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DNA-directed RNA polymerase I subunit RPA1 [Rattus norvegicus]
Protein Classification
DNA-directed RNA polymerase I subunit RPA1 ( domain architecture ID 11546233 )
DNA-directed RNA polymerase I subunit RPA1 is the largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
16-1011
0e+00
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain]
Cd Length: 779
Bit Score: 1294.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 16 SF GM YSAEE LK KLSVK S ITNP RYV DSLG N P SAD GLYD L ALGP A D SKEV CSTC VQDFN NC S GH L GHI D LPL T VYNPL L FD K 95
Cdd:cd01435 1 SF SF YSAEE IR KLSVK E ITNP VTF DSLG H P VPG GLYD P ALGP L D KDDI CSTC GLNYL NC P GH F GHI E LPL P VYNPL F FD L 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 96 LY L LLRGSC LN CH MLTCPRAAIH L L V CQ LK V LD V G A L QAVY EL E rilsrfleetsdpsafeiqeeleeytskilqnnllg 175
Cdd:cd01435 81 LY K LLRGSC FY CH RFRISKWEVK L F V AK LK L LD K G L L VEAA EL D ------------------------------------ 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 176 sqgahvknvcesrsklvahfwkthmaakrcphcktgrsvvrkehnskltitypamvhkksgqkdaelpegapaapgidea 255
Cdd:cd01435 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 256 qmgkrgyltpssaqehlfaiwknegfflnylfsglddigpess F NPS MFFLD FIV VPP S R Y RP INR LGD QM F T N G Q T V N L 335
Cdd:cd01435 125 ------------------------------------------- F GYD MFFLD VLL VPP N R F RP PSF LGD KV F E N P Q N V L L 161
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 336 QAVM KD AVL IR K LLA V M A Q EQKL pcemteitidkendssgaidr S F L S L LP G QSLTD KL Y N I W IR LQS H VN IV FDS DMDK 415
Cdd:cd01435 162 SKIL KD NQQ IR D LLA S M R Q AESQ --------------------- S K L D L IS G KTNSE KL I N A W LQ LQS A VN EL FDS TKAP 220
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 416 LMLE K - Y PGI R Q I LEKKEGLFR KH MMGKRV D YAARSVI C PD MY I N TNEIGIP M VFA T KLT Y P Q PVTP W NV Q ELRQAVING 494
Cdd:cd01435 221 KSGK K s P PGI K Q L LEKKEGLFR MN MMGKRV N YAARSVI S PD PF I E TNEIGIP L VFA K KLT F P E PVTP F NV E ELRQAVING 300
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 495 P N V H PGA SMVIN EDG SRTA LSA VDATQ R E A V AK Q LL TP S TGIPKPQ G A K V V C RH VKN GD IL LLNRQPTLH R PSI Q AH RAH 574
Cdd:cd01435 301 P D V Y PGA NAIED EDG RLIL LSA LSEER R K A L AK L LL LL S SAKLLLN G P K K V Y RH LLD GD VV LLNRQPTLH K PSI M AH KVR 380
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 575 I LP E EK V LRLHYANCK A YNADFDGDEMN A HFPQSEL G RAEAY VL A C TD Q QYLVP K DG Q PL A GLIQDH M VSG ANM T I R GC F 654
Cdd:cd01435 381 V LP G EK T LRLHYANCK S YNADFDGDEMN L HFPQSEL A RAEAY YI A S TD N QYLVP T DG K PL R GLIQDH V VSG VLL T S R DT F 460
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 655 FTRE Q Y ME LVY RG L T ----- DK V GR V KL F PPAILKP F PLWTGKQV V ST L L I N I IP EDYTP LNL T GK A K IGS K AWVKEK pr 729
Cdd:cd01435 461 FTRE E Y QQ LVY AA L R plfts DK D GR I KL L PPAILKP K PLWTGKQV I ST I L K N L IP GNAPL LNL S GK K K TKK K VGGGKW -- 538
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 730 pvpdfd PDSMC ESQVIIR E GELL C GVLDK AHY G S SAYGLVH CC YE I YGGET S G RV L TC L A RLFTAYLQ l Y RGFT L G V ED I 809
Cdd:cd01435 539 ------ GGGSE ESQVIIR N GELL T GVLDK SQF G A SAYGLVH AV YE L YGGET A G KL L SA L G RLFTAYLQ - M RGFT C G I ED L 611
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 810 L VK P N AD VM R QR I IEESTQC G PR A VRAA L N L peaascdeiqgkwqdahlgkdqrdfnmidmkfke EV N HYSNE I N KAC M P 889
Cdd:cd01435 612 L LT P K AD EK R RK I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P 657
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 890 F GL HRQ FPENNLQ M MVQSGAKGS T VN TM QISCLLGQ I ELEGRR P PLM A SGK S LP C F E PY EFT PRAGGF V T G RFLTGIRP P 969
Cdd:cd01435 658 K GL LKP FPENNLQ L MVQSGAKGS M VN AS QISCLLGQ Q ELEGRR V PLM V SGK T LP S F P PY DTS PRAGGF I T D RFLTGIRP Q 737
970 980 990 1000
....*....|....*....|....*....|....*....|..
gi 1939159911 970 E F FFHCMAGREGL V DTAVKTSRSGYLQRC I IKHLEGL VIQ YD 1011
Cdd:cd01435 738 E Y FFHCMAGREGL I DTAVKTSRSGYLQRC L IKHLEGL KVN YD 779
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
965-1666
5.64e-159
RNA polymerase Rpb1, domain 5; 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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 494.95
E-value: 5.64e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 965 G IR P P EFFFH C M A GREGL V DTAVKT SR SGYLQR CII K H LE G LV IQ YD L TVR D S D G SV VQFLYGEDGLD IP K TQFLQPKQF 1044
Cdd:pfam04998 1 G LT P Q EFFFH T M G GREGL I DTAVKT AE SGYLQR RLV K A LE D LV VT YD D TVR N S G G EI VQFLYGEDGLD PL K IEKQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1045 P F LASNY E VIM K SKH L HEV L SRADPQKVLRHFRAIKKW hhrhssallrkgaflsfsqkiqaavkalnlegktqngrspet 1124
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1125 qqmlqmwheldeqsrrkyqkraapcpdps LSVWRPDIHF A SVSE T FEKKIDDY S QEWAAQAEKSHNRSELSLDR L RTLLQ 1204
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1205 L KW Q R SL CD PGEAVG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM V a S A NIK T P MMS V PV F NTK - KA L R 1283
Cdd:pfam04998 170 L LY Q Q SL IN PGEAVG II AAQSIGEP G TQMTLNTFHFAG VASK NVTLG V PRL K EI IN V - S K NIK S P SLT V YL F DEV g RE L E 248
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1284 RV K SLKKQLTR V C LG E V LQKVD I QESFCMGEKQNKFR V YELRFQ F LPHAYYQQ E KCLR PE DI L HFMET R FF K L L MEA IKK 1363
Cdd:pfam04998 249 KA K KVYGAIEK V T LG S V VESGE I LYDPDPFNTPIISD V KGVVKF F DIIDEVTN E EEID PE TG L LILVI R LL K I L NKS IKK 328
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1364 KNSKAS afrsvntrratqkdlddtedsgrnrreeerdeeeegnivdaeaeegdadasdtkrkekqeeevdyeseeegeee 1443
Cdd:pfam04998 329 VVKSEV -------------------------------------------------------------------------- 334
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1444 eeedvqeeenikgegahqthepdeeegsgleeessqnpprr HS R PQGAEAM E R R IQ A VR E SHS FI EDYQYDTEESLWCQV 1523
Cdd:pfam04998 335 ----------------------------------------- IP R SIRNKVD E G R DI A IG E ITA FI IKISKKIRQDTGGLR 373
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1524 T V KLPL M KINFDMSS LV V SL AH N AIVYTTK GI T R C L L NE TINS K N E KEF VL N TEG I NL PELFKYSEVL D LR R LY SNDIH A 1603
Cdd:pfam04998 374 R V DELF M EEDPKLAI LV A SL LG N ITLRGIP GI K R I L V NE DDKG K V E PDW VL E TEG V NL LRVLLVPGFV D AG R IL SNDIH E 453
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1939159911 1604 VANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI QSSSSPLQ 1666
Cdd:pfam04998 454 ILEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
Name
Accession
Description
Interval
E-value
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
16-1011
0e+00
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain]
Cd Length: 779
Bit Score: 1294.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 16 SF GM YSAEE LK KLSVK S ITNP RYV DSLG N P SAD GLYD L ALGP A D SKEV CSTC VQDFN NC S GH L GHI D LPL T VYNPL L FD K 95
Cdd:cd01435 1 SF SF YSAEE IR KLSVK E ITNP VTF DSLG H P VPG GLYD P ALGP L D KDDI CSTC GLNYL NC P GH F GHI E LPL P VYNPL F FD L 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 96 LY L LLRGSC LN CH MLTCPRAAIH L L V CQ LK V LD V G A L QAVY EL E rilsrfleetsdpsafeiqeeleeytskilqnnllg 175
Cdd:cd01435 81 LY K LLRGSC FY CH RFRISKWEVK L F V AK LK L LD K G L L VEAA EL D ------------------------------------ 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 176 sqgahvknvcesrsklvahfwkthmaakrcphcktgrsvvrkehnskltitypamvhkksgqkdaelpegapaapgidea 255
Cdd:cd01435 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 256 qmgkrgyltpssaqehlfaiwknegfflnylfsglddigpess F NPS MFFLD FIV VPP S R Y RP INR LGD QM F T N G Q T V N L 335
Cdd:cd01435 125 ------------------------------------------- F GYD MFFLD VLL VPP N R F RP PSF LGD KV F E N P Q N V L L 161
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 336 QAVM KD AVL IR K LLA V M A Q EQKL pcemteitidkendssgaidr S F L S L LP G QSLTD KL Y N I W IR LQS H VN IV FDS DMDK 415
Cdd:cd01435 162 SKIL KD NQQ IR D LLA S M R Q AESQ --------------------- S K L D L IS G KTNSE KL I N A W LQ LQS A VN EL FDS TKAP 220
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 416 LMLE K - Y PGI R Q I LEKKEGLFR KH MMGKRV D YAARSVI C PD MY I N TNEIGIP M VFA T KLT Y P Q PVTP W NV Q ELRQAVING 494
Cdd:cd01435 221 KSGK K s P PGI K Q L LEKKEGLFR MN MMGKRV N YAARSVI S PD PF I E TNEIGIP L VFA K KLT F P E PVTP F NV E ELRQAVING 300
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 495 P N V H PGA SMVIN EDG SRTA LSA VDATQ R E A V AK Q LL TP S TGIPKPQ G A K V V C RH VKN GD IL LLNRQPTLH R PSI Q AH RAH 574
Cdd:cd01435 301 P D V Y PGA NAIED EDG RLIL LSA LSEER R K A L AK L LL LL S SAKLLLN G P K K V Y RH LLD GD VV LLNRQPTLH K PSI M AH KVR 380
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 575 I LP E EK V LRLHYANCK A YNADFDGDEMN A HFPQSEL G RAEAY VL A C TD Q QYLVP K DG Q PL A GLIQDH M VSG ANM T I R GC F 654
Cdd:cd01435 381 V LP G EK T LRLHYANCK S YNADFDGDEMN L HFPQSEL A RAEAY YI A S TD N QYLVP T DG K PL R GLIQDH V VSG VLL T S R DT F 460
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 655 FTRE Q Y ME LVY RG L T ----- DK V GR V KL F PPAILKP F PLWTGKQV V ST L L I N I IP EDYTP LNL T GK A K IGS K AWVKEK pr 729
Cdd:cd01435 461 FTRE E Y QQ LVY AA L R plfts DK D GR I KL L PPAILKP K PLWTGKQV I ST I L K N L IP GNAPL LNL S GK K K TKK K VGGGKW -- 538
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 730 pvpdfd PDSMC ESQVIIR E GELL C GVLDK AHY G S SAYGLVH CC YE I YGGET S G RV L TC L A RLFTAYLQ l Y RGFT L G V ED I 809
Cdd:cd01435 539 ------ GGGSE ESQVIIR N GELL T GVLDK SQF G A SAYGLVH AV YE L YGGET A G KL L SA L G RLFTAYLQ - M RGFT C G I ED L 611
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 810 L VK P N AD VM R QR I IEESTQC G PR A VRAA L N L peaascdeiqgkwqdahlgkdqrdfnmidmkfke EV N HYSNE I N KAC M P 889
Cdd:cd01435 612 L LT P K AD EK R RK I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P 657
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 890 F GL HRQ FPENNLQ M MVQSGAKGS T VN TM QISCLLGQ I ELEGRR P PLM A SGK S LP C F E PY EFT PRAGGF V T G RFLTGIRP P 969
Cdd:cd01435 658 K GL LKP FPENNLQ L MVQSGAKGS M VN AS QISCLLGQ Q ELEGRR V PLM V SGK T LP S F P PY DTS PRAGGF I T D RFLTGIRP Q 737
970 980 990 1000
....*....|....*....|....*....|....*....|..
gi 1939159911 970 E F FFHCMAGREGL V DTAVKTSRSGYLQRC I IKHLEGL VIQ YD 1011
Cdd:cd01435 738 E Y FFHCMAGREGL I DTAVKTSRSGYLQRC L IKHLEGL KVN YD 779
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
11-1032
1.39e-165
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 525.96
E-value: 1.39e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 11 R LQG I S FG MY S A EE LK K L SV KS I TNPRYV D SL G N P SAD GL Y D LA LG PA D SKEV C S TC VQDFNN C S GH L GHI D L PLT V YNP 90
Cdd:PRK08566 8 R IGS I K FG LL S P EE IR K M SV TK I ITADTY D DD G Y P IDG GL M D PR LG VI D PGLR C K TC GGRAGE C P GH F GHI E L ARP V IHV 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 91 LLFDKL Y L LLR GS C LN C hmltcpraaihllvcqlkvldv G alqavyele R IL srf L E E tsdpsafeiq EE L EEY TS K I lq 170
Cdd:PRK08566 88 GFAKLI Y K LLR AT C RE C ---------------------- G --------- R LK --- L T E ---------- EE I EEY LE K L -- 121
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 171 n NL L GSQ G AHVKNVCESRS K LV A hfwkthm AAKR CPHC KTGRSVVRK E hns K L T IT Y pa MVH K KSGQ K daelpegapaap 250
Cdd:PRK08566 122 - ER L KEW G SLADDLIKEVK K EA A ------- KRMV CPHC GEKQYKIKF E --- K P T TF Y -- EER K EGLV K ------------ 176
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 251 gideaqmgkrgy LTPS SAQ E H L FA I WKNEGFF L nylfs G LD dig PE SS f N P SMFF L DFIV VPP SRY RP - I nrlgdq MFTN 329
Cdd:PRK08566 177 ------------ LTPS DIR E R L EK I PDEDLEL L ----- G IN --- PE VA - R P EWMV L TVLP VPP VTV RP s I ------ TLET 229
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 330 GQ TVN lqavm K D av L IR KL LAVMAQE Q K L pcemteitid KEN DSS GA idrsflsll P g Q SLTDK L yni W IR LQ S HV NIV F 409
Cdd:PRK08566 230 GQ RSE ----- D D -- L TH KL VDIIRIN Q R L ---------- KEN IEA GA --------- P - Q LIIED L --- W EL LQ Y HV TTY F 279
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 410 D SDM dklmleky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT NE I G I P MVF A TK LT Y 475
Cdd:PRK08566 280 D NEI -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI NE V G V P EAI A KE LT V 351
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 476 P QP VT P WN VQ ELR QA V I NGP NV HPGA SM VI NE DG S R TA L SAVD atq R E AV A KQ L ltpstgip K P qg AKV V C RH VKN GDI L 555
Cdd:PRK08566 352 P ER VT E WN IE ELR EY V L NGP EK HPGA NY VI RP DG R R IK L TDKN --- K E EL A EK L -------- E P -- GWI V E RH LID GDI V 418
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 556 L L NRQP T LHR P SI Q AHR AHI LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQY L V P KD G Q P LA 635
Cdd:PRK08566 419 L F NRQP S LHR M SI M AHR VRV LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQ T E EA RAEA RI L MLVQEHI L S P RY G G P II 497
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 636 G L IQDH m V SGA NM - T IRGCF FT R E QYME L VYRG ltd KVGRVKLFP PAI LKPF P L WTGKQ VV S TL L inii P E D ytp LNL TG 714
Cdd:PRK08566 498 G G IQDH - I SGA YL l T RKSTL FT K E EALD L LRAA --- GIDELPEPE PAI ENGK P Y WTGKQ IF S LF L ---- P K D --- LNL EF 566
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 715 KAKI G S K awvkekprpv P D FDPDSM CE -- SQ V I I RE G E LL C GV L DK AHY G SSAYGLVHCCYEI YG G E TSG R V L TCLA RL F 792
Cdd:PRK08566 567 KAKI C S G ---------- C D ECKKED CE hd AY V V I KN G K LL E GV I DK KAI G AEQGSILDRIVKE YG P E RAR R F L DSVT RL A 636
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 793 TAYLQ L y RGFT L G VE D ILVKPN A DVMRQR IIEE stqcgpr A VRAALN L P EA ASCD E IQ --- G KWQDAH L gkdqrdfnmi D 869
Cdd:PRK08566 637 IRFIM L - RGFT T G ID D EDIPEE A KEEIDE IIEE ------- A EKRVEE L I EA YENG E LE plp G RTLEET L ---------- E 698
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 870 MK FKEEVNHYSN E INK - A CMPF G lhrqf PE N NLQM M VQS GA K GS TV N TM Q ISCLL GQ IELE G R R PPLMASGKS LP C F E P Y 948
Cdd:PRK08566 699 MK IMQVLGKARD E AGE i A EKYL G ----- LD N PAVI M ART GA R GS ML N LT Q MAACV GQ QSVR G E R IRRGYRDRT LP H F K P G 773
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 949 EFTPR A G GFV TGRFLT G IR P P EFFFH C M A GREGLVDTAV K TS R SGY L QR CI I KH L EG L VIQ YD L TVRD SD G SV VQF L YGE 1028
Cdd:PRK08566 774 DLGAE A R GFV RSSYKS G LT P T EFFFH A M G GREGLVDTAV R TS Q SGY M QR RL I NA L QD L KVE YD G TVRD TR G NI VQF K YGE 853
....
gi 1939159911 1029 DG L D 1032
Cdd:PRK08566 854 DG V D 857
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
965-1666
5.64e-159
RNA polymerase Rpb1, domain 5; 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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 494.95
E-value: 5.64e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 965 G IR P P EFFFH C M A GREGL V DTAVKT SR SGYLQR CII K H LE G LV IQ YD L TVR D S D G SV VQFLYGEDGLD IP K TQFLQPKQF 1044
Cdd:pfam04998 1 G LT P Q EFFFH T M G GREGL I DTAVKT AE SGYLQR RLV K A LE D LV VT YD D TVR N S G G EI VQFLYGEDGLD PL K IEKQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1045 P F LASNY E VIM K SKH L HEV L SRADPQKVLRHFRAIKKW hhrhssallrkgaflsfsqkiqaavkalnlegktqngrspet 1124
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1125 qqmlqmwheldeqsrrkyqkraapcpdps LSVWRPDIHF A SVSE T FEKKIDDY S QEWAAQAEKSHNRSELSLDR L RTLLQ 1204
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1205 L KW Q R SL CD PGEAVG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM V a S A NIK T P MMS V PV F NTK - KA L R 1283
Cdd:pfam04998 170 L LY Q Q SL IN PGEAVG II AAQSIGEP G TQMTLNTFHFAG VASK NVTLG V PRL K EI IN V - S K NIK S P SLT V YL F DEV g RE L E 248
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1284 RV K SLKKQLTR V C LG E V LQKVD I QESFCMGEKQNKFR V YELRFQ F LPHAYYQQ E KCLR PE DI L HFMET R FF K L L MEA IKK 1363
Cdd:pfam04998 249 KA K KVYGAIEK V T LG S V VESGE I LYDPDPFNTPIISD V KGVVKF F DIIDEVTN E EEID PE TG L LILVI R LL K I L NKS IKK 328
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1364 KNSKAS afrsvntrratqkdlddtedsgrnrreeerdeeeegnivdaeaeegdadasdtkrkekqeeevdyeseeegeee 1443
Cdd:pfam04998 329 VVKSEV -------------------------------------------------------------------------- 334
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1444 eeedvqeeenikgegahqthepdeeegsgleeessqnpprr HS R PQGAEAM E R R IQ A VR E SHS FI EDYQYDTEESLWCQV 1523
Cdd:pfam04998 335 ----------------------------------------- IP R SIRNKVD E G R DI A IG E ITA FI IKISKKIRQDTGGLR 373
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1524 T V KLPL M KINFDMSS LV V SL AH N AIVYTTK GI T R C L L NE TINS K N E KEF VL N TEG I NL PELFKYSEVL D LR R LY SNDIH A 1603
Cdd:pfam04998 374 R V DELF M EEDPKLAI LV A SL LG N ITLRGIP GI K R I L V NE DDKG K V E PDW VL E TEG V NL LRVLLVPGFV D AG R IL SNDIH E 453
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1939159911 1604 VANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI QSSSSPLQ 1666
Cdd:pfam04998 454 ILEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1206-1712
6.03e-154
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain]
Cd Length: 309
Bit Score: 472.83
E-value: 6.03e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1206 K WQ RSL CD PGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM V AS A NIKTP M M SV P VF N T K K A L R r V 1285
Cdd:cd02735 1 K YM RSL VE PGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM T AS K NIKTP S M TL P LK N G K S A E R - A 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1286 KS LKK Q L T RV C L GE V LQ KV DIQ E sfcmgekqnkfrvyelrfqflphayyqqekclrped IL HFM E TR F F KLL meaikkkn 1365
Cdd:cd02735 80 ET LKK R L S RV T L SD V VE KV EVT E ------------------------------------ IL KTI E RV F K KLL -------- 115
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1366 skasafrsvntrratqkdlddtedsgrnrreeerdeeeegnivdaeaeegdadasdtkrkekqeeevdyeseeegeeeee 1445
Cdd:cd02735 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1446 edvqeeenikgegahqthepdeeegsgleeessqnpprrhsrpqgaeamerriqavreshsfiedyqydtee SL WC Q VT V 1525
Cdd:cd02735 116 ------------------------------------------------------------------------ GK WC E VT I 123
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1526 KLPL MKINFDMS S L V VS LA HN A IVYTTK GITRC LLN E TINSKNE K E f VLN TEG I NL PE L F K Y S EV LD LR R L Y S NDIHA VA 1605
Cdd:cd02735 124 KLPL SSPKLLLL S I V EK LA RK A VIREIP GITRC FVV E EDKGGKT K Y - LVI TEG V NL AA L W K F S DI LD VN R I Y T NDIHA ML 202
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1606 NTYGIEAA L R V I E KEI KD VF A VYGIAVDPRHLSL V ADYM C FEG V Y K P L NR F G IQ SS S SPLQ Q M T FET SFQ FLK Q AT MM G S 1685
Cdd:cd02735 203 NTYGIEAA R R A I V KEI SN VF K VYGIAVDPRHLSL I ADYM T FEG G Y R P F NR I G ME SS T SPLQ K M S FET TLA FLK K AT LN G D 282
490 500
....*....|....*....|....*..
gi 1939159911 1686 H D E L K SPS AC LVVGK V V K GGTGLF E L K 1712
Cdd:cd02735 283 I D N L S SPS SR LVVGK P V N GGTGLF D L L 309
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
302-645
6.63e-105
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 337.18
E-value: 6.63e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 302 SMFF L DFIV VPP SRY RP INR L GDQM F - TNGQ T VN L QAVM K DAVLIRK LL AVM A QEQKLPC E mteitidkendssgaidrs 380
Cdd:smart00663 1 EWMI L TVLP VPP PCL RP SVQ L DGGR F a EDDL T HL L RDII K RNNRLKR LL ELG A PSIIIRN E ------------------- 61
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 381 flsllpgqsltdklyni WIR LQ SH V NIVF D SDMDKLMLE K ---- YPGIR Q I L EK KEG L FR KHMM GKRVD YA ARSVI C PD M 456
Cdd:smart00663 62 ----------------- KRL LQ EA V DTLI D NEGLPRANQ K sgrp LKSLS Q R L KG KEG R FR QNLL GKRVD FS ARSVI T PD P 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 457 YINT NE I G I P MVF A TK LT Y P QP VTP W N VQE LR QA V I NGP nvh P GA SMV I N ed G SR T A L SAVD atq REAV A KQ L LTPS tgi 536
Cdd:smart00663 125 NLKL NE V G V P KEI A LE LT F P EI VTP L N IDK LR KL V R NGP --- N GA KYI I R -- G KK T N L KLAK --- KSKI A NH L KIGD --- 193
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 537 pkpqgak V V C RHV KN GD IL L L NRQPTLHR P SIQAHR AHI L p E E K VL RL HYAN C KA YNADFDGDEMN A H F PQS ELG RAEA Y 616
Cdd:smart00663 194 ------- I V E RHV ID GD VV L F NRQPTLHR M SIQAHR VRV L - E G K TI RL NPLV C SP YNADFDGDEMN L H V PQS LEA RAEA R 265
330 340
....*....|....*....|....*....
gi 1939159911 617 V L ACTDQQY L V PK D G Q P LA G L IQD HMVSG 645
Cdd:smart00663 266 E L MLVPNNI L S PK N G K P II G P IQD MLLGL 294
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
441-621
4.46e-86
RNA polymerase Rpb1, domain 2; 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, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498
Cd Length: 166
Bit Score: 278.03
E-value: 4.46e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 441 GKRVD YA AR S VI C PD MYINTN E I G I P MV FA TK LT Y P QP VTP W N VQE LRQ A V I NGPNV H PGA SMV I NED G S R TA L SA vdat 520
Cdd:pfam00623 1 GKRVD FS AR T VI S PD PNLKLD E V G V P IS FA KT LT F P EI VTP Y N IKR LRQ L V E NGPNV Y PGA NYI I RIN G A R RD L RY ---- 76
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 521 Q REAVA K Q L LTPST gipkpqgakv V C RHV KN GD IL L L NRQP T LHR P SI QA HR AHI LP e E K VL RL HYANCKA YNADFDGDE 600
Cdd:pfam00623 77 Q KRRLD K E L EIGDI ---------- V E RHV ID GD VV L F NRQP S LHR L SI MG HR VRV LP - G K TF RL NLSVTTP YNADFDGDE 145
170 180
....*....|....*....|.
gi 1939159911 601 MN A H F PQSE LG RAEA YV L ACT 621
Cdd:pfam00623 146 MN L H V PQSE EA RAEA EE L MLV 166
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1179-1711
1.51e-49
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 181.02
E-value: 1.51e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1179 Q E WAAQAE K SHNRSELS LD RLRTLLQLKWQ RSL C DPGEAVG LL AAQSIGEP S TQMT LN TFH F AG RG E M NVTLG I PRL R EI 1258
Cdd:TIGR02389 8 K E LEETVK K REISDKEE LD EIIKRVEEEYL RSL I DPGEAVG IV AAQSIGEP G TQMT MR TFH Y AG VA E L NVTLG L PRL I EI 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1259 LM v A SANIK TP M M SVPVF - NTK K ALRRVKSLK K QLTRVC L GE V LQKVD I Q esfcmgekqnkfr VYELRFQFLPHAYYQQ E 1337
Cdd:TIGR02389 88 VD - A RKTPS TP S M TIYLE d EYE K DREKAEEVA K KIEATK L ED V AKDIS I D ------------- LADMTVIIELDEEQLK E 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1338 KCLRPE D I lhfmetrffkll ME AIKK K nskasafrsvntrratq K DLDDT E DS grnrreeerdee EEG N IVDAEAEE g DA 1417
Cdd:TIGR02389 154 RGITVD D V ------------ EK AIKK A ----------------- K LGKVI E ID ------------ MDN N TITIKPGN - PS 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1418 DASDT K R KEK qeeevdyeseeegeeeeeedv QEEEN IKG egahqthepdeeegsgleeessqnpprrhsrpqgaeamerr 1497
Cdd:TIGR02389 192 LKELR K L KEK --------------------- IKNLH IKG ----------------------------------------- 209
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1498 iqavreshsfiedyqydteeslwcqvtvklplmkinfdmsslvvslahnaivyt T KGI T R C llne T I NSKNE k E F V LN TE 1577
Cdd:TIGR02389 210 ------------------------------------------------------ I KGI K R V ---- V I RKEGD - E Y V IY TE 230
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1578 G I NL P E LF K YSE V l D LR R LYS NDIH AV A NTY GIEAA LRV I EK EIK DVFAVY G IA VD P RHL S LVAD Y M CFE G VYKPLN R F G 1657
Cdd:TIGR02389 231 G S NL K E VL K LEG V - D KT R TTT NDIH EI A EVL GIEAA RNA I IE EIK RTLEEQ G LD VD I RHL M LVAD L M TWD G EVRQIG R H G 309
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*
gi 1939159911 1658 I Q - SSS S P L QQMT FE TSFQF L KQ A TMM G SH DELK SPSACLV VG KVVKG GTG LFE L 1711
Cdd:TIGR02389 310 I S g EKA S V L ARAA FE VTVKH L LD A AIR G EV DELK GVIENII VG QPIPL GTG DVD L 364
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1166-1711
1.16e-45
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 170.03
E-value: 1.16e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1166 VS ET F E K K ID D Y S -------- Q E WAAQA E K s HNRS E LSLDRLRTLLQLKWQ RSL CD PGEAVG LL AAQSIGEP S TQMT LN T 1237
Cdd:PRK04309 3 SE ET L E E K LE D A S lelpqklk E E LREKL E E - RKLT E EEVEEIIEEVVREYL RSL VE PGEAVG VV AAQSIGEP G TQMT MR T 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1238 FH F AG RG E M NVTLG I PRL R EI l MV A SANIK TPMM SVPV ----- FNTK KA lrrv KSLKKQLTRVC L GEVLQKVDIQ esfcm 1312
Cdd:PRK04309 82 FH Y AG VA E I NVTLG L PRL I EI - VD A RKEPS TPMM TIYL kdeya YDRE KA ---- EEVARKIEATT L ENLAKDISVD ----- 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1313 gekqnkfr VYELRFQFLPHAYYQQEKC L RPE D I lhfmetrffkll M EAI K KK N skasafrsvntrratqkd LDDT E DS G r 1392
Cdd:PRK04309 152 -------- LANMTIIIELDEEMLEDRG L TVD D V ------------ K EAI E KK K ------------------ GGEV E IE G - 192
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1393 nrreeerdeeeeg N IVDAEAE E gdadasdtkrkekqeeevdyeseeegeeeeeedvqeeenikgegahqthepdeeegsg 1472
Cdd:PRK04309 193 ------------- N TLIISPK E ---------------------------------------------------------- 201
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1473 leeessqnpprrhsrpqgaeamerriqavreshsfi ED Y Q ydteeslwcqvtvkl P L M K I nfdmsslv VSLAH N AIVYTT 1552
Cdd:PRK04309 202 ------------------------------------ PS Y R --------------- E L R K L -------- AEKIR N IKIKGI 222
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1553 KGI T R cllne T I NS K NEK E F V LN TEG I NL P E LF K YSE V l D LR R LYS N D IH AVANTY GIEAA LRV I EK EIK DVFAVY G IA V 1632
Cdd:PRK04309 223 KGI K R ----- V I IR K EGD E Y V IY TEG S NL K E VL K VEG V - D AT R TTT N N IH EIEEVL GIEAA RNA I IE EIK NTLEEQ G LD V 296
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1633 D P RH LS LVAD Y M CFE G VYKPLN R F G IQ - SSS S P L QQMT FE TSFQF L KQ A TMM G SH DELK SPSACLV VG KVVKG GTG LF EL 1711
Cdd:PRK04309 297 D I RH IM LVAD M M TWD G EVRQIG R H G VS g EKA S V L ARAA FE VTVKH L LD A AVR G EV DELK GVTENII VG QPIPL GTG DV EL 376
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
428-1259
6.62e-41
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain]
Cd Length: 1140
Bit Score: 165.61
E-value: 6.62e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 428 L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L typqp VT P WNVQE L - RQAVI ng P N VHPGAS M VIN 506
Cdd:TIGR02386 313 L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPELKMYQC G L P KKM A LE L ----- FK P FIIKR L i DRELA -- A N IKSAKK M IEQ 385
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 507 ED gsrtal SA V - D AT qr E A V A K Q lltpstgip K P qgakvvcrhvkngdi L LLNR Q PTLHR PS IQA HRA h I L P E E K VL RLH 585
Cdd:TIGR02386 386 ED ------ PE V w D VL -- E D V I K E --------- H P --------------- V LLNR A PTLHR LG IQA FEP - V L V E G K AI RLH 432
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 586 YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V PKDG Q P LAGLI QD hmvsgan M TI r G CF ftreq Y MELVY 665
Cdd:TIGR02386 433 PLV C T A F NADFDGD Q M AV H V P L S PEAQ AEA RA L MLASNNI L N PKDG K P IVTPS QD ------- M VL - G LY ----- Y LTTEK 499
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 666 R G ltd KV G RV K L F ppailkpfplwtgkqvv S TLLIN I IPE D YTPLN L TGKAKIGSKAWVK E KP ------- RPV P DFD P ds 738
Cdd:TIGR02386 500 P G --- AK G EG K I F ----------------- S NVDEA I RAY D NGKVH L HALIGVRTSGEIL E TT vgrvifn EIL P EGF P -- 557
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 739 mcesqv I I REG E llcg V L D K AHYG S sayg L VHCC YE IY G G E TSGRV L TCLAR L FTA Y LQLY r G F T LGVE DI L V KPN advm 818
Cdd:TIGR02386 558 ------ Y I NDN E ---- P L S K KEIS S ---- L IDLL YE VH G I E ETAEM L DKIKA L GFK Y ATKS - G T T ISAS DI V V PDE ---- 618
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 819 RQR I IE E STQ cgpravraalnlpeaa SCDE IQ GKWQDAHLGKDQ R DFNMIDM -- KF K EE V NH - YSNEIN K acmpfglh RQ 895
Cdd:TIGR02386 619 KYE I LK E ADK ---------------- EVAK IQ KFYNKGLITDEE R YRKVVSI ws ET K DK V TD a MMKLLK K -------- DT 674
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 896 FPE N NLQ MM VQ SGA K G STVNTM Q ISCLL G qielegrrpp LMA -- SG KSLP cfepyef T P raggf VTGR F LT G IRPP E F F F 973
Cdd:TIGR02386 675 YKF N PIF MM AD SGA R G NISQFR Q LAGMR G ---------- LMA kp SG DIIE ------- L P ----- IKSS F RE G LTVL E Y F I 732
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 974 HCMAG R E GL V DTA V KT SR SGYL Q R ciikhle G LV - IQY D LT VR DS D - G S vvqflyg E D G LDI pktqflqpkqfpflasny 1051
Cdd:TIGR02386 733 STHGA R K GL A DTA L KT AD SGYL T R ------- R LV d VAQ D VV VR EE D c G T ------- E E G IEV ------------------ 780
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1052 E V I MKS K H l HEVL S RA D pq KVLRHFR A IKKWH hrhssallrkgaflsfsqkiqaavkalnlegktqngrs P E T QQMLQMW 1131
Cdd:TIGR02386 781 E A I VEG K D - EIIE S LK D -- RIVGRYS A EDVYD -------------------------------------- P D T GKLIAEA 819
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1132 HE L deqsrrkyqkraapcpdpslsvwrpdihfas VS E TFEK KI D dysqew AAQA EK SHN RS E L SLDRLRTLL Q LKWQ R S L 1211
Cdd:TIGR02386 820 NT L ------------------------------- IT E EIAE KI E ------ NSGI EK VKV RS V L TCESEHGVC Q KCYG R D L 862
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 1939159911 1212 C ----- DP GEAVG LL AAQSIGEP S TQ M T LN TFH --- F AG RGE m NV T L G I PR LR E IL 1259
Cdd:TIGR02386 863 A tgklv EI GEAVG VI AAQSIGEP G TQ L T MR TFH tgg V AG ASG - DI T Q G L PR VK E LF 917
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
431-997
9.70e-32
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain]
Cd Length: 1165
Bit Score: 135.67
E-value: 9.70e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 431 K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq AVIN gpnvhpgas MVINEDGS 510
Cdd:COG0086 324 K Q G R FR QNLL GKRVDY SG RSVI VVGPELKLHQC G L P KKM A LE L FK P ------------- FIYR --------- KLEERGLA 381
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 511 R T AL SA VDATQ RE avakqlltpstgip K P QGAKVVCRHV K NGDI LL l NR Q PTLHR PS IQA HRA h I L P E E K VLR LH YAN C K 590
Cdd:COG0086 382 T T IK SA KKMVE RE -------------- E P EVWDILEEVI K EHPV LL - NR A PTLHR LG IQA FEP - V L I E G K AIQ LH PLV C T 445
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 591 A Y NADFDGD E M NA H F P Q S ELGRA EA YV L ACTDQQY L V P KD G Q P LAGLI QD h MV S G AN - M T I ------- R G CF F TREQYME 662
Cdd:COG0086 446 A F NADFDGD Q M AV H V P L S LEAQL EA RL L MLSTNNI L S P AN G K P IIVPS QD - MV L G LY y L T R eregakg E G MI F ADPEEVL 524
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 663 LV Y R - G LT D KVG R V K LFPPAILKP fplw T GK Q V VS T --- L L I N - I I P EDYTPL N - LTG K AK I G skawvkekprpvpdfdp 736
Cdd:COG0086 525 RA Y E n G AV D LHA R I K VRITEDGEQ ---- V GK I V ET T vgr Y L V N e I L P QEVPFY N q VIN K KH I E ----------------- 583
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 737 dsmcesq VIIR E gellcgvldkahygssayglvhc C Y EIY G GETSGRV L TC L AR L ft AYLQLY R - G FTL G VE D IL V KPN a 815
Cdd:COG0086 584 ------- VIIR Q ----------------------- M Y RRC G LKETVIF L DR L KK L -- GFKYAT R a G ISI G LD D MV V PKE - 630
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 816 dvm R Q R I I EE ST qcgp RA V raalnlpeaasc D EI QGKWQDAHLGKDQ R DFNM ID mkfke EVNHY S N E INKAC M P f GLHR Q 895
Cdd:COG0086 631 --- K Q E I F EE AN ---- KE V ------------ K EI EKQYAEGLITEPE R YNKV ID ----- GWTKA S L E TESFL M A - AFSS Q 685
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 896 fpe N NLQ MM VQ SGA K GS T vntmqiscll G Q IE - L E G R R p P LMA -- SG kslpcf EPY E f TP ----- R A G gfvtgrfl T G IR 967
Cdd:COG0086 686 --- N TTY MM AD SGA R GS A ---------- D Q LR q L A G M R - G LMA kp SG ------ NII E - TP igsnf R E G -------- L G VL 736
570 580 590
....*....|....*....|....*....|
gi 1939159911 968 pp E F F FHCMAG R E GL V DTA V KT SR SGYL Q R 997
Cdd:COG0086 737 -- E Y F ISTHGA R K GL A DTA L KT AD SGYL T R 764
Name
Accession
Description
Interval
E-value
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
16-1011
0e+00
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain]
Cd Length: 779
Bit Score: 1294.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 16 SF GM YSAEE LK KLSVK S ITNP RYV DSLG N P SAD GLYD L ALGP A D SKEV CSTC VQDFN NC S GH L GHI D LPL T VYNPL L FD K 95
Cdd:cd01435 1 SF SF YSAEE IR KLSVK E ITNP VTF DSLG H P VPG GLYD P ALGP L D KDDI CSTC GLNYL NC P GH F GHI E LPL P VYNPL F FD L 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 96 LY L LLRGSC LN CH MLTCPRAAIH L L V CQ LK V LD V G A L QAVY EL E rilsrfleetsdpsafeiqeeleeytskilqnnllg 175
Cdd:cd01435 81 LY K LLRGSC FY CH RFRISKWEVK L F V AK LK L LD K G L L VEAA EL D ------------------------------------ 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 176 sqgahvknvcesrsklvahfwkthmaakrcphcktgrsvvrkehnskltitypamvhkksgqkdaelpegapaapgidea 255
Cdd:cd01435 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 256 qmgkrgyltpssaqehlfaiwknegfflnylfsglddigpess F NPS MFFLD FIV VPP S R Y RP INR LGD QM F T N G Q T V N L 335
Cdd:cd01435 125 ------------------------------------------- F GYD MFFLD VLL VPP N R F RP PSF LGD KV F E N P Q N V L L 161
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 336 QAVM KD AVL IR K LLA V M A Q EQKL pcemteitidkendssgaidr S F L S L LP G QSLTD KL Y N I W IR LQS H VN IV FDS DMDK 415
Cdd:cd01435 162 SKIL KD NQQ IR D LLA S M R Q AESQ --------------------- S K L D L IS G KTNSE KL I N A W LQ LQS A VN EL FDS TKAP 220
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 416 LMLE K - Y PGI R Q I LEKKEGLFR KH MMGKRV D YAARSVI C PD MY I N TNEIGIP M VFA T KLT Y P Q PVTP W NV Q ELRQAVING 494
Cdd:cd01435 221 KSGK K s P PGI K Q L LEKKEGLFR MN MMGKRV N YAARSVI S PD PF I E TNEIGIP L VFA K KLT F P E PVTP F NV E ELRQAVING 300
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 495 P N V H PGA SMVIN EDG SRTA LSA VDATQ R E A V AK Q LL TP S TGIPKPQ G A K V V C RH VKN GD IL LLNRQPTLH R PSI Q AH RAH 574
Cdd:cd01435 301 P D V Y PGA NAIED EDG RLIL LSA LSEER R K A L AK L LL LL S SAKLLLN G P K K V Y RH LLD GD VV LLNRQPTLH K PSI M AH KVR 380
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 575 I LP E EK V LRLHYANCK A YNADFDGDEMN A HFPQSEL G RAEAY VL A C TD Q QYLVP K DG Q PL A GLIQDH M VSG ANM T I R GC F 654
Cdd:cd01435 381 V LP G EK T LRLHYANCK S YNADFDGDEMN L HFPQSEL A RAEAY YI A S TD N QYLVP T DG K PL R GLIQDH V VSG VLL T S R DT F 460
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 655 FTRE Q Y ME LVY RG L T ----- DK V GR V KL F PPAILKP F PLWTGKQV V ST L L I N I IP EDYTP LNL T GK A K IGS K AWVKEK pr 729
Cdd:cd01435 461 FTRE E Y QQ LVY AA L R plfts DK D GR I KL L PPAILKP K PLWTGKQV I ST I L K N L IP GNAPL LNL S GK K K TKK K VGGGKW -- 538
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 730 pvpdfd PDSMC ESQVIIR E GELL C GVLDK AHY G S SAYGLVH CC YE I YGGET S G RV L TC L A RLFTAYLQ l Y RGFT L G V ED I 809
Cdd:cd01435 539 ------ GGGSE ESQVIIR N GELL T GVLDK SQF G A SAYGLVH AV YE L YGGET A G KL L SA L G RLFTAYLQ - M RGFT C G I ED L 611
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 810 L VK P N AD VM R QR I IEESTQC G PR A VRAA L N L peaascdeiqgkwqdahlgkdqrdfnmidmkfke EV N HYSNE I N KAC M P 889
Cdd:cd01435 612 L LT P K AD EK R RK I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P 657
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 890 F GL HRQ FPENNLQ M MVQSGAKGS T VN TM QISCLLGQ I ELEGRR P PLM A SGK S LP C F E PY EFT PRAGGF V T G RFLTGIRP P 969
Cdd:cd01435 658 K GL LKP FPENNLQ L MVQSGAKGS M VN AS QISCLLGQ Q ELEGRR V PLM V SGK T LP S F P PY DTS PRAGGF I T D RFLTGIRP Q 737
970 980 990 1000
....*....|....*....|....*....|....*....|..
gi 1939159911 970 E F FFHCMAGREGL V DTAVKTSRSGYLQRC I IKHLEGL VIQ YD 1011
Cdd:cd01435 738 E Y FFHCMAGREGL I DTAVKTSRSGYLQRC L IKHLEGL KVN YD 779
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
11-1036
4.30e-175
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain]
Cd Length: 861
Bit Score: 550.70
E-value: 4.30e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 11 R LQ GI S FG MY S A EE LK K L SV KS I TN P RYV D SL G N P SAD GL Y D LA LG PADSKEV C S TC VQDFNN C S GH L GHI D L PLT V YNP 90
Cdd:cd02582 3 R IK GI K FG LL S P EE IR K M SV VE I IT P DTY D ED G Y P IEG GL M D PR LG VIEPGLR C K TC GNTAGE C P GH F GHI E L ARP V IHV 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 91 LLFDKL Y L LLR GS C LN C HMLTC P raaihllvcqlkvldvgalqavyelerilsrfleetsdpsafei Q EE L E E Y TSK I LQ 170
Cdd:cd02582 83 GFAKHI Y D LLR AT C RS C GRILL P -------------------------------------------- E EE I E K Y LER I RR 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 171 nnllgsqga HVKNVC E SRSKLVAHFW K THMAA K R CPHC KTGRSVVRK E HNSKLTITYPAMVH K ksgqkdaelpegapaap 250
Cdd:cd02582 119 --------- LKEKWP E LVKRVIEKVK K KAKKR K V CPHC GAPQYKIKL E KPTTFYEEKEEGEV K ----------------- 172
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 251 gideaqmgkrgy LTPS SAQ E H L FA I WKNEGFF L N ylfsgldd I G P ESS f N P SMFF L DFIV VPP SRY RP - I nrlgdq MFTN 329
Cdd:cd02582 173 ------------ LTPS EIR E R L EK I PDEDLEL L G -------- I D P KTA - R P EWMV L TVLP VPP VTV RP s I ------ TLET 225
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 330 G QTVN lqavm K D av L IR KL LAVMAQE Q K L pcemteitid KEN DSS GA idrsflsll P GQSLT D klyn I W IR LQ S HV NIV F 409
Cdd:cd02582 226 G ERSE ----- D D -- L TH KL VDIIRIN Q R L ---------- KEN IEA GA --------- P QLIIE D ---- L W DL LQ Y HV TTY F 275
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 410 D SDM dklmleky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT NE I G I P MVF A TK LT Y 475
Cdd:cd02582 276 D NEI -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI NE V G V P EDI A KE LT V 347
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 476 P QP VT P WN VQEL R QA V I NGP NVH PGA SM VI NE DG S R TA L SA V D atq RE AV A KQ L ltpstgip K P qg AKV V C RH VKN GDI L 555
Cdd:cd02582 348 P ER VT E WN IEKM R KL V L NGP DKW PGA NY VI RP DG R R IR L RY V N --- RE EL A ER L -------- E P -- GWI V E RH LID GDI V 414
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 556 L L NRQP T LHR P SI Q AHR AHI LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQSE LG RAEA YV L ACTDQQY L V P KD G Q P LA 635
Cdd:cd02582 415 L F NRQP S LHR M SI M AHR VRV LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQSE EA RAEA RE L MLVQEHI L S P RY G G P II 493
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 636 G L IQD H m V SGA NM - T IRGCF FT R E QYME L VYRGLT D kvgr VK L FP PAIL K P F PLWTGKQ VV S TL L inii P E D ytp LN LT G 714
Cdd:cd02582 494 G G IQD Y - I SGA YL l T RKTTL FT K E EALQ L LSAAGY D ---- GL L PE PAIL E P K PLWTGKQ LF S LF L ---- P K D --- LN FE G 561
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 715 KAK IG S KAWVKE kprpvpdf D P D SMCESQ V I I RE G E LL C GV L DK AHY G SSAY G - L V H CCYEI YG G E TSG R V L TCLA RL FT 793
Cdd:cd02582 562 KAK VC S GCSECK -------- D E D CPNDGY V V I KN G K LL E GV I DK KAI G AEQP G s L L H RIAKE YG N E VAR R F L DSVT RL AI 633
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 794 AYLQ L Y r GFT L G VE D ILVKPN A DVMRQR II E E stqcgpr A VRAALN L P E AASCD E IQ --- G K wqdahl GKDQ rdfn MID M 870
Cdd:cd02582 634 RFIE L R - GFT I G ID D EDIPEE A RKEIEE II K E ------- A EKKVYE L I E QYKNG E LE plp G R ------ TLEE ---- TLE M 695
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 871 K FKEEVNHYSN E IN K - A CMPFG lhrqf P E NN LQM M VQS GA K GS TV N TM Q ISCL LGQ IELE G R R PPLMASGKS LP C F E P YE 949
Cdd:cd02582 696 K IMQVLGKARD E AG K v A SKYLD ----- P F NN AVI M ART GA R GS ML N LT Q MAAC LGQ QSVR G E R INRGYRNRT LP H F K P GD 770
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 950 FT P R A G GFV TGR F LT G IR P P EFFFH C M A GREGLVDTAV K TS R SGY L QR CI I KH L EG L VIQ YD L TVRDS D G SVV QF L YGED 1029
Cdd:cd02582 771 LG P E A R GFV RSS F RD G LS P T EFFFH A M G GREGLVDTAV R TS Q SGY M QR RL I NA L QD L YVE YD G TVRDS R G NII QF K YGED 850
....*..
gi 1939159911 1030 G L D IP K T 1036
Cdd:cd02582 851 G V D PA K S 857
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
11-1032
1.39e-165
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 525.96
E-value: 1.39e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 11 R LQG I S FG MY S A EE LK K L SV KS I TNPRYV D SL G N P SAD GL Y D LA LG PA D SKEV C S TC VQDFNN C S GH L GHI D L PLT V YNP 90
Cdd:PRK08566 8 R IGS I K FG LL S P EE IR K M SV TK I ITADTY D DD G Y P IDG GL M D PR LG VI D PGLR C K TC GGRAGE C P GH F GHI E L ARP V IHV 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 91 LLFDKL Y L LLR GS C LN C hmltcpraaihllvcqlkvldv G alqavyele R IL srf L E E tsdpsafeiq EE L EEY TS K I lq 170
Cdd:PRK08566 88 GFAKLI Y K LLR AT C RE C ---------------------- G --------- R LK --- L T E ---------- EE I EEY LE K L -- 121
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 171 n NL L GSQ G AHVKNVCESRS K LV A hfwkthm AAKR CPHC KTGRSVVRK E hns K L T IT Y pa MVH K KSGQ K daelpegapaap 250
Cdd:PRK08566 122 - ER L KEW G SLADDLIKEVK K EA A ------- KRMV CPHC GEKQYKIKF E --- K P T TF Y -- EER K EGLV K ------------ 176
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 251 gideaqmgkrgy LTPS SAQ E H L FA I WKNEGFF L nylfs G LD dig PE SS f N P SMFF L DFIV VPP SRY RP - I nrlgdq MFTN 329
Cdd:PRK08566 177 ------------ LTPS DIR E R L EK I PDEDLEL L ----- G IN --- PE VA - R P EWMV L TVLP VPP VTV RP s I ------ TLET 229
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 330 GQ TVN lqavm K D av L IR KL LAVMAQE Q K L pcemteitid KEN DSS GA idrsflsll P g Q SLTDK L yni W IR LQ S HV NIV F 409
Cdd:PRK08566 230 GQ RSE ----- D D -- L TH KL VDIIRIN Q R L ---------- KEN IEA GA --------- P - Q LIIED L --- W EL LQ Y HV TTY F 279
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 410 D SDM dklmleky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT NE I G I P MVF A TK LT Y 475
Cdd:PRK08566 280 D NEI -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI NE V G V P EAI A KE LT V 351
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 476 P QP VT P WN VQ ELR QA V I NGP NV HPGA SM VI NE DG S R TA L SAVD atq R E AV A KQ L ltpstgip K P qg AKV V C RH VKN GDI L 555
Cdd:PRK08566 352 P ER VT E WN IE ELR EY V L NGP EK HPGA NY VI RP DG R R IK L TDKN --- K E EL A EK L -------- E P -- GWI V E RH LID GDI V 418
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 556 L L NRQP T LHR P SI Q AHR AHI LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQY L V P KD G Q P LA 635
Cdd:PRK08566 419 L F NRQP S LHR M SI M AHR VRV LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQ T E EA RAEA RI L MLVQEHI L S P RY G G P II 497
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 636 G L IQDH m V SGA NM - T IRGCF FT R E QYME L VYRG ltd KVGRVKLFP PAI LKPF P L WTGKQ VV S TL L inii P E D ytp LNL TG 714
Cdd:PRK08566 498 G G IQDH - I SGA YL l T RKSTL FT K E EALD L LRAA --- GIDELPEPE PAI ENGK P Y WTGKQ IF S LF L ---- P K D --- LNL EF 566
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 715 KAKI G S K awvkekprpv P D FDPDSM CE -- SQ V I I RE G E LL C GV L DK AHY G SSAYGLVHCCYEI YG G E TSG R V L TCLA RL F 792
Cdd:PRK08566 567 KAKI C S G ---------- C D ECKKED CE hd AY V V I KN G K LL E GV I DK KAI G AEQGSILDRIVKE YG P E RAR R F L DSVT RL A 636
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 793 TAYLQ L y RGFT L G VE D ILVKPN A DVMRQR IIEE stqcgpr A VRAALN L P EA ASCD E IQ --- G KWQDAH L gkdqrdfnmi D 869
Cdd:PRK08566 637 IRFIM L - RGFT T G ID D EDIPEE A KEEIDE IIEE ------- A EKRVEE L I EA YENG E LE plp G RTLEET L ---------- E 698
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 870 MK FKEEVNHYSN E INK - A CMPF G lhrqf PE N NLQM M VQS GA K GS TV N TM Q ISCLL GQ IELE G R R PPLMASGKS LP C F E P Y 948
Cdd:PRK08566 699 MK IMQVLGKARD E AGE i A EKYL G ----- LD N PAVI M ART GA R GS ML N LT Q MAACV GQ QSVR G E R IRRGYRDRT LP H F K P G 773
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 949 EFTPR A G GFV TGRFLT G IR P P EFFFH C M A GREGLVDTAV K TS R SGY L QR CI I KH L EG L VIQ YD L TVRD SD G SV VQF L YGE 1028
Cdd:PRK08566 774 DLGAE A R GFV RSSYKS G LT P T EFFFH A M G GREGLVDTAV R TS Q SGY M QR RL I NA L QD L KVE YD G TVRD TR G NI VQF K YGE 853
....
gi 1939159911 1029 DG L D 1032
Cdd:PRK08566 854 DG V D 857
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
965-1666
5.64e-159
RNA polymerase Rpb1, domain 5; 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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 494.95
E-value: 5.64e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 965 G IR P P EFFFH C M A GREGL V DTAVKT SR SGYLQR CII K H LE G LV IQ YD L TVR D S D G SV VQFLYGEDGLD IP K TQFLQPKQF 1044
Cdd:pfam04998 1 G LT P Q EFFFH T M G GREGL I DTAVKT AE SGYLQR RLV K A LE D LV VT YD D TVR N S G G EI VQFLYGEDGLD PL K IEKQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1045 P F LASNY E VIM K SKH L HEV L SRADPQKVLRHFRAIKKW hhrhssallrkgaflsfsqkiqaavkalnlegktqngrspet 1124
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1125 qqmlqmwheldeqsrrkyqkraapcpdps LSVWRPDIHF A SVSE T FEKKIDDY S QEWAAQAEKSHNRSELSLDR L RTLLQ 1204
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1205 L KW Q R SL CD PGEAVG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM V a S A NIK T P MMS V PV F NTK - KA L R 1283
Cdd:pfam04998 170 L LY Q Q SL IN PGEAVG II AAQSIGEP G TQMTLNTFHFAG VASK NVTLG V PRL K EI IN V - S K NIK S P SLT V YL F DEV g RE L E 248
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1284 RV K SLKKQLTR V C LG E V LQKVD I QESFCMGEKQNKFR V YELRFQ F LPHAYYQQ E KCLR PE DI L HFMET R FF K L L MEA IKK 1363
Cdd:pfam04998 249 KA K KVYGAIEK V T LG S V VESGE I LYDPDPFNTPIISD V KGVVKF F DIIDEVTN E EEID PE TG L LILVI R LL K I L NKS IKK 328
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1364 KNSKAS afrsvntrratqkdlddtedsgrnrreeerdeeeegnivdaeaeegdadasdtkrkekqeeevdyeseeegeee 1443
Cdd:pfam04998 329 VVKSEV -------------------------------------------------------------------------- 334
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1444 eeedvqeeenikgegahqthepdeeegsgleeessqnpprr HS R PQGAEAM E R R IQ A VR E SHS FI EDYQYDTEESLWCQV 1523
Cdd:pfam04998 335 ----------------------------------------- IP R SIRNKVD E G R DI A IG E ITA FI IKISKKIRQDTGGLR 373
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1524 T V KLPL M KINFDMSS LV V SL AH N AIVYTTK GI T R C L L NE TINS K N E KEF VL N TEG I NL PELFKYSEVL D LR R LY SNDIH A 1603
Cdd:pfam04998 374 R V DELF M EEDPKLAI LV A SL LG N ITLRGIP GI K R I L V NE DDKG K V E PDW VL E TEG V NL LRVLLVPGFV D AG R IL SNDIH E 453
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1939159911 1604 VANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI QSSSSPLQ 1666
Cdd:pfam04998 454 ILEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
21-1015
4.08e-155
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain]
Cd Length: 816
Bit Score: 495.53
E-value: 4.08e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 21 S A E ELKK LS VKSI TN PR - Y VDSLGN P SAD G LY D LA LG PA D SKEV C S TC VQDFNN C S GH L G H I D L P L T V YN pllfdklyll 99
Cdd:cd02583 2 S P E DIIR LS EVEV TN RN l Y DIETRK P LPY G VL D PR LG TS D KDGI C E TC GLNLAD C V GH F G Y I K L E L P V FH ---------- 71
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 100 lrgsclnchmltcpraaihllvcqlkvld V G ALQ A VYE - L ER I L --- SR F L eetsdpsafe IQ EE LEEYTS K I L QN --- N 172
Cdd:cd02583 72 ----------------------------- I G YFK A IIN i L QC I C ktc SR V L ---------- LP EE EKRKFL K R L RR pnl D 112
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 173 L L GSQGAHV K NVCESRSK lvahfwkthmaa KR CPHC K tgrsvvrkehnskltitypamv HK K SG Q K D aelpegapaapgi 252
Cdd:cd02583 113 N L QKKALKK K ILEKCKKV ------------ RK CPHC G ---------------------- LL K KA Q E D ------------- 145
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 253 deaqmgkrgy L T P SSAQEHLFA I wk NEGFFLNY L FSG L DD igpessf N P SMFF L DF I V VPP SRY RP inrlgdqmftngqt 332
Cdd:cd02583 146 ---------- L N P LKVLNLFKN I -- PPEDVELL L MNP L AG ------- R P ENLI L TR I P VPP LCI RP -------------- 192
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 333 vnlq A V MK D A vlirkll AVMAQ E QK L PCEMT EI T id KE ND S sga I DRSFLSLLPG Q sltd K LYNI W IR LQ SHVNIVFD S D 412
Cdd:cd02583 193 ---- S V VM D E ------- KSGTN E DD L TVKLS EI I -- FL ND V --- I KKHLEKGAKT Q ---- K IMED W DF LQ LQCALYIN S E 252
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 413 MDK L M L EKY P ----- G IR Q I L EK K E G L FR KHMM GKRVD YAA R S VI C PD MYINTNEI G I P MVF A TK LTYP QP VT PW N VQE L 487
Cdd:cd02583 253 LPG L P L SMQ P kkpir G FC Q R L KG K Q G R FR GNLS GKRVD FSG R T VI S PD PNLRIDQV G V P EHV A KI LTYP ER VT RY N IEK L 332
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 488 R QA V I NGP N VHPGA SM VI NE DG SRT - A L SAVD atq R EAV A KQ L ltp ST G I pkpqgak V V C RH VKN GDI L L L NRQP T LHR P 566
Cdd:cd02583 333 R KL V L NGP D VHPGA NF VI KR DG GKK k F L KYGN --- R RKI A RE L --- KI G D ------- I V E RH LED GDI V L F NRQP S LHR L 399
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 567 SI Q AHRA HIL P e EKVL R LHYAN C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQYLV P KD G Q PL AGLI QD HMVSGA 646
Cdd:cd02583 400 SI M AHRA KVM P - WRTF R FNECV C TP YNADFDGDEMN L H V PQ T E EA RAEA LE L MGVKNNLVT P RN G E PL IAAT QD FLTASY 478
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 647 NM T IRGC FF T R E Q YME L V y RGLT D KVGRVK L F PPAILKP FP LWTGKQ VV S t LL INIIPEDYTPL NL TG K A K IGS K awvke 726
Cdd:cd02583 479 LL T SKDV FF D R A Q FCQ L C - SYML D GEIKID L P PPAILKP VE LWTGKQ IF S - LL LRPNKKSPVLV NL EA K E K SYT K ----- 551
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 727 kprpvpdf DPDS MC -- ESQ V I IR EG ELLCG V LDK AHY GS SAYGLVH cc Y EI --- YG G E TSGRVLTC LA R L FTAY L QL y RG 801
Cdd:cd02583 552 -------- KSPD MC pn DGY V V IR NS ELLCG R LDK STL GS GSKNSLF -- Y VL lrd YG P E AAAAAMNR LA K L SSRW L SN - RG 620
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 802 F TL G VE D il V K P NADVMRQR -- IIEES tqcgpravraalnlpe A A S CDE IQGKWQDAH L g KD Q RDFNMID --- M K FKE E V 876
Cdd:cd02583 621 F SI G ID D -- V T P SKELLKKK ee LVDNG ---------------- Y A K CDE YIKQYKKGK L - EL Q PGCTAEQ tle A K ISG E L 681
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 877 NHYSNEIN KAC MPF g LH rqf PE N NLQM M VQS G A KGS TV N TM Q - I S C l L GQ IELE G R R P P LMASGKS LP C F EPYEF TP R A G 955
Cdd:cd02583 682 SKIREDAG KAC LKE - LH --- KS N SPLI M ALC G S KGS NI N IS Q m I A C - V GQ QIIS G K R I P NGFEDRT LP H F PRNSK TP A A K 756
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 956 GFV TGR F LT G IR P P EFFFH C M A GREGLVDTAVKT SRS GY L QR CII K H LE G L VI QYD L TVR 1015
Cdd:cd02583 757 GFV ANS F YS G LT P T EFFFH T M S GREGLVDTAVKT AET GY M QR RLM K A LE D L SV QYD G TVR 816
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1206-1712
6.03e-154
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain]
Cd Length: 309
Bit Score: 472.83
E-value: 6.03e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1206 K WQ RSL CD PGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM V AS A NIKTP M M SV P VF N T K K A L R r V 1285
Cdd:cd02735 1 K YM RSL VE PGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM T AS K NIKTP S M TL P LK N G K S A E R - A 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1286 KS LKK Q L T RV C L GE V LQ KV DIQ E sfcmgekqnkfrvyelrfqflphayyqqekclrped IL HFM E TR F F KLL meaikkkn 1365
Cdd:cd02735 80 ET LKK R L S RV T L SD V VE KV EVT E ------------------------------------ IL KTI E RV F K KLL -------- 115
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1366 skasafrsvntrratqkdlddtedsgrnrreeerdeeeegnivdaeaeegdadasdtkrkekqeeevdyeseeegeeeee 1445
Cdd:cd02735 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1446 edvqeeenikgegahqthepdeeegsgleeessqnpprrhsrpqgaeamerriqavreshsfiedyqydtee SL WC Q VT V 1525
Cdd:cd02735 116 ------------------------------------------------------------------------ GK WC E VT I 123
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1526 KLPL MKINFDMS S L V VS LA HN A IVYTTK GITRC LLN E TINSKNE K E f VLN TEG I NL PE L F K Y S EV LD LR R L Y S NDIHA VA 1605
Cdd:cd02735 124 KLPL SSPKLLLL S I V EK LA RK A VIREIP GITRC FVV E EDKGGKT K Y - LVI TEG V NL AA L W K F S DI LD VN R I Y T NDIHA ML 202
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1606 NTYGIEAA L R V I E KEI KD VF A VYGIAVDPRHLSL V ADYM C FEG V Y K P L NR F G IQ SS S SPLQ Q M T FET SFQ FLK Q AT MM G S 1685
Cdd:cd02735 203 NTYGIEAA R R A I V KEI SN VF K VYGIAVDPRHLSL I ADYM T FEG G Y R P F NR I G ME SS T SPLQ K M S FET TLA FLK K AT LN G D 282
490 500
....*....|....*....|....*..
gi 1939159911 1686 H D E L K SPS AC LVVGK V V K GGTGLF E L K 1712
Cdd:cd02735 283 I D N L S SPS SR LVVGK P V N GGTGLF D L L 309
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
8-1711
1.38e-150
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 498.01
E-value: 1.38e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 8 PWRRLQ GI S FG MY S AEELK K LSVKS IT N P RYV D SL G N P SAD GL Y D LA LG PADSKEV C S TC VQDFN NC S GH L GHI D L PLT V 87
Cdd:PRK14977 5 AVKAID GI I FG LI S PADAR K IGFAE IT A P EAY D ED G L P VQG GL L D GR LG TIEPGQK C L TC GNLAA NC P GH F GHI E L AEP V 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 88 YNPLLF D KLYL LL RGS C LN C HM L TC P R aaihllvcqlkvldvgalqavyelerilsrfleet S D PSA F EIQ EE LEEYTSK 167
Cdd:PRK14977 85 IHIAFI D NIKD LL NST C HK C AK L KL P Q ----------------------------------- E D LNV F KLI EE AHAAARD 129
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 168 I lqnnllg SQGAHVKNVC E SRSKL V AHFW K TH maa K R CPHC kt G RSVVR kehnsk L TITY P AMV hkksgqkdaelpegap 247
Cdd:PRK14977 130 I ------- PEKRIDDEII E EVRDQ V KVYA K KA --- K E CPHC -- G APQHE ------ L EFEE P TIF ---------------- 175
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 248 aapg I DEAQMGKR g Y L T P SSAQEHLFA I WKNEGFFLNY lfsglddi G P ESS f N P SMFF L DFIV VPP SRY RP inrlgdqmf 327
Cdd:PRK14977 176 ---- I EKTEIEEH - R L L P IEIRDIFEK I IDDDLELIGF -------- D P KKA - R P EWAV L QAFL VPP LTA RP --------- 232
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 328 tngq TVN L Q - AVMKDAV L IRK L LAVMAQE QKL pcemteitid KE NDSS GA idrsflsll P GQSLT D klyn IWIR LQ S H VN 406
Cdd:PRK14977 233 ---- SII L E t GERSEDD L THI L VDIIKAN QKL ---------- KE SKDA GA --------- P PLIVE D ---- EVDH LQ Y H TS 285
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 407 IV FD SDMDKLMLEKYP G IR ------- Q I L EK KEG L FR KHMM GKRVD YA AR S VI C PD MY I NTN E I G I P MVF A T KLT Y P QP V 479
Cdd:PRK14977 286 TF FD NATAGIPQAHHK G SG rplkslf Q R L KG KEG R FR GNLI GKRVD FS AR T VI S PD PM I DID E V G V P EAI A M KLT I P EI V 365
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 480 TPW N VQELRQA VINGP NVH PGA SMVINE DG SRTA L SAVDATQRE A --- V A K QL ltpstgipkp QGAKV V C RH VKN GDI LL 556
Cdd:PRK14977 366 NEN N IEKMKEL VINGP DEF PGA NAIRKG DG TKIR L DFLEDKGKD A lre A A E QL ---------- EIGDI V E RH LAD GDI VI 435
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 557 L NRQP T LH RP SI Q AHR AHI LP E e KVL RLH Y A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQYLV P KD G Q P LA G 636
Cdd:PRK14977 436 F NRQP S LH KL SI L AHR VKV LP G - ATF RLH P A V C PP YNADFDGDEMN L H V PQ I E DA RAEA IE L MGVKDNLIS P RT G G P II G 514
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 637 LI QD HMVSGANM T IRGCF F TREQYMELVYR - G L TD K vgrvk L FP PAI - L K PF P L WTGKQ VV S TL L inii P E D ytp L N LT G 714
Cdd:PRK14977 515 AL QD FITAAYLI T KDDAL F DKNEASNIAML a G I TD P ----- L PE PAI k T K DG P A WTGKQ LF S LF L ---- P K D --- F N FE G 582
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 715 K AK I -- G SKAWV K ekprpvpdf DP DSMCESQ V I I R EGEL LC GV L D KAHY G SSAYG --- L VHCCYEI YG GETSGRV L TCLA 789
Cdd:PRK14977 583 I AK W sa G KAGEA K --------- DP SCLGDGY V L I K EGEL IS GV I D DNII G ALVEE pes L IDRIAKD YG EAVAIEF L NKIL 653
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 790 RLFTAYLQL Y r GF TL G VE D ILV k P NAD vm R Q R I IEESTQCGPRAVRAALNLPEAASCDEIQ GK WQ dah L GKDQRDFNMID 869
Cdd:PRK14977 654 IIAKKEILH Y - GF SN G PG D LII - P DEA -- K Q E I EDDIQGMKDEVSDLIDQRKITRKITIYK GK EE --- L LRGMKEEEALE 726
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 870 MKFKE E VNHY ---- SNEI N K a C MP fglhrqf PE N NLQM M VQS GA K GS TV N TM QI SCL LGQ IELEG R RPPLMAS G K ----- 940
Cdd:PRK14977 727 ADIVN E LDKA rdka GSSA N D - C ID ------- AD N AGKI M AKT GA R GS MA N LA QI AGA LGQ QKRKT R IGFVLTG G R lhegy 798
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 941 --- S L PC F EPYEFT P R A G GFV TGRFLT G IRPP EFFFH C M A GREGL V D T A VK T SR SGY L QR CIIKH LE GLVIQ YD L TVRD S 1017
Cdd:PRK14977 799 kdr A L SH F QEGDDN P D A H GFV KNNYRE G LNAA EFFFH A M G GREGL I D K A RR T ED SGY F QR RLANA LE DIRLE YD E TVRD P 878
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1018 D G SVV QF LY GEDG L D IP K TQFLQP kqfpflasnyevimkskhlhevlsr ADPQKVLR hfraikkwhhrhssallrkgafl 1097
Cdd:PRK14977 879 H G HII QF KF GEDG I D PQ K LDHGEA ------------------------- FNLERIIE ----------------------- 910
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1098 sf S QKI qaavkalnlegktqngrspetqqmlqmwheld E QSRRKYQ K raapcpdpslsvwrpdihfasvs ETF E KKIDD Y 1177
Cdd:PRK14977 911 -- K QKI -------------------------------- E DRGKGAS K ----------------------- DEI E ELAKE Y 933
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1178 SQEWA A QAE K S ----- H N r S EL SL D R L RTL --- LQLKWQRSLCD PG E A V G LLA AQSI G EP S TQMTL N TFH F AG RGE M N VT 1249
Cdd:PRK14977 934 TKTFN A NLP K L ladai H G - A EL KE D E L EAI cae GKEGFEKAKVE PG Q A I G IIS AQSI A EP G TQMTL R TFH A AG IKA M D VT 1012
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1250 L G IP R LR E i L MV A S A NIK TP M M SV pvfntkkalrrvkslkkqltrvclgevlqkvdiqesfcmgekqnkfrvyelrfqfl 1329
Cdd:PRK14977 1013 H G LE R FI E - L VD A R A KPS TP T M DI -------------------------------------------------------- 1035
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1330 phay Y QQEK C lrpedilhfmetrffkllmeai K KKNS KA safrsvntr RATQKD L DDTE dsgrnrreeerdeeeegni V D 1409
Cdd:PRK14977 1036 ---- Y LDDE C ---------------------- K EDIE KA --------- IEIARN L KELK ------------------- V R 1061
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1410 A EAEEGDA D ASDTKRKE K qeeevdyeseeegeeeeeedvqeeenikgegahqthepdeeegsgleeessqnp P RRHSRPQ 1489
Cdd:PRK14977 1062 A LIADSAI D NANEIKLI K ------------------------------------------------------ P DKRALEN 1087
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1490 G AEA MER RIQAVRESHSFIE d YQYDT E ES L wcq VTVK L PLMKINFDMSSLVVSLAH --- NAI V YTTKG I T R CLL n E TINS 1566
Cdd:PRK14977 1088 G CIP MER FAEIEAALAKGKK - FEMEL E DD L --- IILD L VEAADRDKPLATLIAIRN kil DKP V KGVPD I E R AWV - E LVEK 1162
1610 1620 1630 1640 1650 1660 1670 1680
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1567 KNEK E FVLN T E G I NL PELFKYSEV l D LRRLYS ND IHAV A N T Y GIEAA LRV I EK E IKDVFAVY G IA VD P R HLS LVAD Y MC F 1646
Cdd:PRK14977 1163 DGRD E WIIQ T S G S NL AAVLEMKCI - D IANTIT ND CFEI A G T L GIEAA RNA I FN E LASILEDQ G LE VD N R YIM LVAD I MC S 1241
1690 1700 1710 1720 1730 1740 1750
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1939159911 1647 E G VYKPLN ------ R F G IQSS - S SPL QQMT FE TSFQFLKQ A TMM G SHDEL K SPSAC L VV G KVVKG G T G LFE L 1711
Cdd:PRK14977 1242 R G TIEAIG lqaagv R H G FAGE k D SPL AKAA FE ITTHTIAH A ALG G EIEKI K GILDA L IM G QNIPI G S G KVD L 1313
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
13-1011
1.25e-145
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain]
Cd Length: 751
Bit Score: 467.40
E-value: 1.25e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 13 QGIS FG MY S AE E LKKL SV KS I TN P RYVDSL G N P SAD GL Y D LAL G PA D SKEV C S TC VQ D FNN C S GH L GHI D L PLT V YN pll 92
Cdd:cd02733 1 KRVQ FG IL S PD E IRAM SV AE I EH P ETYENG G G P KLG GL N D PRM G TI D RNSR C Q TC GG D MKE C P GH F GHI E L AKP V FH --- 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 93 fdklylllrgsclnchmltcpraaihllvcqlkvld V G A L QAVY elerilsrfleetsdpsafeiqeeleeyts KIL qnn 172
Cdd:cd02733 78 ------------------------------------ I G F L TKIL ------------------------------ KIL --- 88
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 173 llgsqgahv KN VC ES rsklvahfwkthmaakrcphcktgrsvvrkehnskltitypamvhkksgqkdaelpegapaapgi 252
Cdd:cd02733 89 --------- RC VC KR ----------------------------------------------------------------- 94
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 253 deaqmgkrg Y L TPSSAQ E HLFA I WKNEGFF L nylfs G L D dig P ES S f N P SMFF L DFIV VPP SRY RP INRLG dq MFTNGQ - 331
Cdd:cd02733 95 --------- E L SAERVL E IFKR I SDEDCRI L ----- G F D --- P KF S - R P DWMI L TVLP VPP PAV RP SVVMD -- GSARSE d 154
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 332 -- T VN L QAVM K DAVLIRK llavmaqeqklpcemteiti DKE N DSSGA I DRSFLS LL pgqsltdklyniwirl Q S HV NIVF 409
Cdd:cd02733 155 dl T HK L ADII K ANNQLKR -------------------- QEQ N GAPAH I IEEDEQ LL ---------------- Q F HV ATYM 198
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 410 D SD --- MDKLMLEK --- YPG IRQ I L EK KEG LF R KHM MGKRVD YA AR S VI C PD MYINTNEI G I P MVF A TK LT Y P QP VTP W N 483
Cdd:cd02733 199 D NE ipg LPQATQKS grp LKS IRQ R L KG KEG RI R GNL MGKRVD FS AR T VI T PD PNLELDQV G V P RSI A MN LT F P EI VTP F N 278
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 484 VQE L RQA V I NGPN VH PGA SMV I NE DG S R TA L SAVD atqre AVAKQL L TP stgipkpq G AK V V c RH VKN GD IL L L NRQP T L 563
Cdd:cd02733 279 IDR L QEL V R NGPN EY PGA KYI I RD DG E R ID L RYLK ----- KASDLH L QY -------- G YI V E - RH LQD GD VV L F NRQP S L 344
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 564 H RP S IQA HR AHI LP e EKVL RL HYANCKA YNADFDGDEMN A H F PQS ELG RAE AYV L ACTDQ Q YLV P KDGQ P LA G LI QD HMV 643
Cdd:cd02733 345 H KM S MMG HR VKV LP - YSTF RL NLSVTTP YNADFDGDEMN L H V PQS LET RAE LKE L MMVPR Q IVS P QSNK P VM G IV QD TLL 423
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 644 SGANM T I R GC F FTRE Q Y M E L VY r G L T D KV G RVK lf P PAILKP F PLWTGKQ VV S T llin IIP E dytp L N LTGK akig S KAW 723
Cdd:cd02733 424 GVRKL T K R DT F LEKD Q V M N L LM - W L P D WD G KIP -- Q PAILKP K PLWTGKQ IF S L ---- IIP K ---- I N NLIR ---- S SSH 488
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 724 VKEKPRPVPDF D pdsmce SQ VII RE GELL C G V L D K AHY G S S AY GL V H CCYEI YG G E TSGRVLTCLA R LFTAY L q L YR GF T 803
Cdd:cd02733 489 HDGDKKWISPG D ------ TK VII EN GELL S G I L C K KTV G A S SG GL I H VIWLE YG P E AARDFIGNIQ R VVNNW L - L HN GF S 561
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 804 L G VE D IL vk PNADV M R -- Q RI I EEST qcgpravraalnlpeaasc DEIQGKWQD A HL G KDQRDFNMIDMK - F KEE VN hys 880
Cdd:cd02733 562 I G IG D TI -- ADKET M K ki Q ET I KKAK ------------------- RDVIKLIEK A QN G ELEPQPGKTLRE s F ENK VN --- 617
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 881 NEI NKA CMPF G LHR Q F --- PE NN LQM MV QS G A KGS TV N TM QI SCLL GQ IEL EG R R P P LMASGKS LP C F EPYEFT P RAG GF 957
Cdd:cd02733 618 RIL NKA RDKA G KSA Q K sls ED NN FKA MV TA G S KGS FI N IS QI IACV GQ QNV EG K R I P FGFRRRT LP H F IKDDYG P ESR GF 697
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....
gi 1939159911 958 V TGRF L T G IR P P EFFFH C M A GREGL V DTAVKT SRS GY L QR CII K HL E GLVIQ YD 1011
Cdd:cd02733 698 V ENSY L R G LT P Q EFFFH A M G GREGL I DTAVKT AET GY I QR RLV K AM E DVMVK YD 751
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
396-1011
6.78e-110
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain]
Cd Length: 528
Bit Score: 360.59
E-value: 6.78e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 396 NI W IR LQ S HV NIVF D SDMDKLMLEKYP ----- GIR Q I L EK KEG L FR KHM MGKRVD YAA RSVI C PD MYINTNEI G I P MVF A 470
Cdd:cd00399 107 ER W RL LQ E HV DTYL D NGIAGQPQTQKS grplr SLA Q R L KG KEG R FR GNL MGKRVD FSG RSVI S PD PNLRLDQV G V P KSI A 186
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 471 TK L typqpvtpwnvqelrqavingpnvhpgasmvinedgsrtalsavdatqreavakqlltpstgipkpqgakvvcrhvk 550
Cdd:cd00399 187 LT L ----------------------------------------------------------------------------- 189
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 551 N GD IL L L NRQP T LH RP SI Q AHR AHI LP E e KVL RL HYAN C KA YNADFDGDEMN A H F PQSE LG RAEA YV L ACTDQQY L V P KD 630
Cdd:cd00399 190 D GD PV L F NRQP S LH KL SI M AHR VRV LP G - STF RL NPLV C SP YNADFDGDEMN L H V PQSE EA RAEA RE L MLVPNNI L S P QN 268
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 631 G Q PL A GL I QD HMVSGANM T I rgcfftreqymelvyrgltdkvgrvklfppailkpfplwt GKQ V VS TL L iniipedytpl 710
Cdd:cd00399 269 G E PL I GL S QD TLLGAYLL T L ---------------------------------------- GKQ I VS AA L ----------- 297
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 711 nltgkakigskawvkekprpvpdfdpdsmcesqviiregellcgvldkahygss AY GL V H CCYEIY G G E TSGRV L TC L A R 790
Cdd:cd00399 298 ------------------------------------------------------ PG GL L H TVTREL G P E KAAKL L SN L Q R 323
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 791 LFTAY L QL y R GF TL G VE D IL vk PNADVMRQR -- I IEE ST qcgpravraalnlpea ASC DE IQGKW Q -- DAHLGKDQRDFN 866
Cdd:cd00399 324 VGFVF L TT - S GF SV G IG D VI -- DDGVIPEEK te L IEE AK ---------------- KKV DE VEEAF Q ag LLTAQEGMTLEE 384
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 867 MIDMKFKEEV N HYSNEINK A CMPF g L HRQFPE N NLQM M VQ SGAKGS TV N TM Q I S CLL GQ IEL EG R R P P LMA S GKS LP C F E 946
Cdd:cd00399 385 SLEDNILDFL N EARDKAGS A ASVN - L DLVSKF N SIYV M AM SGAKGS FI N IR Q M S ACV GQ QSV EG K R I P RGF S DRT LP H F S 463
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1939159911 947 PYEFT P R A G GF VTGR FL T G IR P P E F FFH C M A GREGLVDTAVKT SR SGYLQR CII K H LE G LV IQ YD 1011
Cdd:cd00399 464 KDDYS P E A K GF IRNS FL E G LT P L E Y FFH A M G GREGLVDTAVKT AE SGYLQR RLV K A LE D LV VH YD 528
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
302-645
6.63e-105
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 337.18
E-value: 6.63e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 302 SMFF L DFIV VPP SRY RP INR L GDQM F - TNGQ T VN L QAVM K DAVLIRK LL AVM A QEQKLPC E mteitidkendssgaidrs 380
Cdd:smart00663 1 EWMI L TVLP VPP PCL RP SVQ L DGGR F a EDDL T HL L RDII K RNNRLKR LL ELG A PSIIIRN E ------------------- 61
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 381 flsllpgqsltdklyni WIR LQ SH V NIVF D SDMDKLMLE K ---- YPGIR Q I L EK KEG L FR KHMM GKRVD YA ARSVI C PD M 456
Cdd:smart00663 62 ----------------- KRL LQ EA V DTLI D NEGLPRANQ K sgrp LKSLS Q R L KG KEG R FR QNLL GKRVD FS ARSVI T PD P 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 457 YINT NE I G I P MVF A TK LT Y P QP VTP W N VQE LR QA V I NGP nvh P GA SMV I N ed G SR T A L SAVD atq REAV A KQ L LTPS tgi 536
Cdd:smart00663 125 NLKL NE V G V P KEI A LE LT F P EI VTP L N IDK LR KL V R NGP --- N GA KYI I R -- G KK T N L KLAK --- KSKI A NH L KIGD --- 193
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 537 pkpqgak V V C RHV KN GD IL L L NRQPTLHR P SIQAHR AHI L p E E K VL RL HYAN C KA YNADFDGDEMN A H F PQS ELG RAEA Y 616
Cdd:smart00663 194 ------- I V E RHV ID GD VV L F NRQPTLHR M SIQAHR VRV L - E G K TI RL NPLV C SP YNADFDGDEMN L H V PQS LEA RAEA R 265
330 340
....*....|....*....|....*....
gi 1939159911 617 V L ACTDQQY L V PK D G Q P LA G L IQD HMVSG 645
Cdd:smart00663 266 E L MLVPNNI L S PK N G K P II G P IQD MLLGL 294
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
441-621
4.46e-86
RNA polymerase Rpb1, domain 2; 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, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498
Cd Length: 166
Bit Score: 278.03
E-value: 4.46e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 441 GKRVD YA AR S VI C PD MYINTN E I G I P MV FA TK LT Y P QP VTP W N VQE LRQ A V I NGPNV H PGA SMV I NED G S R TA L SA vdat 520
Cdd:pfam00623 1 GKRVD FS AR T VI S PD PNLKLD E V G V P IS FA KT LT F P EI VTP Y N IKR LRQ L V E NGPNV Y PGA NYI I RIN G A R RD L RY ---- 76
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 521 Q REAVA K Q L LTPST gipkpqgakv V C RHV KN GD IL L L NRQP T LHR P SI QA HR AHI LP e E K VL RL HYANCKA YNADFDGDE 600
Cdd:pfam00623 77 Q KRRLD K E L EIGDI ---------- V E RHV ID GD VV L F NRQP S LHR L SI MG HR VRV LP - G K TF RL NLSVTTP YNADFDGDE 145
170 180
....*....|....*....|.
gi 1939159911 601 MN A H F PQSE LG RAEA YV L ACT 621
Cdd:pfam00623 146 MN L H V PQSE EA RAEA EE L MLV 166
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1206-1712
2.52e-53
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain]
Cd Length: 410
Bit Score: 193.19
E-value: 2.52e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1206 KWQ RSL CD PGE A VG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM VA S a NIKTP mm S VP V F --- NTK K AL 1282
Cdd:cd02584 18 RFN RSL VH PGE M VG TI AAQSIGEP A TQMTLNTFHFAG VSAK NVTLG V PRL K EI IN VA K - NIKTP -- S LT V Y lep GFA K DE 94
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1283 RRV K SLKKQ L TRVC L GE V LQKVD I qesfcmgekqnkfrvyelrfqflpha YY -- QQEKCLRP ED i LH F M E TR F fkl LMEA 1360
Cdd:cd02584 95 EKA K KIQSR L EHTT L KD V TAATE I -------------------------- YY dp DPQNTVIE ED - KE F V E SY F --- EFPD 144
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1361 IKKKNSKA S AF -- R - SVNTRRA T Q K D L D dtedsgrnrreeerdeee EGN I VDAEA EE gdadasdtkrkekqeeevdyese 1437
Cdd:cd02584 145 EDVEQDRL S PW ll R i ELDRKKM T D K K L S ------------------ MEQ I AKKIK EE ----------------------- 183
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1438 eegeeeeeedvqeeeni KGEGAHQTHEP D E eegsgleeessqnpprrhsrpqg AE AMER RI QAVRES ---- HSFIE D YQY 1513
Cdd:cd02584 184 ----------------- FKDDLNVIFSD D N ----------------------- AE KLVI RI RIINDD eeke EDSED D VFL 223
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1514 DTE ES - LWCQV T V K L - PLMKIN F DMSSLVV slahna I V YTTK G IT rcllnetins K NEK E F VL N T E G I NL P E LFKYSE V l 1591
Cdd:cd02584 224 KKI ES n MLSDM T L K G i EGIRKV F IREENKK ------ K V DIET G EF ---------- K KRE E W VL E T D G V NL R E VLSHPG V - 286
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1592 D LR R LY SNDI HAVANTY GIEAA LRVIE KE IKD V FAVY G IA V DP RHL S L VA D Y M CFE G VYKPLN R F GI - QSSSS PL QQMT F 1670
Cdd:cd02584 287 D PT R TT SNDI VEIFEVL GIEAA RKALL KE LRN V ISFD G SY V NY RHL A L LC D V M TQR G HLMAIT R H GI n RQDTG PL MRCS F 366
490 500 510 520
....*....|....*....|....*....|....*....|..
gi 1939159911 1671 E TSFQF L KQ A TMM G SH D E LK SP S ACLVV G KVVKG GTG L F E L K 1712
Cdd:cd02584 367 E ETVDI L LE A AAF G ET D D LK GV S ENIML G QLAPI GTG C F D L L 408
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1180-1711
8.00e-53
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain]
Cd Length: 363
Bit Score: 190.15
E-value: 8.00e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1180 E WAAQAE K S H NRSELSLDRLRTLLQLKWQ RSL CD PGEAVG LL AAQSIGEP S TQMTL N TFH F AG RG E M NVTLG I PRL R EI L 1259
Cdd:cd06528 5 E KLEEVL K E H GLTLSEAEEIIKEVLREYL RSL IE PGEAVG IV AAQSIGEP G TQMTL R TFH Y AG VA E I NVTLG L PRL I EI V 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1260 M v A SANIK TP M M SVPV - FNT K KALRRVKSLKKQLTRVC L GEVLQKVD I Q esfcmgekqnkfr VYEL R FQFLPHAYYQQEK 1338
Cdd:cd06528 85 D - A RKEPS TP T M TIYL e EEY K YDREKAEEVARKIEETT L ENLAEDIS I D ------------- LFNM R ITIELDEEMLEDR 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1339 CLRPE D I lhfmetrffkll ME AI K K KNSKA safrsvntrratqkdlddtedsgrnrreeerdeeeegnivda EA EEGD AD 1418
Cdd:cd06528 151 GITVD D V ------------ LK AI E K LKKGK ------------------------------------------ VG EEGD VT 176
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1419 ASDT K RK E K qeeevdyeseeegeeeeeedvqeeenikgegahqthepdeeegsgleeessqnpprrhsrpqgaeamer R I 1498
Cdd:cd06528 177 LIVL K AE E P --------------------------------------------------------------------- S I 187
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1499 QAV R E shsf IED yqydteeslwcqvtvklplm KI nfdmsslvvsla H N AIVYTT KGI T R cllne T I NS K N E K E F V LN TEG 1578
Cdd:cd06528 188 KEL R K ---- LAE -------------------- KI ------------ L N TKIKGI KGI K R ----- V I VR K E E D E Y V IY TEG 226
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1579 I NL PELF K YSE V l D LR R LYS N D IH AVANTY GIEAA LRV I EK EIK DVFAVY G IA VD P RH LS LVAD Y M CFE G VYKPLN R F GI 1658
Cdd:cd06528 227 S NL KAVL K VEG V - D PT R TTT N N IH EIEEVL GIEAA RNA I IN EIK RTLEEQ G LD VD I RH IM LVAD I M TYD G EVRQIG R H GI 305
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....
gi 1939159911 1659 QSS - S S P L QQMT FE TSFQF L KQ A TMM G SH DEL KSPSACLV VG KVVKG GTG LF EL 1711
Cdd:cd06528 306 AGE k P S V L ARAA FE VTVKH L LD A AVR G EV DEL RGVIENII VG QPIPL GTG DV EL 359
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
430-1015
7.54e-51
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain]
Cd Length: 744
Bit Score: 193.78
E-value: 7.54e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 430 KK E GL -- FRKHMM GKR VDYAA RSV ICP D M Y INT NEIGIP MVF A TK LT YPQP V TP WN VQE L RQAVINGP nvhpgas MVINE 507
Cdd:cd10506 199 KK S GL kw MKDLLL GKR SGHSF RSV VVG D P Y LEL NEIGIP CEI A ER LT VSER V SS WN RER L QEYCDLTL ------- LLKGV 271
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 508 D G S R TA lsavdat Q R EAVAKQLL T PST G ipkpqga K V VC R HVKN GD IL L L NR Q P TL H RP S IQ A HRAHI LP EEK V LRLHYA 587
Cdd:cd10506 272 I G V R RN ------- G R LVGVRSHN T LQI G ------- D V IH R PLVD GD VV L V NR P P SI H QH S LI A LSVKV LP TNS V VSINPL 337
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 588 N C KAYNA DFDGD EMNAHF PQS ELG RAE AYV L ACTDQ Q YLVPKD GQ P L AG L I QD HMVSGAN MT I RG C F FTRE Q YME L VYRG 667
Cdd:cd10506 338 C C SPFRG DFDGD CLHGYI PQS LQA RAE LEE L VALPK Q LISSQS GQ N L LS L T QD SLLAAHL MT E RG V F LDKA Q MQQ L QMLC 417
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 668 LTDKV grvklf PPAI L K PF ---- PLWTGKQ VVST LL inii P E D ytp L NLTG kakigskawvkekprpv P DFD pdsmcesq 743
Cdd:cd10506 418 PSQLP ------ PPAI I K SP psng PLWTGKQ LFQM LL ---- P T D --- L DYSF ----------------- P SNL -------- 459
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 744 V I I RE GEL L c GVLDKAHYGSSAY G LV - HCCYEIYG G ETSG r V L TCLAR L FTAY L QL y RGF TLGVE D ILVKPNA d VM RQ RI 822
Cdd:cd10506 460 V F I SD GEL I - SSSGGSSWLRDSE G NL f SILVKHGP G KALD - F L DSAQG L LCEW L SM - RGF SVSLS D LYLSSDS - YS RQ KM 535
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 823 IEE s TQC G P R AVR aalnlp E A ASCDEIQGK - WQ D AHL G KDQRDFNMI D ------ MKF K EEVN --------- HYSNE I NKA 886
Cdd:cd10506 536 IEE - ISL G L R EAE ------ I A CNIKQLLVD s RK D FLS G SGEENDVSS D verviy ERQ K SAAL sqasvsafk QVFRD I QNL 608
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 887 CMPFGLH rqfp E N N L QM M VQS G A KGS TVNTM Q I S CL LG - Q IE L EG --- R R P ------------- P LMASGKSLP C F E P Y E 949
Cdd:cd10506 609 VYKYASK ---- D N S L LA M IKA G S KGS LLKLV Q Q S GC LG l Q LS L VK lsy R I P rqlscaawnsqks P RVIEKDGSE C T E S Y I 684
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1939159911 950 ftpr AG G F V TGR FL T G IR P P E F F F H CMAG R EGLVDTAVKT sr S G Y L Q R CIIKHLEGLVIQ YD L TVR 1015
Cdd:cd10506 685 ---- PY G V V ESS FL D G LN P L E C F V H SITS R DSSFSSNADL -- P G T L F R KLMFFMRDIYVA YD G TVR 744
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1179-1711
1.51e-49
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 181.02
E-value: 1.51e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1179 Q E WAAQAE K SHNRSELS LD RLRTLLQLKWQ RSL C DPGEAVG LL AAQSIGEP S TQMT LN TFH F AG RG E M NVTLG I PRL R EI 1258
Cdd:TIGR02389 8 K E LEETVK K REISDKEE LD EIIKRVEEEYL RSL I DPGEAVG IV AAQSIGEP G TQMT MR TFH Y AG VA E L NVTLG L PRL I EI 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1259 LM v A SANIK TP M M SVPVF - NTK K ALRRVKSLK K QLTRVC L GE V LQKVD I Q esfcmgekqnkfr VYELRFQFLPHAYYQQ E 1337
Cdd:TIGR02389 88 VD - A RKTPS TP S M TIYLE d EYE K DREKAEEVA K KIEATK L ED V AKDIS I D ------------- LADMTVIIELDEEQLK E 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1338 KCLRPE D I lhfmetrffkll ME AIKK K nskasafrsvntrratq K DLDDT E DS grnrreeerdee EEG N IVDAEAEE g DA 1417
Cdd:TIGR02389 154 RGITVD D V ------------ EK AIKK A ----------------- K LGKVI E ID ------------ MDN N TITIKPGN - PS 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1418 DASDT K R KEK qeeevdyeseeegeeeeeedv QEEEN IKG egahqthepdeeegsgleeessqnpprrhsrpqgaeamerr 1497
Cdd:TIGR02389 192 LKELR K L KEK --------------------- IKNLH IKG ----------------------------------------- 209
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1498 iqavreshsfiedyqydteeslwcqvtvklplmkinfdmsslvvslahnaivyt T KGI T R C llne T I NSKNE k E F V LN TE 1577
Cdd:TIGR02389 210 ------------------------------------------------------ I KGI K R V ---- V I RKEGD - E Y V IY TE 230
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1578 G I NL P E LF K YSE V l D LR R LYS NDIH AV A NTY GIEAA LRV I EK EIK DVFAVY G IA VD P RHL S LVAD Y M CFE G VYKPLN R F G 1657
Cdd:TIGR02389 231 G S NL K E VL K LEG V - D KT R TTT NDIH EI A EVL GIEAA RNA I IE EIK RTLEEQ G LD VD I RHL M LVAD L M TWD G EVRQIG R H G 309
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*
gi 1939159911 1658 I Q - SSS S P L QQMT FE TSFQF L KQ A TMM G SH DELK SPSACLV VG KVVKG GTG LFE L 1711
Cdd:TIGR02389 310 I S g EKA S V L ARAA FE VTVKH L LD A AIR G EV DELK GVIENII VG QPIPL GTG DVD L 364
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1206-1709
2.06e-47
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain]
Cd Length: 300
Bit Score: 172.40
E-value: 2.06e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1206 K WQ R SLCD PG E AVG LL AAQSIGEP S TQMTL N TFHFAG RGE MN V TLG I PR LR EI l MV AS A NI K TP MMSVPVF N TK -- K AL R 1283
Cdd:cd02736 1 K YM R AKVE PG T AVG AI AAQSIGEP G TQMTL K TFHFAG VAS MN I TLG V PR IK EI - IN AS K NI S TP IITAKLE N DR de K SA R 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1284 R VK S lkk QLTRVC LGEV LQKVDI qesfcmgekqnkfrvyelrfqflphayyqqek CLR P E D I lh FME trf F KL LMEA I K K 1363
Cdd:cd02736 80 I VK G --- RIEKTY LGEV ASYIEE -------------------------------- VYS P D D C -- YIL --- I KL DKKI I E K 119
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1364 K nskasafrsvntrratqkdlddtedsgrnrreeerdeeeegnivdaeaeegdadasdtkrkekqeeevdyeseeegeee 1443
Cdd:cd02736 120 L ------------------------------------------------------------------------------- 120
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1444 eeedvqeeenikgegahqthepdeeegsgleeessqnpprrhsrpqgaeamerriqavreshsfiedyqydteeslwcqv 1523
Cdd:cd02736 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1524 tv K L PLMKIN F DMS SL VVS L A h NAI V YTTKGIT R CLL N E tin S K NEKEFV L NT EG IN L PELFKYSE V l DLR R LY SN D I HA 1603
Cdd:cd02736 121 -- Q L SKSNLY F LLQ SL KRK L P - DVV V SGIPEVK R AVI N K --- D K KKGKYK L LV EG YG L RAVMNTPG V - IGT R TT SN H I ME 193
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1604 V ANTY GIEAA LRV I EK EI KDVFAVY G IAV DPRH LS L V AD Y M C F E G VYKPLN RFGI QS - SS S P L QQMT FE TSFQF L KQ A TM 1682
Cdd:cd02736 194 V EKVL GIEAA RST I IN EI QYTMKSH G MSI DPRH IM L L AD L M T F K G EVLGIT RFGI AK m KE S V L MLAS FE KTTDH L FN A AL 273
490 500
....*....|....*....|....*..
gi 1939159911 1683 M G SH D ELKSP S A C LVV GK VVKG GTGLF 1709
Cdd:cd02736 274 H G RK D SIEGV S E C IIM GK PMPI GTGLF 300
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1166-1711
1.16e-45
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 170.03
E-value: 1.16e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1166 VS ET F E K K ID D Y S -------- Q E WAAQA E K s HNRS E LSLDRLRTLLQLKWQ RSL CD PGEAVG LL AAQSIGEP S TQMT LN T 1237
Cdd:PRK04309 3 SE ET L E E K LE D A S lelpqklk E E LREKL E E - RKLT E EEVEEIIEEVVREYL RSL VE PGEAVG VV AAQSIGEP G TQMT MR T 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1238 FH F AG RG E M NVTLG I PRL R EI l MV A SANIK TPMM SVPV ----- FNTK KA lrrv KSLKKQLTRVC L GEVLQKVDIQ esfcm 1312
Cdd:PRK04309 82 FH Y AG VA E I NVTLG L PRL I EI - VD A RKEPS TPMM TIYL kdeya YDRE KA ---- EEVARKIEATT L ENLAKDISVD ----- 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1313 gekqnkfr VYELRFQFLPHAYYQQEKC L RPE D I lhfmetrffkll M EAI K KK N skasafrsvntrratqkd LDDT E DS G r 1392
Cdd:PRK04309 152 -------- LANMTIIIELDEEMLEDRG L TVD D V ------------ K EAI E KK K ------------------ GGEV E IE G - 192
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1393 nrreeerdeeeeg N IVDAEAE E gdadasdtkrkekqeeevdyeseeegeeeeeedvqeeenikgegahqthepdeeegsg 1472
Cdd:PRK04309 193 ------------- N TLIISPK E ---------------------------------------------------------- 201
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1473 leeessqnpprrhsrpqgaeamerriqavreshsfi ED Y Q ydteeslwcqvtvkl P L M K I nfdmsslv VSLAH N AIVYTT 1552
Cdd:PRK04309 202 ------------------------------------ PS Y R --------------- E L R K L -------- AEKIR N IKIKGI 222
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1553 KGI T R cllne T I NS K NEK E F V LN TEG I NL P E LF K YSE V l D LR R LYS N D IH AVANTY GIEAA LRV I EK EIK DVFAVY G IA V 1632
Cdd:PRK04309 223 KGI K R ----- V I IR K EGD E Y V IY TEG S NL K E VL K VEG V - D AT R TTT N N IH EIEEVL GIEAA RNA I IE EIK NTLEEQ G LD V 296
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1633 D P RH LS LVAD Y M CFE G VYKPLN R F G IQ - SSS S P L QQMT FE TSFQF L KQ A TMM G SH DELK SPSACLV VG KVVKG GTG LF EL 1711
Cdd:PRK04309 297 D I RH IM LVAD M M TWD G EVRQIG R H G VS g EKA S V L ARAA FE VTVKH L LD A AVR G EV DELK GVTENII VG QPIPL GTG DV EL 376
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
624-809
5.90e-44
RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507
Cd Length: 158
Bit Score: 157.02
E-value: 5.90e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 624 QY L V P KD G Q P LA G LI QD HMVSGANM T IRGC FF T RE QY M E L VYR G ltdkvgr VK L FP PAILKP F - PLWTGKQ VV S T LL I N i 702
Cdd:pfam04983 1 NI L S P QN G K P II G PS QD MVLGAYLL T REDT FF D RE EV M Q L LMY G ------- IV L PH PAILKP I k PLWTGKQ TF S R LL P N - 72
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 703 ipedyt PL N LT GK A K IGS kawvkekprpvpdf DPDSMCE S Q V I I RE GEL LC GV L DK AHY G S S AYG L V H CC Y EI YG G E TSG 782
Cdd:pfam04983 73 ------ EI N PK GK P K TNE -------------- EDLCEND S Y V L I NN GEL IS GV I DK KTV G K S LGS L I H II Y KE YG P E ETA 132
170 180
....*....|....*....|....*..
gi 1939159911 783 RV L TC L AR L FTA YL QLY r GF TL G VE DI 809
Cdd:pfam04983 133 KF L DR L QK L GFR YL TKS - GF SI G ID DI 158
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
428-1259
6.62e-41
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain]
Cd Length: 1140
Bit Score: 165.61
E-value: 6.62e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 428 L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L typqp VT P WNVQE L - RQAVI ng P N VHPGAS M VIN 506
Cdd:TIGR02386 313 L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPELKMYQC G L P KKM A LE L ----- FK P FIIKR L i DRELA -- A N IKSAKK M IEQ 385
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 507 ED gsrtal SA V - D AT qr E A V A K Q lltpstgip K P qgakvvcrhvkngdi L LLNR Q PTLHR PS IQA HRA h I L P E E K VL RLH 585
Cdd:TIGR02386 386 ED ------ PE V w D VL -- E D V I K E --------- H P --------------- V LLNR A PTLHR LG IQA FEP - V L V E G K AI RLH 432
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 586 YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V PKDG Q P LAGLI QD hmvsgan M TI r G CF ftreq Y MELVY 665
Cdd:TIGR02386 433 PLV C T A F NADFDGD Q M AV H V P L S PEAQ AEA RA L MLASNNI L N PKDG K P IVTPS QD ------- M VL - G LY ----- Y LTTEK 499
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 666 R G ltd KV G RV K L F ppailkpfplwtgkqvv S TLLIN I IPE D YTPLN L TGKAKIGSKAWVK E KP ------- RPV P DFD P ds 738
Cdd:TIGR02386 500 P G --- AK G EG K I F ----------------- S NVDEA I RAY D NGKVH L HALIGVRTSGEIL E TT vgrvifn EIL P EGF P -- 557
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 739 mcesqv I I REG E llcg V L D K AHYG S sayg L VHCC YE IY G G E TSGRV L TCLAR L FTA Y LQLY r G F T LGVE DI L V KPN advm 818
Cdd:TIGR02386 558 ------ Y I NDN E ---- P L S K KEIS S ---- L IDLL YE VH G I E ETAEM L DKIKA L GFK Y ATKS - G T T ISAS DI V V PDE ---- 618
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 819 RQR I IE E STQ cgpravraalnlpeaa SCDE IQ GKWQDAHLGKDQ R DFNMIDM -- KF K EE V NH - YSNEIN K acmpfglh RQ 895
Cdd:TIGR02386 619 KYE I LK E ADK ---------------- EVAK IQ KFYNKGLITDEE R YRKVVSI ws ET K DK V TD a MMKLLK K -------- DT 674
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 896 FPE N NLQ MM VQ SGA K G STVNTM Q ISCLL G qielegrrpp LMA -- SG KSLP cfepyef T P raggf VTGR F LT G IRPP E F F F 973
Cdd:TIGR02386 675 YKF N PIF MM AD SGA R G NISQFR Q LAGMR G ---------- LMA kp SG DIIE ------- L P ----- IKSS F RE G LTVL E Y F I 732
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 974 HCMAG R E GL V DTA V KT SR SGYL Q R ciikhle G LV - IQY D LT VR DS D - G S vvqflyg E D G LDI pktqflqpkqfpflasny 1051
Cdd:TIGR02386 733 STHGA R K GL A DTA L KT AD SGYL T R ------- R LV d VAQ D VV VR EE D c G T ------- E E G IEV ------------------ 780
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1052 E V I MKS K H l HEVL S RA D pq KVLRHFR A IKKWH hrhssallrkgaflsfsqkiqaavkalnlegktqngrs P E T QQMLQMW 1131
Cdd:TIGR02386 781 E A I VEG K D - EIIE S LK D -- RIVGRYS A EDVYD -------------------------------------- P D T GKLIAEA 819
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1132 HE L deqsrrkyqkraapcpdpslsvwrpdihfas VS E TFEK KI D dysqew AAQA EK SHN RS E L SLDRLRTLL Q LKWQ R S L 1211
Cdd:TIGR02386 820 NT L ------------------------------- IT E EIAE KI E ------ NSGI EK VKV RS V L TCESEHGVC Q KCYG R D L 862
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 1939159911 1212 C ----- DP GEAVG LL AAQSIGEP S TQ M T LN TFH --- F AG RGE m NV T L G I PR LR E IL 1259
Cdd:TIGR02386 863 A tgklv EI GEAVG VI AAQSIGEP G TQ L T MR TFH tgg V AG ASG - DI T Q G L PR VK E LF 917
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
427-997
9.91e-38
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain]
Cd Length: 659
Bit Score: 152.29
E-value: 9.91e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 427 I L EK K E G L FR KHMM GKRVDY AA RSVI C -- P DMYIN tn EI G I P MVF A TK L typqp VT P WNVQ EL rqa VIN G -- PN VHPGAS 502
Cdd:cd01609 235 M L KG K Q G R FR QNLL GKRVDY SG RSVI V vg P ELKLH -- QC G L P KEM A LE L ----- FK P FVIR EL --- IER G la PN IKSAKK 304
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 503 M VINE D gsrtalsavdatqr EA V AKQ L ltpstgipkpqg AK V VCR H V kngdi L LLNR Q PTLHR PS IQA HRA h I L P E E K VL 582
Cdd:cd01609 305 M IERK D -------------- PE V WDI L ------------ EE V IKG H P ----- V LLNR A PTLHR LG IQA FEP - V L I E G K AI 352
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 583 R LH YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA Y VL ACTDQQY L V P KD G Q P LAGLI QD h MV S ganmtir G CF ftreq Y ME 662
Cdd:cd01609 353 Q LH PLV C T A F NADFDGD Q M AV H V P L S LEAQ AEA R VL MLSSNNI L S P AS G K P IVTPS QD - MV L ------- G LY ----- Y LT 419
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 663 LVYR G LTDK ------ VGRV klfppailkpfplwtgkqvvst LLIN I I PE DYTPL N L T - G K AKIGS kawvkekprpvpdfd 735
Cdd:cd01609 420 KERK G DKGE giiett VGRV ---------------------- IFNE I L PE GLPFI N K T l K K KVLKK --------------- 462
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 736 pdsmcesqv I I R E gellcgvldkahygssayglvhc CY EI YG G E TSGRV L TCLAR L ftaylqlyr GF -------- TLGVE 807
Cdd:cd01609 463 --------- L I N E ----------------------- CY DR YG L E ETAEL L DDIKE L --------- GF kyatrsgi SISID 501
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 808 DI L V K P N advm RQR II E E STQ cgpravraalnlpeaa SCD EI QGKWQDAH L GKDQ R DFNM I D -- MKFK E E V nhy SNEIN K 885
Cdd:cd01609 502 DI V V P P E ---- KKE II K E AEE ---------------- KVK EI EKQYEKGL L TEEE R YNKV I E iw TEVT E K V --- ADAMM K 558
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 886 AC mpfglh RQF P E N NLQ MM VQ SGA K GS TVNTM Q ISCLL G qielegrrpp LMA -- SGK SLP cfepyef T P raggf VTGR F L 963
Cdd:cd01609 559 NL ------ DKD P F N PIY MM AD SGA R GS KSQIR Q LAGMR G ---------- LMA kp SGK IIE ------- L P ----- IKSN F R 610
570 580 590
....*....|....*....|....*....|....
gi 1939159911 964 T G IRPP E F F FHCMAG R E GL V DTA V KT SR SGYL Q R 997
Cdd:cd01609 611 E G LTVL E Y F ISTHGA R K GL A DTA L KT AD SGYL T R 644
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1187-1707
3.01e-35
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 142.64
E-value: 3.01e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1187 K SHNRS ELS L D RLRTL L QL --- KWQ R SLC DP G EAVG LL AAQSIGEP S TQMT LN TFH F AG RG EMNVTLG I PRL R EI l MV A S 1263
Cdd:PRK14897 151 K AMKKK ELS D D EYEEI L RR ire EYE R ARV DP Y EAVG IV AAQSIGEP G TQMT MR TFH Y AG VA EMNVTLG L PRL I EI - VD A R 229
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1264 ANIK TP M M SVPV fnt KK AL R ---- R V KSLK K QLTRVC L GE V LQKV - DI Q E s FCMGEKQNKFRV yelrfqflphayyq Q E K 1338
Cdd:PRK14897 230 KKPS TP T M TIYL --- KK DY R edee K V REVA K KIENTT L ID V ADII t DI A E - MSVVVELDEEKM -------------- K E R 291
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1339 CLRPE DI lhfmetrffkll ME AI K K KNS K A safrsvntrratqkdlddtedsgrnrreeerdeeeegnivd A E AE egdad 1418
Cdd:PRK14897 292 LIEYD DI ------------ LA AI S K LTF K T ----------------------------------------- V E ID ----- 313
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1419 a SDTK R KEK Q eeevdyeseeegeeeeeedvqeeenikgegahqth E P deeegsgleeessqnpprrhsrpqgaeamerri 1498
Cdd:PRK14897 314 - DGII R LKP Q ----------------------------------- Q P --------------------------------- 324
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1499 qavresh SF IED Y Q yd TE E SL wcqvt VK L PLMK I nfdmsslvvslahnaivytt KGI T R CLLNE tin SKN E KEF V LN T E G 1578
Cdd:PRK14897 325 ------- SF KKL Y L -- LA E KV ----- KS L TIKG I -------------------- KGI K R AIARK --- END E RRW V IY T Q G 367
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1579 I NL PELFKYS EV l D LR R L Y S NDI HAV A NTY GIEAA LRV I EK E I K DVFAVY G IA VD P RH LS LVAD Y M C F E G VY K PLN R F GI 1658
Cdd:PRK14897 368 S NL KDVLEID EV - D PT R T Y T NDI IEI A TVL GIEAA RNA I IH E A K RTLQEQ G LN VD I RH IM LVAD M M T F D G SV K AIG R H GI 446
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1659 QS - S SS P L QQMT FE TSFQF L KQ A TMM G SH D E L KSPSACLV VG KVVKG GTG 1707
Cdd:PRK14897 447 SG e K SS V L ARAA FE ITGKH L LR A GIL G EV D K L AGVAENII VG QPITL GTG 496
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
401-1242
3.80e-32
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 137.75
E-value: 3.80e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 401 LQ SH V NIV FD SDMDKLMLE --- K Y P -- GIRQ I LEK K E G L FR KHMM GKRVD YAA RSVI CPDMYINTN E I G I P MVF A TK L TY 475
Cdd:PRK09603 1688 LQ EA V DVL FD NGRSTNAVK gan K R P lk SLSE I IKG K Q G R FR QNLL GKRVD FSG RSVI VVGPNLKMD E C G L P KNM A LE L FK 1767
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 476 P QPVTP wnvqelrqavingpnvhpgasmv IN E D G SR T A L S avdat Q REAVAK Q lltpstgip K PQGAKVVCRHVKN G DIL 555
Cdd:PRK09603 1768 P HLLSK ----------------------- LE E R G YA T T L K ----- Q AKRMIE Q --------- K SNEVWECLQEITE G YPV 1810
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 556 LLNR Q PTLH RP SIQA HRAHIL p EE K VLR LH YAN C K A Y NADFDGD E M NA H F P Q S ELGR AE AY VL ACTDQQY L V P KD G QPL A 635
Cdd:PRK09603 1811 LLNR A PTLH KQ SIQA FHPKLI - DG K AIQ LH PLV C S A F NADFDGD Q M AV H V P L S QEAI AE CK VL MLSSMNI L L P AS G KAV A 1889
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 636 GLI QD h MV S G A nmtirgcfftre Q Y ME L VYR G LT dkv G RV KLF PPAILKPFPLW T GKQVVSTLLINI ip EDYTPLNLT - G 714
Cdd:PRK09603 1890 IPS QD - MV L G L ------------ Y Y LS L EKS G VK --- G EH KLF SSVNEIITAID T KELDIHAKIRVL -- DQGNIIATS a G 1951
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 715 KAK I G S K awvkekprp V PDF D P DSMCES qviiregellcg VLD K AHY G S sayg LV HCCYEIY G GETSGRV L TC L AR L FTA 794
Cdd:PRK09603 1952 RMI I K S I --------- L PDF I P TDLWNR ------------ PMK K KDI G V ---- LV DYVHKVG G IGITATF L DN L KT L GFR 2006
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 795 Y l QLYR G FTLGV EDI LVKPN advm R Q RII E ESTQ cgpravraalnlpeaa SCDE IQ GKW q D AH L GK DQ RDF N M I d MKFKE 874
Cdd:PRK09603 2007 Y - ATKA G ISISM EDI ITPKD ---- K Q KMV E KAKV ---------------- EVKK IQ QQY - D QG L LT DQ ERY N K I - IDTWT 2063
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 875 EVN hys NEIN K AC M PFGLHRQFPE N NLQ MM VQ SGA K GS TVNTM Q I S CLL G qielegrrpp LM AS gksl P CFEPY E f TP ra 954
Cdd:PRK09603 2064 EVN --- DKMS K EM M TAIAKDKEGF N SIY MM AD SGA R GS AAQIR Q L S AMR G ---------- LM TK ---- P DGSII E - TP -- 2123
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 955 ggf VTGR F LT G IRPP E F F FHCMAG R E GL V DTA V KT SRS GYL Q R CI I K hlegl V I Q YDLT V R D SD G S vvqflyg ED G LD I P 1034
Cdd:PRK09603 2124 --- IISN F KE G LNVL E Y F NSTHGA R K GL A DTA L KT ANA GYL T R KL I D ----- V S Q NVKV V S D DC G T ------- HE G IE I T 2188
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1035 K ---- TQFLQ P KQ fpflasny E V I MKSKH L HE V L sra DP QK vlrhfraikkwhhrh SSA LL RKGAFL -- SFSQ K I - Q A AV 1107
Cdd:PRK09603 2189 D iavg SELIE P LE -------- E R I FGRVL L ED V I --- DP IT --------------- NEI LL YADTLI de EGAK K V v E A GI 2242
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1108 K ALNL egktqng R S P E T Q qmlqmwheldeqsrr K YQ K RA - A P C PDPS L S vwrpdihfasvsetf E K K iddysqewaaqae 1186
Cdd:PRK09603 2243 K SITI ------- R T P V T C --------------- K AP K GV c A K C YGLN L G --------------- E G K ------------- 2272
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 1939159911 1187 kshnrselsldrlrtllqlkwqrs LCD PGEAVG LL AAQSIGEP S TQ M TL N TFH FA G 1242
Cdd:PRK09603 2273 ------------------------ MSY PGEAVG VV AAQSIGEP G TQ L TL R TFH VG G 2304
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
431-997
9.70e-32
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain]
Cd Length: 1165
Bit Score: 135.67
E-value: 9.70e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 431 K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq AVIN gpnvhpgas MVINEDGS 510
Cdd:COG0086 324 K Q G R FR QNLL GKRVDY SG RSVI VVGPELKLHQC G L P KKM A LE L FK P ------------- FIYR --------- KLEERGLA 381
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 511 R T AL SA VDATQ RE avakqlltpstgip K P QGAKVVCRHV K NGDI LL l NR Q PTLHR PS IQA HRA h I L P E E K VLR LH YAN C K 590
Cdd:COG0086 382 T T IK SA KKMVE RE -------------- E P EVWDILEEVI K EHPV LL - NR A PTLHR LG IQA FEP - V L I E G K AIQ LH PLV C T 445
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 591 A Y NADFDGD E M NA H F P Q S ELGRA EA YV L ACTDQQY L V P KD G Q P LAGLI QD h MV S G AN - M T I ------- R G CF F TREQYME 662
Cdd:COG0086 446 A F NADFDGD Q M AV H V P L S LEAQL EA RL L MLSTNNI L S P AN G K P IIVPS QD - MV L G LY y L T R eregakg E G MI F ADPEEVL 524
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 663 LV Y R - G LT D KVG R V K LFPPAILKP fplw T GK Q V VS T --- L L I N - I I P EDYTPL N - LTG K AK I G skawvkekprpvpdfdp 736
Cdd:COG0086 525 RA Y E n G AV D LHA R I K VRITEDGEQ ---- V GK I V ET T vgr Y L V N e I L P QEVPFY N q VIN K KH I E ----------------- 583
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 737 dsmcesq VIIR E gellcgvldkahygssayglvhc C Y EIY G GETSGRV L TC L AR L ft AYLQLY R - G FTL G VE D IL V KPN a 815
Cdd:COG0086 584 ------- VIIR Q ----------------------- M Y RRC G LKETVIF L DR L KK L -- GFKYAT R a G ISI G LD D MV V PKE - 630
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 816 dvm R Q R I I EE ST qcgp RA V raalnlpeaasc D EI QGKWQDAHLGKDQ R DFNM ID mkfke EVNHY S N E INKAC M P f GLHR Q 895
Cdd:COG0086 631 --- K Q E I F EE AN ---- KE V ------------ K EI EKQYAEGLITEPE R YNKV ID ----- GWTKA S L E TESFL M A - AFSS Q 685
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 896 fpe N NLQ MM VQ SGA K GS T vntmqiscll G Q IE - L E G R R p P LMA -- SG kslpcf EPY E f TP ----- R A G gfvtgrfl T G IR 967
Cdd:COG0086 686 --- N TTY MM AD SGA R GS A ---------- D Q LR q L A G M R - G LMA kp SG ------ NII E - TP igsnf R E G -------- L G VL 736
570 580 590
....*....|....*....|....*....|
gi 1939159911 968 pp E F F FHCMAG R E GL V DTA V KT SR SGYL Q R 997
Cdd:COG0086 737 -- E Y F ISTHGA R K GL A DTA L KT AD SGYL T R 764
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
428-1261
2.44e-29
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 128.07
E-value: 2.44e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 428 L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L T yp Q P VTPWNVQ EL RQ A V ingp N V hpgasmvine 507
Cdd:PRK14906 409 L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPHLKLHQC G L P SAM A LE L F -- K P FVMKRLV EL EY A A ---- N I ---------- 472
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 508 dgs RT A LS AVD atqreavakqlltpstgipkp Q GA KV V --- CRH V KNGDIL LLNR Q PTLHR PS IQA HRA h I L P E E K VLR L 584
Cdd:PRK14906 473 --- KA A KR AVD --------------------- R GA SY V wdv LEE V IQDHPV LLNR A PTLHR LG IQA FEP - V L V E G K AIK L 527
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 585 H YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA Y VL ACTDQQYLV P KD G Q PL AGLI QD hmvsgan M T I RGCFF T R E qymelv 664
Cdd:PRK14906 528 H PLV C T A F NADFDGD Q M AV H V P L S TQAQ AEA R VL MLSSNNIKS P AH G R PL TVPT QD ------- M I I GVYYL T T E ------ 594
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 665 y R GLTDKV GR VKLFPPAI L KPFPLWTGKQVVSTLLIN i IPE D Y T PLNLT G KAKIGSKAWVK E KPRPVPD F D pdsmces QV 744
Cdd:PRK14906 595 - R DGFEGE GR TFADFDDA L NAYDARADLDLQAKIVVR - LSR D M T VRGSY G DLEETKAGERI E TTVGRII F N ------- QV 665
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 745 IIREGEL L CGVLD K AHY G S sayg LV HC C YEI Y GGETSGRV L TCLARLFTA Y LQL y R G F T LG V E D ILVKPNAD vmrq R I IE 824
Cdd:PRK14906 666 LPEDYPY L NYKMV K KDI G R ---- LV ND C CNR Y STAEVEPI L DGIKKTGFH Y ATR - A G L T VS V Y D ATIPDDKP ---- E I LA 736
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 825 E ST qcgpravraalnlpea ASCDE I QGKWQ D AH L GKDQ R DFNMI D M kfkee VNHYSN E INK A cmpfg LHRQ F P E N N - LQ M 903
Cdd:PRK14906 737 E AD ---------------- EKVAA I DEDYE D GF L SERE R HKQVV D I ----- WTEATE E VGE A ----- MLAG F D E D N p IY M 790
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 904 M VQ SGA K G STVNTM Q ISCLL G qielegrrpp LMA SG K SLPCFE P yeftpraggf VTGR F LT G IRPP E F F FHCMAG R E GLV 983
Cdd:PRK14906 791 M AD SGA R G NIKQIR Q LAGMR G ---------- LMA DM K GEIIDL P ---------- IKAN F RE G LSVL E Y F ISTHGA R K GLV 850
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 984 DTA VK T SR SGYL Q R CIIK hleglv IQY D LT VR DS D - G S vvqflyg ED G LDI P ktq FLQ PK qfpfla SNYEVIMKSKH L H E 1062
Cdd:PRK14906 851 DTA LR T AD SGYL T R RLVD ------ VAQ D VI VR EE D c G T ------- DE G VTY P --- LVK PK ------ GDVDTNLIGRC L L E 908
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1063 VLSRAD pqkvlrhfraikkwhhrh SSA LL RK G AFLSFSQKIQAA V K A lnlegktqn G RSPETQQM L QMW H elde QSRRKY 1142
Cdd:PRK14906 909 DVCDPN ------------------ GEV LL SA G DYIESMDDLKRL V E A --------- G VTKVQIRT L MTC H ---- AEYGVC 957
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1143 QK raap C PDPS L SVW RP dihfasvsetfekkiddysqewaaqaekshnrselsldrlrtllqlkwqrsl CDP G E AVG LL A 1222
Cdd:PRK14906 958 QK ---- C YGWD L ATR RP ---------------------------------------------------- VNI G T AVG II A 981
810 820 830
....*....|....*....|....*....|....*....
gi 1939159911 1223 AQSIGEP S TQ M T LN TFH FA G RGEMNV T L G I PR LR E ILMV 1261
Cdd:PRK14906 982 AQSIGEP G TQ L T MR TFH SG G VAGDDI T Q G L PR VA E LFEA 1020
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
431-1258
4.44e-28
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 124.02
E-value: 4.44e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 431 K E G L FR KHMM GKRVDY AA RSVI C -- P D -- MY intn EI G I P MVF A TK L typqp VT P WNVQE L RQ avingpnv HPG A SMV in 506
Cdd:PRK00566 324 K Q G R FR QNLL GKRVDY SG RSVI V vg P E lk LH ---- QC G L P KKM A LE L ----- FK P FIMKK L VE -------- RGL A TTI -- 384
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 507 edgs RT A LSA V DA t QREA V AKQ L ltpstgipkpqg AK V VCR H V kngdi L LLNR Q PTLHR PS IQA HRA h I L P E E K VLR LH Y 586
Cdd:PRK00566 385 ---- KS A KKM V ER - EDPE V WDV L ------------ EE V IKE H P ----- V LLNR A PTLHR LG IQA FEP - V L I E G K AIQ LH P 441
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 587 AN C K A Y NADFDGD E M NA H F P Q S ELGR AEA Y VL ACTDQQY L V P KD G Q P LAGLI QD h MV S G AN - M T I ------- R G CF F TRE 658
Cdd:PRK00566 442 LV C T A F NADFDGD Q M AV H V P L S LEAQ AEA R VL MLSSNNI L S P AN G K P IIVPS QD - MV L G LY y L T R eregakg E G MV F SSP 520
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 659 QYMELV Y R ---- G L TDKV g R V KL fppailkpfplw T G K QV V S T ---- LLI N - I I PE DYTPL N LT --- G K AK I GS kawvke 726
Cdd:PRK00566 521 EEALRA Y E ngev D L HARI - K V RI ------------ T S K KL V E T tvgr VIF N e I L PE GLPFI N VN kpl K K KE I SK ------ 581
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 727 kprpvpdfdpdsmcesqviiregellcgvldkahygssayg LVHCC Y EI YG GETSGRV L TCLAR L ftaylqlyr GF ---- 802
Cdd:PRK00566 582 ----------------------------------------- IINEV Y RR YG LKETVIF L DKIKD L --------- GF kyat 611
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 803 ---- TL G VE DI LVK P N advm RQR IIEE STQ cgpravraalnlp E A asc D EI QGKWQDAHLGKDQ R DFNM ID -- M K FKE EV 876
Cdd:PRK00566 612 rsgi SI G ID DI VIP P E ---- KKE IIEE AEK ------------- E V --- A EI EKQYRRGLITDGE R YNKV ID iw S K ATD EV 671
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 877 nhy SNEIN K A c MP fgl HR Q FPE N NLQ MM VQ SGA K G stv NTM QI SC L L G qie LE G rrpp LMA -- SG KSLP cfepyef TP ra 954
Cdd:PRK00566 672 --- AKAMM K N - LS --- KD Q ESF N PIY MM AD SGA R G --- SAS QI RQ L A G --- MR G ---- LMA kp SG EIIE ------- TP -- 725
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 955 ggf VTGR F LT G IRPP E F F F -- H cma G - R E GL V DTA V KT SR SGYL Q R -------- C I IKH ----- LE G LVI qydl T VRDSD 1018
Cdd:PRK00566 726 --- IKSN F RE G LTVL E Y F I st H --- G a R K GL A DTA L KT AD SGYL T R rlvdvaqd V I VRE ddcgt DR G IEV ---- T AIIEG 795
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1019 G S V V ---- QFLY G ---- ED GL D i P K T Q flqpkqfpflasny EVI MKSKH L hevlsr A D PQKV lrhfraikkwhhrhssal 1090
Cdd:PRK00566 796 G E V I eple ERIL G rvla ED VV D - P E T G -------------- EVI VPAGT L ------ I D EEIA ------------------ 836
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1091 lrkgaflsfs Q KI QA A ---- VK A lnlegktqng RS PE T qqmlqmwheldeqsrrkyqkraap C pdpslsvwrpdihfasv 1166
Cdd:PRK00566 837 ---------- D KI EE A giee VK I ---------- RS VL T ------------------------ C ----------------- 855
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1167 setfekkiddysqewaaqae KSHN -------- R S e L S ldrlrtllqlkw QRS L CDP GEAVG LL AAQSIGEP S TQ M T LN TF 1238
Cdd:PRK00566 856 -------------------- ETRH gvcakcyg R D - L A ------------ TGK L VNI GEAVG VI AAQSIGEP G TQ L T MR TF 902
890 900
....*....|....*....|
gi 1939159911 1239 H FA G rge MNV T L G I PR LR E I 1258
Cdd:PRK00566 903 H TG G --- VDI T G G L PR VA E L 919
rpoC1
CHL00018 RNA polymerase beta' subunit
427-645
2.36e-27
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 120.01
E-value: 2.36e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 427 IL E K KEG L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq A VI N G pnvhpgasm V I N 506
Cdd:CHL00018 359 VI E G KEG R FR ENLL GKRVDY SG RSVI VVGPSLSLHQC G L P REI A IE L FQ P ------------- F VI R G --------- L I R 416
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 507 EDGSRTAL savdatqrea V AK QLLTPSTG I PKP qgakv VCRH V KN G DIL LLNR Q PTLHR PS IQA HRA h IL P E EKVLR LH Y 586
Cdd:CHL00018 417 QHLASNIR ---------- A AK SKIREKEP I VWE ----- ILQE V MQ G HPV LLNR A PTLHR LG IQA FQP - IL V E GRAIC LH P 480
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 1939159911 587 AN CK AY NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V P KD G Q P LAGLI QD h M VS G 645
Cdd:CHL00018 481 LV CK GF NADFDGD Q M AV H V P L S LEAQ AEA RL L MFSHMNL L S P AI G D P ISVPS QD - M LL G 538
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
851-958
3.67e-26
RNA polymerase Rpb1, domain 4; 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, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598
Cd Length: 108
Bit Score: 104.37
E-value: 3.67e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 851 GK WQ D AHLGKDQRD F NMIDMKFKEEVNHYSNE I NKACMP fglhrqf P E N NLQ MM VQ SGAKGS TV N TM QI SCLL GQ IEL EG 930
Cdd:pfam05000 8 GK LE D IWGMTLEES F EALINNILNKARDPAGN I ASKSLD ------- P N N SIY MM AD SGAKGS II N IS QI AGCR GQ QNV EG 80
90 100
....*....|....*....|....*...
gi 1939159911 931 R R P P LMA SG KS LP C F EPYEFT P RAG GFV 958
Cdd:pfam05000 81 K R I P FGF SG RT LP H F KKDDEG P ESR GFV 108
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1600-1708
4.30e-24
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain]
Cd Length: 158
Bit Score: 100.18
E-value: 4.30e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1600 D IH AVANTY GIEAA LRV I EK EI KD V F A VY G IA VD P RH LS L V AD Y M CFE G VYKPLN R F G - IQ S SS SPL QQMT FE TSFQF L K 1678
Cdd:cd00630 49 S IH EMLEAL GIEAA RET I IR EI QK V L A SQ G VS VD R RH IE L I AD V M TYS G GLRGVT R S G f RA S KT SPL MRAS FE KTTKH L L 128
90 100 110
....*....|....*....|....*....|
gi 1939159911 1679 Q A TMM G SH DEL KSP S ACLVV G KVVKG GTG L 1708
Cdd:cd00630 129 D A AAA G EK DEL EGV S ENIIL G RPAPL GTG S 158
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
379-1009
5.46e-24
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 110.87
E-value: 5.46e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 379 R SF LSL L P GQSL tdk LY N IWIR LQ SH V NIV FD SDMDKLMLE K Y ------ PG I RQI L EK K E G L FR KHMM GKRVDY AA RSVI 452
Cdd:PRK14844 1712 R KL LSL N P PEIM --- IR N EKRM LQ EA V DSL FD NSRRNALVN K A gavgyk KS I SDM L KG K Q G R FR QNLL GKRVDY SG RSVI 1788
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 453 CPDMYINT N EI G I P MVF A TK L TY P QPVTPWNVQEL rqavin G P NVHPGASMVIN E dgsrtalsavdatqreavakqlltp 532
Cdd:PRK14844 1789 VVGPTLKL N QC G L P KRM A LE L FK P FVYSKLKMYGM ------ A P TIKFASKLIRA E ------------------------- 1837
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 533 stgip KP QGAKVVCRHV K NGDI LL l NR Q PTLHR PS IQA HRA h IL P E E K VLR LH YAN C K A Y NADFDGD E M NA H F P Q S ELGR 612
Cdd:PRK14844 1838 ----- KP EVWDMLEEVI K EHPV LL - NR A PTLHR LG IQA FEP - IL I E G K AIQ LH PLV C T A F NADFDGD Q M AV H V P I S LEAQ 1910
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 613 A EA Y VL ACTDQQY L V P KD G Q P L agliqdh M V SGANMTIRGCFF T REQYM E lvyrgltdkvgrvklfppail KPF P LWTGK 692
Cdd:PRK14844 1911 L EA R VL MMSTNNV L S P SN G R P I ------- I V PSKDIVLGIYYL T LQEPK E --------------------- DDL P SFGAF 1962
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 693 QV V STL L IN iipedytplnlt G KAK I G S K aw V K EKPRPVP df DPDSMCESQVIIRE G E L LCGVLDKA H ygssayglvhcc 772
Cdd:PRK14844 1963 CE V EHS L SD ------------ G TLH I H S S -- I K YRMEYIN -- SSGETHYKTICTTP G R L ILWQIFPK H ------------ 2014
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 773 y E IY G GETSGR VLT cl ARLF T AYLQ L - YR -- G FTLG V E dilvkp NA D VMRQRII E ES T QC G PRAV R AALNL PE -- A ASC D 847
Cdd:PRK14844 2015 - E NL G FDLINQ VLT -- VKEI T SIVD L v YR nc G QSAT V A ------ FS D KLMVLGF E YA T FS G VSFS R CDMVI PE tk A THV D 2085
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 848 EIQ G ------- KW QD AHLGKDQ R DFNM ID m KFKEEVNHYS N EIN KA CMPFGLHRQF pe N NLQ MMV Q SGA K GST VNTM Q IS 920
Cdd:PRK14844 2086 HAR G eikkfsm QY QD GLITRSE R YNKV ID - EWSKCTDMIA N DML KA ISIYDGNSKY -- N SVY MMV N SGA R GST SQMK Q LA 2162
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 921 CLL G qielegrrpp LM AS gksl P CF E PY E f TP raggf VTGR F LT G IRPP E F F FHCMAG R E GL V DTA V KT SR SGYL ----- 995
Cdd:PRK14844 2163 GMR G ---------- LM TK ---- P SG E II E - TP ----- IISN F RE G LNVF E Y F NSTHGA R K GL A DTA L KT AN SGYL trrlv 2222
650 660
....*....|....*....|..
gi 1939159911 996 --- Q R CI I ----- K HLE GLV IQ 1009
Cdd:PRK14844 2223 dvs Q N CI V tkhdc K TKN GLV VR 2244
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1215-1263
9.69e-24
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain]
Cd Length: 158
Bit Score: 99.41
E-value: 9.69e-24
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1939159911 1215 GEAVG L LAAQSIGEP S TQMTL N TFHFAG RGE MNVTLG I PRL R EIL MV AS 1263
Cdd:cd00630 1 GEAVG V LAAQSIGEP G TQMTL R TFHFAG VAS MNVTLG L PRL K EIL NA AS 49
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1554-1712
6.63e-23
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 106.52
E-value: 6.63e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1554 GI T R C L LNET i NSK N EK E F VL N T E G I NL P E L FK Y s E VL D LR R LYS N D I HAVANTY GIEAA LRV I EK E IKDVFAVY G IA VD 1633
Cdd:PRK14898 690 GI E R V L VKKE - EHE N DE E Y VL Y T Q G S NL R E V FK I - E GV D TS R TTT N N I IEIQEVL GIEAA RNA I IN E MMNTLEQQ G LE VD 767
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1634 P RHL S LVAD Y M CFE G VY KP LN R F G IQ - SSS S P L QQMT FE TSFQF L KQ A TMM G SH D E LK SPSACLV VGK VV K G GTG LFE L K 1712
Cdd:PRK14898 768 I RHL M LVAD I M TAD G EV KP IG R H G VA g EKG S V L ARAA FE ETVKH L YD A AEH G EV D K LK GVIENVI VGK PI K L GTG CVD L R 847
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
427-646
8.96e-23
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 105.22
E-value: 8.96e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 427 I L E K K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L typqp VT P WNVQE L - RQ AVI N gp N VHPGASMVI 505
Cdd:PRK02625 338 I I E G K Q G R FR QNLL GKRVDY SG RSVI VVGPKLKMHQC G L P KEM A IE L ----- FQ P FVIHR L i RQ GIV N -- N IKAAKKLIQ 410
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 506 NE D gsrtalsavdatqreavakqlltpstgipk P QGAK V V c RH V KN G DIL LLNR Q PTLHR PS IQA HRA h IL P E EKVLR LH 585
Cdd:PRK02625 411 RA D ------------------------------ P EVWQ V L - EE V IE G HPV LLNR A PTLHR LG IQA FEP - IL V E GRAIQ LH 458
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1939159911 586 YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V P KD G Q P LAGLI QD h MV S G A 646
Cdd:PRK02625 459 PLV C P A F NADFDGD Q M AV H V P L S LEAQ AEA RL L MLASNNI L S P AT G E P IVTPS QD - MV L G C 518
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1215-1259
7.84e-12
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain]
Cd Length: 204
Bit Score: 66.40
E-value: 7.84e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 1939159911 1215 GEAVG LL AAQSIGEP S TQ M T LN TFH FA G RGE m NV T L G I PR LR E IL 1259
Cdd:cd02655 6 GEAVG II AAQSIGEP G TQ L T MR TFH TG G VAT - DI T Q G L PR VE E LF 49
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
21-90
1.76e-11
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain]
Cd Length: 528
Bit Score: 69.00
E-value: 1.76e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1939159911 21 S A EE LK K L SV KSITN P RYV D SLGNPS - AD G L YD LA LG PA D SK E V C S TC VQDF N N C S GH L GHI D L PLT V YNP 90
Cdd:cd00399 2 S P EE IR K W SV AKVIK P ETI D NRTLKA e RG G K YD PR LG SI D RC E K C G TC GTGL N D C P GH F GHI E L AKP V FHV 72
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
10-89
4.11e-11
RNA polymerase Rpb1, domain 1; 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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595
Cd Length: 320
Bit Score: 66.16
E-value: 4.11e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 10 RRLQG I S FG MY S A EE LK K L SV KSI T N P R - Y VDSLGN P SAD GL Y D LAL G PA D SKEV C S TC VQDFNN C S GH L GHI D L PLT V Y 88
Cdd:pfam04997 2 KKIKE I Q FG IA S P EE IR K W SV GEV T K P E t Y NYGSLK P EEG GL L D ERM G TI D KDYE C E TC GKKKKD C P GH F GHI E L AKP V F 81
.
gi 1939159911 89 N 89
Cdd:pfam04997 82 H 82
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1589-1711
1.12e-09
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain]
Cd Length: 381
Bit Score: 62.44
E-value: 1.12e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1589 EVL D LR R LYSND I HAVANTY GI E AA LRVIEKEIKDVFAVY G IA V DPR HL S LVAD Y M CFE G VYKP LN RF G IQ ------ SS S 1662
Cdd:cd02737 250 DLI D WE R SMPYS I QQIKSVL GI D AA FEQFVQRLESAVSMT G KS V LRE HL L LVAD S M TYS G EFVG LN AK G YK aqrrsl KI S 329
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1663 S P LQQMT F ETSFQFLKQ A TMM G SH D E L KSPSACLVV GK VVKG GTG - L FE L 1711
Cdd:cd02737 330 A P FTEAC F SSPIKCFLK A AKK G AS D S L SGVLDACAW GK EAPV GTG s K FE I 379
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1210-1239
4.10e-09
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 61.88
E-value: 4.10e-09
10 20 30
....*....|....*....|....*....|
gi 1939159911 1210 S L CDP GEAVG LL A A QSIGEP S TQ M TL N TFH 1239
Cdd:CHL00117 310 D L VEL GEAVG II A G QSIGEP G TQ L TL R TFH 339
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
1166-1242
9.43e-09
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain]
Cd Length: 1227
Bit Score: 60.63
E-value: 9.43e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1939159911 1166 VSETFE K K I DD ysqewa A QAEKSHN RS E L SLDRL R TLLQLKWQR SL C ----- D P GEAVG LL AAQSIGEP S TQ M T LN TFH F 1240
Cdd:TIGR02388 261 IDPDLA K T I ET ------ A GISEVVV RS P L TCEAA R SVCRKCYGW SL A hahlv D L GEAVG II AAQSIGEP G TQ L T MR TFH T 334
..
gi 1939159911 1241 A G 1242
Cdd:TIGR02388 335 G G 336
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
1211-1242
1.34e-08
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 60.01
E-value: 1.34e-08
10 20 30
....*....|....*....|....*....|..
gi 1939159911 1211 L C D P GEAVG LL AAQSIGEP S TQ M T LN TFH FA G 1242
Cdd:PRK02597 307 L V D L GEAVG II AAQSIGEP G TQ L T MR TFH TG G 338
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1186-1235
9.75e-05
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 47.20
E-value: 9.75e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1939159911 1186 EK SHN R SELSLDRLRTLLQL --- KWQRS L CD P G EAVG LL AAQSIGEP S TQM T L 1235
Cdd:PRK14898 25 EK LSK R DGVTEEMVEEIIDE vvs AYLNA L VE P Y EAVG IV AAQSIGEP G TQM S L 77
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
