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) | 2e-44 | |
| pfam00623 | 165 | pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, do | 2e-38 | |
| COG0086 | 808 | COG0086, RpoC, DNA-directed RNA polymerase, beta' | 1e-32 | |
| pfam11523 | 76 | pfam11523, DUF3223, Protein of unknown function (D | 2e-27 | |
| pfam04983 | 158 | pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, do | 2e-10 | |
| TIGR02387 | 619 | TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase | 8e-09 | |
| CHL00018 | 663 | CHL00018, rpoC1, RNA polymerase beta' subunit | 1e-08 | |
| PRK09603 | 2890 | PRK09603, PRK09603, bifunctional DNA-directed RNA | 2e-08 | |
| PRK02625 | 627 | PRK02625, rpoC1, DNA-directed RNA polymerase subun | 3e-08 | |
| PRK14906 | 1460 | PRK14906, PRK14906, DNA-directed RNA polymerase su | 4e-08 | |
| PRK14844 | 2836 | PRK14844, PRK14844, bifunctional DNA-directed RNA | 2e-07 | |
| cd00630 | 158 | cd00630, RNAP_largest_subunit_C, Largest subunit o | 6e-07 | |
| TIGR02386 | 1140 | TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, | 2e-06 | |
| TIGR02390 | 867 | TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymer | 1e-04 | |
| PRK00566 | 1156 | PRK00566, PRK00566, DNA-directed RNA polymerase su | 1e-04 | |
| cd02736 | 300 | cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) o | 2e-04 | |
| PRK08566 | 882 | PRK08566, PRK08566, DNA-directed RNA polymerase su | 6e-04 | |
| pfam04997 | 330 | pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, do | 6e-04 | |
| cd02735 | 309 | cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of | 7e-04 | |
| PRK14977 | 1321 | PRK14977, PRK14977, bifunctional DNA-directed RNA | 0.002 | |
| pfam04998 | 447 | pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do | 0.004 |
| >gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus | Back alignment and domain information |
|---|
Score = 240 bits (614), Expect = 4e-71
Identities = 106/307 (34%), Positives = 152/307 (49%), Gaps = 25/307 (8%)
Query: 141 DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRS-GTPNFESQ 199
+ IL LPVPP CL P + + D +L+ ++K+ ++ G P+ +
Sbjct: 1 EWMILTVLPVPPPCLR-PSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIR 59
Query: 200 EVESNDLQLAVGQYLEV----RGTAKSSRDVDARFGVSQDPNSTTKAWLEK----MRTLF 251
+ LQ AV ++ R KS R P + L+ R
Sbjct: 60 NEKRL-LQEAVDTLIDNEGLPRANQKSGR-----------PLKSLSQRLKGKEGRFRQNL 107
Query: 252 IRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKL-CLT 310
+ K FS+RSVIT D ++NE+GVP EIA +TF E V NI+ L++LV N
Sbjct: 108 LGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGPNGAK 167
Query: 311 YSDGSSSYSLR--EGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHD 368
Y +L+ + SK L+ G +V R ++DGD V NR PT H+ S+QA V V +
Sbjct: 168 YIIRGKKTNLKLAKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLE 227
Query: 369 DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLA 428
T+++NPL+C P +ADFDGD ++L PQSL A+AE EL V +LS NG +
Sbjct: 228 GKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPI 287
Query: 429 TDALLSL 435
D LL L
Sbjct: 288 QDMLLGL 294
|
Length = 295 |
| >gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2 | Back alignment and domain information |
|---|
| >gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >gnl|CDD|221127 pfam11523, DUF3223, Protein of unknown function (DUF3223) | Back alignment and domain information |
|---|
| >gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3 | Back alignment and domain information |
|---|
| >gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit | Back alignment and domain information |
|---|
| >gnl|CDD|214336 CHL00018, rpoC1, 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|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; 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|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1 | Back alignment and domain information |
|---|
| >gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5 | Back alignment and domain information |
|---|
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
| ID | Alignment Graph | Length |
Definition |
Probability |
| Query | 1714 | |||
| KOG0261 | 1386 | consensus RNA polymerase III, large subunit [Trans | 100.0 | |
| PRK14977 | 1321 | bifunctional DNA-directed RNA polymerase A'/A'' su | 100.0 | |
| KOG0260 | 1605 | consensus RNA polymerase II, large subunit [Transc | 100.0 | |
| KOG0262 | 1640 | consensus RNA polymerase I, large subunit [Transcr | 100.0 | |
| TIGR02390 | 868 | RNA_pol_rpoA1 DNA-directed RNA polymerase subunit | 100.0 | |
| PRK08566 | 882 | DNA-directed RNA polymerase subunit A'; Validated | 100.0 | |
| TIGR02386 | 1140 | rpoC_TIGR DNA-directed RNA polymerase, beta' subun | 100.0 | |
| PRK00566 | 1156 | DNA-directed RNA polymerase subunit beta'; Provisi | 100.0 | |
| PRK14906 | 1460 | DNA-directed RNA polymerase subunit beta'/alpha do | 100.0 | |
| PRK14844 | 2836 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| PRK09603 | 2890 | bifunctional DNA-directed RNA polymerase subunit b | 100.0 | |
| COG0086 | 808 | RpoC DNA-directed RNA polymerase, beta' subunit/16 | 100.0 | |
| PRK02625 | 627 | rpoC1 DNA-directed RNA polymerase subunit gamma; P | 100.0 | |
| TIGR02387 | 619 | rpoC1_cyan DNA-directed RNA polymerase, gamma subu | 100.0 | |
| CHL00018 | 663 | rpoC1 RNA polymerase beta' subunit | 100.0 | |
| smart00663 | 295 | RPOLA_N RNA polymerase I subunit A N-terminus. | 100.0 | |
| PF00623 | 166 | RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; Int | 100.0 | |
| TIGR02389 | 367 | RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit | 100.0 | |
| cd06528 | 363 | RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R | 100.0 | |
| PRK04309 | 383 | DNA-directed RNA polymerase subunit A''; Validated | 100.0 | |
| PRK14897 | 509 | unknown domain/DNA-directed RNA polymerase subunit | 100.0 | |
| cd02584 | 410 | RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti | 100.0 | |
| cd02737 | 381 | RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher | 100.0 | |
| cd02736 | 300 | RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot | 100.0 | |
| TIGR02388 | 1227 | rpoC2_cyan DNA-directed RNA polymerase, beta'' sub | 100.0 | |
| PRK02597 | 1331 | rpoC2 DNA-directed RNA polymerase subunit beta'; P | 100.0 | |
| PF04998 | 277 | RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int | 100.0 | |
| cd02735 | 309 | RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic | 100.0 | |
| CHL00117 | 1364 | rpoC2 RNA polymerase beta'' subunit; Reviewed | 100.0 | |
| PF04997 | 337 | RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; Int | 100.0 | |
| PRK14898 | 858 | DNA-directed RNA polymerase subunit A''; Provision | 100.0 | |
| PF04983 | 158 | RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; Int | 99.95 | |
| cd00630 | 158 | RNAP_largest_subunit_C Largest subunit of RNA poly | 99.94 | |
| PF11523 | 76 | DUF3223: Protein of unknown function (DUF3223); In | 99.93 | |
| cd02655 | 204 | RNAP_beta'_C Largest subunit (beta') of Bacterial | 99.89 | |
| PF05000 | 108 | RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; Int | 99.48 | |
| TIGR02388 | 1227 | rpoC2_cyan DNA-directed RNA polymerase, beta'' sub | 99.14 | |
| CHL00117 | 1364 | rpoC2 RNA polymerase beta'' subunit; Reviewed | 99.14 | |
| PRK02597 | 1331 | rpoC2 DNA-directed RNA polymerase subunit beta'; P | 99.07 | |
| COG0086 | 808 | RpoC DNA-directed RNA polymerase, beta' subunit/16 | 98.93 | |
| KOG0260 | 1605 | consensus RNA polymerase II, large subunit [Transc | 97.96 | |
| PF04990 | 135 | RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; Int | 97.49 | |
| COG5164 | 607 | SPT5 Transcription elongation factor [Transcriptio | 96.22 | |
| PRK14898 | 858 | DNA-directed RNA polymerase subunit A''; Provision | 94.59 | |
| KOG1999 | 1024 | consensus RNA polymerase II transcription elongati | 93.3 | |
| KOG1999 | 1024 | consensus RNA polymerase II transcription elongati | 92.48 | |
| COG5164 | 607 | SPT5 Transcription elongation factor [Transcriptio | 88.77 |
| >KOG0261 consensus RNA polymerase III, large subunit [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=3.2e-240 Score=2129.27 Aligned_cols=1052 Identities=24% Similarity=0.356 Sum_probs=908.3
Q ss_pred CCCCcccccceeeEEEecCCHHHHHHhcccccc------cc-----cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 000291 4 NTSSTILEGQIVGIRFGLATQKEICTASISDCS------IS-----HASQLANPFLGLPLEFGKCESCGTSEPGKCEGHF 72 (1714)
Q Consensus 4 ~~~~~~~~~~I~~I~F~l~S~eEI~k~Sv~~~~------I~-----~~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHF 72 (1714)
|-.....+.+|++|+|+++|++||++.+++++. +. .++|++|||||++++...|+|||.++ .+|+|||
T Consensus 3 ~~~e~~~~kki~~i~F~~~s~~ei~~~a~v~v~~~~LY~~~~~~~P~~~G~LD~rMGvs~K~~~C~TCg~~l-a~C~GHf 81 (1386)
T KOG0261|consen 3 QFREDEIPKKIKHIQFSILSPEEIRQQAEVEVSSKDLYDISTQRAPLPNGPLDPRMGVSNKKDKCATCGEGL-ADCIGHF 81 (1386)
T ss_pred ccccccccceeeeEeeccCCHHHHHhcceEEeeccchhhhhcccCCCcCCCcCcccCCCCCCCccchhccch-hhccccc
Confidence 345667889999999999999999999987541 11 14799999999999999999999996 7999999
Q ss_pred eeEEcCcccccccchHHHHHHHHHHHhhhc-------------------------cchHHHHHHHHH--------H----
Q 000291 73 GYIELPIPIYHPSHISELKLTMYAFQLQIK-------------------------NDGVAQRLLSSC--------C---- 115 (1714)
Q Consensus 73 GhIeL~~PVfHpgf~k~I~~IL~~iC~ri~-------------------------~~g~~kri~~~C--------C---- 115 (1714)
||++|++||||+|||+.+++||||||+.|- +.++.++|+.+| |
T Consensus 82 Gy~~L~LPVFhiGyfk~ti~iLq~ICK~Cs~ilL~~~~k~~fl~~lr~p~~~~l~k~~l~kri~~~CkK~~~C~hCg~~N 161 (1386)
T KOG0261|consen 82 GYLKLALPVFHIGYFKATIQILQCICKNCSSILLSEEDKRQFLKKLRNPGLDNLRKKALLKRIVAKCKKVNTCSHCGALN 161 (1386)
T ss_pred ceEeecceeeeehhHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhhccccccccCCcC
Confidence 999999999999999999999999987552 123456666666 3
Q ss_pred ----------------------------------------------------------HHHHHHhcCChHHHHhhccC-C
Q 000291 116 ----------------------------------------------------------EVKEMLKRIPEETRKKLAGK-G 136 (1714)
Q Consensus 116 ----------------------------------------------------------eV~~IfkkI~~ed~~~L~~~-~ 136 (1714)
.|+++|++|++.|+++|++. .
T Consensus 162 G~VKK~~~~lkIiHd~~~~~~k~~~~~~~~~~~~~~~~~~n~e~~~~~~~~~~~LnPl~vLnLFk~i~~~D~eLLg~~~~ 241 (1386)
T KOG0261|consen 162 GTVKKAAALLKIIHDRFKLVKKSDPLVTNERGEFKTAISHNKELEGHLSSCCEELNPLVVLNLFKQIKEDDCELLGMDSE 241 (1386)
T ss_pred ceeeccccceeEeeehhhccccccchhhhhHHHHHHHhhcCcchHhHHHHHHhhcChHHHHHHHhhCCccccceeeeccC
Confidence 67899999999999999653 2
Q ss_pred CCCCCcEEEeeccCCCCCCCCCcccCC-CccccchhHHHHHHHHHHHHHHHHhh-hcCCCCccchhhhhhHHHHHHHHHH
Q 000291 137 YFPQDGYILEYLPVPPNCLSVPDISDG-VSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYL 214 (1714)
Q Consensus 137 ~~~pe~~il~~lpVPP~~~Rp~~~~~g-~~~~~~Dlt~~~l~~Il~~n~~lk~~-~~g~p~~~~~~~~~~~LQ~~v~~~~ 214 (1714)
.-+|+.+|++++||||.|+||++++++ ....+||+|+ +|.+|+-.|..|++. ..|.|.... ...|+.||.+|+.||
T Consensus 242 ~~~P~~Li~t~~~vPP~cIRPSV~~~~k~gtnEDDlT~-KltEIi~tn~vik~~~~~g~~~~~i-mE~Wd~lQl~~AlyI 319 (1386)
T KOG0261|consen 242 EGRPENLIITRVPVPPVCIRPSVMSEDKAGTNEDDLTM-KLTEIILTNDVIKKHLSKGTPINLI-MEDWDFLQLQVALYI 319 (1386)
T ss_pred cCCchheEEEeccCCccccccceeecCCCCCCccchhh-hhhhhhhHHHHHHHHhhcCCCchhh-hhhhHHHHHHHHHhh
Confidence 346889999999999999999999877 3567899999 699999999999975 567765554 456999999999999
Q ss_pred hh--cCCCcCCCCCCCCCCCCCCCCchhhhhHhhhhhcccccCCCCccceeEeCCCCCccccccchhhcccccccccccc
Q 000291 215 EV--RGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVN 292 (1714)
Q Consensus 215 ~~--~~~~~~~~~~~~~~~~~k~~~~~ik~k~gr~R~~l~GKRvdfSaRsVI~pdP~l~~~evgvP~~~A~~Lt~pe~vt 292 (1714)
++ +|.+....+. .......+++|||+||||+||.||||||||||||||||||+|+|||||..||+.|||||+||
T Consensus 320 NSEl~g~~~~~~p~----kp~RGf~QRLKGKqGRFRgNLSGKRVDFSGRTVISPDPNL~IdeVgVP~rvAkiLTfpE~Vt 395 (1386)
T KOG0261|consen 320 NSELPGIPINMAPK----KPTRGFVQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDEVGVPIRVAKILTFPERVT 395 (1386)
T ss_pred cccCCCCCCCCCCC----CchHHHHHHhcccCCceeccccCceeeccCceeeCCCCCcceeeccchHHHHHHhcchhhcc
Confidence 84 4544321110 00011237899999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHccCcc-------ccCCCCceEEeccCCCC--ccccCCcceeeheeeccceEEEeCCCcccccccccee
Q 000291 293 VHNINYLQELVDNKLCL-------TYSDGSSSYSLREGSKG--HTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALS 363 (1714)
Q Consensus 293 ~~Ni~~l~~lv~~g~~~-------~~~~~~~~~~l~~~~~~--~~~l~~g~iV~Rhl~dgd~VL~NRqPsLHr~Sima~~ 363 (1714)
.+||++||+||+|||.+ +.+..+.+..|+|++|. +..|++||+|||||+|||+|||||||||||||||+|+
T Consensus 396 ~~Ni~klr~lV~NGP~vhPGANyv~~r~~~~kr~L~yg~R~kiA~eLk~GdvVERHL~DgDvVLFNRQPSLHkmSIM~H~ 475 (1386)
T KOG0261|consen 396 RANIRKLRQLVRNGPNVHPGANYVVQRGEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHR 475 (1386)
T ss_pred HHHHHHHHHHHhcCCCCCCCcchhhhcccchhhHhhcCcHHHHHHhhccchHHHhhcccCCEEEEcCCchHHHHHHHHHH
Confidence 99999999999999962 11233345557777654 4689999999999999999999999999999999999
Q ss_pred eEecCCCeEEecccccCCCCCccccccccccCCCCHHHHHHHHHhcccccccccCCCCCceEeechhhHhHHHhhh-ccc
Q 000291 364 VYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKY 442 (1714)
Q Consensus 364 ~~v~~~~t~rln~~vC~pyNADFDGDeMnlHvPQS~eAraEa~~Lm~~~~nilsp~~G~Piigl~QD~llg~~llt-kd~ 442 (1714)
+||+|++|||||.|||+||||||||||||+||||++||||||.+||.+++||++|++|+|||+++||||+|+|||| ||+
T Consensus 476 akV~p~RTfRFNEcvCtPYNADFDGDEMNlHvPQTEEAraEA~~LMgvknNlvTPr~GEpiiAAtQDFiTg~YLlt~KDt 555 (1386)
T KOG0261|consen 476 AKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQDFITGGYLLTHKDT 555 (1386)
T ss_pred hhcccCceeeccccccCCcCCCCCcccccccCCchHHHHHHHHHHhccccccccCCCCCceeehhhhhhhcceeeecccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999997 999
Q ss_pred cCCHHHHHHhhcccc-----cccccccccccccccccceeeeccccCCCCcc------------------------c-cC
Q 000291 443 FLDKAFTQQLAMFAL-----SPLPRPALSKARCSARWTALQILQSVLPPGFD------------------------S-CG 492 (1714)
Q Consensus 443 fl~~~~~~~l~~~~~-----~~lp~PaI~Kp~~~~lWTGKQl~s~~LP~~~~------------------------~-~~ 492 (1714)
||+|+++.||+.++. +.+|||||+||. .|||||||||+++.++.+ | .+
T Consensus 556 F~dRa~~~ql~s~~~d~~~~i~lppPaI~KP~--~LwTGKQ~fsvlirpn~~s~v~~Nl~~k~k~~~~~~~k~~~mc~nD 633 (1386)
T KOG0261|consen 556 FLDRAEFSQLCSYMSDAMTHIDLPPPAILKPV--ELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSFEMCPND 633 (1386)
T ss_pred cccHHHHHHHHHHHhccccccCCCChhhcCce--eeeccCEEEEEEeccCCCCceEEeeccccceeecccCCCcccCCCC
Confidence 999999999986653 579999999999 999999999999954321 1 36
Q ss_pred CEEEEEcceecccccccCcccch-HHHHHHHHHHhhCHHHHHhchhhhHHHHHHHHHhcCceeeeCCcccCHHHHHHHHH
Q 000291 493 DRYLIKKSEVLKGDFDRDTIPSV-INEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQK 571 (1714)
Q Consensus 493 ~~viI~~Gell~G~ldK~~lg~s-~~~Li~~i~~~~G~~~a~~fLd~lqrL~~~~L~~~GFSiGi~Dl~~~~~~~~~i~~ 571 (1714)
+.|+|+|++|+.|.+||+++|.. ..+||+.|.++||+.+|++.|+++.+|+.+||..+||||||+|+.+.+.+.+++.+
T Consensus 634 g~v~irns~l~sG~ldKs~lG~g~k~~lfy~llrDyg~~aAa~am~rlaklc~r~lgnrGFSIGi~DVqPg~~L~~~k~~ 713 (1386)
T KOG0261|consen 634 GYVIIRNSELISGVLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEILSQEKEE 713 (1386)
T ss_pred CeEEEecchhhhcccccccccCCCccceEeeehhhcchHHHHHHHHHHHHhhhhhccccccccccCCCCccHHHHHHHHH
Confidence 77899999999999999999985 68999999999999999999999999999999999999999999999999998888
Q ss_pred HHHHHHHHHHHhhh-------------hhHHHHHHHHHHHHHHHHHHHHHHHHh----cCCcccccccccchhhhhHHHH
Q 000291 572 EIQALYSLLYHRMS-------------TQNELVDLQIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQ 634 (1714)
Q Consensus 572 ~i~~~~~~~~~~~~-------------~~~e~le~~i~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi 634 (1714)
.++..|..+.++.. ..+++||+.+..+|+.+|+.+++.|++ .|+..+|+.||||||.+||+||
T Consensus 714 lv~~gY~kc~~~I~e~~kG~L~~qpg~~~eetLEa~I~~~Ls~IRe~~G~~C~~eL~~~NsPliMa~CGSKGS~INiSQM 793 (1386)
T KOG0261|consen 714 LVNRGYAKCDEKIEEYNKGKLQLQPGCNEEETLEAEILSELSTIREEAGKICIRELHPRNSPLIMALCGSKGSKINISQM 793 (1386)
T ss_pred HHHhHHHHHHHHHHHHhccccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccChHHHHHhcCCCCcccHHHH
Confidence 88888877766543 336899999999999999999999996 4888999999999999999999
Q ss_pred hHhccceecCCCccccccccccccccccccCCCCCCCCCCccceecCcccccCCccceEEeeccccceeeecccccCCCC
Q 000291 635 AGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPG 714 (1714)
Q Consensus 635 ~g~lGQQ~~~g~r~~~r~l~~~~~~~f~~~~p~~~d~~~~a~GfV~ssF~~GL~P~EfFfHamagREGLiDTAvkTA~sG 714 (1714)
++|||||.+.|.| ++.++.+|.+|||+++ ...|+|+|||.||||+||+|.|||||+|+|||||||||||||+||
T Consensus 794 vACVGQQ~ISG~R-vPdGf~dRsLPHF~r~-----Sk~P~aKGFV~NSFySGLTptEFfFHtm~GREGLVDTAVKTAETG 867 (1386)
T KOG0261|consen 794 VACVGQQIISGHR-VPDGFEDRSLPHFERH-----SKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETG 867 (1386)
T ss_pred HHHhhhhhhcCCc-CCCccccccCcccccc-----CCCccccchhhhhcccCCCchhhheeecccccchhhhhhhhhhhh
Confidence 9999999999776 6788999999999864 567899999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHhceEEEeccccccccCCceeEEEeccccccc---------------------------------------
Q 000291 715 TLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKS--------------------------------------- 755 (1714)
Q Consensus 715 YLqRrLvk~ledl~v~YD~Tvr~~~~~~IiQf~yg~dg~~~--------------------------------------- 755 (1714)
||||||||.||||.++||+|||++ .+.||||+||+||+|+
T Consensus 868 YMqRRLmK~LEDL~~~YDgTVR~s-~~~vvqF~YG~DglDPa~mEg~~~pv~f~r~~~~~~~~~~~~~~~~l~~~el~e~ 946 (1386)
T KOG0261|consen 868 YMQRRLMKSLEDLSVQYDGTVRNS-NGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFPHRHDPPLSSEELDET 946 (1386)
T ss_pred hHHHHHHHHHHHHHHhhcCceecC-CCcEEEEeecCCCCChhhhcCCCCchhHHHHHHHHHhcCCCCCCCCCCHHHHHHH
Confidence 999999999999999999999995 7999999999999762
Q ss_pred --------------------------------------------------------------------------cCcCCC
Q 000291 756 --------------------------------------------------------------------------HSLFPA 761 (1714)
Q Consensus 756 --------------------------------------------------------------------------~~lv~~ 761 (1714)
+..++|
T Consensus 947 ~~~~l~~~f~~~~~~F~~~~~~~i~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~Ep 1026 (1386)
T KOG0261|consen 947 LEEELLRKFTEKGDPFVHELREFIASLSKKIKKLQDKYGDECGPKFCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEP 1026 (1386)
T ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCC
Confidence 124699
Q ss_pred CceeEEeccccCChhHHHHhhcCCC-------CCCCchHHHHHHHHhhccCCCCCCCceEEEEcCCCCCCCccccHHHHH
Q 000291 762 GEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAY 834 (1714)
Q Consensus 762 GepVG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~ 834 (1714)
|.+||++||||||||+|||||+||| |+|+|+||+||||++.++++|+ .++-.|..++ ++..|+
T Consensus 1027 GTavGAi~aQSIGEPGTQMTLKTFHFAGVASMNiTlGVPRIkEIINAsk~ISTP----IItA~L~n~~------d~~~Ar 1096 (1386)
T KOG0261|consen 1027 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKTISTP----IITAELENPH------DERSAR 1096 (1386)
T ss_pred cchhhhhhcccCCCCCceeeeeeeeecceeeeeeccCcchHHHHHhhhcccCcc----ceeeeecCch------hHHHHH
Confidence 9999999999999999999999987 8999999999999999987766 4555565543 888999
Q ss_pred HHHhhhccccHhhhhheeEEEecCCccccCCCceEEEEEecHHHHHHhcC--ChhhhHHHHHHhh-hhh-----------
Q 000291 835 MVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRI--SMHDILPKCQETL-KSF----------- 900 (1714)
Q Consensus 835 ~V~~~le~vtl~dv~~~i~I~y~~~~~~~~~~~wv~~i~Ld~e~L~~~~l--t~~~I~~k~~~~~-~~~----------- 900 (1714)
.||.+||+++|.||++.|...|.++.. .+.|.||.+.+...+| ++++|...|-+.- ...
T Consensus 1097 ~VKgRiEKt~L~dv~~yieeV~~p~~~-------fl~i~vd~~~I~~l~L~i~~~~I~~sI~~s~~~k~~~~~v~v~~~~ 1169 (1386)
T KOG0261|consen 1097 VVKGRIEKTTLGDVCSYIEEVYGPDSC-------FLLIRVDLKRISLLQLEITIESIAYSILKSPKRKVKPNDVRVVGET 1169 (1386)
T ss_pred HHhhhhhhhhHHHHHHHHHHHhCCcce-------EEEEEecHhHHhhhhccccHHHHHHHHhcCCccccCCcceEEecce
Confidence 999999999999999999999999976 7889999988877665 4778887655421 110
Q ss_pred -----hhcchh---hHHHHHhhccccccccccc--ccccccccCCCcceEEEEEcccC-----CcccccceecccccchH
Q 000291 901 -----CKKKKM---KKVVQFFKNTSLSISECCS--FQQSCADKRSNMPCLMFVLRGAS-----DSYLDKLSGVLANMIYP 965 (1714)
Q Consensus 901 -----~~~~~~---~~i~~~~~~~~~~~~~~gi--~~~~~~~~~~~~~~l~~~~~~~~-----~~~~vd~~~~~~n~I~~ 965 (1714)
....++ +--.+.+++.+..+.+||+ +++.+++-++..-...+.++|.+ .++||.-++|.+|++.+
T Consensus 1170 ~~~v~~~~~~~~S~~~~lq~lk~~L~~Vvv~gip~vnr~vi~~de~~~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~E 1249 (1386)
T KOG0261|consen 1170 TLRVTPVSDTKSSVYYNLQRLKRSLPNVVVKGIPEVNRAVINIDEKRGLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLE 1249 (1386)
T ss_pred eEEEeecccccchhhhhHHHHHhhCCceEEecCcchhhhheeecccCCceEEEEeccchHHHhccCCccccccccCceEE
Confidence 000000 1126777777778888999 78888776422221334799987 78999999999999988
Q ss_pred HH--------HHHhhhhhHHHHHHHHHHHHHhhcccccceeeeeccceeeeceEeeeccccccccccCcccccccccccc
Q 000291 966 VL--------LETIIKENWWVRQRLSASVTMVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATL 1037 (1714)
Q Consensus 966 i~--------r~~IIkgi~w~r~~l~~~~~~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~ 1037 (1714)
|. |.+||.||. .++..-|.+||+||+|||||.|||.|+|+||||+|++++++|+|+.||||+|
T Consensus 1250 v~~vLGIEAAR~~II~EI~-------ytM~~HGmsiD~RHiMLLaDvMTyrGEVlGITRfGl~KM~~SVL~lASFEkT-- 1320 (1386)
T KOG0261|consen 1250 VEKVLGIEAARTTIISEIG-------YTMSNHGMSIDPRHIMLLADVMTYRGEVLGITRFGLAKMKDSVLMLASFEKT-- 1320 (1386)
T ss_pred eehhhchHHHHHHHHHHHH-------HHHHhcCcccCHHHHHHHHHHhhhcceeeeeeehhhHHHHHHHHHHHhhhhh--
Confidence 76 666666655 6667777889999999999999999999999999999999999999999998
Q ss_pred cCcHHHHHHHHhhcCCCCCCchhhhhhcCCcccccccceEEEEeccCCcccccCCccchhhcccc
Q 000291 1038 FMPRKCFEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQDDGVDVYDFLHM 1102 (1714)
Q Consensus 1038 ~~~~~~l~~Aa~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~~~~~~~~~~~~y~~l~~ 1102 (1714)
.+||++||.++.+|.+.||+|+||+|+|+++|||. |+|++..+. +..++....|++-|..
T Consensus 1321 ---~DhLF~AA~~~k~D~I~GVSEcIIlG~pm~iGTG~-fkl~~~~~~-~~~~~~~~~if~~~~~ 1380 (1386)
T KOG0261|consen 1321 ---ADHLFDAAAYGKKDAIEGVSECIILGIPMCIGTGI-FKLLQRTDD-KKVLKPKPPIFSSLNL 1380 (1386)
T ss_pred ---hHHHHHHHHhcCcccccchhhheecccceeccccH-HHHHHhcCC-cccCCCCCCccccccc
Confidence 89999999999999999999999999999999999 999997655 3333334556665543
|
|
| >PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional | Back alignment and domain information |
|---|
| >KOG0260 consensus RNA polymerase II, large subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0262 consensus RNA polymerase I, large subunit [Transcription] | Back alignment and domain information |
|---|
| >TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A' | Back alignment and domain information |
|---|
| >PRK08566 DNA-directed RNA polymerase subunit A'; Validated | Back alignment and domain information |
|---|
| >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form | Back alignment and domain information |
|---|
| >PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional | Back alignment and domain information |
|---|
| >PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional | Back alignment and domain information |
|---|
| >PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed | Back alignment and domain information |
|---|
| >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional | Back alignment and domain information |
|---|
| >TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit | Back alignment and domain information |
|---|
| >CHL00018 rpoC1 RNA polymerase beta' subunit | Back alignment and domain information |
|---|
| >smart00663 RPOLA_N RNA polymerase I subunit A N-terminus | Back alignment and domain information |
|---|
| >PF00623 RNA_pol_Rpb1_2: RNA polymerase Rpb1, domain 2; InterPro: IPR000722 RNA polymerases catalyse the DNA dependent polymerisation of RNA from DNA, using the four ribonucleoside triphosphates as substrates | Back alignment and domain information |
|---|
| >TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A'' | Back alignment and domain information |
|---|
| >cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP) | Back alignment and domain information |
|---|
| >PRK04309 DNA-directed RNA polymerase subunit A''; Validated | Back alignment and domain information |
|---|
| >PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional | Back alignment and domain information |
|---|
| >cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain | Back alignment and domain information |
|---|
| >cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain | Back alignment and domain information |
|---|
| >cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain | Back alignment and domain information |
|---|
| >TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain | Back alignment and domain information |
|---|
| >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
| >PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >PRK14898 DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function | Back alignment and domain information |
|---|
| >cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain | Back alignment and domain information |
|---|
| >PF05000 RNA_pol_Rpb1_4: RNA polymerase Rpb1, domain 4; InterPro: IPR007083 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit | Back alignment and domain information |
|---|
| >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed | Back alignment and domain information |
|---|
| >PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional | Back alignment and domain information |
|---|
| >COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription] | Back alignment and domain information |
|---|
| >KOG0260 consensus RNA polymerase II, large subunit [Transcription] | Back alignment and domain information |
|---|
| >PF04990 RNA_pol_Rpb1_7: RNA polymerase Rpb1, domain 7; InterPro: IPR007073 RNA polymerases catalyse the DNA dependent polymerisation of RNA | Back alignment and domain information |
|---|
| >COG5164 SPT5 Transcription elongation factor [Transcription] | Back alignment and domain information |
|---|
| >PRK14898 DNA-directed RNA polymerase subunit A''; Provisional | Back alignment and domain information |
|---|
| >KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription] | Back alignment and domain information |
|---|
| >KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription] | Back alignment and domain information |
|---|
| >COG5164 SPT5 Transcription elongation factor [Transcription] | 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 | 1714 | ||||
| 3h0g_A | 1752 | Rna Polymerase Ii From Schizosaccharomyces Pombe Le | 3e-46 | ||
| 4a3c_A | 1732 | Rna Polymerase Ii Initial Transcribing Complex With | 3e-42 | ||
| 1i3q_A | 1733 | Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio | 3e-42 | ||
| 3j0k_A | 1455 | Orientation Of Rna Polymerase Ii Within The Human V | 2e-41 | ||
| 2pmz_A | 880 | Archaeal Rna Polymerase From Sulfolobus Solfataricu | 1e-38 | ||
| 2waq_A | 880 | The Complete Structure Of The Archaeal 13-Subunit D | 1e-35 | ||
| 3iyd_D | 1413 | Three-Dimensional Em Structure Of An Intact Activat | 4e-12 | ||
| 3lu0_D | 1407 | Molecular Model Of Escherichia Coli Core Rna Polyme | 4e-12 | ||
| 4gzy_D | 1534 | Crystal Structures Of Bacterial Rna Polymerase Paus | 2e-09 | ||
| 1iw7_D | 1524 | Crystal Structure Of The Rna Polymerase Holoenzyme | 2e-09 | ||
| 2gho_D | 1233 | Recombinant Thermus Aquaticus Rna Polymerase For St | 2e-09 | ||
| 1i6v_D | 1264 | Thermus Aquaticus Core Rna Polymerase-Rifampicin Co | 3e-09 | ||
| 1hqm_D | 1265 | Crystal Structure Of Thermus Aquaticus Core Rna Pol | 3e-09 | ||
| 1l9u_D | 1524 | Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A | 3e-09 | ||
| 2k0m_A | 104 | Solution Nmr Structure Of The Uncharacterized Prote | 8e-06 |
| >pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 1752 | Back alignment and structure |
|
| >pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt Dna-Rna Hybrid Length = 1732 | Back alignment and structure |
| >pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 1733 | Back alignment and structure |
| >pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 1455 | Back alignment and structure |
| >pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus Length = 880 | Back alignment and structure |
| >pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna- Directed Rna Polymerase Length = 880 | Back alignment and structure |
| >pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 1413 | Back alignment and structure |
| >pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase Length = 1407 | Back alignment and structure |
| >pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused Elongation Complexes Length = 1534 | Back alignment and structure |
| >pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 1524 | Back alignment and structure |
| >pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural Studies Length = 1233 | Back alignment and structure |
| >pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 1264 | Back alignment and structure |
| >pdb|1HQM|D Chain D, 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 = 1265 | Back alignment and structure |
| >pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 1524 | Back alignment and structure |
| >pdb|2K0M|A Chain A, Solution Nmr Structure Of The Uncharacterized Protein From Rhodospirillum Rubrum Gene Locus Rru_a0810. Northeast Structural Genomics Target Rrr43 Length = 104 | Back alignment and structure |
Structure Templates Detected by RPS-BLAST
Original result of RPS-BLAST against PDB70 database
| >4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A 2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A Length = 880 | Back alignment and structure |
|---|
Score = 310 bits (796), Expect = 5e-89
Identities = 217/883 (24%), Positives = 338/883 (38%), Gaps = 184/883 (20%)
Query: 13 QIVGIRFGLATQKEICTASISDCSISHASQ-----------LANPFLGLPLEFGKCESCG 61
I GI+FG+ + EI +S +I + +P LG+ KC +CG
Sbjct: 5 NIKGIKFGILSPDEI--RKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG 62
Query: 62 TSEPGKCEGHFGYIELPIPIYHPSHISELKLTM-------YAFQLQIKNDGVAQRLLSSC 114
+ G C GHFG+IEL P+ H + + + ++ R+ ++
Sbjct: 63 NTL-GNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAI 121
Query: 115 --------------------------------------------CEVKEMLKRI-PEETR 129
E KE + ++ P + R
Sbjct: 122 KKRWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEGVAKLTPSDIR 181
Query: 130 KKLAGKGYFPQDGYIL--------------EYLPVPPNCL--SVPDISDGVSTMSSDLSI 173
++L + D IL LPVPP + S+ + + DL+
Sbjct: 182 ERL--EKVPESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSI--MIESGIRAEDDLTH 237
Query: 174 AMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDVDARF 230
L +++ E ++ S +G P +++ + LQ V Y E+ G S
Sbjct: 238 -KLVDIVRINERLKESIDAGAPQLIIEDLW-DLLQYHVATYFDNEIPGLPPSKHR----- 290
Query: 231 GVSQDPNSTTKAWLEK----MRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRIT 286
S P T L+ R K FSSR+VI+ D ++E+GVP IA+ +T
Sbjct: 291 --SGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLT 348
Query: 287 FEERVNVHNINYLQELVDN-------KLCLTYSDGS--SSYSLREGSKGHTFLRPGQVVH 337
ER+ NI L++ V N + DG +++ + + L PG VV
Sbjct: 349 VPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVE 408
Query: 338 RRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQ 397
R + DGD V NR P+ H+ S+ A V V T ++N L+C P +ADFDGD ++L PQ
Sbjct: 409 RHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQ 468
Query: 398 SLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFKK-YFLDKAFTQQLAMFA 456
S A AE E+ V K +++ G + A D + ++ K L K QQ+ A
Sbjct: 469 SEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVA 528
Query: 457 LSP--LPRPALSKARCSARWTALQILQSVLPPGF------------------DSCGDRY- 495
L PA+ R +T Q++ + LP F D D Y
Sbjct: 529 DVKIDLGEPAILAPR--EYYTGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYV 586
Query: 496 LIKKSEVLKGDFDRDTI-PSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSV 554
+IK +L+G FD+ I I+ + E E D+L + + + GF++
Sbjct: 587 VIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTM 646
Query: 555 SLEDFSLSKAALWNIQKEIQALYS------LLYHRMSTQN----------ELVDLQIENH 598
LED SL I EI Y + E L +
Sbjct: 647 RLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDK 706
Query: 599 IRHVKMLVAKFILKSS-TLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGK-----FYSKT 652
+R +A L + + + +V + Q A LG Q S RG+ + ++T
Sbjct: 707 LRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQ-SVRGERIKRGYMTRT 765
Query: 653 LVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGL-- 710
L HF+ P D++ P A+ G I F GL P E H+ RE GL
Sbjct: 766 L-----PHFK---PYDIS-PEAR-GFIYSSFRTGLKPTELFFHAAGGRE-------GLVD 808
Query: 711 -----SEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDY 748
S+ G + + L+ L D+ YDGTVR+ +IQ Y
Sbjct: 809 TAVRTSQSGYMQRRLINALSDLRAEYDGTVRS-LYGEVIQVAY 850
|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752 | Back alignment and structure |
|---|
| >2k0m_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Rhodospirillum rubrum atcc 11170} Length = 104 | 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} Length = 436 | 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} Length = 436 | 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 |
|---|
| >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 |
|---|
| >4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C Length = 395 | Back alignment and structure |
|---|
| >1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D Length = 1265 | Back alignment and structure |
|---|
| >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 | Back alignment and structure |
|---|
| >3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D* Length = 1407 | Back alignment and structure |
|---|
Structure Templates Detected by HHsearch
Original result of HHsearch against PDB70 database
No hit with probability above 80.00
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 |
| 1714 | ||||
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 2e-76 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 7e-12 | |
| d1twfa_ | 1449 | e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c | 2e-04 | |
| d1smyd_ | 1504 | e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus t | 4e-60 |
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | 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-prime domain: RBP1 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Score = 278 bits (711), Expect = 2e-76
Identities = 190/862 (22%), Positives = 350/862 (40%), Gaps = 70/862 (8%)
Query: 116 EVKEMLKRIPEETRKKLAGKGYFPQ-DGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIA 174
E+ + K I + L F + + IL LPVPP + + DL+
Sbjct: 205 EILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTF- 263
Query: 175 MLKKVLK-QVEIIRSSRSGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDVDARFG 231
L +LK + + +G P+ +E ES LQ V Y+ ++ G ++ +
Sbjct: 264 KLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATYMDNDIAGQPQALQKSGRPVK 322
Query: 232 VSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERV 291
+ K ++R + K FS+R+VI+GD ++++GVP IA+ +T+ E V
Sbjct: 323 SIRA---RLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVV 379
Query: 292 NVHNINYLQELVDN------KLCLTYSDGSSSYSLRE-GSKGHTFLRPGQVVHRRIMDGD 344
+NI+ L +LV N D LR G L+ G V R IMD D
Sbjct: 380 TPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDND 439
Query: 345 TVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAE 404
V NR P+ HK S+ A V V T ++N + P +ADFDGD ++L PQS +AE
Sbjct: 440 PVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAE 499
Query: 405 VLELFSVEKQLLSSHNGNLNLQLATDALLSLKVM-FKKYFLDKAFTQQLAMFALS---PL 460
+ +L +V Q++S + + + D L ++ + + F++ + + +
Sbjct: 500 LSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVI 559
Query: 461 PRPALSKARCSARWTALQILQSVLPPG------------FDSCGDRYLIKKSEVLKGDFD 508
P PA + W+ QIL +P G + LI +++ G +
Sbjct: 560 PTPA--IIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVE 617
Query: 509 RDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAAL-- 566
+ T+ S ++ + EKGP+ + F ++Q ++ L +GFS + D +
Sbjct: 618 KKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMRE 677
Query: 567 ------------WNIQKEIQALYSLLYHRMSTQNELVD--LQIENHIRHVKMLVAKFILK 612
++ KE QA H M+ + D ++ N R +A+ LK
Sbjct: 678 ITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLK 737
Query: 613 SSTLGY-LIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNY 671
++ + S + + Q + +G Q S GK + V+ HF + +Y
Sbjct: 738 DLNNVKQMVMAGSKGSFINIAQMSACVGQQ-SVEGKRIAFGFVDRTLPHFSKD-----DY 791
Query: 672 PTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICY 731
G ++ + GL P E H++ RE ++ ++ +E G + + L+ L D+++ Y
Sbjct: 792 SPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHY 851
Query: 732 DGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSPSSNNS 791
D T RN ++IQF Y + + + + A +L++ + + S
Sbjct: 852 DNTTRNSL-GNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPS 910
Query: 792 WELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVE 851
+L + +D + D R+ + A R +++A
Sbjct: 911 LLESGSEILGDLK-LQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQT 969
Query: 852 FLIEYKKPEIISDDEGLVGHIHLNKILLEDLRI--SMHDILPKCQETLKSFCKKKKM--- 906
F I++ KP ++ + ++G K L E+L + ++I+ Q +
Sbjct: 970 FHIDHTKPSDLTIKDIVLG----VKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRL 1025
Query: 907 --KKVVQFFKNTSLSISECCSF 926
++V+Q ++ T + S
Sbjct: 1026 ATRRVLQEYRLTKQAFDWVLSN 1047
|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449 | Back information, alignment and structure |
|---|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} Length = 1504 | 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 | 1714 | |||
| d1twfa_ | 1449 | RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta | 100.0 | |
| d1smyd_ | 1504 | RNA-polymerase beta-prime {Thermus thermophilus [T | 100.0 |
| >d1twfa_ e.29.1.2 (A:) RBP1 {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-prime domain: RBP1 species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=100.00 E-value=0 Score=1944.59 Aligned_cols=1052 Identities=22% Similarity=0.345 Sum_probs=882.1
Q ss_pred CCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCC-------CC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf 7778645531106898249979998705565201-------46---8888899889999998888989999997988552
Q 000291 4 NTSSTILEGQIVGIRFGLATQKEICTASISDCSI-------SH---ASQLANPFLGLPLEFGKCESCGTSEPGKCEGHFG 73 (1714)
Q Consensus 4 ~~~~~~~~~~I~~I~F~l~S~eEI~~~Sv~~~~I-------~~---~~gl~DprLG~~~~~~~C~TCg~~~~~~CpGHFG 73 (1714)
+.-...|.++|.+|+|+++||+||+++|+.++.. ++ .+||+|||||+++++..|+||+.+. .+||||||
T Consensus 3 ~~~~~~p~~~i~~i~f~~~s~eeIr~~S~~ei~~~~~~~~~~~~p~~~Gl~d~rlG~~~~~~~C~tC~~~~-~~CpGHfG 81 (1449)
T d1twfa_ 3 QQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGM-NECPGHFG 81 (1449)
T ss_dssp CSCCCSCBCCCCEEECCBCCHHHHHHTCCCCCCCSCCSCTTSCCSCCSSSSCSSSCCCTTCCCSSSCCCCT-TSCCCCCC
T ss_pred CCCCCCCCCEECEEEEEECCHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCC-CCCCCCCE
T ss_conf 87886765640667999258999998535698077856289999999997666338999869998999877-49999987
Q ss_pred EEECCCCCCCCCCHHHHHHHHHHHHHHHC------CCHH-------------HHHHHHHH--------------------
Q ss_conf 68867522344455889999999976422------6128-------------99999879--------------------
Q 000291 74 YIELPIPIYHPSHISELKLTMYAFQLQIK------NDGV-------------AQRLLSSC-------------------- 114 (1714)
Q Consensus 74 hIeL~~PVfHp~fik~I~~IL~~iC~ri~------~~g~-------------~k~i~~~C-------------------- 114 (1714)
||||++|||||+||+.++++|+++|++|- .... ...+...|
T Consensus 82 hIeL~~PV~h~~f~~~~~~~L~~~C~~C~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (1449)
T d1twfa_ 82 HIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLV 161 (1449)
T ss_dssp CEEEEEEEECGGGHHHHHHHHHHBCTTTCCBSCCTTSHHHHHHHTCCSHHHHHHHHHHHHTTCCBCCSEECCSSCTTSCE
T ss_pred EEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHHEECCCCCCCHHHHHHHH
T ss_conf 56726625438999999999998521057785166389999887530566556789987423143000010013256665
Q ss_pred ----H--------------------------------------HHHHHHHCCCHHHHHHHCCC-CCCCCCCEEEEECCCC
Q ss_conf ----9--------------------------------------99999805995789841148-9999873899630689
Q 000291 115 ----C--------------------------------------EVKEMLKRIPEETRKKLAGK-GYFPQDGYILEYLPVP 151 (1714)
Q Consensus 115 ----C--------------------------------------eV~~IlkkI~~ed~~~L~~~-g~~~pe~lil~~lPVP 151 (1714)
| +++++|++|+++++.+|... ...+|+||||++||||
T Consensus 162 ~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~~i~~~~~~~l~~~~~~~~p~~~~l~~lpV~ 241 (1449)
T d1twfa_ 162 SRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVP 241 (1449)
T ss_dssp ECCSCCCBCCCCEECSSCEEEEECSSSSCTTSCSCEEEEECHHHHHHHHTTSCHHHHHHTTCBTTTBCGGGGEEEEECCC
T ss_pred HCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHEECCHHHHHHHHHHCCHHHHHHHCCCCCCCCHHHEEEEEEECC
T ss_conf 23787767743433347777788775320344535431489999999997388868987478867898678876623369
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCC
Q ss_conf 98887872028986445224799999999999999862-0699973201324437999999998611877678-887777
Q 000291 152 PNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSS-RDVDAR 229 (1714)
Q Consensus 152 P~~iRp~~~~~g~~~~~~Dlt~~~l~~Ii~~n~~l~~~-~~g~p~~~~~~~~~~~LQ~~v~~~~~~~~~~k~~-~~~~~r 229 (1714)
|+|+||++..++..+.++|+|. +|++||+.|++|+.. ..++|..+. .++|.+||.+|+.|+|+....++. .....
T Consensus 242 P~~~RP~~~~~~~~~~~~dlt~-~~~~Ii~~n~~l~~~~~~~~~~~~~-~~~~~~LQ~~v~~~~dn~~~~~~~~~~~~~- 318 (1449)
T d1twfa_ 242 PPPVRPSISFNESQRGEDDLTF-KLADILKANISLETLEHNGAPHHAI-EEAESLLQFHVATYMDNDIAGQPQALQKSG- 318 (1449)
T ss_dssp CTTTSCCCCCSSSCCCCCHHHH-HHHHHHHHHHHHHHHHSSCCCHHHH-HHHHHHHHHHHHHHHCCCSSCCCCCSSCTT-
T ss_pred CCCCCCCEEECCCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCCCHHHH-HHHHHHHHHHHHHHCCCCCCCCCHHCCCCC-
T ss_conf 9876871694898626786899-9999999999999998739957789-999999999999843556568840004667-
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf 78778998302456733210002458797663168289997633233112300124324312223199999999816765
Q 000291 230 FGVSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCL 309 (1714)
Q Consensus 230 ~~~~k~~~~~~k~k~~~~R~~l~gKRvdfsaRsVI~pDP~l~~~evgiP~~~A~~Lt~pe~vt~~Ni~~l~~lv~~g~~~ 309 (1714)
...+.+.+++++|.||||+|||||||||||||||+|||+|+++|||||..||++|||||+||+||+++|+++|.|||..
T Consensus 319 -~~~k~i~~~L~gK~GrfR~nl~GKRVd~s~RsVI~pdp~l~~~evGvP~~~A~~Lt~pe~v~~~n~~~l~~~v~ng~~~ 397 (1449)
T d1twfa_ 319 -RPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNE 397 (1449)
T ss_dssp -CCCCCSTTSCTTTTTTSSGGGTTCSCCSEEEEEEEECTTSCTTEEEEEHHHHTTCEEEEECCTTTHHHHHHHHHHTTTS
T ss_pred -CCCCCHHHHHCCCHHHHHHHCCCCCCCCCCCEEECCCCCCCEEECCCHHHHHHHCCCCEEECHHHHHHHHHHHHCCCCC
T ss_conf -7762066675161044321126553366653045258753100121189999618978254089999999999708744
Q ss_pred ------CCCCCCCEEEECCCCC-CCCCCCCCCEEEHEEECCCEEEEECCCCCCCCCCCCEEEEECCCCEEEECCCCCCCC
Q ss_conf ------3579995288136998-864567853322201126648770888665355321366734888288445566878
Q 000291 310 ------TYSDGSSSYSLREGSK-GHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPL 382 (1714)
Q Consensus 310 ------~~~~~~~~~~l~~~~~-~~~~l~~G~~V~R~l~dgd~Vl~NRqPsLHr~Sima~~~~i~~~~t~rln~~~C~~y 382 (1714)
+....+..+.|++..+ ....|++||+|+|||+|||+|||||||||||+|||||+|++++++||||||+||+||
T Consensus 398 ~pga~~~~~~~g~~~~l~~~~~~~~~~l~~g~~V~r~l~~gd~Vl~NRqPtLHr~si~a~~~~v~~~ktirl~~~vc~~y 477 (1449)
T d1twfa_ 398 HPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPY 477 (1449)
T ss_dssp SSCEEEEECTTCCEEETTSCTTTTCCCCCTTCEEEEECCTTCEEEEECSSCCSGGGEEEEEEEEESSSSEEECGGGHHHH
T ss_pred CCCCCCEECCCCCEEEEECCHHHHHHHCCCCCEEEEEEECCEEEEECCCCCHHHHCCCCCEEEEECCCEEEECCCCCCCC
T ss_conf 77620000046726988511122211036663899997247068954764133311012246861485478521101111
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEECHHHHHHHHHHH-CCCCCCHHHHHHHHCCCC---C
Q ss_conf 886654520246778799999998850663312347999953751035676888652-136679999998610134---5
Q 000291 383 SADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMF-KKYFLDKAFTQQLAMFAL---S 458 (1714)
Q Consensus 383 NADFDGDeMNihvPQs~eAraEa~~Lm~v~~qilsp~~G~Piigl~QD~llg~~llt-kd~fl~~~~~~~l~~~~~---~ 458 (1714)
||||||||||+|+|||++|||||++||++.+||++|++|+|+++++||+|+|+|+|| +++|++++++++++|+.. .
T Consensus 478 NADFDGDeMnvhvPqs~~A~aEa~~Lm~~~~nilsp~~G~pi~~~~QD~~lg~y~LT~~~~f~~~~~~~~~~~~~~~~~~ 557 (1449)
T d1twfa_ 478 NADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDG 557 (1449)
T ss_dssp TCCSSSCEEEEECCCSHHHHHHHHHHTBGGGGSEETTTTEESCCCCHHHHHHHHHHHSTTCEEEHHHHHHHHHHSTTCCS
T ss_pred CCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf 45545654789716888899999998641325346667862431021304231201136445789999999973545465
Q ss_pred CCCCCCCCCCCCCCCCCEEEECCCCCCCCCCC------------CCCEEEEECCEECCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 65522220232345540121012448998322------------597799976521333355676423378899999984
Q 000291 459 PLPRPALSKARCSARWTALQILQSVLPPGFDS------------CGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFE 526 (1714)
Q Consensus 459 ~lp~PaI~Kp~~~~lWTGKQi~s~~LP~~~~~------------~~~~viI~~Gell~g~ldK~~lg~s~~~Li~~i~~~ 526 (1714)
.+|+|+|+||. ++|||||+||++||..+.+ .++.++|++|+|+.|.+||+++|++.++|+|.+++.
T Consensus 558 ~~~~p~~~~~~--~~~tgkqi~s~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~g~l~~g~l~k~~~g~~~~~li~~i~~~ 635 (1449)
T d1twfa_ 558 VIPTPAIIKPK--PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTRE 635 (1449)
T ss_dssp CCCCCSBCSSS--CEEEHHHHHHHHSCTTCCEEECCTTCCTTCTTCCSEEEETTEEEESCCCHHHHSSCTTSHHHHHHHH
T ss_pred CCCCCEEEEEE--ECCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCEEEEECCEEEECCCHHHHCCCCCCCCCCCCCCC
T ss_conf 44687077632--0125646899972687302321578621156776599877866643102644165434520000000
Q ss_pred HCHHHHHHCHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHH
Q ss_conf 29799996042229999999984074331077545999999999999999999987554-------------45789999
Q 000291 527 KGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMS-------------TQNELVDL 593 (1714)
Q Consensus 527 ~G~~~a~~fLd~lq~L~~~~L~~~GFSiGl~Dl~~~~~~~~~i~~~i~~~~~~~~~~~~-------------~~~~~le~ 593 (1714)
||+.+|+.||+.+|+|+++||+++|||+|++|+++++...+++.+.+.+....+.++.. ..++.++.
T Consensus 636 ~G~~~~~~~l~~~~~l~~~~l~~~Gfs~gi~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 715 (1449)
T d1twfa_ 636 KGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFED 715 (1449)
T ss_dssp HCHHHHHHHHHHHHHHHHHHHHTTCBCCCGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCTTCCHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCHHEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 03799999998887789999986521005212124420468888888887665788999998766413568727899999
Q ss_pred HHHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 9999999999999999971----398421202111013556777867114614079951234552011122233498998
Q 000291 594 QIENHIRHVKMLVAKFILK----SSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDL 669 (1714)
Q Consensus 594 ~~~~~l~~~~~~i~~~~~~----~n~l~~Mi~SGSKGS~~Ni~Qi~g~lGqQ~~~ggr~~~r~l~~~~~~~f~~~~p~~~ 669 (1714)
.+...++++++.+.+.+.+ .|++.+|+.||||||+.|++||+||||||.++|+| +..+..++++|||.+ +
T Consensus 716 ~v~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGakGs~~n~~Qi~g~~Gqq~~~g~r-i~~~~~~r~lp~f~~-----~ 789 (1449)
T d1twfa_ 716 NVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKR-IAFGFVDRTLPHFSK-----D 789 (1449)
T ss_dssp HHHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHTSSCCHHHHHHHHSCCEECCBTTBS-CCCCBTTBSSTTSCT-----T
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHEECCCCCCCCCHHHHHHHHHHHCCCCCC-CCCCCCCCCCCCCCC-----C
T ss_conf 9999999999999998766440255267641211457831468887665332015753-554666666666788-----9
Q ss_pred CCCCCCCCEECCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHCEEEEECCCCCCCCCCCEEEEEEC
Q ss_conf 99988652002744446896530786225431023224444798832478999874138972351113468961388812
Q 000291 670 NYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYA 749 (1714)
Q Consensus 670 d~~~ea~GfI~nSF~~GL~P~EfFfHsmagREGLiDTAvkTA~sGYL~RrLv~~led~~v~YD~Tvr~~~~~~IiQf~yg 749 (1714)
+..|+++|||.+||++||+|+|||||||||||||||||+|||+|||||||||++|||++|+||+|||+ ++|+||||.||
T Consensus 790 ~~~~~~~GfI~~sf~~GL~p~Eyf~h~~~gReGLiDTAvkTa~sGYl~RrLvk~ledv~v~yD~tvr~-~~g~IiQf~YG 868 (1449)
T d1twfa_ 790 DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRN-SLGNVIQFIYG 868 (1449)
T ss_dssp CCSTTTTTEECSCTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCEECTTSCEEC-TTCCEEESSGG
T ss_pred CCCCCCCCCCCCHHHHHHCCHHEEEEECCCHHHHHHHCCCCCCCHHHHHHHHHHHCCEEEEECCCCCC-CCCEEEEEEEC
T ss_conf 99813267603235541120212543123021133320254640889999999755759974686676-89559999975
Q ss_pred CCCCCC--------------------------------------------------------------------------
Q ss_conf 344544--------------------------------------------------------------------------
Q 000291 750 VNARKS-------------------------------------------------------------------------- 755 (1714)
Q Consensus 750 ~~g~~~-------------------------------------------------------------------------- 755 (1714)
+||+|+
T Consensus 869 eDg~d~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~~~i~~~~~~~l~~~r~~l~~~~~~ 948 (1449)
T d1twfa_ 869 EDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVD 948 (1449)
T ss_dssp GTTBCGGGEEEEECGGGSSCHHHHHHHHCCCTTCTTTSCCTTTBTTHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred CCCCCCEEEEEEECCEECCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 75543117887531424252487665500000465444575676545777411888888789999998878889987157
Q ss_pred --------------------------------------------------------------------------------
Q ss_conf --------------------------------------------------------------------------------
Q 000291 756 -------------------------------------------------------------------------------- 755 (1714)
Q Consensus 756 -------------------------------------------------------------------------------- 755 (1714)
T Consensus 949 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 1028 (1449)
T d1twfa_ 949 GEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATR 1028 (1449)
T ss_dssp CCCEEEEESCHHHHHHHHHHHTTCCTTSCBCCCHHHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHEECCCCHHHHHHCCCCCCEEEEEECCCCCHH
T ss_conf 54343576009999986455410255764445489999988888764301014311223330154200222001432023
Q ss_pred -------------------------CCCCCCCCEEEEECCCCCCHHHHHHHHCCCC-------CCCCCHHHHHHHHHHHC
Q ss_conf -------------------------6767899605872123479067887424799-------99986577999997311
Q 000291 756 -------------------------HSLFPAGEPVGVLAATAMSNPAYKAVLDSSP-------SSNNSWELMKEILLCRV 803 (1714)
Q Consensus 756 -------------------------~~l~~~Ge~VG~laaqsigepatq~~L~t~~-------~~~~g~~rlkEil~~~~ 803 (1714)
++++.|||+||++||||||||+|||||+||| ++|+|+||++||+++.+
T Consensus 1029 ~~~~~~~l~~~~~~~~~~~~~~ky~~slv~pGEaVGiiAAQSIGEP~TQmTLnTFH~AG~~~~nvT~GiPRl~EIl~ask 1108 (1449)
T d1twfa_ 1029 RVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAK 1108 (1449)
T ss_dssp HHHHTSCCCHHHHHHHHHHHHHHHHHHBCCTTCCHHHHHHHHHHHHHTTCCC----------CCSCCHHHHHHHHTTTCS
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCEEEECCCCCCHHHHHHEEEEC
T ss_conf 43444366899998899888888766455136751212122216613355554322112443001355043332222002
Q ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHEEEEEECCCCCCC--------------------
Q ss_conf 378998874199972788888763228999999863210138654421377753896445--------------------
Q 000291 804 SFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIIS-------------------- 863 (1714)
Q Consensus 804 ~~k~~~~d~~~~l~L~~~~~~~~~~~e~~a~~V~~~Le~v~l~dv~~~i~i~y~~~~~~~-------------------- 863 (1714)
+ +++|.|+++|.+.... ++..++.++..+++++|++++....|.|.++...+
T Consensus 1109 ~----iktp~~~v~l~~~~~~----~~~~~k~~~~~i~~~~l~~vv~~~~v~~~~~~~~~~i~~~~~~i~~~~~~~~~~~ 1180 (1449)
T d1twfa_ 1109 N----MKTPSLTVYLEPGHAA----DQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEA 1180 (1449)
T ss_dssp S----CSSCEEEEEBCSSSSS----CHHHHHHHHHHHSCEEGGGTEEEEEEEECCCSSSCSSGGGHHHHHTSSCC-----
T ss_pred C----CCCCCEEEEECCCCCH----HHHHHHHHHHEEEEEECCCEEEEEEEEECCCCCEEEEEEECCEEEEEEEECCCHH
T ss_conf 5----6786215774022103----5999886653146630010466459997377733899875134367778425122
Q ss_pred -----CCCCEEEEEEECHHHHHHHCCCHHHHHHHHHHHHHHHH--------------------H-------CCHHHHHHH
Q ss_conf -----89961899994598898705895445899998555454--------------------2-------002368999
Q 000291 864 -----DDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFC--------------------K-------KKKMKKVVQ 911 (1714)
Q Consensus 864 -----~~~~wv~~i~Ld~e~L~~~~lt~~~I~~k~~~~~~~~~--------------------~-------~~~~~~i~~ 911 (1714)
..++|++++++|++.+..+++++.+|..++...+..-. . +.....+..
T Consensus 1181 ~~~~~~~~~~ilrl~l~~~~~~~k~i~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~l~ 1260 (1449)
T d1twfa_ 1181 EQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLK 1260 (1449)
T ss_dssp -----CCCSEEEEEEECHHHHHHTTCCHHHHHHHHHHHHGGGEEEEECCTTSSSCEEEEEEC----------CCTTHHHH
T ss_pred EEEECCCCCCEEEEEECHHHCCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHH
T ss_conf 02301357723899971555146788778878999986089858994688864478853667753210003656689999
Q ss_pred HHH-CCCCCCCCCCC--CCCCCCCC--------CC---CCCEEEEEECCCC-----CCCCCCCEECCCCCCHHHHHHHHH
Q ss_conf 840-25333322222--23512155--------89---9566999972368-----754431000012540379888765
Q 000291 912 FFK-NTSLSISECCS--FQQSCADK--------RS---NMPCLMFVLRGAS-----DSYLDKLSGVLANMIYPVLLETII 972 (1714)
Q Consensus 912 ~~~-~~~~~~~~~gi--~~~~~~~~--------~~---~~~~l~~~~~~s~-----~~~~vd~~~~~~n~I~ei~l~tII 972 (1714)
.+. ..+....++|+ +.++++.+ .+ ......+.++|.+ ..+.+|..++++|+|++|+. +
T Consensus 1261 ~i~~~~l~~~~v~Gi~~I~rv~i~~~~~~~~~~~~~~~~~~~~vl~teG~nl~~~l~~~~iD~~~~~sNdI~dil~---~ 1337 (1449)
T d1twfa_ 1261 KIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIME---V 1337 (1449)
T ss_dssp HHHHHHHHHCEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHH---H
T ss_pred HHHHHCCCCCEEECCCCEEEEEEECCCCEEECCCCCCCCCCCEEEECCCCCHHHHHCCCCCCCCCCCCCCHHHHHH---H
T ss_conf 8774133880870788847999962465341788737258709998683878888606991642074086999999---7
Q ss_pred HHHHHHHHHHHHHHH----HHHCCCCCCEEEEECCCEEEECEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 555899999899888----7622555220233304603202076425521012234743224521102358177999998
Q 000291 973 KENWWVRQRLSASVT----MVAKGVLKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAA 1048 (1714)
Q Consensus 973 kgi~w~r~~l~~~~~----~~~~~V~~rHl~LlAd~MT~~G~~~~~~r~G~~~~~~s~l~~a~Fe~~t~~~~~~~l~~Aa 1048 (1714)
.||+++|+.|..++. .+|..||+|||.||||+||++|.++||||+||+++..|++++||||+| .++|.+||
T Consensus 1338 lGIEAar~~ii~EI~~V~~~~Gi~Id~rHi~LIad~MT~~G~~~~i~R~gi~~~~~S~l~~aSFEeT-----~~vL~~AA 1412 (1449)
T d1twfa_ 1338 LGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEET-----VEILFEAG 1412 (1449)
T ss_dssp HCHHHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTTTBSSCCCSSSCSSSCSSCCTTSSCCSSCS-----HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEECHHHHHHHHHHHCCCCEEEECCHHHHCCCCCCHHHHHHCHHH-----HHHHHHHH
T ss_conf 7299999999999999998659588799999999997758857101189814698589887006439-----99999999
Q ss_pred HHCCCCCCCCHHHHHHCCCCCCCCCCCEEEEEECCCCC
Q ss_conf 32198878822446415875553456528999606774
Q 000291 1049 EKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLWQTENE 1086 (1714)
Q Consensus 1049 ~~g~~D~l~gv~~~ii~Gk~~~~GTG~~~~l~~~~~~~ 1086 (1714)
.+|++|.|+|++||||+|+++|+|||+ |||++|.+.+
T Consensus 1413 i~g~~D~L~G~senIi~G~~ip~GTG~-fdll~d~~~l 1449 (1449)
T d1twfa_ 1413 ASAELDDCRGVSENVILGQMAPIGTGA-FDVMIDEESL 1449 (1449)
T ss_dssp HHTCEECCCSHHHHHHTTCCCSSGGGS-SEEEECSCCC
T ss_pred HCCCCCCCCCCHHHEECCCCCCCCCCC-CEEEECHHHC
T ss_conf 639914278807870268988986516-2888665319
|
| >d1smyd_ e.29.1.2 (D:) RNA-polymerase beta-prime {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
|---|