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RecName: Full=DNA-directed RNA polymerase 133 kDa polypeptide
Protein Classification
List of domain hits
Name
Accession
Description
Interval
E-value
Ricin_B_lectin super family
cl47023 Ricin-type beta-trefoil lectin domain;
313-1140
6.72e-89
Ricin-type beta-trefoil lectin domain;
PRK08565 :Pssm-ID: 481363 [Multi-domain]
Cd Length: 1103
Bit Score: 311.12
E-value: 6.72e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 313 HNF LPH MNYT P - D QL K GF Y MISLLRKF L YCI Y YTS R Y PD - R D SMVCH R ILTY G KYFET L AHDELENYIGNIRND i MNNHK 390
Cdd:PRK08565 287 KYL LPH LGTS P e D RI K KA Y FLGQMASK L LEL Y LGR R E PD d K D HYANK R LRLA G DLLAE L FRVAFKQLVKDLKYQ - LEKSY 365
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 391 N RG t YAVNIHVLTT P G ----- LN HA FS -- SLLS G KFKK S DGSY RT hphy SWMQNI S IP R S V gfypdqvk I S KM ------ F 457
Cdd:PRK08565 366 A RG - RKLDLRAIVR P D iiter IR HA LA tg NWVG G RTGV S QLLD RT ---- NYLSTL S HL R R V -------- V S PL srgqph F 432
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 458 SV R KY H PS Q YLYF C SSDV PE r GP QV GLV SQ L SVLSS I T - NILTS E YLDLEKK ----- IC E YIRSY Y KDDISYFET G FP I T 531
Cdd:PRK08565 433 EA R DL H GT Q WGRI C PFET PE - GP NC GLV KN L ALMAQ I S v GVDEE E VEEILYE lgvvp VE E AREEE Y ISWSRVYLN G RL I G 511
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 532 IEN alvasl NPNMICDFVTDF RR RKRM gffg NL EV GITLVRD - HM NE IRI N IGA GR LV RP FL VV D NG ELMMD vc P E LESR 610
Cdd:PRK08565 512 YHP ------ DGEELAEKIREL RR SGKI ---- SD EV NVAYIET g EI NE VYV N CDS GR VR RP LI VV E NG KPKLT -- R E HVEK 579
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 611 L D -- DM TF S D IQ K E fp H VIE MV D I E QFTFSN V CESV qkfrmms K D ERKQYDLCDF -- PA EF rd G YV AS SLVGIN HN SG PR 686
Cdd:PRK08565 580 L K kg EL TF D D LV K M -- G VIE YL D A E EEENAY V ALDP ------- E D LTPEHTHLEI wp PA IL -- G IT AS IIPYPE HN QS PR 648
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 687 AILGC A Q AKQ AISCLSSDI R NKI D NGI HL M - YP E RP I V ISK ALE TSKIAANCF GQ HVTI A LM SY K G I N Q ED G II IK K QF I 765
Cdd:PRK08565 649 NTYQA A M AKQ SLGLYAANF R IRT D TRG HL L h YP Q RP L V QTR ALE IIGYNDRPA GQ NAVV A VL SY T G Y N I ED A II MN K AS I 728
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 766 Q RG ------- GLDIVTAK K H ------ QV EIP LE N FNNKERDR sn A Y S KL ESN G L V RLNAFLES GD AMARNI S S - R T LE DD 831
Cdd:PRK08565 729 E RG larstff RTYETEER K Y pggqed KI EIP EP N VRGYRGEE -- Y Y R KL DED G I V SPEVEVKG GD VLIGKT S P p R F LE EL 806
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 832 FA -------- RD NQISFDVS EK - YT D M yksrvervq V EL T DK ------ VKVRV LTM ke R R P I LGDKF TT R TS QKG TVAYI 896
Cdd:PRK08565 807 EE lslglqer RD TSVTVRHG EK g IV D T --------- V LI T ES pegnkl VKVRV RDL -- R I P E LGDKF AS R HG QKG VIGML 875
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 897 ADETEL P YD E N GI T PD V IIN STS I F SR K T ISM L I E V I l TAAYS A K pynnkg E N R P V CFPSSNETSIDTYM - QFA K QC Y EH 975
Cdd:PRK08565 876 VPQEDM P FT E D GI V PD L IIN PHA I P SR M T VGQ L L E S I - AGKVA A L ------ E G R F V DATPFYGEPEEELR k ELL K LG Y KP 948
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 976 lnpkl TEK E lsdkifcek IL YD PE T DKPYASKV F F G PI YY LR L R H LTQ DK ATV R C RG KKTK L I RQ AN EGR K R G GG IK FGE 1055
Cdd:PRK08565 949 ----- DGT E --------- VM YD GR T GEKIKAPI F I G VV YY QK L H H MVA DK IHA R A RG PVQI L T RQ PT EGR A R E GG LR FGE 1014
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1056 MERDCLI A HGAA NTIT E V L K DS EEDY q DV Y I CE N CG D IA -- AQI K SINT C LRC - S K L N L SP lltk IDTTHVS K VF L TQMN 1132
Cdd:PRK08565 1015 MERDCLI G HGAA MLLK E R L L DS SDKT - TI Y V CE L CG H IA wy DRR K NKYV C PIH g D K G N I SP ---- VEVSYAF K LL L QELM 1089
....*...
gi 1767232066 1133 AR G VKVK L 1140
Cdd:PRK08565 1090 SM G ISPR L 1097
rpo132
pfam12415 Poxvirus DNA dependent RNA polymerase; This domain family is found in viruses, and is ...
247-277
5.45e-12
Poxvirus DNA dependent RNA polymerase; This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with pfam04566, pfam00562, pfam04567, pfam04560, pfam04565. This family is the second largest subunit of the poxvirus DNA dependent RNA polymerase. It has structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Pssm-ID: 289200
Cd Length: 32
Bit Score: 60.90
E-value: 5.45e-12
10 20 30
....*....|....*....|....*....|.
gi 1767232066 247 FIR R SLSYDMPPEV V YLVNAII D S A K RLT ES 277
Cdd:pfam12415 2 FIR N SLSYDMPPEV I YLVNAII E S T K EII ES 32
Name
Accession
Description
Interval
E-value
PRK08565
PRK08565 DNA-directed RNA polymerase subunit B; Provisional
313-1140
6.72e-89
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain]
Cd Length: 1103
Bit Score: 311.12
E-value: 6.72e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 313 HNF LPH MNYT P - D QL K GF Y MISLLRKF L YCI Y YTS R Y PD - R D SMVCH R ILTY G KYFET L AHDELENYIGNIRND i MNNHK 390
Cdd:PRK08565 287 KYL LPH LGTS P e D RI K KA Y FLGQMASK L LEL Y LGR R E PD d K D HYANK R LRLA G DLLAE L FRVAFKQLVKDLKYQ - LEKSY 365
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 391 N RG t YAVNIHVLTT P G ----- LN HA FS -- SLLS G KFKK S DGSY RT hphy SWMQNI S IP R S V gfypdqvk I S KM ------ F 457
Cdd:PRK08565 366 A RG - RKLDLRAIVR P D iiter IR HA LA tg NWVG G RTGV S QLLD RT ---- NYLSTL S HL R R V -------- V S PL srgqph F 432
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 458 SV R KY H PS Q YLYF C SSDV PE r GP QV GLV SQ L SVLSS I T - NILTS E YLDLEKK ----- IC E YIRSY Y KDDISYFET G FP I T 531
Cdd:PRK08565 433 EA R DL H GT Q WGRI C PFET PE - GP NC GLV KN L ALMAQ I S v GVDEE E VEEILYE lgvvp VE E AREEE Y ISWSRVYLN G RL I G 511
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 532 IEN alvasl NPNMICDFVTDF RR RKRM gffg NL EV GITLVRD - HM NE IRI N IGA GR LV RP FL VV D NG ELMMD vc P E LESR 610
Cdd:PRK08565 512 YHP ------ DGEELAEKIREL RR SGKI ---- SD EV NVAYIET g EI NE VYV N CDS GR VR RP LI VV E NG KPKLT -- R E HVEK 579
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 611 L D -- DM TF S D IQ K E fp H VIE MV D I E QFTFSN V CESV qkfrmms K D ERKQYDLCDF -- PA EF rd G YV AS SLVGIN HN SG PR 686
Cdd:PRK08565 580 L K kg EL TF D D LV K M -- G VIE YL D A E EEENAY V ALDP ------- E D LTPEHTHLEI wp PA IL -- G IT AS IIPYPE HN QS PR 648
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 687 AILGC A Q AKQ AISCLSSDI R NKI D NGI HL M - YP E RP I V ISK ALE TSKIAANCF GQ HVTI A LM SY K G I N Q ED G II IK K QF I 765
Cdd:PRK08565 649 NTYQA A M AKQ SLGLYAANF R IRT D TRG HL L h YP Q RP L V QTR ALE IIGYNDRPA GQ NAVV A VL SY T G Y N I ED A II MN K AS I 728
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 766 Q RG ------- GLDIVTAK K H ------ QV EIP LE N FNNKERDR sn A Y S KL ESN G L V RLNAFLES GD AMARNI S S - R T LE DD 831
Cdd:PRK08565 729 E RG larstff RTYETEER K Y pggqed KI EIP EP N VRGYRGEE -- Y Y R KL DED G I V SPEVEVKG GD VLIGKT S P p R F LE EL 806
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 832 FA -------- RD NQISFDVS EK - YT D M yksrvervq V EL T DK ------ VKVRV LTM ke R R P I LGDKF TT R TS QKG TVAYI 896
Cdd:PRK08565 807 EE lslglqer RD TSVTVRHG EK g IV D T --------- V LI T ES pegnkl VKVRV RDL -- R I P E LGDKF AS R HG QKG VIGML 875
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 897 ADETEL P YD E N GI T PD V IIN STS I F SR K T ISM L I E V I l TAAYS A K pynnkg E N R P V CFPSSNETSIDTYM - QFA K QC Y EH 975
Cdd:PRK08565 876 VPQEDM P FT E D GI V PD L IIN PHA I P SR M T VGQ L L E S I - AGKVA A L ------ E G R F V DATPFYGEPEEELR k ELL K LG Y KP 948
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 976 lnpkl TEK E lsdkifcek IL YD PE T DKPYASKV F F G PI YY LR L R H LTQ DK ATV R C RG KKTK L I RQ AN EGR K R G GG IK FGE 1055
Cdd:PRK08565 949 ----- DGT E --------- VM YD GR T GEKIKAPI F I G VV YY QK L H H MVA DK IHA R A RG PVQI L T RQ PT EGR A R E GG LR FGE 1014
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1056 MERDCLI A HGAA NTIT E V L K DS EEDY q DV Y I CE N CG D IA -- AQI K SINT C LRC - S K L N L SP lltk IDTTHVS K VF L TQMN 1132
Cdd:PRK08565 1015 MERDCLI G HGAA MLLK E R L L DS SDKT - TI Y V CE L CG H IA wy DRR K NKYV C PIH g D K G N I SP ---- VEVSYAF K LL L QELM 1089
....*...
gi 1767232066 1133 AR G VKVK L 1140
Cdd:PRK08565 1090 SM G ISPR L 1097
RNA_pol_B_RPB2
cd00653 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
327-1141
8.44e-82
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain]
Cd Length: 866
Bit Score: 286.39
E-value: 8.44e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 327 KGFYM I SLL RK FLYCIYYTSRYP D R D SMVCH R ILTY G KYFET L AHDE L ENYIGNIR ---- NDIMNNHKNRGTYAV N IHVL 402
Cdd:cd00653 209 RFEDL I YMI RK LILLVLGKGKLD D I D HLGNK R VRLA G ELLQN L FRSG L KRLEREVK eklq KQLSKKKDLTPQLLI N SKPI 288
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 403 T T p G LNHAFSS lls G KFK - K SDGSY R THP ----- HYSWMQNI S IP R SV --- G FYPDQ vkis K M F S VR KY HPS QYLYF C SS 473
Cdd:cd00653 289 T S - G IKEFLAT --- G NWG s K RFLMQ R SGL sqvld RLNPLSEL S HK R RI ssl G LFRER ---- K G F E VR DL HPS HWGRI C PI 360
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 474 DV PE r G PQV GLV SQ L SVLSS I T niltseyldlekkiceyirsyykddisyfetgfpitienalvaslnpnmicdfvtdfr 553
Cdd:cd00653 361 ET PE - G ENC GLV KN L ALMAR I S ---------------------------------------------------------- 381
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 554 rrkrmgffgnlevgitlvrdhmneiriniga GR LV RP FLV V DN gelmmdvcpelesrlddmtfsdiqkefph VIEMVD I E 633
Cdd:cd00653 382 ------------------------------- GR IE RP YRI V EK ----------------------------- EVTHIE I S 401
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 634 QFT fsnvcesvqkfr MM S kderkqydlcdfpaefrdgy VA S SL VG - IN HN SG PR AILGCAQA KQA ISCLSSDIRNKI D NG 712
Cdd:cd00653 402 PSQ ------------ IL S -------------------- VA A SL IP f PE HN QS PR NLYQSNMQ KQA VGTPALNQQYRM D TK 449
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 713 IH - L M YP ER P I V ISKAL E --- TSKIAA ncf GQ HVTI A L MSY K G I N Q ED G III K K QFIQ RG - GLD I VT a KK HQV E IPLENF 787
Cdd:cd00653 450 LY l L L YP QK P L V GTGIE E yia FGELPL --- GQ NAIV A V MSY S G Y N F ED A III N K SSVD RG f FRS I HY - KK YEI E LRKTKN 525
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 788 NNK E RD R SN ------- AYSK L ESN G LV R LN A FL E S GD AMARN I SSRTLEDD --- F ARDNQISF D V S E KY TDMY K SR V ER V 857
Cdd:cd00653 526 GPE E IT R GD ipnvsee KLKN L DED G II R PG A RV E P GD ILVGK I TPKGETES tpi F GEKARDVR D T S L KY PGGE K GI V DD V 605
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 858 QV --- EL T D KV -- K V R V LTMKE R R P IL GDKF TT R TS QKG TVAY I ADETEL P YD E N GI T PD V I I N STSIF SR K TI SM L I E V 932
Cdd:cd00653 606 KI fsr EL N D GG nk L V K V YIRQK R K P QI GDKF AS R HG QKG VISK I LPQEDM P FT E D GI P PD I I L N PHGFP SR M TI GQ L L E S 685
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 933 I L T -- A A YSA K PY nnkgen RPVC F PSSN E TS I DTY mq FAKQCYEHLN pklte KE lsdkifcek I LYD PE T DK P YASKV F F 1010
Cdd:cd00653 686 L L G ka G A LLG K FG ------ DATP F DGAE E ED I SEL -- LGEAGLNYYG ----- KE --------- V LYD GR T GE P LEAPI F V 743
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1011 GP I YY L RL R H LTQ DK ATV R CR G KKTK L I RQ ANE GR K RGGG IK FGEMERD C LIAHGAA NTIT E V L KDSEE D YQ d VYI C EN C 1090
Cdd:cd00653 744 GP V YY Q RL K H MVD DK IHA R ST G PYSL L T RQ PLK GR S RGGG QR FGEMERD A LIAHGAA YLLQ E R L TIKSD D VV - ARV C VK C 822
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|.
gi 1767232066 1091 G D I A aqik S I N T C LR C S K lnl SPLLT K IDTTHVS K VFLTQMNARGVKVK L D 1141
Cdd:cd00653 823 G I I L ---- S A N L C RL C K K --- GTNIS K VGIPYAF K LLFQELQSMNIDPR L K 866
RNA_pol_Rpb2_6
pfam00562 RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
674-1047
3.17e-66
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain]
Cd Length: 371
Bit Score: 228.18
E-value: 3.17e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 674 S SL VGI - N HN SG PR AILG CA QA KQA ISCLSSDIRNKI D NGIHLM - YP ER P I V ISK A L E --- TSKIAA ncf GQ HVTI A L MS 748
Cdd:pfam00562 2 A SL IPF v D HN QS PR NTYQ CA MG KQA MGIYTLNKFYRS D QNTYVL c YP QK P L V KTG A V E agg FGELPL --- GQ NAIV A V MS 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 749 Y K G I NQED G III K K QFIQ RG GLDIVTA K KHQVEI - P L ---- E NFNNKERDRSN A YS KL ESN G L VR LN A FLES GD A ---- M 819
Cdd:pfam00562 79 Y T G Y NQED A III N K SSVD RG FFTSIHI K EIEARK t K L gpie E ITRDIPNVSEE A LK KL DED G I VR VG A EVKP GD I lvgk V 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 820 ARNISSRT L EDD F ARDNQISF D V S E K YTDMYKSR V ER V Q V - EL TDKV -- K V R V LTMKE R R P IL GDKF TT R TS QKG T V AY I 896
Cdd:pfam00562 159 GPTELTKL L RAI F GEKARDVK D T S L K VPPGEEGV V DD V I V f EL PPGG ik M V K V YIRQK R K P EV GDKF AS R HG QKG V V SR I 238
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 897 ADETEL P YD E N GI T PD V I I N STSIF SR K TI SM L I E VI L -- T AA YSAKPYNN kgenr PV c F p SSNE T SID tym QFAKQCYE 974
Cdd:pfam00562 239 LPQEDM P FT E D GI P PD I I L N PHGVP SR M TI GQ L L E TH L gk A AA LLGVFVDA ----- TP - F - DGAS T EVE --- DIGELLEK 308
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1767232066 975 H - L N PKLT E kelsdkifcek I LYD PE T DK P YASKV F F GPIYY LR L R H LTQ DK ATV R CR G KKTK L I RQ ANE GR K R 1047
Cdd:pfam00562 309 A g Y N YYGK E ----------- V LYD GR T GE P FEAPI F V GPIYY QK L K H MVD DK IHA R ST G PYSL L T RQ PLG GR A R 371
RpoB
COG0085 DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
672-1082
4.66e-45
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain]
Cd Length: 1001
Bit Score: 177.22
E-value: 4.66e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 672 VA S SL VG - IN H NSGP RA IL G CAQAK QA ISC L SSD ----------- I R NKIDNG I H lmyp E RPIV ----- IS K -------- 726
Cdd:COG0085 523 VA T SL IP f LE H DDAN RA LM G ANMQR QA VPL L RPE apllhyplqkf Q R SNQGTC I N ---- Q RPIV rvgdr VE K gdvladgp 598
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 727 A LETSKI A A ncf GQ HVTI A L M SYK G I N Q ED G III KKQFIQRGG L DIVTAKKHQV E -------------- IP lenfn N KER 792
Cdd:COG0085 599 A TDNGEL A L --- GQ NLLV A F M PWE G Y N Y ED A III SERLVKDDV L TSIHIEEYEI E ardtklgpeeitrd IP ----- N VSE 670
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 793 D rsn A YSK L ESN G LV R LN A FLES GD AMARNIS ---------- S R T L EDD F A ------ RD N qi S FD V -- S EK ytdmyk SR V 854
Cdd:COG0085 671 E --- A LRN L DED G II R IG A EVKG GD ILVGKVT pkgeteltpe E R L L RAI F G ekarev RD T -- S LR V ph G EK ------ GK V 739
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 855 ER V Q V ------- EL TDK V -- K VRV LTMKE R RPIL GDK FTT R TSQ KG TVAY I ADETEL P YD E N G ITP D VII N STSIF SR KT 925
Cdd:COG0085 740 ID V K V fsreegd EL PPG V nk L VRV YVAQK R KIEV GDK LAG R HGN KG VISR I LPQEDM P FL E D G TPV D IVL N PLGVP SR MN 819
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 926 ISMLI E VI L TA A YSAKPYNNKG enr PV c F PSSN E TS I DTYMQF A K qcyeh L N P kltekel SD K I fcek I LYD PE T DK P YA 1005
Cdd:COG0085 820 VGQVL E TH L GW A AALLGRRVAT --- PV - F DGAP E EE I RELLEK A G ----- L P P ------- DG K E ---- V LYD GR T GE P FD 879
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1767232066 1006 SK V FF G PI YYL R L R H LTQ DK ATV R CR G KKTKLIR Q ANE G RKRG GG IK FGEME RDC L I A H GAA N T IT E V L KDSEE D YQ 1082
Cdd:COG0085 880 NP V TV G YM YYL K L H H MVD DK IHA R ST G PYSLITQ Q PLG G KAQF GG QR FGEME VWA L E A Y GAA Y T LQ E R L TIKSD D VC 956
rpo132
pfam12415 Poxvirus DNA dependent RNA polymerase; This domain family is found in viruses, and is ...
247-277
5.45e-12
Poxvirus DNA dependent RNA polymerase; This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with pfam04566, pfam00562, pfam04567, pfam04560, pfam04565. This family is the second largest subunit of the poxvirus DNA dependent RNA polymerase. It has structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Pssm-ID: 289200
Cd Length: 32
Bit Score: 60.90
E-value: 5.45e-12
10 20 30
....*....|....*....|....*....|.
gi 1767232066 247 FIR R SLSYDMPPEV V YLVNAII D S A K RLT ES 277
Cdd:pfam12415 2 FIR N SLSYDMPPEV I YLVNAII E S T K EII ES 32
Name
Accession
Description
Interval
E-value
PRK08565
PRK08565 DNA-directed RNA polymerase subunit B; Provisional
313-1140
6.72e-89
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain]
Cd Length: 1103
Bit Score: 311.12
E-value: 6.72e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 313 HNF LPH MNYT P - D QL K GF Y MISLLRKF L YCI Y YTS R Y PD - R D SMVCH R ILTY G KYFET L AHDELENYIGNIRND i MNNHK 390
Cdd:PRK08565 287 KYL LPH LGTS P e D RI K KA Y FLGQMASK L LEL Y LGR R E PD d K D HYANK R LRLA G DLLAE L FRVAFKQLVKDLKYQ - LEKSY 365
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 391 N RG t YAVNIHVLTT P G ----- LN HA FS -- SLLS G KFKK S DGSY RT hphy SWMQNI S IP R S V gfypdqvk I S KM ------ F 457
Cdd:PRK08565 366 A RG - RKLDLRAIVR P D iiter IR HA LA tg NWVG G RTGV S QLLD RT ---- NYLSTL S HL R R V -------- V S PL srgqph F 432
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 458 SV R KY H PS Q YLYF C SSDV PE r GP QV GLV SQ L SVLSS I T - NILTS E YLDLEKK ----- IC E YIRSY Y KDDISYFET G FP I T 531
Cdd:PRK08565 433 EA R DL H GT Q WGRI C PFET PE - GP NC GLV KN L ALMAQ I S v GVDEE E VEEILYE lgvvp VE E AREEE Y ISWSRVYLN G RL I G 511
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 532 IEN alvasl NPNMICDFVTDF RR RKRM gffg NL EV GITLVRD - HM NE IRI N IGA GR LV RP FL VV D NG ELMMD vc P E LESR 610
Cdd:PRK08565 512 YHP ------ DGEELAEKIREL RR SGKI ---- SD EV NVAYIET g EI NE VYV N CDS GR VR RP LI VV E NG KPKLT -- R E HVEK 579
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 611 L D -- DM TF S D IQ K E fp H VIE MV D I E QFTFSN V CESV qkfrmms K D ERKQYDLCDF -- PA EF rd G YV AS SLVGIN HN SG PR 686
Cdd:PRK08565 580 L K kg EL TF D D LV K M -- G VIE YL D A E EEENAY V ALDP ------- E D LTPEHTHLEI wp PA IL -- G IT AS IIPYPE HN QS PR 648
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 687 AILGC A Q AKQ AISCLSSDI R NKI D NGI HL M - YP E RP I V ISK ALE TSKIAANCF GQ HVTI A LM SY K G I N Q ED G II IK K QF I 765
Cdd:PRK08565 649 NTYQA A M AKQ SLGLYAANF R IRT D TRG HL L h YP Q RP L V QTR ALE IIGYNDRPA GQ NAVV A VL SY T G Y N I ED A II MN K AS I 728
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 766 Q RG ------- GLDIVTAK K H ------ QV EIP LE N FNNKERDR sn A Y S KL ESN G L V RLNAFLES GD AMARNI S S - R T LE DD 831
Cdd:PRK08565 729 E RG larstff RTYETEER K Y pggqed KI EIP EP N VRGYRGEE -- Y Y R KL DED G I V SPEVEVKG GD VLIGKT S P p R F LE EL 806
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 832 FA -------- RD NQISFDVS EK - YT D M yksrvervq V EL T DK ------ VKVRV LTM ke R R P I LGDKF TT R TS QKG TVAYI 896
Cdd:PRK08565 807 EE lslglqer RD TSVTVRHG EK g IV D T --------- V LI T ES pegnkl VKVRV RDL -- R I P E LGDKF AS R HG QKG VIGML 875
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 897 ADETEL P YD E N GI T PD V IIN STS I F SR K T ISM L I E V I l TAAYS A K pynnkg E N R P V CFPSSNETSIDTYM - QFA K QC Y EH 975
Cdd:PRK08565 876 VPQEDM P FT E D GI V PD L IIN PHA I P SR M T VGQ L L E S I - AGKVA A L ------ E G R F V DATPFYGEPEEELR k ELL K LG Y KP 948
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 976 lnpkl TEK E lsdkifcek IL YD PE T DKPYASKV F F G PI YY LR L R H LTQ DK ATV R C RG KKTK L I RQ AN EGR K R G GG IK FGE 1055
Cdd:PRK08565 949 ----- DGT E --------- VM YD GR T GEKIKAPI F I G VV YY QK L H H MVA DK IHA R A RG PVQI L T RQ PT EGR A R E GG LR FGE 1014
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1056 MERDCLI A HGAA NTIT E V L K DS EEDY q DV Y I CE N CG D IA -- AQI K SINT C LRC - S K L N L SP lltk IDTTHVS K VF L TQMN 1132
Cdd:PRK08565 1015 MERDCLI G HGAA MLLK E R L L DS SDKT - TI Y V CE L CG H IA wy DRR K NKYV C PIH g D K G N I SP ---- VEVSYAF K LL L QELM 1089
....*...
gi 1767232066 1133 AR G VKVK L 1140
Cdd:PRK08565 1090 SM G ISPR L 1097
RNA_pol_B_RPB2
cd00653 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
327-1141
8.44e-82
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain]
Cd Length: 866
Bit Score: 286.39
E-value: 8.44e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 327 KGFYM I SLL RK FLYCIYYTSRYP D R D SMVCH R ILTY G KYFET L AHDE L ENYIGNIR ---- NDIMNNHKNRGTYAV N IHVL 402
Cdd:cd00653 209 RFEDL I YMI RK LILLVLGKGKLD D I D HLGNK R VRLA G ELLQN L FRSG L KRLEREVK eklq KQLSKKKDLTPQLLI N SKPI 288
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 403 T T p G LNHAFSS lls G KFK - K SDGSY R THP ----- HYSWMQNI S IP R SV --- G FYPDQ vkis K M F S VR KY HPS QYLYF C SS 473
Cdd:cd00653 289 T S - G IKEFLAT --- G NWG s K RFLMQ R SGL sqvld RLNPLSEL S HK R RI ssl G LFRER ---- K G F E VR DL HPS HWGRI C PI 360
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 474 DV PE r G PQV GLV SQ L SVLSS I T niltseyldlekkiceyirsyykddisyfetgfpitienalvaslnpnmicdfvtdfr 553
Cdd:cd00653 361 ET PE - G ENC GLV KN L ALMAR I S ---------------------------------------------------------- 381
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 554 rrkrmgffgnlevgitlvrdhmneiriniga GR LV RP FLV V DN gelmmdvcpelesrlddmtfsdiqkefph VIEMVD I E 633
Cdd:cd00653 382 ------------------------------- GR IE RP YRI V EK ----------------------------- EVTHIE I S 401
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 634 QFT fsnvcesvqkfr MM S kderkqydlcdfpaefrdgy VA S SL VG - IN HN SG PR AILGCAQA KQA ISCLSSDIRNKI D NG 712
Cdd:cd00653 402 PSQ ------------ IL S -------------------- VA A SL IP f PE HN QS PR NLYQSNMQ KQA VGTPALNQQYRM D TK 449
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 713 IH - L M YP ER P I V ISKAL E --- TSKIAA ncf GQ HVTI A L MSY K G I N Q ED G III K K QFIQ RG - GLD I VT a KK HQV E IPLENF 787
Cdd:cd00653 450 LY l L L YP QK P L V GTGIE E yia FGELPL --- GQ NAIV A V MSY S G Y N F ED A III N K SSVD RG f FRS I HY - KK YEI E LRKTKN 525
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 788 NNK E RD R SN ------- AYSK L ESN G LV R LN A FL E S GD AMARN I SSRTLEDD --- F ARDNQISF D V S E KY TDMY K SR V ER V 857
Cdd:cd00653 526 GPE E IT R GD ipnvsee KLKN L DED G II R PG A RV E P GD ILVGK I TPKGETES tpi F GEKARDVR D T S L KY PGGE K GI V DD V 605
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 858 QV --- EL T D KV -- K V R V LTMKE R R P IL GDKF TT R TS QKG TVAY I ADETEL P YD E N GI T PD V I I N STSIF SR K TI SM L I E V 932
Cdd:cd00653 606 KI fsr EL N D GG nk L V K V YIRQK R K P QI GDKF AS R HG QKG VISK I LPQEDM P FT E D GI P PD I I L N PHGFP SR M TI GQ L L E S 685
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 933 I L T -- A A YSA K PY nnkgen RPVC F PSSN E TS I DTY mq FAKQCYEHLN pklte KE lsdkifcek I LYD PE T DK P YASKV F F 1010
Cdd:cd00653 686 L L G ka G A LLG K FG ------ DATP F DGAE E ED I SEL -- LGEAGLNYYG ----- KE --------- V LYD GR T GE P LEAPI F V 743
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1011 GP I YY L RL R H LTQ DK ATV R CR G KKTK L I RQ ANE GR K RGGG IK FGEMERD C LIAHGAA NTIT E V L KDSEE D YQ d VYI C EN C 1090
Cdd:cd00653 744 GP V YY Q RL K H MVD DK IHA R ST G PYSL L T RQ PLK GR S RGGG QR FGEMERD A LIAHGAA YLLQ E R L TIKSD D VV - ARV C VK C 822
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|.
gi 1767232066 1091 G D I A aqik S I N T C LR C S K lnl SPLLT K IDTTHVS K VFLTQMNARGVKVK L D 1141
Cdd:cd00653 823 G I I L ---- S A N L C RL C K K --- GTNIS K VGIPYAF K LLFQELQSMNIDPR L K 866
PRK07225
PRK07225 DNA-directed RNA polymerase subunit B'; Validated
548-1143
2.37e-76
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain]
Cd Length: 605
Bit Score: 264.52
E-value: 2.37e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 548 F V TDF R RRK R M G FFGN l EV GIT l VRDHM NE IR IN IG AGR LV RP FL VV D NGE LM md VCP E LESR L D -- DM TF S D IQ K E fp H 625
Cdd:PRK07225 23 L V EEI R EAR R S G EISE - EV NVS - YKEET NE VI IN TD AGR AR RP LI VV E NGE PL -- LTE E HIEK L K ng EL TF D D LV K Q -- G 96
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 626 VIE MV D I E Q ftfsnvcesvqkfrmmskd E RKQ Y d LCDFPAEFRDGYV ----- A S SLV GI -------- N HN SG PR AIL G CA 692
Cdd:PRK07225 97 VIE YL D A E E ------------------- E ENA Y - IAVYEEDLTEEHT hleid P S LIL GI gagmipyp E HN AS PR ITM G AG 156
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 693 QA KQ AISCLSSDIRNKI D NGI HL M - YP ER P I V ISKAL E TSKIAANCF GQ HVTI A L MSY K G I N Q ED GI I IK K QF I Q RG gld 771
Cdd:PRK07225 157 MI KQ SLGLPAANYKLRP D TRG HL L h YP QV P L V KTQTQ E IIGFDERPA GQ NFVV A V MSY E G Y N I ED AL I MN K AS I E RG --- 233
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 772 iv TAKK H ------------------ QV EIP LENFNNK erd R S - N AY SK L ESN GLV RLNAFLES GD AMARNI S S - R T LE -- 829
Cdd:PRK07225 234 -- LGRS H ffrtyegeerrypggqed RF EIP DKDVRGY --- R G e E AY RH L DED GLV NPETEVKE GD VLIGKT S P p R F LE ep 308
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 830 DDF A ------ R DNQISFDVS E K - YT D M yksrvervq V E LT D -------- KV K VR vltm KE R R P I LGDKF TT R TS QKG TVA 894
Cdd:PRK07225 309 DDF G ispekr R ETSVTMRSG E E g IV D T --------- V I LT E teegsrlv KV R VR ---- DL R I P E LGDKF AS R HG QKG VIG 375
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 895 Y I ADETEL P YD E N G IT PD V IIN STS I F SR K T ISMLI E V I LTAAY S A kpynnkg E N R P V --- C F PSSN E TSIDT ym QFA K Q 971
Cdd:PRK07225 376 L I VPQEDM P FT E S G VV PD L IIN PHA I P SR M T VGHVL E M I GGKVG S L ------- E G R R V dgt A F SGED E EDLRE -- ALE K L 446
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 972 CY EH lnpkl T E KE lsdkifcek IL YD PE T DKPYASKV F F G P IYY LR L R H LTQD K ATV R C RG KKTK L I RQ AN EGR K R G GG I 1051
Cdd:PRK07225 447 GF EH ----- T G KE --------- VM YD GI T GEKIEAEI F V G V IYY QK L H H MVAN K LHA R S RG PVQV L T RQ PT EGR A R E GG L 512
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1052 K FGEMERD C LI A HGAA NTIT E V L K D s E E D YQDV Y I C EN CG D IA AQI K SI N T -- C LR C - SKLNLS P lltk IDTTHVS K VF L 1128
Cdd:PRK07225 513 R FGEMERD V LI G HGAA MLLK E R L L D - E S D KVEI Y V C AK CG M IA IYD K KR N R ky C PI C g EETDIY P ---- VEMSYAF K LL L 587
650
....*....|....*
gi 1767232066 1129 TQMNAR G VKVK L DF E 1143
Cdd:PRK07225 588 DELKSL G IAPR L EL E 602
RNA_pol_Rpb2_6
pfam00562 RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
674-1047
3.17e-66
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain]
Cd Length: 371
Bit Score: 228.18
E-value: 3.17e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 674 S SL VGI - N HN SG PR AILG CA QA KQA ISCLSSDIRNKI D NGIHLM - YP ER P I V ISK A L E --- TSKIAA ncf GQ HVTI A L MS 748
Cdd:pfam00562 2 A SL IPF v D HN QS PR NTYQ CA MG KQA MGIYTLNKFYRS D QNTYVL c YP QK P L V KTG A V E agg FGELPL --- GQ NAIV A V MS 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 749 Y K G I NQED G III K K QFIQ RG GLDIVTA K KHQVEI - P L ---- E NFNNKERDRSN A YS KL ESN G L VR LN A FLES GD A ---- M 819
Cdd:pfam00562 79 Y T G Y NQED A III N K SSVD RG FFTSIHI K EIEARK t K L gpie E ITRDIPNVSEE A LK KL DED G I VR VG A EVKP GD I lvgk V 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 820 ARNISSRT L EDD F ARDNQISF D V S E K YTDMYKSR V ER V Q V - EL TDKV -- K V R V LTMKE R R P IL GDKF TT R TS QKG T V AY I 896
Cdd:pfam00562 159 GPTELTKL L RAI F GEKARDVK D T S L K VPPGEEGV V DD V I V f EL PPGG ik M V K V YIRQK R K P EV GDKF AS R HG QKG V V SR I 238
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 897 ADETEL P YD E N GI T PD V I I N STSIF SR K TI SM L I E VI L -- T AA YSAKPYNN kgenr PV c F p SSNE T SID tym QFAKQCYE 974
Cdd:pfam00562 239 LPQEDM P FT E D GI P PD I I L N PHGVP SR M TI GQ L L E TH L gk A AA LLGVFVDA ----- TP - F - DGAS T EVE --- DIGELLEK 308
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1767232066 975 H - L N PKLT E kelsdkifcek I LYD PE T DK P YASKV F F GPIYY LR L R H LTQ DK ATV R CR G KKTK L I RQ ANE GR K R 1047
Cdd:pfam00562 309 A g Y N YYGK E ----------- V LYD GR T GE P FEAPI F V GPIYY QK L K H MVD DK IHA R ST G PYSL L T RQ PLG GR A R 371
RpoB
COG0085 DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
672-1082
4.66e-45
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain]
Cd Length: 1001
Bit Score: 177.22
E-value: 4.66e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 672 VA S SL VG - IN H NSGP RA IL G CAQAK QA ISC L SSD ----------- I R NKIDNG I H lmyp E RPIV ----- IS K -------- 726
Cdd:COG0085 523 VA T SL IP f LE H DDAN RA LM G ANMQR QA VPL L RPE apllhyplqkf Q R SNQGTC I N ---- Q RPIV rvgdr VE K gdvladgp 598
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 727 A LETSKI A A ncf GQ HVTI A L M SYK G I N Q ED G III KKQFIQRGG L DIVTAKKHQV E -------------- IP lenfn N KER 792
Cdd:COG0085 599 A TDNGEL A L --- GQ NLLV A F M PWE G Y N Y ED A III SERLVKDDV L TSIHIEEYEI E ardtklgpeeitrd IP ----- N VSE 670
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 793 D rsn A YSK L ESN G LV R LN A FLES GD AMARNIS ---------- S R T L EDD F A ------ RD N qi S FD V -- S EK ytdmyk SR V 854
Cdd:COG0085 671 E --- A LRN L DED G II R IG A EVKG GD ILVGKVT pkgeteltpe E R L L RAI F G ekarev RD T -- S LR V ph G EK ------ GK V 739
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 855 ER V Q V ------- EL TDK V -- K VRV LTMKE R RPIL GDK FTT R TSQ KG TVAY I ADETEL P YD E N G ITP D VII N STSIF SR KT 925
Cdd:COG0085 740 ID V K V fsreegd EL PPG V nk L VRV YVAQK R KIEV GDK LAG R HGN KG VISR I LPQEDM P FL E D G TPV D IVL N PLGVP SR MN 819
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 926 ISMLI E VI L TA A YSAKPYNNKG enr PV c F PSSN E TS I DTYMQF A K qcyeh L N P kltekel SD K I fcek I LYD PE T DK P YA 1005
Cdd:COG0085 820 VGQVL E TH L GW A AALLGRRVAT --- PV - F DGAP E EE I RELLEK A G ----- L P P ------- DG K E ---- V LYD GR T GE P FD 879
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1767232066 1006 SK V FF G PI YYL R L R H LTQ DK ATV R CR G KKTKLIR Q ANE G RKRG GG IK FGEME RDC L I A H GAA N T IT E V L KDSEE D YQ 1082
Cdd:COG0085 880 NP V TV G YM YYL K L H H MVD DK IHA R ST G PYSLITQ Q PLG G KAQF GG QR FGEME VWA L E A Y GAA Y T LQ E R L TIKSD D VC 956
rpoB
CHL00207 RNA polymerase beta subunit; Provisional
722-1074
6.41e-26
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain]
Cd Length: 1077
Bit Score: 115.96
E-value: 6.41e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 722 IVISKALET S KI A anc F GQ H V TI A L M SYK G I N Q ED G I I I K K QF ---------- I QRGGLDIVTA K KHQV EI PLENF N NK E 791
Cdd:CHL00207 633 LADGSDIDN S EL A --- L GQ N V LV A Y M PWE G Y N F ED A I L I N K RL vyedlftsih I EKYEIELRQT K LGSE EI TRNIP N VS E 709
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 792 RDRS N aysk L ES NG LVRLNAFLES GD AMARN I SSRTLE D D ---------- F ARDNQISF D V S EKYTDMYKS RV ER V QVEL 861
Cdd:CHL00207 710 YSLK N ---- L DE NG IISIGSKVLA GD ILVGK I TPKGES D Q lpegkllrai F GEKAKDVK D T S LRMPNGGYG RV IK V EIFS 785
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 862 TD K --------- V K V RV LTMKE R RPIL GDK FTT R TSQ KG TVAY I ADETEL PY DEN G IT PD V I I N STSIF SR KTISM L I E V 932
Cdd:CHL00207 786 RS K gdelkfgyy L K I RV FIAQI R KIQV GDK LAG R HGN KG IISR I LPRQDM PY LPD G TP PD I I L N PLGVP SR MNVGQ L F E C 865
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 933 I L ta AYSAKPY N NK genrp VCFPSSN E TSIDT Y MQFA kq CYEH LN p KLTE K ELSDKI F ----- CEKI L Y D PE T DKPYASK 1007
Cdd:CHL00207 866 L L -- GLAGDNL N KR ----- FKILPFD E MYGSE Y SRIL -- INNK LN - QASI K NNEYWL F nsyhp GKMV L R D GR T GYKFKNP 935
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1767232066 1008 V FF G PI Y Y L R L R HL TQ DK ATV R CR G KKTKLIR Q ANE G RKRG GG IK FGEME RDC L I A H GAA N T IT E V L 1074
Cdd:CHL00207 936 V TV G IA Y M L K L I HL VD DK IHA R TT G PYSLVTQ Q PLG G KAQH GG QR FGEME VWA L E A F GAA Y T LK E L L 1002
RNA_pol_Rpb2_3
pfam04565 RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
428-493
4.52e-17
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain]
Cd Length: 67
Bit Score: 76.41
E-value: 4.52e-17
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1767232066 428 THPHYSWMQNI S IP R S V GFYPDQV - KIS K MFS VR KY HPS QYLYF C SSDV PE r GP QV GLV SQ L SVLSS 493
Cdd:pfam04565 2 VLDRTNYLSTL S HL R R V NSPRGGL f REM K TTE VR DL HPS HWGRI C PVET PE - GP NC GLV KH L ALYAR 67
RNA_pol_Rpb2_7
pfam04560 RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1049-1141
3.61e-16
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain]
Cd Length: 87
Bit Score: 74.55
E-value: 3.61e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 1049 GG IK FGEMER DC LIA H GAA N T IT E V L KDS e E D YQD V YI C EN CG DI AA qiks I N T C LR C - SKLNL SP lltk IDTTHVS K VF 1127
Cdd:pfam04560 1 GG LR FGEMER WA LIA Y GAA H T LQ E R L TIK - S D AYE V DV C GR CG LY AA ---- Y N K C PI C k GETDI SP ---- GYIPESF K LL 71
90
....*....|....
gi 1767232066 1128 LTQMNAR G VKVK L D 1141
Cdd:pfam04560 72 FQELQSL G IDPR L L 85
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
864-1080
6.04e-13
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 73.80
E-value: 6.04e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 864 KVK VRVL T mk E R RPIL GDK FTT R TSQ KG T V AY I ADETEL PY DEN G ITP D VII N STSIF SR KT I SMLI E VI L --------- 934
Cdd:PRK09603 1077 KVK LYIA T -- K R KLKV GDK MAG R HGN KG I V SN I VPVADM PY TAD G EPV D IVL N PLGVP SR MN I GQIL E MH L glvgkefgk 1154
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 935 --------- T AAYS ---------- A KPY N N K GENRPVCFPSSNETSIDT Y ------- MQF A KQCY E HLN pklte K E LSD K 988
Cdd:PRK09603 1155 qiasmledk T KDFA kelrakmlei A NAI N E K DPLTIHALENCSDEELLE Y akdwskg VKM A IPVF E GIS ----- Q E KFY K 1229
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 989 I F - CE KI ------- LYD PE T DKPYASK V FF G PI Y YLR L R HL TQD K ATV R CR G KKTKLIR Q ANE G RKRG GG IK FGEME RDC 1060
Cdd:PRK09603 1230 L F e LA KI amdgkmd LYD GR T GEKMRER V NV G YM Y MIK L H HL VDE K VHA R ST G PYSLVTH Q PVG G KALF GG QR FGEME VWA 1309
250 260
....*....|....*....|
gi 1767232066 1061 L I A H GAA N T IT E V L KDSEE D 1080
Cdd:PRK09603 1310 L E A Y GAA H T LK E M L TIKSD D 1329
rpo132
pfam12415 Poxvirus DNA dependent RNA polymerase; This domain family is found in viruses, and is ...
247-277
5.45e-12
Poxvirus DNA dependent RNA polymerase; This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with pfam04566, pfam00562, pfam04567, pfam04560, pfam04565. This family is the second largest subunit of the poxvirus DNA dependent RNA polymerase. It has structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Pssm-ID: 289200
Cd Length: 32
Bit Score: 60.90
E-value: 5.45e-12
10 20 30
....*....|....*....|....*....|.
gi 1767232066 247 FIR R SLSYDMPPEV V YLVNAII D S A K RLT ES 277
Cdd:pfam12415 2 FIR N SLSYDMPPEV I YLVNAII E S T K EII ES 32
rpoB
CHL00001 RNA polymerase beta subunit
737-1074
6.99e-10
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain]
Cd Length: 1070
Bit Score: 63.38
E-value: 6.99e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 737 CF G QH V TI A L M SYK G I N Q ED GII I KKQFIQR ggl DI V T A --- K K HQVEIPLENFN ---- N KE RDRSN A YS -- K L ES NG L V 807
Cdd:CHL00001 650 AL G KN V LV A Y M PWE G Y N F ED AVL I SERLVYE --- DI Y T S fhi R K YEIQTHVTSQG peri T KE IPHLE A HL lr N L DK NG I V 726
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 808 R L NAFL E S GD AMARNI ------- SS RTL E DDFA R D --- N Q I S ----------------- F DV SEKYTDMYK S - RV E RVQ V 859
Cdd:CHL00001 727 M L GSWV E T GD ILVGKL tpqeaee SS YAP E GRLL R A ifg I Q V S tsketclklpiggrgrv I DV RWIQKKGGS S y NP E TIH V 806
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 860 ELTD K VKVR V ltmkerrpil GDK FTT R TSQ KG TVAY I ADETEL PY DEN G ITP D VII N STSIF SR KTISMLI E VI L TA A -- 937
Cdd:CHL00001 807 YILQ K REIQ V ---------- GDK VAG R HGN KG IISK I LPRQDM PY LQD G TPV D MVL N PLGVP SR MNVGQIF E CL L GL A gd 876
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 938 ----- Y SAK P YNNKG E --- N R PVC F PSSN E T S ID T Y mqfakqcyehl NP KLT E K E LSD K ifce KI L Y D PE T DK P YASK V F 1009
Cdd:CHL00001 877 llnrh Y RIA P FDERY E qea S R KLV F SELY E A S KQ T A ----------- NP WVF E P E YPG K ---- SR L F D GR T GD P FEQP V T 941
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1767232066 1010 F G PI Y Y L R L R H LTQ DK ATV R CR G KKTKLIR Q ANE GR KRG GG IKF GEME RDC L IAH G A A NTIT E V L 1074
Cdd:CHL00001 942 I G KA Y I L K L I H QVD DK IHA R SS G PYALVTQ Q PLR GR SKQ GG QRV GEME VWA L EGF G V A YILQ E M L 1006
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
821-1080
3.51e-08
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 58.09
E-value: 3.51e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 821 RN IS S -- RT L ED DF ar D NQI S FDVSE kytdm Y K SR VE RVQ ------ VELTDK VKV RVLTMKERR P il GDK FTT R TSQ KG T 892
Cdd:PRK14844 1026 QS IS E qv KS L KK DF -- D EKV S HAIAQ ----- F K RK VE KLH egydlp QGVSMS VKV FIAVKHSLQ P -- GDK MAG R HGN KG V 1096
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 893 VAYIADETEL PY D E N G ITP D V I I N STSIF SR KTISMLI E V --------------- IL T --------------------- A 936
Cdd:PRK14844 1097 ISRVVPVEDM PY L E D G TPV D I I L N PLGVP SR MNVGQIL E T hvgwackklgekvgn IL D einkiksafckgirslnddnf T 1176
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 937 AYS A KPYN NK G --------- ENRPVCF P SS N E ------ TSIDT Y MQFA K QC Y EH L NPK L T E -------------- KEL SD 987
Cdd:PRK14844 1177 KFA A AYLD NK K ienidddei TASVLNT P NK N A lndeln ELVEN Y LNSC K SA Y SN L RNF L I E vyscgsnvsicnni RDI SD 1256
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1767232066 988 ------------------------------ K I F C -------- EKI LYD PETDKPYAS KV FF G PI Y Y L R L R HL TQD K ATV R 1029
Cdd:PRK14844 1257 nnliefarklrdgipvaapvfegpkdeqia K L F E lagldnsg QAV LYD GCSGEKFDR KV TV G YM Y M L K L H HL VDG K IHA R 1336
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 1767232066 1030 CR G KKTKLIR Q ANE G RKRG GG IK FGEME RDC L I A H GAA N T IT E V L KDSEE D 1080
Cdd:PRK14844 1337 SV G PYSLVTQ Q PLG G KSHF GG QR FGEME CWA L Q A Y GAA Y T LQ E M L TVKSD D 1387
Blast search parameters
Data Source:
Precalculated data, version = cdd.v.3.21
Preset Options: Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
