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RNA polymerase III subunit A [Drosophila melanogaster]
Protein Classification
DNA-directed RNA polymerase III subunit RPC1 ( domain architecture ID 10118853 )
DNA-directed RNA polymerase III subunit RPC1 is the largest and is a catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
24-889
0e+00
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: 1550.98
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 24 GADE I QQEAL V RIISK NLY - QAQ R Q P V PYGVLD R R M G I S T KD AM CETCG QG L NE C I GHFGY LD L A LPVFHIG H F RST INI 102
Cdd:cd02583 2 SPED I IRLSE V EVTNR NLY d IET R K P L PYGVLD P R L G T S D KD GI CETCG LN L AD C V GHFGY IK L E LPVFHIG Y F KAI INI 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 103 LQ M ICK V C AH V M L KP E DRQLYE K K L HN PN FSY L G KKAL HVQM L A K A KKV T KCPHCG S pnggvkkgpgllkilhdpykgrk 182
Cdd:cd02583 82 LQ C ICK T C SR V L L PE E EKRKFL K R L RR PN LDN L Q KKAL KKKI L E K C KKV R KCPHCG L ----------------------- 138
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 183 mdslftsnmnemlrstqtnrdlnstlg NYSTA E E L T PL M VL D LF EQ IP QR DV A LL G M CSHDAH P KH LI V TR VF VPP A CIR 262
Cdd:cd02583 139 --------------------------- LKKAQ E D L N PL K VL N LF KN IP PE DV E LL L M NPLAGR P EN LI L TR IP VPP L CIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 263 PSV LSEV K A GT T EDDLT M K Q SEI LLI NDVI QR H MAT G G K IEL I H EDWDFLQL HV ALY FH SE IS G I P IN M A PKK TT RG IV Q 342
Cdd:cd02583 192 PSV VMDE K S GT N EDDLT V K L SEI IFL NDVI KK H LEK G A K TQK I M EDWDFLQL QC ALY IN SE LP G L P LS M Q PKK PI RG FC Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 343 RLKGKQGRFR C NLSGKRVDFSGRTVISPDPNL M I N QVGVP VR VAKILTYPERV NPA NI RHM R E LV R NGP SM HPGAN Y V QQ 422
Cdd:cd02583 272 RLKGKQGRFR G NLSGKRVDFSGRTVISPDPNL R I D QVGVP EH VAKILTYPERV TRY NI EKL R K LV L NGP DV HPGAN F V IK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 423 R GSSF KK Y L A YGNR E K V A Q ELK C GD V VERHL R DGDIVLFNRQPSLH KM SIM C HRAKV Q P Q RTFRFNEC A CTPYNADFDGD 502
Cdd:cd02583 352 R DGGK KK F L K YGNR R K I A R ELK I GD I VERHL E DGDIVLFNRQPSLH RL SIM A HRAKV M P W RTFRFNEC V CTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 503 EMNLH L PQTEEARAEAL I LMG NQS NLVTP K NGE I LIAATQDF I T GG YLLT Q K E VF LTKEEAM QL AACF L AN E dst MH I K L 582
Cdd:cd02583 432 EMNLH V PQTEEARAEAL E LMG VKN NLVTP R NGE P LIAATQDF L T AS YLLT S K D VF FDRAQFC QL CSYM L DG E --- IK I D L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 583 PPPA L LKP RR LWTGKQ M FSLL M RPN DD S Q V RL N MVN K GRN YT R - NK D L C S ND SWIH IRNSEL M CG VM DK A T M GSG T K QCI 661
Cdd:cd02583 509 PPPA I LKP VE LWTGKQ I FSLL L RPN KK S P V LV N LEA K EKS YT K k SP D M C P ND GYVV IRNSEL L CG RL DK S T L GSG S K NSL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 662 FY L LLRD F G ESH A TK AM W RLA RIA S YF L Q NRGFS F GI S DVTPSK K LL QH KE L L LN NGYAKC N EYI ELL K A G T L QC QPGCT 741
Cdd:cd02583 589 FY V LLRD Y G PEA A AA AM N RLA KLS S RW L S NRGFS I GI D DVTPSK E LL KK KE E L VD NGYAKC D EYI KQY K K G K L EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 742 P E E TLE SVMLR ELS A IRE Q A A K T C FA ELH PT NS A LIMAL S GSKGSNINISQMIACVGQQ A ISGKR V PNGFE N R A LPHF E R 821
Cdd:cd02583 669 A E Q TLE AKISG ELS K IRE D A G K A C LK ELH KS NS P LIMAL C GSKGSNINISQMIACVGQQ I ISGKR I PNGFE D R T LPHF P R 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281360912 822 H S AI PAA R GFV Q NSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGY L QRRL V K C LEDL V V H YDGTVR 889
Cdd:cd02583 749 N S KT PAA K GFV A NSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGY M QRRL M K A LEDL S V Q YDGTVR 816
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1013-1353
2.84e-175
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: 522.55
E-value: 2.84e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1013 R Y N RA VT EPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNIT Q GVPRI V EIINA T K T ISTPIITA E LEN CHSMEF AR Q 1092
Cdd:cd02736 1 K Y M RA KV EPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNIT L GVPRI K EIINA S K N ISTPIITA K LEN DRDEKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1093 VK A RIEKT T L A E LS SY V E V V CG P YS CY LA I GV D MAR I KL L G L hidldtivfsilksrmrvkptqvevvasqsrivvrvea 1172
Cdd:cd02736 81 VK G RIEKT Y L G E VA SY I E E V YS P DD CY IL I KL D KKI I EK L Q L -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1173 t RT S TINAE L AR L ALS L QN VVV A G L P NIN RAVI AV D D ar QPPT YKL CI EGYGLR D V IA T Y GV V G K RT R SN N I C E IYQT LG 1252
Cdd:cd02736 123 - SK S NLYFL L QS L KRK L PD VVV S G I P EVK RAVI NK D K -- KKGK YKL LV EGYGLR A V MN T P GV I G T RT T SN H I M E VEKV LG 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1253 IEAAR TI I MS EI TEV M EG HGMS V D W RHIMLLA SQ MT AR GEVLGITR H G L AKM R ESV FN LASFEKT A DHLF D AA YY G QT D A 1332
Cdd:cd02736 200 IEAAR ST I IN EI QYT M KS HGMS I D P RHIMLLA DL MT FK GEVLGITR F G I AKM K ESV LM LASFEKT T DHLF N AA LH G RK D S 279
330 340
....*....|....*....|.
gi 281360912 1333 I N GVSE R II L G M P AC IGTG I F 1353
Cdd:cd02736 280 I E GVSE C II M G K P MP IGTG L F 300
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
24-889
0e+00
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: 1550.98
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 24 GADE I QQEAL V RIISK NLY - QAQ R Q P V PYGVLD R R M G I S T KD AM CETCG QG L NE C I GHFGY LD L A LPVFHIG H F RST INI 102
Cdd:cd02583 2 SPED I IRLSE V EVTNR NLY d IET R K P L PYGVLD P R L G T S D KD GI CETCG LN L AD C V GHFGY IK L E LPVFHIG Y F KAI INI 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 103 LQ M ICK V C AH V M L KP E DRQLYE K K L HN PN FSY L G KKAL HVQM L A K A KKV T KCPHCG S pnggvkkgpgllkilhdpykgrk 182
Cdd:cd02583 82 LQ C ICK T C SR V L L PE E EKRKFL K R L RR PN LDN L Q KKAL KKKI L E K C KKV R KCPHCG L ----------------------- 138
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 183 mdslftsnmnemlrstqtnrdlnstlg NYSTA E E L T PL M VL D LF EQ IP QR DV A LL G M CSHDAH P KH LI V TR VF VPP A CIR 262
Cdd:cd02583 139 --------------------------- LKKAQ E D L N PL K VL N LF KN IP PE DV E LL L M NPLAGR P EN LI L TR IP VPP L CIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 263 PSV LSEV K A GT T EDDLT M K Q SEI LLI NDVI QR H MAT G G K IEL I H EDWDFLQL HV ALY FH SE IS G I P IN M A PKK TT RG IV Q 342
Cdd:cd02583 192 PSV VMDE K S GT N EDDLT V K L SEI IFL NDVI KK H LEK G A K TQK I M EDWDFLQL QC ALY IN SE LP G L P LS M Q PKK PI RG FC Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 343 RLKGKQGRFR C NLSGKRVDFSGRTVISPDPNL M I N QVGVP VR VAKILTYPERV NPA NI RHM R E LV R NGP SM HPGAN Y V QQ 422
Cdd:cd02583 272 RLKGKQGRFR G NLSGKRVDFSGRTVISPDPNL R I D QVGVP EH VAKILTYPERV TRY NI EKL R K LV L NGP DV HPGAN F V IK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 423 R GSSF KK Y L A YGNR E K V A Q ELK C GD V VERHL R DGDIVLFNRQPSLH KM SIM C HRAKV Q P Q RTFRFNEC A CTPYNADFDGD 502
Cdd:cd02583 352 R DGGK KK F L K YGNR R K I A R ELK I GD I VERHL E DGDIVLFNRQPSLH RL SIM A HRAKV M P W RTFRFNEC V CTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 503 EMNLH L PQTEEARAEAL I LMG NQS NLVTP K NGE I LIAATQDF I T GG YLLT Q K E VF LTKEEAM QL AACF L AN E dst MH I K L 582
Cdd:cd02583 432 EMNLH V PQTEEARAEAL E LMG VKN NLVTP R NGE P LIAATQDF L T AS YLLT S K D VF FDRAQFC QL CSYM L DG E --- IK I D L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 583 PPPA L LKP RR LWTGKQ M FSLL M RPN DD S Q V RL N MVN K GRN YT R - NK D L C S ND SWIH IRNSEL M CG VM DK A T M GSG T K QCI 661
Cdd:cd02583 509 PPPA I LKP VE LWTGKQ I FSLL L RPN KK S P V LV N LEA K EKS YT K k SP D M C P ND GYVV IRNSEL L CG RL DK S T L GSG S K NSL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 662 FY L LLRD F G ESH A TK AM W RLA RIA S YF L Q NRGFS F GI S DVTPSK K LL QH KE L L LN NGYAKC N EYI ELL K A G T L QC QPGCT 741
Cdd:cd02583 589 FY V LLRD Y G PEA A AA AM N RLA KLS S RW L S NRGFS I GI D DVTPSK E LL KK KE E L VD NGYAKC D EYI KQY K K G K L EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 742 P E E TLE SVMLR ELS A IRE Q A A K T C FA ELH PT NS A LIMAL S GSKGSNINISQMIACVGQQ A ISGKR V PNGFE N R A LPHF E R 821
Cdd:cd02583 669 A E Q TLE AKISG ELS K IRE D A G K A C LK ELH KS NS P LIMAL C GSKGSNINISQMIACVGQQ I ISGKR I PNGFE D R T LPHF P R 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281360912 822 H S AI PAA R GFV Q NSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGY L QRRL V K C LEDL V V H YDGTVR 889
Cdd:cd02583 749 N S KT PAA K GFV A NSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGY M QRRL M K A LEDL S V Q YDGTVR 816
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
13-919
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 942.75
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 13 K K I SHVQ FG ISGAD EI QQEALVR II SKNL Y QAQRQ P VPY G VL D R R M G ISTKDAM C E TCG QGLN EC I GHFG YLD LA L PV F H 92
Cdd:PRK08566 7 K R I GSIK FG LLSPE EI RKMSVTK II TADT Y DDDGY P IDG G LM D P R L G VIDPGLR C K TCG GRAG EC P GHFG HIE LA R PV I H 86
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 93 I G HFRSTINI L QMI C KV C AHVM L KP E DRQL Y EK KL HNPNFSYLGKKA L HVQMLAK A K K VTK CPHCG SP nggvkkgpg LL K 172
Cdd:PRK08566 87 V G FAKLIYKL L RAT C RE C GRLK L TE E EIEE Y LE KL ERLKEWGSLADD L IKEVKKE A A K RMV CPHCG EK --------- QY K 157
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 173 I LHD - P Y kgrkmdslfts NMN E mlrst QTNRD L N stlgnystae E LTP LMVLDLF E Q IP QR D VA LLG MCSHD A H P KHLIV 251
Cdd:PRK08566 158 I KFE k P T ----------- TFY E ----- ERKEG L V ---------- K LTP SDIRERL E K IP DE D LE LLG INPEV A R P EWMVL 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 252 T RVF VPP ACI RPS VLS E vk A G - TT EDDLT M K QSE I LL IN DVIQRHMAT G GK i E LI H ED - W DF LQ L HV AL YF HS EI S GIP i 329
Cdd:PRK08566 212 T VLP VPP VTV RPS ITL E -- T G q RS EDDLT H K LVD I IR IN QRLKENIEA G AP - Q LI I ED l W EL LQ Y HV TT YF DN EI P GIP - 287
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 330 nma P ----- KKTTRGIV QRLKGK Q GRFR C NLSGKRV D FS G RTVISPDPNL M IN Q VGVP VRV AK I LT Y PERV NPA NI RHM R 404
Cdd:PRK08566 288 --- P arhrs GRPLKTLA QRLKGK E GRFR G NLSGKRV N FS A RTVISPDPNL S IN E VGVP EAI AK E LT V PERV TEW NI EEL R 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 405 E L V R NGP SM HPGANYV QQR - G SSF K ky L AYG N R E KV A QE L KC G DV VERHL R DGDIVLFNRQPSLH K MSIM C HR AK V Q P QR 483
Cdd:PRK08566 365 E Y V L NGP EK HPGANYV IRP d G RRI K -- L TDK N K E EL A EK L EP G WI VERHL I DGDIVLFNRQPSLH R MSIM A HR VR V L P GK 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 484 TFR F N ECA C T PYNADFDGDEMNLH L PQTEEARAEA L ILM GN Q SNLVT P KN G EIL I AAT QD F I T G G YLLT Q K EVFL TKEEA 563
Cdd:PRK08566 443 TFR L N LAV C P PYNADFDGDEMNLH V PQTEEARAEA R ILM LV Q EHILS P RY G GPI I GGI QD H I S G A YLLT R K STLF TKEEA 522
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 564 MQ L aacf L ANEDST m HIKL P P PA LLKPRRL WTGKQ M FSL LM r P N D dsqvr LN MVN K GRN ---- YTRN K DL C SN D SWIH I R 639
Cdd:PRK08566 523 LD L ---- L RAAGID - ELPE P E PA IENGKPY WTGKQ I FSL FL - P K D ----- LN LEF K AKI csgc DECK K ED C EH D AYVV I K 591
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 640 N SE L MC GV M DK ATM G SGTKQ c I FYLLLRDF G ESH A TKAMWRLA R I A SY F LQN RGF SF GI S D VTPSKKLLQHKELLLNNGY 719
Cdd:PRK08566 592 N GK L LE GV I DK KAI G AEQGS - I LDRIVKEY G PER A RRFLDSVT R L A IR F IML RGF TT GI D D EDIPEEAKEEIDEIIEEAE 670
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 720 AKCN E Y IE LLKA G T L QCQ PG C T P EETLE SVMLRE L SAI R EQ A AKTCFAE L HPT N S A L IMA LS G SK GS NI N IS QM I ACVGQ 799
Cdd:PRK08566 671 KRVE E L IE AYEN G E L EPL PG R T L EETLE MKIMQV L GKA R DE A GEIAEKY L GLD N P A V IMA RT G AR GS ML N LT QM A ACVGQ 750
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 800 Q AIS G K R VPN G FEN R A LPHF ERHSAIPA ARGFV QN S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GY L QRRL VKC L E D 879
Cdd:PRK08566 751 Q SVR G E R IRR G YRD R T LPHF KPGDLGAE ARGFV RS S YK SGLTPTEFFFH A M G GREGLVDTAV R T SQS GY M QRRL INA L Q D 830
890 900 910 920
....*....|....*....|....*....|....*....|
gi 281360912 880 L V V H YDGTVR NAVNEM V DTI YG G DG L DP VSME t RN KPVD L 919
Cdd:PRK08566 831 L K V E YDGTVR DTRGNI V QFK YG E DG V DP MKSD - HG KPVD V 869
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-919
0e+00
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.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 879.82
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 13 KKI SHVQ FG ISGAD EI QQEAL V RIISKNL Y QAQRQ P VPY G VL D R R M G ISTKDAM C E TCG QGLN EC I GHFG YLD LA L PV F H 92
Cdd:TIGR02390 2 KKI GSIK FG LLSPE EI RKMSV V EVVTADT Y DDDGY P IEG G LM D P R L G VIEPGLR C K TCG GKVG EC P GHFG HIE LA R PV V H 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 93 I G HFRSTIN IL QMI C KV C AHVM L KP E DRQL Y EK K LHNPNFSY - LGKKA L HVQMLAK A K K VT KCPHCG SPNGGV K kgpgll 171
Cdd:TIGR02390 82 V G FAKEIYK IL RAT C RK C GRIT L TE E EIEQ Y LE K INKLKEEG g DLAST L IEKIVKE A A K RM KCPHCG EEQKKI K ------ 155
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 172 ki LHD P YKGRKMDS lftsnmnemlrstqtnrdlnstlgny STAEE LTP LMVLDLF E Q IP QR D VA LLG MCSHD A H P KHLIV 251
Cdd:TIGR02390 156 -- FEK P TYFYEEGK -------------------------- EGDVK LTP SEIRERL E K IP DE D AE LLG INPKV A R P EWMVL 207
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 252 T RVF VPP ACI RPS VLS E v KAGTT EDDLT M K QSE I LL IN DVIQRHMAT G GKIEL I HED W DF LQ L HVA L YF HS E IS GIP - IN 330
Cdd:TIGR02390 208 T VLP VPP VTV RPS ITL E - TGERS EDDLT H K LVD I IR IN QRLKENIEA G APQLI I EDL W EL LQ Y HVA T YF DN E LP GIP p AR 286
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 331 MAPKKTTRGIV QRLKGK Q GRFR C NLSGKRV D FS G RTVISPDPN LM IN Q VGVP VRV AK I LT Y PERV N P A NI RHM RE L V R NG 410
Cdd:TIGR02390 287 HRSGRPLKTLA QRLKGK E GRFR G NLSGKRV N FS A RTVISPDPN IS IN E VGVP EQI AK E LT V PERV T P W NI DEL RE Y V L NG 366
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 411 P SMH PGANYV - QQR G SSF K ky LAYG N R E KV A QE L KC G D VVERHL R DGDIVLFNRQPSLH K MS I M C H RA KV Q P QR TFR F N E 489
Cdd:TIGR02390 367 P DSW PGANYV i RPD G RRI K -- IRDE N K E EL A ER L EP G W VVERHL I DGDIVLFNRQPSLH R MS M M G H KV KV L P GK TFR L N L 444
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 490 CA C T PYNADFDGDEMNLH L PQTEEARAEA LI LM GNQSNLV TP KN G EIL I AATQ D F I T G G YLLT Q K EVFL TKEE AMQ - L AA 568
Cdd:TIGR02390 445 AV C P PYNADFDGDEMNLH V PQTEEARAEA RE LM LVEEHIL TP RY G GPI I GGIH D Y I S G A YLLT H K STLF TKEE VQT i L GV 524
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 569 CFLANED stmhikl P P PA LL KP RRL WTGKQ M FS LLM r P N D dsqvr LN MVNKGRN ---- YTRN K DL C SN D SWIH I R N SE L M 644
Cdd:TIGR02390 525 AGYFGDP ------- P E PA IE KP KEY WTGKQ I FS AFL - P E D ----- LN FEGRAKI csgs DACK K EE C PH D AYVV I K N GK L L 591
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 645 C GV M DK ATM G S g T K QC I FYLLL R DF G ESH A TKAMWRLA R IASY F LQN RGF SF GI S D VTPS K KLLQHK E L L LNNGYAKCNE 724
Cdd:TIGR02390 592 K GV I DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT R LFIR F ITL RGF TT GI D D IDIP K EAKEEI E E L IEKAEKRVDN 670
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 725 Y IE LLKA G T L QCQ PG C T P EETLE SVMLRE L SAI R EQ A AKTCFAE L H P T N S A L IMA LS G SK GS NI NI S QM I A C VGQQ AIS G 804
Cdd:TIGR02390 671 L IE RYRN G E L EPL PG R T V EETLE MKIMEV L GKA R DE A GEVAEKY L D P E N H A V IMA RT G AR GS LL NI T QM A A M VGQQ SVR G 750
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 805 K R VPN G FE NR A LPHF ERHSAIPA ARGFV QN SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GY L QRRL VKC L E DL V V H Y 884
Cdd:TIGR02390 751 G R IRR G YR NR T LPHF KKGDIGAK ARGFV RS SF KK GL D PTE Y FFH AAG GREGLVDTAV R T SQS GY M QRRL INA L Q DL Y V E Y 830
890 900 910
....*....|....*....|....*....|....*
gi 281360912 885 DGTVR NAVNEMVDTI YG G DG L DP VSME t RN KPVD L 919
Cdd:TIGR02390 831 DGTVR DTRGNLIQFK YG E DG V DP MKSD - HG KPVD V 864
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1013-1353
2.84e-175
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: 522.55
E-value: 2.84e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1013 R Y N RA VT EPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNIT Q GVPRI V EIINA T K T ISTPIITA E LEN CHSMEF AR Q 1092
Cdd:cd02736 1 K Y M RA KV EPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNIT L GVPRI K EIINA S K N ISTPIITA K LEN DRDEKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1093 VK A RIEKT T L A E LS SY V E V V CG P YS CY LA I GV D MAR I KL L G L hidldtivfsilksrmrvkptqvevvasqsrivvrvea 1172
Cdd:cd02736 81 VK G RIEKT Y L G E VA SY I E E V YS P DD CY IL I KL D KKI I EK L Q L -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1173 t RT S TINAE L AR L ALS L QN VVV A G L P NIN RAVI AV D D ar QPPT YKL CI EGYGLR D V IA T Y GV V G K RT R SN N I C E IYQT LG 1252
Cdd:cd02736 123 - SK S NLYFL L QS L KRK L PD VVV S G I P EVK RAVI NK D K -- KKGK YKL LV EGYGLR A V MN T P GV I G T RT T SN H I M E VEKV LG 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1253 IEAAR TI I MS EI TEV M EG HGMS V D W RHIMLLA SQ MT AR GEVLGITR H G L AKM R ESV FN LASFEKT A DHLF D AA YY G QT D A 1332
Cdd:cd02736 200 IEAAR ST I IN EI QYT M KS HGMS I D P RHIMLLA DL MT FK GEVLGITR F G I AKM K ESV LM LASFEKT T DHLF N AA LH G RK D S 279
330 340
....*....|....*....|.
gi 281360912 1333 I N GVSE R II L G M P AC IGTG I F 1353
Cdd:cd02736 280 I E GVSE C II M G K P MP IGTG L F 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
249-549
3.94e-145
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 443.11
E-value: 3.94e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 249 L I V T RVF VPP A C I RPSV LSEVKA g TT EDDLT MKQSE I LLI N DVIQ R HMAT G GKIEL I HEDWDF LQ LH V ALYFHS E i SGIP 328
Cdd:smart00663 3 M I L T VLP VPP P C L RPSV QLDGGR - FA EDDLT HLLRD I IKR N NRLK R LLEL G APSII I RNEKRL LQ EA V DTLIDN E - GLPR 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 329 I N MAPKKTTRGIV QRLKGK Q GRFR C NL S GKRVDFS G R T VI S PDPNL MI N Q VGVP VRV A KI LT Y PE R V N P A NI RHM R E LVR 408
Cdd:smart00663 81 A N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KL N E VGVP KEI A LE LT F PE I V T P L NI DKL R K LVR 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 409 NGP smh P GA N Y VQQ rgs SF K KY L AYGNRE K V A QE LK C GD V VERH LR DGD I VLFNRQP S LH K MSI MC HR AK V QPQR T F R F N 488
Cdd:smart00663 161 NGP --- N GA K Y IIR --- GK K TN L KLAKKS K I A NH LK I GD I VERH VI DGD V VLFNRQP T LH R MSI QA HR VR V LEGK T I R L N 234
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281360912 489 ECA C T PYNADFDGDEMNLH L PQ TE EARAEA LI LM GNQS N LVT PKNG EIL I AAT QD FIT G G Y 549
Cdd:smart00663 235 PLV C S PYNADFDGDEMNLH V PQ SL EARAEA RE LM LVPN N ILS PKNG KPI I GPI QD MLL G L Y 295
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
839-1309
1.66e-119
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: 383.24
E-value: 1.66e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 839 GLTP T EFFFHTM A GREGL V DTAVKTAE T GYLQRRLVK C LEDLVV H YD G TVRN AVN E M V DTI YG G DGLDP VSM E TRNKPV d 918
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GYLQRRLVK A LEDLVV T YD D TVRN SGG E I V QFL YG E DGLDP LKI E KQGRFT - 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 919 LVHQYDN L RAQ hpqg KDRP L NAEEMSEALET L L rtp EFA E ARDDFKLDV R NHINTVSK ----------- RI G QLQ KR YEK 987
Cdd:pfam04998 80 IEFSDLK L EDK ---- FKND L LDDLLLLSEFS L S --- YKK E ILVRDSKLG R DRLSKEAQ eratllfelll KS G LES KR VRS 152
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 988 CIDL - CHQIE CL TTE qllqfvrr INDR Y NRAVTE PG T AVG A IAAQSIGEPGTQMTL K TFHFAGVAS M N I T Q GVPR IV EII 1066
Cdd:pfam04998 153 ELTC n SKAFV CL LCY -------- GRLL Y QQSLIN PG E AVG I IAAQSIGEPGTQMTL N TFHFAGVAS K N V T L GVPR LK EII 224
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1067 N AT K T I ST P II T AE L ENCHSM E F -- A RQ V KAR IEK T TL AELSSYV E VVCG P YS --------------- CYLAIG V DM --- 1126
Cdd:pfam04998 225 N VS K N I KS P SL T VY L FDEVGR E L ek A KK V YGA IEK V TL GSVVESG E ILYD P DP fntpiisdvkgvvkf FDIIDE V TN eee 304
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1127 ------ AR I KLLG L HID L DTIVFSIL KS --------------- RMRVKPTQVEVVASQSR I VVRVEAT R TSTINAELARL 1185
Cdd:pfam04998 305 idpetg LL I LVIR L LKI L NKSIKKVV KS eviprsirnkvdegr DIAIGEITAFIIKISKK I RQDTGGL R RVDELFMEEDP 384
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1186 A L S ------ L Q N VVVA G L P N I N R AVIAV DD A - RQP P TYK L CI EG YG L RD V IATY G V V GK - R TR SN N I C EI YQT LGIEAAR 1257
Cdd:pfam04998 385 K L A ilvasl L G N ITLR G I P G I K R ILVNE DD K g KVE P DWV L ET EG VN L LR V LLVP G F V DA g R IL SN D I H EI LEI LGIEAAR 464
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|..
gi 281360912 1258 TIIMS EI TE V MEGH G MSVDW RH IM L L A S QMT AR G EVLG I T RHG LA K MRE S VF 1309
Cdd:pfam04998 465 NALLN EI RN V YRFQ G IYIND RH LE L I A D QMT RK G YIMA I G RHG IN K AEL S AL 516
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
998-1356
4.83e-96
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 314.09
E-value: 4.83e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 998 LT T E QLLQFVRRINDR Y N R AVT EPG T AVG AI AAQSIGEPGTQMT LK TFH F AGVA SM N I T Q G V PR IV EI IN A T K TI STP II 1077
Cdd:PRK04309 35 LT E E EVEEIIEEVVRE Y L R SLV EPG E AVG VV AAQSIGEPGTQMT MR TFH Y AGVA EI N V T L G L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1078 T AE L -- E NCHSM E F A RQ V KAR IE K TTL AE L SSYVE V vc GPYSCYLA I GV D MARIKLL G lh IDL D TIV f SILKSRMRV kpt 1155
Cdd:PRK04309 115 T IY L kd E YAYDR E K A EE V ARK IE A TTL EN L AKDIS V -- DLANMTII I EL D EEMLEDR G -- LTV D DVK - EAIEKKKGG --- 186
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1156 qv EV VASQSRIVVRVEATRTS tina EL AR LA LSLQ N VVVA G LPN I N R AV I AVDDAR qppt Y KLCI EG YG L RD V IATY GV V 1235
Cdd:PRK04309 187 -- EV EIEGNTLIISPKEPSYR ---- EL RK LA EKIR N IKIK G IKG I K R VI I RKEGDE ---- Y VIYT EG SN L KE V LKVE GV D 256
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1236 GK RT RS NNI C EI YQT LGIEAAR TI I MS EI TEVM E GH G MS VD W RHIML L A SQ MT AR GEV LG I T RHG LAKMRE SV FNL A S FE 1315
Cdd:PRK04309 257 AT RT TT NNI H EI EEV LGIEAAR NA I IE EI KNTL E EQ G LD VD I RHIML V A DM MT WD GEV RQ I G RHG VSGEKA SV LAR A A FE 336
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 281360912 1316 K T AD HL F DAA YY G QT D AIN GV S E R II L G M P ACI GTG IFK L L 1356
Cdd:PRK04309 337 V T VK HL L DAA VR G EV D ELK GV T E N II V G Q P IPL GTG DVE L T 377
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
12-355
3.62e-95
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: 309.22
E-value: 3.62e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 12 N KKI SHV QFGI SGAD EI QQEALVRIISKNL Y Q - AQRQ P VPY G V LD R RMG IST KD AM CETCG QGLNE C I GHFG YLD LA L PV 90
Cdd:pfam04997 1 L KKI KEI QFGI ASPE EI RKWSVGEVTKPET Y N y GSLK P EEG G L LD E RMG TID KD YE CETCG KKKKD C P GHFG HIE LA K PV 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 91 FHIG H F RS T IN IL QMI CK V C AHVM L K P EDRQ L YE K KLHNPNFSY L GKK A LHV qm L AKA KK VTK C P HCG SP NG GVKKGPGL 170
Cdd:pfam04997 81 FHIG F F KK T LK IL ECV CK Y C SKLL L D P GKPK L FN K DKKRLGLEN L KMG A KAI -- L ELC KK KDL C E HCG GK NG VCGSQQPV 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 171 LKILH dpykgrkmdslft SNMNEMLRSTQTNRDL nstlgnysta E E L T P LM VL DL F EQ I PQR DV AL LG MCSHDAH P KHL I 250
Cdd:pfam04997 159 SRKEG ------------- LKLKAAIKKSKEEEEK ---------- E I L N P EK VL KI F KR I SDE DV EI LG FNPSGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 251 V T RVF VPP A CIRPSV LSEVK a GTT EDDLT M K QSE I LLI N DVIQRHMAT G GKIEL I H E D W DF LQ L HVA LY F HS EI S G I - P I 329
Cdd:pfam04997 216 L T VLP VPP P CIRPSV QLDGG - RRA EDDLT H K LRD I IKR N NRLKKLLEL G APSHI I R E E W RL LQ E HVA TL F DN EI P G L p P A 294
330 340
....*....|....*....|....*.
gi 281360912 330 NMAP K KTTRG I V QRLKGK Q GRFR C NL 355
Cdd:pfam04997 295 LQKS K RPLKS I S QRLKGK E GRFR G NL 320
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
982-1356
5.31e-87
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: 288.10
E-value: 5.31e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 982 Q K RYEKCIDLCHQI E CLTT E Q L LQFVR R INDR Y N R AVTE PG T AVG AI AAQSIGEPGTQMT LK TFH F AGVA SM N I T Q G V PR 1061
Cdd:TIGR02389 4 E K LLKELEETVKKR E ISDK E E L DEIIK R VEEE Y L R SLID PG E AVG IV AAQSIGEPGTQMT MR TFH Y AGVA EL N V T L G L PR 83
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1062 IV EI IN A T KT I STP II T AE LE NCH -- SM E F A RQ V KAR IE K T T L AELSS yvevvcgpyscyl A I GV D M A RIKLL glh I D LD 1139
Cdd:TIGR02389 84 LI EI VD A R KT P STP SM T IY LE DEY ek DR E K A EE V AKK IE A T K L EDVAK ------------- D I SI D L A DMTVI --- I E LD 147
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1140 T ivf SI LK S R MRVKPTQVEVVASQSRIV V RVEATRTS TI NA -------- EL AR L ALSLQ N VVVA G LPN I N R A VI AVDDAR 1211
Cdd:TIGR02389 148 E --- EQ LK E R GITVDDVEKAIKKAKLGK V IEIDMDNN TI TI kpgnpslk EL RK L KEKIK N LHIK G IKG I K R V VI RKEGDE 224
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1212 qppt Y KLCI EG YG L RD V IATY GV VGK RT RS N N I C EI YQT LGIEAAR TI I MS EI TEVM E GH G MS VD W RH I ML L A SQ MT AR G 1291
Cdd:TIGR02389 225 ---- Y VIYT EG SN L KE V LKLE GV DKT RT TT N D I H EI AEV LGIEAAR NA I IE EI KRTL E EQ G LD VD I RH L ML V A DL MT WD G 300
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281360912 1292 EV LG I T RHG LAKMRE SV FNL A S FE K T AD HL F DAA YY G QT D AIN GV S E R II L G M P ACI GTG IFK L L 1356
Cdd:TIGR02389 301 EV RQ I G RHG ISGEKA SV LAR A A FE V T VK HL L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L V 365
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
312-1210
8.54e-60
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: 225.42
E-value: 8.54e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 312 LQ LH V ALY F HSEIS G IPINM A P K KTTRGIVQR LKGKQGRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY 391
Cdd:COG0086 289 LQ EA V DAL F DNGRR G RAVTG A N K RPLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KKM A LE L FK 368
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 392 P ER vnpanirh M R E L VRN G psmhp G A NYV qqrg S S F KK YL aygnr E KVAQ E LK cg D VV E RHLR d GDI VL F NR Q P S LH KMS 471
Cdd:COG0086 369 P FI -------- Y R K L EER G ----- L A TTI ---- K S A KK MV ----- E REEP E VW -- D IL E EVIK - EHP VL L NR A P T LH RLG 423
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 472 I MCHRAKVQPQRTFRFNECA CT PY NADFDGD E M NL H L P QTE EA RA EA LI LM GNQS N LVT P K NG EIL I AAT QD FIT G G Y L L 551
Cdd:COG0086 424 I QAFEPVLIEGKAIQLHPLV CT AF NADFDGD Q M AV H V P LSL EA QL EA RL LM LSTN N ILS P A NG KPI I VPS QD MVL G L Y Y L 503
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 552 T QKE -------- V F LTK EE A mq L A A cf LA N EDSTM H iklppp A LL K P R RLWT G K Q MFSLLM ---- R pnddsq VRL N MV - N 618
Cdd:COG0086 504 T RER egakgegm I F ADP EE V -- L R A -- YE N GAVDL H ------ A RI K V R ITED G E Q VGKIVE ttvg R ------ YLV N EI l P 567
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 619 KGRNYT r N KDL cs N DSW I H -- IR NSELM CG V md K A T mgsgtkq C IF YLL L RDF G ESH AT K A mwrlariasyflqnr G F S F 696
Cdd:COG0086 568 QEVPFY - N QVI -- N KKH I E vi IR QMYRR CG L -- K E T ------- V IF LDR L KKL G FKY AT R A --------------- G I S I 620
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 697 G IS D VTPS K K llqh K ELLLNNGYAKCN E YIELLKA G TL qcqpgc T PE E TLES V ML r ELSAIREQAAKTCF A ELHPT N SAL 776
Cdd:COG0086 621 G LD D MVVP K E ---- K QEIFEEANKEVK E IEKQYAE G LI ------ T EP E RYNK V ID - GWTKASLETESFLM A AFSSQ N TTY 689
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 777 I MA L SG SK GS NINIS Q MIACV G QQ A isgkr V P N G -- F E NRAL phferh S AIPA argfvqnsfys GL TPT E F F FH T MAG R E 854
Cdd:COG0086 690 M MA D SG AR GS ADQLR Q LAGMR G LM A ----- K P S G ni I E TPIG ------ S NFRE ----------- GL GVL E Y F IS T HGA R K 747
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 855 GL V DTA V KTA ET GYL Q RRLV KCLE D LV V HYD -- GT V R NA vn EMVDTIY GG DGLD P VS -- MET R NKPV D L V H qydnlraqh 930
Cdd:COG0086 748 GL A DTA L KTA DS GYL T RRLV DVAQ D VI V TEE dc GT D R GI -- TVTAIKE GG EVIE P LK er ILG R VAAE D V V D --------- 816
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 931 pqgkdr P LNA E EMSE A LETL lr TP E F AE ARDD fkldvrnhintvs KR I GQLQK R YEKCIDLCHQIECLTTEQL L QFVRRI 1010
Cdd:COG0086 817 ------ P GTG E VLVP A GTLI -- DE E V AE IIEE ------------- AG I DSVKV R SVLTCETRGGVCAKCYGRD L ARGHLV 875
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1011 N D rynravtep G T AVG A IAAQSIGEPGTQ M T LK TFH FA G V AS M ---- NITQGVPRIVEII N AT K TISTPIITAELENCH S 1086
Cdd:COG0086 876 N I --------- G E AVG V IAAQSIGEPGTQ L T MR TFH IG G A AS R aaee SSIEAKAGGIVRL N NL K VVVNEEGKGVVVSRN S 946
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1087 MEFARQVKA R I E KTTLAELSSYVE VV C G PYSCYLA I GVDMARIKLLGLHIDLDTI VF SILKSRMRVKPTQV E VVASQ S RI 1166
Cdd:COG0086 947 ELVIVDDGG R R E EEYKVPYGGVLV VV G G GVVVGGG I VAEWDPHTPPIIEEVGGGV VF DDIVEGGVIVEKTD E ETGGL S IV 1026
890 900 910 920
....*....|....*....|....*....|....*....|....
gi 281360912 1167 V VRVE A T R TSTINAEL A RLA L SLQNVVVAGLPNINR A VIAVDDA 1210
Cdd:COG0086 1027 V EDDK A R R GGGKLLIR A LKL L DAVGLSLLLGGTDAA A AGVIIGG 1070
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
24-889
0e+00
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: 1550.98
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 24 GADE I QQEAL V RIISK NLY - QAQ R Q P V PYGVLD R R M G I S T KD AM CETCG QG L NE C I GHFGY LD L A LPVFHIG H F RST INI 102
Cdd:cd02583 2 SPED I IRLSE V EVTNR NLY d IET R K P L PYGVLD P R L G T S D KD GI CETCG LN L AD C V GHFGY IK L E LPVFHIG Y F KAI INI 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 103 LQ M ICK V C AH V M L KP E DRQLYE K K L HN PN FSY L G KKAL HVQM L A K A KKV T KCPHCG S pnggvkkgpgllkilhdpykgrk 182
Cdd:cd02583 82 LQ C ICK T C SR V L L PE E EKRKFL K R L RR PN LDN L Q KKAL KKKI L E K C KKV R KCPHCG L ----------------------- 138
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 183 mdslftsnmnemlrstqtnrdlnstlg NYSTA E E L T PL M VL D LF EQ IP QR DV A LL G M CSHDAH P KH LI V TR VF VPP A CIR 262
Cdd:cd02583 139 --------------------------- LKKAQ E D L N PL K VL N LF KN IP PE DV E LL L M NPLAGR P EN LI L TR IP VPP L CIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 263 PSV LSEV K A GT T EDDLT M K Q SEI LLI NDVI QR H MAT G G K IEL I H EDWDFLQL HV ALY FH SE IS G I P IN M A PKK TT RG IV Q 342
Cdd:cd02583 192 PSV VMDE K S GT N EDDLT V K L SEI IFL NDVI KK H LEK G A K TQK I M EDWDFLQL QC ALY IN SE LP G L P LS M Q PKK PI RG FC Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 343 RLKGKQGRFR C NLSGKRVDFSGRTVISPDPNL M I N QVGVP VR VAKILTYPERV NPA NI RHM R E LV R NGP SM HPGAN Y V QQ 422
Cdd:cd02583 272 RLKGKQGRFR G NLSGKRVDFSGRTVISPDPNL R I D QVGVP EH VAKILTYPERV TRY NI EKL R K LV L NGP DV HPGAN F V IK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 423 R GSSF KK Y L A YGNR E K V A Q ELK C GD V VERHL R DGDIVLFNRQPSLH KM SIM C HRAKV Q P Q RTFRFNEC A CTPYNADFDGD 502
Cdd:cd02583 352 R DGGK KK F L K YGNR R K I A R ELK I GD I VERHL E DGDIVLFNRQPSLH RL SIM A HRAKV M P W RTFRFNEC V CTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 503 EMNLH L PQTEEARAEAL I LMG NQS NLVTP K NGE I LIAATQDF I T GG YLLT Q K E VF LTKEEAM QL AACF L AN E dst MH I K L 582
Cdd:cd02583 432 EMNLH V PQTEEARAEAL E LMG VKN NLVTP R NGE P LIAATQDF L T AS YLLT S K D VF FDRAQFC QL CSYM L DG E --- IK I D L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 583 PPPA L LKP RR LWTGKQ M FSLL M RPN DD S Q V RL N MVN K GRN YT R - NK D L C S ND SWIH IRNSEL M CG VM DK A T M GSG T K QCI 661
Cdd:cd02583 509 PPPA I LKP VE LWTGKQ I FSLL L RPN KK S P V LV N LEA K EKS YT K k SP D M C P ND GYVV IRNSEL L CG RL DK S T L GSG S K NSL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 662 FY L LLRD F G ESH A TK AM W RLA RIA S YF L Q NRGFS F GI S DVTPSK K LL QH KE L L LN NGYAKC N EYI ELL K A G T L QC QPGCT 741
Cdd:cd02583 589 FY V LLRD Y G PEA A AA AM N RLA KLS S RW L S NRGFS I GI D DVTPSK E LL KK KE E L VD NGYAKC D EYI KQY K K G K L EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 742 P E E TLE SVMLR ELS A IRE Q A A K T C FA ELH PT NS A LIMAL S GSKGSNINISQMIACVGQQ A ISGKR V PNGFE N R A LPHF E R 821
Cdd:cd02583 669 A E Q TLE AKISG ELS K IRE D A G K A C LK ELH KS NS P LIMAL C GSKGSNINISQMIACVGQQ I ISGKR I PNGFE D R T LPHF P R 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 281360912 822 H S AI PAA R GFV Q NSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGY L QRRL V K C LEDL V V H YDGTVR 889
Cdd:cd02583 749 N S KT PAA K GFV A NSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGY M QRRL M K A LEDL S V Q YDGTVR 816
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
13-919
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 942.75
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 13 K K I SHVQ FG ISGAD EI QQEALVR II SKNL Y QAQRQ P VPY G VL D R R M G ISTKDAM C E TCG QGLN EC I GHFG YLD LA L PV F H 92
Cdd:PRK08566 7 K R I GSIK FG LLSPE EI RKMSVTK II TADT Y DDDGY P IDG G LM D P R L G VIDPGLR C K TCG GRAG EC P GHFG HIE LA R PV I H 86
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 93 I G HFRSTINI L QMI C KV C AHVM L KP E DRQL Y EK KL HNPNFSYLGKKA L HVQMLAK A K K VTK CPHCG SP nggvkkgpg LL K 172
Cdd:PRK08566 87 V G FAKLIYKL L RAT C RE C GRLK L TE E EIEE Y LE KL ERLKEWGSLADD L IKEVKKE A A K RMV CPHCG EK --------- QY K 157
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 173 I LHD - P Y kgrkmdslfts NMN E mlrst QTNRD L N stlgnystae E LTP LMVLDLF E Q IP QR D VA LLG MCSHD A H P KHLIV 251
Cdd:PRK08566 158 I KFE k P T ----------- TFY E ----- ERKEG L V ---------- K LTP SDIRERL E K IP DE D LE LLG INPEV A R P EWMVL 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 252 T RVF VPP ACI RPS VLS E vk A G - TT EDDLT M K QSE I LL IN DVIQRHMAT G GK i E LI H ED - W DF LQ L HV AL YF HS EI S GIP i 329
Cdd:PRK08566 212 T VLP VPP VTV RPS ITL E -- T G q RS EDDLT H K LVD I IR IN QRLKENIEA G AP - Q LI I ED l W EL LQ Y HV TT YF DN EI P GIP - 287
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 330 nma P ----- KKTTRGIV QRLKGK Q GRFR C NLSGKRV D FS G RTVISPDPNL M IN Q VGVP VRV AK I LT Y PERV NPA NI RHM R 404
Cdd:PRK08566 288 --- P arhrs GRPLKTLA QRLKGK E GRFR G NLSGKRV N FS A RTVISPDPNL S IN E VGVP EAI AK E LT V PERV TEW NI EEL R 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 405 E L V R NGP SM HPGANYV QQR - G SSF K ky L AYG N R E KV A QE L KC G DV VERHL R DGDIVLFNRQPSLH K MSIM C HR AK V Q P QR 483
Cdd:PRK08566 365 E Y V L NGP EK HPGANYV IRP d G RRI K -- L TDK N K E EL A EK L EP G WI VERHL I DGDIVLFNRQPSLH R MSIM A HR VR V L P GK 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 484 TFR F N ECA C T PYNADFDGDEMNLH L PQTEEARAEA L ILM GN Q SNLVT P KN G EIL I AAT QD F I T G G YLLT Q K EVFL TKEEA 563
Cdd:PRK08566 443 TFR L N LAV C P PYNADFDGDEMNLH V PQTEEARAEA R ILM LV Q EHILS P RY G GPI I GGI QD H I S G A YLLT R K STLF TKEEA 522
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 564 MQ L aacf L ANEDST m HIKL P P PA LLKPRRL WTGKQ M FSL LM r P N D dsqvr LN MVN K GRN ---- YTRN K DL C SN D SWIH I R 639
Cdd:PRK08566 523 LD L ---- L RAAGID - ELPE P E PA IENGKPY WTGKQ I FSL FL - P K D ----- LN LEF K AKI csgc DECK K ED C EH D AYVV I K 591
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 640 N SE L MC GV M DK ATM G SGTKQ c I FYLLLRDF G ESH A TKAMWRLA R I A SY F LQN RGF SF GI S D VTPSKKLLQHKELLLNNGY 719
Cdd:PRK08566 592 N GK L LE GV I DK KAI G AEQGS - I LDRIVKEY G PER A RRFLDSVT R L A IR F IML RGF TT GI D D EDIPEEAKEEIDEIIEEAE 670
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 720 AKCN E Y IE LLKA G T L QCQ PG C T P EETLE SVMLRE L SAI R EQ A AKTCFAE L HPT N S A L IMA LS G SK GS NI N IS QM I ACVGQ 799
Cdd:PRK08566 671 KRVE E L IE AYEN G E L EPL PG R T L EETLE MKIMQV L GKA R DE A GEIAEKY L GLD N P A V IMA RT G AR GS ML N LT QM A ACVGQ 750
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 800 Q AIS G K R VPN G FEN R A LPHF ERHSAIPA ARGFV QN S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GY L QRRL VKC L E D 879
Cdd:PRK08566 751 Q SVR G E R IRR G YRD R T LPHF KPGDLGAE ARGFV RS S YK SGLTPTEFFFH A M G GREGLVDTAV R T SQS GY M QRRL INA L Q D 830
890 900 910 920
....*....|....*....|....*....|....*....|
gi 281360912 880 L V V H YDGTVR NAVNEM V DTI YG G DG L DP VSME t RN KPVD L 919
Cdd:PRK08566 831 L K V E YDGTVR DTRGNI V QFK YG E DG V DP MKSD - HG KPVD V 869
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
13-907
0e+00
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: 940.13
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 13 K K I SHVQ FG ISGAD EI QQEAL V R II SKNL Y QAQRQ P VPY G VL D R R M G ISTKDAM C E TCG QGLN EC I GHFG YLD LA L PV F H 92
Cdd:cd02582 2 K R I KGIK FG LLSPE EI RKMSV V E II TPDT Y DEDGY P IEG G LM D P R L G VIEPGLR C K TCG NTAG EC P GHFG HIE LA R PV I H 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 93 I G HFRSTINI L QMI C KV C AHVM L KP E DRQL Y EKKLHN - PNFSYLGK K ALHVQMLA KAKK VTK CPHCG S P nggvkkgpg LL 171
Cdd:cd02582 82 V G FAKHIYDL L RAT C RS C GRIL L PE E EIEK Y LERIRR l KEKWPELV K RVIEKVKK KAKK RKV CPHCG A P --------- QY 152
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 172 KI LHD - P YKGRKMD slftsnmnemlrstqtnrdlnstlgn YSTAEE LTP LMVLDLF E Q IP QR D VA LLG MCSHD A H P KHLI 250
Cdd:cd02582 153 KI KLE k P TTFYEEK -------------------------- EEGEVK LTP SEIRERL E K IP DE D LE LLG IDPKT A R P EWMV 206
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 251 V T RVF VPP ACI RPS VLS E vk A G - TT EDDLT M K QSE I LL IN DVIQRHMAT G GK i E LI H ED - WD F LQ L HV AL YF HS EI S GIP 328
Cdd:cd02582 207 L T VLP VPP VTV RPS ITL E -- T G e RS EDDLT H K LVD I IR IN QRLKENIEA G AP - Q LI I ED l WD L LQ Y HV TT YF DN EI P GIP 283
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 329 I nm A PKKTT R --- GIV QRLKGK Q GRFR C NLSGKRV D FS G RTVISPDPNL M IN Q VGVP VRV AK I LT Y PERV NPA NI RH MR E 405
Cdd:cd02582 284 P -- A RHRSG R plk TLA QRLKGK E GRFR G NLSGKRV N FS A RTVISPDPNL S IN E VGVP EDI AK E LT V PERV TEW NI EK MR K 361
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 406 LV R NGP SMH PGANYV QQRGSS f KKY L A Y G NRE KV A QE L KC G DV VERHL R DGDIVLFNRQPSLH K MSIM C HR AK V Q P QR TF 485
Cdd:cd02582 362 LV L NGP DKW PGANYV IRPDGR - RIR L R Y V NRE EL A ER L EP G WI VERHL I DGDIVLFNRQPSLH R MSIM A HR VR V L P GK TF 440
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 486 R F N ECA C T PYNADFDGDEMNLH L PQ T EEARAEA LI LM GN Q SNLVT P KN G EIL I AAT QD F I T G G YLLT Q K EVFL TKEEA M Q 565
Cdd:cd02582 441 R L N LAV C P PYNADFDGDEMNLH V PQ S EEARAEA RE LM LV Q EHILS P RY G GPI I GGI QD Y I S G A YLLT R K TTLF TKEEA L Q 520
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 566 L AA cf L A NE D S tmhi K LP P PA L L K P RR LWTGKQ M FSL LM r P N D dsqvr LN MVN K ---- GRNYTRNKDL C S ND SWIH I R N S 641
Cdd:cd02582 521 L LS -- A A GY D G ---- L LP E PA I L E P KP LWTGKQ L FSL FL - P K D ----- LN FEG K akvc SGCSECKDED C P ND GYVV I K N G 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 642 E L MC GV M DK ATM G SGTKQCIFYLLLRDF G ESH A TKAMWRLA R I A SY F LQN RGF SF GI S D VTPSKKLLQHK E LLLNNGYA K 721
Cdd:cd02582 589 K L LE GV I DK KAI G AEQPGSLLHRIAKEY G NEV A RRFLDSVT R L A IR F IEL RGF TI GI D D EDIPEEARKEI E EIIKEAEK K 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 722 CN E Y IE LL K A G T L QCQ PG C T P EETLE SVMLRE L SAI R EQ A A K TCFAE L H P T N S A L IMA LS G SK GS NI N IS QM I AC V GQQ A 801
Cdd:cd02582 669 VY E L IE QY K N G E L EPL PG R T L EETLE MKIMQV L GKA R DE A G K VASKY L D P F N N A V IMA RT G AR GS ML N LT QM A AC L GQQ S 748
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 802 IS G K R VPN G FE NR A LPHF ERHSAI P A ARGFV QN SF YS GL T PTEFFFH T M A GREGLVDTAV K T AET GY L QRRL VKC L E DL V 881
Cdd:cd02582 749 VR G E R INR G YR NR T LPHF KPGDLG P E ARGFV RS SF RD GL S PTEFFFH A M G GREGLVDTAV R T SQS GY M QRRL INA L Q DL Y 828
890 900
....*....|....*....|....*.
gi 281360912 882 V H YDGTVR NAVNEMVDTI YG G DG L DP 907
Cdd:cd02582 829 V E YDGTVR DSRGNIIQFK YG E DG V DP 854
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-919
0e+00
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.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 879.82
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 13 KKI SHVQ FG ISGAD EI QQEAL V RIISKNL Y QAQRQ P VPY G VL D R R M G ISTKDAM C E TCG QGLN EC I GHFG YLD LA L PV F H 92
Cdd:TIGR02390 2 KKI GSIK FG LLSPE EI RKMSV V EVVTADT Y DDDGY P IEG G LM D P R L G VIEPGLR C K TCG GKVG EC P GHFG HIE LA R PV V H 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 93 I G HFRSTIN IL QMI C KV C AHVM L KP E DRQL Y EK K LHNPNFSY - LGKKA L HVQMLAK A K K VT KCPHCG SPNGGV K kgpgll 171
Cdd:TIGR02390 82 V G FAKEIYK IL RAT C RK C GRIT L TE E EIEQ Y LE K INKLKEEG g DLAST L IEKIVKE A A K RM KCPHCG EEQKKI K ------ 155
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 172 ki LHD P YKGRKMDS lftsnmnemlrstqtnrdlnstlgny STAEE LTP LMVLDLF E Q IP QR D VA LLG MCSHD A H P KHLIV 251
Cdd:TIGR02390 156 -- FEK P TYFYEEGK -------------------------- EGDVK LTP SEIRERL E K IP DE D AE LLG INPKV A R P EWMVL 207
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 252 T RVF VPP ACI RPS VLS E v KAGTT EDDLT M K QSE I LL IN DVIQRHMAT G GKIEL I HED W DF LQ L HVA L YF HS E IS GIP - IN 330
Cdd:TIGR02390 208 T VLP VPP VTV RPS ITL E - TGERS EDDLT H K LVD I IR IN QRLKENIEA G APQLI I EDL W EL LQ Y HVA T YF DN E LP GIP p AR 286
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 331 MAPKKTTRGIV QRLKGK Q GRFR C NLSGKRV D FS G RTVISPDPN LM IN Q VGVP VRV AK I LT Y PERV N P A NI RHM RE L V R NG 410
Cdd:TIGR02390 287 HRSGRPLKTLA QRLKGK E GRFR G NLSGKRV N FS A RTVISPDPN IS IN E VGVP EQI AK E LT V PERV T P W NI DEL RE Y V L NG 366
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 411 P SMH PGANYV - QQR G SSF K ky LAYG N R E KV A QE L KC G D VVERHL R DGDIVLFNRQPSLH K MS I M C H RA KV Q P QR TFR F N E 489
Cdd:TIGR02390 367 P DSW PGANYV i RPD G RRI K -- IRDE N K E EL A ER L EP G W VVERHL I DGDIVLFNRQPSLH R MS M M G H KV KV L P GK TFR L N L 444
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 490 CA C T PYNADFDGDEMNLH L PQTEEARAEA LI LM GNQSNLV TP KN G EIL I AATQ D F I T G G YLLT Q K EVFL TKEE AMQ - L AA 568
Cdd:TIGR02390 445 AV C P PYNADFDGDEMNLH V PQTEEARAEA RE LM LVEEHIL TP RY G GPI I GGIH D Y I S G A YLLT H K STLF TKEE VQT i L GV 524
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 569 CFLANED stmhikl P P PA LL KP RRL WTGKQ M FS LLM r P N D dsqvr LN MVNKGRN ---- YTRN K DL C SN D SWIH I R N SE L M 644
Cdd:TIGR02390 525 AGYFGDP ------- P E PA IE KP KEY WTGKQ I FS AFL - P E D ----- LN FEGRAKI csgs DACK K EE C PH D AYVV I K N GK L L 591
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 645 C GV M DK ATM G S g T K QC I FYLLL R DF G ESH A TKAMWRLA R IASY F LQN RGF SF GI S D VTPS K KLLQHK E L L LNNGYAKCNE 724
Cdd:TIGR02390 592 K GV I DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT R LFIR F ITL RGF TT GI D D IDIP K EAKEEI E E L IEKAEKRVDN 670
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 725 Y IE LLKA G T L QCQ PG C T P EETLE SVMLRE L SAI R EQ A AKTCFAE L H P T N S A L IMA LS G SK GS NI NI S QM I A C VGQQ AIS G 804
Cdd:TIGR02390 671 L IE RYRN G E L EPL PG R T V EETLE MKIMEV L GKA R DE A GEVAEKY L D P E N H A V IMA RT G AR GS LL NI T QM A A M VGQQ SVR G 750
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 805 K R VPN G FE NR A LPHF ERHSAIPA ARGFV QN SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GY L QRRL VKC L E DL V V H Y 884
Cdd:TIGR02390 751 G R IRR G YR NR T LPHF KKGDIGAK ARGFV RS SF KK GL D PTE Y FFH AAG GREGLVDTAV R T SQS GY M QRRL INA L Q DL Y V E Y 830
890 900 910
....*....|....*....|....*....|....*
gi 281360912 885 DGTVR NAVNEMVDTI YG G DG L DP VSME t RN KPVD L 919
Cdd:TIGR02390 831 DGTVR DTRGNLIQFK YG E DG V DP MKSD - HG KPVD V 864
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
13-1363
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 866.65
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 13 K K I SHVQ FG ISGADEIQQEALVR I ISKNL Y QAQRQ PV PY G V LD R R M G ISTKDAM C E TCG QGLNE C I GHFG YLD LA L PV F H 92
Cdd:PRK14977 7 K A I DGII FG LISPADARKIGFAE I TAPEA Y DEDGL PV QG G L LD G R L G TIEPGQK C L TCG NLAAN C P GHFG HIE LA E PV I H 86
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 93 I GHFRSTINI L QMI C KV CA HVM L KP ED RQLYE -- KKL H NP n FSYLGK K ALHVQMLAK -------- AKK VTK CPHCG S P NG 162
Cdd:PRK14977 87 I AFIDNIKDL L NST C HK CA KLK L PQ ED LNVFK li EEA H AA - ARDIPE K RIDDEIIEE vrdqvkvy AKK AKE CPHCG A P QH 165
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 163 GV kkgpgllk ILHD P YK grkmdslftsnmne MLRS T QTN rdlnstlgnyst AEE L T P LMVL D L FE Q I PQR D VA L L G MCSH 242
Cdd:PRK14977 166 EL -------- EFEE P TI -------------- FIEK T EIE ------------ EHR L L P IEIR D I FE K I IDD D LE L I G FDPK 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 243 D A H P KHLIVTRVF VPP ACI RPS VLS E VKA g TT EDDLT MKQSE I LLI N DVIQRHMAT G GKIELIHEDW D F LQ L H VALY F HS 322
Cdd:PRK14977 212 K A R P EWAVLQAFL VPP LTA RPS IIL E TGE - RS EDDLT HILVD I IKA N QKLKESKDA G APPLIVEDEV D H LQ Y H TSTF F DN 290
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 323 EIS GIP INM -- APKKTTRGIV QRLKGK Q GRFR C NL S GKRVDFS G RTVISPDP NLM I NQ VGVP VRV A KI LT Y PE R VN PA NI 400
Cdd:PRK14977 291 ATA GIP QAH hk GSGRPLKSLF QRLKGK E GRFR G NL I GKRVDFS A RTVISPDP MID I DE VGVP EAI A MK LT I PE I VN EN NI 370
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 401 RH M R ELV R NGP SMH PGAN YVQ q R G SSF K KY L AYGNRE ------ KV A QE L KC GD V VERHL R DGDIV L FNRQPSLHK M SI MC 474
Cdd:PRK14977 371 EK M K ELV I NGP DEF PGAN AIR - K G DGT K IR L DFLEDK gkdalr EA A EQ L EI GD I VERHL A DGDIV I FNRQPSLHK L SI LA 449
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 475 HR A KV Q P QR TFR FNECA C T PYNADFDGDEMNLH L PQ T E E ARAEA LI LMG NQS NL VT P KN G EIL I A A T QDFIT GG YL L T QK 554
Cdd:PRK14977 450 HR V KV L P GA TFR LHPAV C P PYNADFDGDEMNLH V PQ I E D ARAEA IE LMG VKD NL IS P RT G GPI I G A L QDFIT AA YL I T KD 529
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 555 EVFLT K E EA MQL A AC flaned STMHIK LP P PA L - L K PRRL WTGKQ M FSL LM r P N D DSQVRLNMVNK G RNYTRNKDL C SN D 633
Cdd:PRK14977 530 DALFD K N EA SNI A ML ------ AGITDP LP E PA I k T K DGPA WTGKQ L FSL FL - P K D FNFEGIAKWSA G KAGEAKDPS C LG D 602
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 634 SWIH I RNS EL MC GV M D KATM G SGTKQ -- CIFYLLLR D F GE SH A TKAMWRLAR IA SYFLQNR GFS F G IS D VTPSKKLL Q HK 711
Cdd:PRK14977 603 GYVL I KEG EL IS GV I D DNII G ALVEE pe SLIDRIAK D Y GE AV A IEFLNKILI IA KKEILHY GFS N G PG D LIIPDEAK Q EI 682
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 712 E LLLNNGYAKCNEY I ELL K A -------- G TLQCQP G CTP EE T LE SVMLR EL SAI R EQ A AKTCFAELHPT N SAL IMA LS G S 783
Cdd:PRK14977 683 E DDIQGMKDEVSDL I DQR K I trkitiyk G KEELLR G MKE EE A LE ADIVN EL DKA R DK A GSSANDCIDAD N AGK IMA KT G A 762
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 784 K GS NI N IS Q MIACV GQQ AI -------- S G K R VPN G FEN RAL P HF ERHSAI P A A R GFV Q N SFYS GL TPT EFFFH T M A GREG 855
Cdd:PRK14977 763 R GS MA N LA Q IAGAL GQQ KR ktrigfvl T G G R LHE G YKD RAL S HF QEGDDN P D A H GFV K N NYRE GL NAA EFFFH A M G GREG 842
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 856 L V D T A VK T AET GY L QRRL VKC LED LVVH YD G TVR NAVNEMVDTIY G G DG L DP VSME t RNKPVD L VHQ ydn LRA Q HPQGKD 935
Cdd:PRK14977 843 L I D K A RR T EDS GY F QRRL ANA LED IRLE YD E TVR DPHGHIIQFKF G E DG I DP QKLD - HGEAFN L ERI --- IEK Q KIEDRG 918
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 936 RPLNAE E msea L E T L L rtpefaearddfkldv RNHIN T VSKRIGQ L qkryek CI D LC H QI E c L TTEQ L LQFVRRINDRYN 1015
Cdd:PRK14977 919 KGASKD E ---- I E E L A ---------------- KEYTK T FNANLPK L ------ LA D AI H GA E - L KEDE L EAICAEGKEGFE 971
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1016 R A VT EPG T A V G A I A AQSI G EPGTQMTL K TFH F AG VAS M NI T Q G VP R IV E IIN A TKTI STP IITAE L -- E NCHSM E F A RQV 1093
Cdd:PRK14977 972 K A KV EPG Q A I G I I S AQSI A EPGTQMTL R TFH A AG IKA M DV T H G LE R FI E LVD A RAKP STP TMDIY L dd E CKEDI E K A IEI 1051
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1094 KARIEKTTLAE L SSYVEV vcg PYSCYLAIGVDMA R IKLL G L h I DLDTIVFSI lks RMRV K PTQV E VVASQSR I VVR - VEA 1172
Cdd:PRK14977 1052 ARNLKELKVRA L IADSAI --- DNANEIKLIKPDK R ALEN G C - I PMERFAEIE --- AALA K GKKF E MELEDDL I ILD l VEA 1124
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1173 TRTSTIN A E L ARLALSLQNVV V A G L P N I N RA VIAVDDARQPPTYKLCIE G YG L RD V IATYGVVGKR T RS N NIC EI YQ TLG 1252
Cdd:PRK14977 1125 ADRDKPL A T L IAIRNKILDKP V K G V P D I E RA WVELVEKDGRDEWIIQTS G SN L AA V LEMKCIDIAN T IT N DCF EI AG TLG 1204
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1253 IEAAR TI I MS E ITEVM E GH G MS VD W R H IML L A SQ M TA RG EVLG I ------ T RHG L A KMRE S VFNL A S FE K T ADHLFD AA Y 1326
Cdd:PRK14977 1205 IEAAR NA I FN E LASIL E DQ G LE VD N R Y IML V A DI M CS RG TIEA I glqaag V RHG F A GEKD S PLAK A A FE I T THTIAH AA L 1284
1370 1380 1390
....*....|....*....|....*....|....*..
gi 281360912 1327 Y G QTDA I N G VSERI I L G MPAC IG T G IFK LL QQHED K Q 1363
Cdd:PRK14977 1285 G G EIEK I K G ILDAL I M G QNIP IG S G KVD LL MDFSG K A 1321
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
18-885
0e+00
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: 834.11
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 18 VQFGI SGA DEI QQEALVR I ISKNL Y QAQRQ P VPY G VL D R RMG ISTKDAM C E TCG QGLN EC I GHFG YLD LA L PVFHIG HFR 97
Cdd:cd02733 3 VQFGI LSP DEI RAMSVAE I EHPET Y ENGGG P KLG G LN D P RMG TIDRNSR C Q TCG GDMK EC P GHFG HIE LA K PVFHIG FLT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 98 STIN IL QMI CK V cahvmlkpedrqlyekklhnpnfsylgkkalhvqmlakakkvtkcphcgspnggvkkgpgllkilhdp 177
Cdd:cd02733 83 KILK IL RCV CK R -------------------------------------------------------------------- 94
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 178 ykgrkmdslftsnmnemlrstqtnrdlnstlgnystae EL TPLM VL DL F EQ I PQR D VAL LG MCSHDAH P KHL I V T RVF VP 257
Cdd:cd02733 95 -------------------------------------- EL SAER VL EI F KR I SDE D CRI LG FDPKFSR P DWM I L T VLP VP 136
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 258 P ACI RPSV lse V KA G TT -- EDDLT M K QSE I LLI N DVIQ R HMAT G GKIEL I H ED WDF LQ L HVA L Y FHS EI S G I P in M A PK K 335
Cdd:cd02733 137 P PAV RPSV --- V MD G SA rs EDDLT H K LAD I IKA N NQLK R QEQN G APAHI I E ED EQL LQ F HVA T Y MDN EI P G L P -- Q A TQ K 211
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 336 TT R --- G I V QRLKGK Q GR F R C NL S GKRVDFS G RTVI S PDPNL MIN QVGVP VRV A KI LT Y PE R V N P A NI RHMR ELVRNGP S 412
Cdd:cd02733 212 SG R plk S I R QRLKGK E GR I R G NL M GKRVDFS A RTVI T PDPNL ELD QVGVP RSI A MN LT F PE I V T P F NI DRLQ ELVRNGP N 291
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 413 MH PGA N Y VQ q R GSSFKKY L A Y GNR e KVAQE L KC G DV VERHL R DGD I VLFNRQPSLHKMS I M C HR A KV Q P QR TFR F N ECAC 492
Cdd:cd02733 292 EY PGA K Y II - R DDGERID L R Y LKK - ASDLH L QY G YI VERHL Q DGD V VLFNRQPSLHKMS M M G HR V KV L P YS TFR L N LSVT 369
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 493 TPYNADFDGDEMNLH L PQ TE E A RAE ALI LM GNQSNL V T P KNGEILIAAT QD FIT G GYL LT QKEV FL T K EEA M Q L AA c F L A 572
Cdd:cd02733 370 TPYNADFDGDEMNLH V PQ SL E T RAE LKE LM MVPRQI V S P QSNKPVMGIV QD TLL G VRK LT KRDT FL E K DQV M N L LM - W L P 448
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 573 NE D stmh I K L P P PA L LKP RR LWTGKQ M FSL LM r P NDDSQV R LNMVNK G RN ytrn K DLCSN D SWIH I R N S EL MC G VMD K A T 652
Cdd:cd02733 449 DW D ---- G K I P Q PA I LKP KP LWTGKQ I FSL II - P KINNLI R SSSHHD G DK ---- K WISPG D TKVI I E N G EL LS G ILC K K T 519
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 653 M G SG t KQCIFYLLLRDF G ESH A TKAMWRLA R IASYF L QNR GFS F GI S D VTPS K KLLQHKELLLNNGYAKCNEY IE LLKA G 732
Cdd:cd02733 520 V G AS - SGGLIHVIWLEY G PEA A RDFIGNIQ R VVNNW L LHN GFS I GI G D TIAD K ETMKKIQETIKKAKRDVIKL IE KAQN G 598
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 733 T L QC QPG C T PE E TL E SVML R E L SAI R EQ A A K TCFAE L HPT N SALI M ALS GSKGS N INISQ M IACVGQQ AIS GKR V P N GF E 812
Cdd:cd02733 599 E L EP QPG K T LR E SF E NKVN R I L NKA R DK A G K SAQKS L SED N NFKA M VTA GSKGS F INISQ I IACVGQQ NVE GKR I P F GF R 678
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 281360912 813 N R A LPHF ERHSAI P AA RGFV Q NS FYS GLTP T EFFFH T M A GREGL V DTAVKTAETGY L QRRLVK CL ED LV V H YD 885
Cdd:cd02733 679 R R T LPHF IKDDYG P ES RGFV E NS YLR GLTP Q EFFFH A M G GREGL I DTAVKTAETGY I QRRLVK AM ED VM V K YD 751
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
19-885
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: 599.56
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 19 Q F GISG A D EI QQEALVR I ISKNLYQAQRQ PVP Y G VL D RRM G IST KD AM C E TCG QGLNE C I GHFG YLD L A LPV FHIGH F RS 98
Cdd:cd01435 1 S F SFYS A E EI RKLSVKE I TNPVTFDSLGH PVP G G LY D PAL G PLD KD DI C S TCG LNYLN C P GHFG HIE L P LPV YNPLF F DL 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 99 TINI L QMI C KV C AHVMLKPEDRQ L YEK KL hnpnfsylgkkalhv QM L A K AKK V TK cphcgspnggvkkgpgll KI L HDP Y 178
Cdd:cd01435 81 LYKL L RGS C FY C HRFRISKWEVK L FVA KL --------------- KL L D K GLL V EA ------------------ AE L DFG Y 127
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 179 kgrkm D SL F TSNMN emlrstqtnrdlnstlgnystaeeltplmvldlfeqipqrdvallgmcshdahpkhlivtrvf VPP 258
Cdd:cd01435 128 ----- D MF F LDVLL --------------------------------------------------------------- VPP 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 259 ACI RP sv L S EVKAGTT E DDLTMKQ S E IL LI N DV I QRHM A T --------------- GGKI E LIHED W DF LQ LH V ALY F H S E 323
Cdd:cd01435 140 NRF RP -- P S FLGDKVF E NPQNVLL S K IL KD N QQ I RDLL A S mrqaesqskldlisg KTNS E KLINA W LQ LQ SA V NEL F D S T 217
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 324 ISGIPINMA P K kttr GI V Q R L KG K Q G R FR C N LS GKRV DFSG R T VISPDP NLMI N QV G V P VRV AK I LT Y PE R V N P A N IRHM 403
Cdd:cd01435 218 KAPKSGKKS P P ---- GI K Q L L EK K E G L FR M N MM GKRV NYAA R S VISPDP FIET N EI G I P LVF AK K LT F PE P V T P F N VEEL 293
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 404 R EL V R NGP SMH PGAN YVQQRGSS f KKY L AYGN --- R EKV A QE L KC ---------- GDV V E RHL R DGD I VL F NRQP S LHK M 470
Cdd:cd01435 294 R QA V I NGP DVY PGAN AIEDEDGR - LIL L SALS eer R KAL A KL L LL lssaklllng PKK V Y RHL L DGD V VL L NRQP T LHK P 372
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 471 SIM C H RAK V Q P - QR T F R FNECA C TP YNADFDGDEMNLH L PQ T E E ARAEA LILMGNQSNLVT P KN G EI L IAAT QD FITG G Y 549
Cdd:cd01435 373 SIM A H KVR V L P g EK T L R LHYAN C KS YNADFDGDEMNLH F PQ S E L ARAEA YYIASTDNQYLV P TD G KP L RGLI QD HVVS G V 452
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 550 LLT QKEV F L T K EE AM QL AAC --- F L ANE D STMH IKL P PPA L LKP RR LWTGKQ MF S LLMRP - NDDSQVR LN MVN K GRNYTR 625
Cdd:cd01435 453 LLT SRDT F F T R EE YQ QL VYA alr P L FTS D KDGR IKL L PPA I LKP KP LWTGKQ VI S TILKN l IPGNAPL LN LSG K KKTKKK 532
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 626 NKDLC ---- S ND S WIH IRN S EL MC GV M DK ATM G S g TKQCI --- F Y L L lrd F G ESH A T K AMWR L A R IASYF LQ N RGF SF GI 698
Cdd:cd01435 533 VGGGK wggg S EE S QVI IRN G EL LT GV L DK SQF G A - SAYGL vha V Y E L --- Y G GET A G K LLSA L G R LFTAY LQ M RGF TC GI 608
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 699 S D vtpskkllqhke LLL NNGY -- AKCNEYIELL K A G T lqcqpg CTPE E T L ESVMLREL S A I R eqaa K T C FAE - L H --- P T 772
Cdd:cd01435 609 E D ------------ LLL TPKA de KRRKILRKAK K L G L ------ EAAA E F L GLKLNKVT S S I I ---- K A C LPK g L L kpf P E 666
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 773 N SALI M AL SG S KGS NI N I SQ MIACV GQQ AIS G K RVP NGFENRA LP H F ERHSAI P A A R GF VQNS F YS G LT P T E F FFH T MAG 852
Cdd:cd01435 667 N NLQL M VQ SG A KGS MV N A SQ ISCLL GQQ ELE G R RVP LMVSGKT LP S F PPYDTS P R A G GF ITDR F LT G IR P Q E Y FFH C MAG 746
890 900 910
....*....|....*....|....*....|...
gi 281360912 853 REGL V DTAVKT AET GYLQR R L V K C LE D L V V H YD 885
Cdd:cd01435 747 REGL I DTAVKT SRS GYLQR C L I K H LE G L K V N YD 779
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
26-885
0e+00
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: 560.51
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 26 D EI QQEALVRI I SKNLY - QAQRQPVPY G VL D R R M G ISTKDAM C E TCG Q GLN E C I GHFG YLD LA L PVFH I G HFRSTINI L Q 104
Cdd:cd00399 4 E EI RKWSVAKV I KPETI d NRTLKAERG G KY D P R L G SIDRCEK C G TCG T GLN D C P GHFG HIE LA K PVFH V G FIKKVPSF L G 83
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 105 mickvcahvmlk PE D rqlyekklhnpnfsylgkkalhvqmlakakkvtkcphcgspnggvkkgpgllkilhdpykgrkmd 184
Cdd:cd00399 84 ------------ PE W ----------------------------------------------------------------- 86
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 185 slftsnmnemlrstqtnrdlnstlgnystaeeltplmvldlfeqipqrdvallgmcshdahpkh L I V T RVF VPP A C I RPS 264
Cdd:cd00399 87 ---------------------------------------------------------------- M I L T CLP VPP P C L RPS 102
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 265 V L sevkagtteddltmkqseillindviqrhmatggkiel I H E D W DF LQ L HV AL Y FHSE I S G I P INMAPKKTT R GIV QRL 344
Cdd:cd00399 103 V I -------------------------------------- I E E R W RL LQ E HV DT Y LDNG I A G Q P QTQKSGRPL R SLA QRL 144
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 345 KGK Q GRFR C NL S GKRVDFSGR T VISPDPNL MIN QVGVP VRV A KI L typervnpanirhmrelvrngpsmhpganyvqqrg 424
Cdd:cd00399 145 KGK E GRFR G NL M GKRVDFSGR S VISPDPNL RLD QVGVP KSI A LT L ----------------------------------- 189
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 425 ssfkkylaygnrekvaqelkcgdvverhlr DGD I VLFNRQPSLHK M SIM C HR AK V Q P QR TFR F N ECA C T PYNADFDGDEM 504
Cdd:cd00399 190 ------------------------------ DGD P VLFNRQPSLHK L SIM A HR VR V L P GS TFR L N PLV C S PYNADFDGDEM 239
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 505 NLH L PQ T EEARAEA LI LM GNQS N LVT P K NGE I LI AAT QD FIT G G YLLT Q kevfltkeeamqlaacflanedstmhiklpp 584
Cdd:cd00399 240 NLH V PQ S EEARAEA RE LM LVPN N ILS P Q NGE P LI GLS QD TLL G A YLLT L ------------------------------- 288
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 585 pallkprrlwt GKQ MF S LLM r P ND dsqvrlnmvnkgrnytrnkdlcsndswihirnselmcgvmdkatmgsgtkqc IFYL 664
Cdd:cd00399 289 ----------- GKQ IV S AAL - P GG ---------------------------------------------------- LLHT 304
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 665 LL R DF G ESH A T K AMWR L A R IASY FL QNR GFS F GI S DV TPSKKLLQH K EL L LNNGYA K CN E YI E LLK AG T L QC Q P G C T P EE 744
Cdd:cd00399 305 VT R EL G PEK A A K LLSN L Q R VGFV FL TTS GFS V GI G DV IDDGVIPEE K TE L IEEAKK K VD E VE E AFQ AG L L TA Q E G M T L EE 384
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 745 T LE SVM L RE L SAI R EQ A AKTCFAE L --- HPT NS ALI MA L SG S KGS N INI S QM I ACVGQQ AIS GKR V P N GF EN R A LPHF ER 821
Cdd:cd00399 385 S LE DNI L DF L NEA R DK A GSAASVN L dlv SKF NS IYV MA M SG A KGS F INI R QM S ACVGQQ SVE GKR I P R GF SD R T LPHF SK 464
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281360912 822 HSAI P A A R GF VQ NSF YS GLTP T E F FFH T M A GREGLVDTAVKTAE T GYLQRRLVK C LEDLVVHYD 885
Cdd:cd00399 465 DDYS P E A K GF IR NSF LE GLTP L E Y FFH A M G GREGLVDTAVKTAE S GYLQRRLVK A LEDLVVHYD 528
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1013-1353
2.84e-175
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: 522.55
E-value: 2.84e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1013 R Y N RA VT EPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNIT Q GVPRI V EIINA T K T ISTPIITA E LEN CHSMEF AR Q 1092
Cdd:cd02736 1 K Y M RA KV EPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNIT L GVPRI K EIINA S K N ISTPIITA K LEN DRDEKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1093 VK A RIEKT T L A E LS SY V E V V CG P YS CY LA I GV D MAR I KL L G L hidldtivfsilksrmrvkptqvevvasqsrivvrvea 1172
Cdd:cd02736 81 VK G RIEKT Y L G E VA SY I E E V YS P DD CY IL I KL D KKI I EK L Q L -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1173 t RT S TINAE L AR L ALS L QN VVV A G L P NIN RAVI AV D D ar QPPT YKL CI EGYGLR D V IA T Y GV V G K RT R SN N I C E IYQT LG 1252
Cdd:cd02736 123 - SK S NLYFL L QS L KRK L PD VVV S G I P EVK RAVI NK D K -- KKGK YKL LV EGYGLR A V MN T P GV I G T RT T SN H I M E VEKV LG 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1253 IEAAR TI I MS EI TEV M EG HGMS V D W RHIMLLA SQ MT AR GEVLGITR H G L AKM R ESV FN LASFEKT A DHLF D AA YY G QT D A 1332
Cdd:cd02736 200 IEAAR ST I IN EI QYT M KS HGMS I D P RHIMLLA DL MT FK GEVLGITR F G I AKM K ESV LM LASFEKT T DHLF N AA LH G RK D S 279
330 340
....*....|....*....|.
gi 281360912 1333 I N GVSE R II L G M P AC IGTG I F 1353
Cdd:cd02736 280 I E GVSE C II M G K P MP IGTG L F 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
249-549
3.94e-145
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 443.11
E-value: 3.94e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 249 L I V T RVF VPP A C I RPSV LSEVKA g TT EDDLT MKQSE I LLI N DVIQ R HMAT G GKIEL I HEDWDF LQ LH V ALYFHS E i SGIP 328
Cdd:smart00663 3 M I L T VLP VPP P C L RPSV QLDGGR - FA EDDLT HLLRD I IKR N NRLK R LLEL G APSII I RNEKRL LQ EA V DTLIDN E - GLPR 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 329 I N MAPKKTTRGIV QRLKGK Q GRFR C NL S GKRVDFS G R T VI S PDPNL MI N Q VGVP VRV A KI LT Y PE R V N P A NI RHM R E LVR 408
Cdd:smart00663 81 A N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KL N E VGVP KEI A LE LT F PE I V T P L NI DKL R K LVR 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 409 NGP smh P GA N Y VQQ rgs SF K KY L AYGNRE K V A QE LK C GD V VERH LR DGD I VLFNRQP S LH K MSI MC HR AK V QPQR T F R F N 488
Cdd:smart00663 161 NGP --- N GA K Y IIR --- GK K TN L KLAKKS K I A NH LK I GD I VERH VI DGD V VLFNRQP T LH R MSI QA HR VR V LEGK T I R L N 234
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281360912 489 ECA C T PYNADFDGDEMNLH L PQ TE EARAEA LI LM GNQS N LVT PKNG EIL I AAT QD FIT G G Y 549
Cdd:smart00663 235 PLV C S PYNADFDGDEMNLH V PQ SL EARAEA RE LM LVPN N ILS PKNG KPI I GPI QD MLL G L Y 295
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
839-1309
1.66e-119
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: 383.24
E-value: 1.66e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 839 GLTP T EFFFHTM A GREGL V DTAVKTAE T GYLQRRLVK C LEDLVV H YD G TVRN AVN E M V DTI YG G DGLDP VSM E TRNKPV d 918
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GYLQRRLVK A LEDLVV T YD D TVRN SGG E I V QFL YG E DGLDP LKI E KQGRFT - 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 919 LVHQYDN L RAQ hpqg KDRP L NAEEMSEALET L L rtp EFA E ARDDFKLDV R NHINTVSK ----------- RI G QLQ KR YEK 987
Cdd:pfam04998 80 IEFSDLK L EDK ---- FKND L LDDLLLLSEFS L S --- YKK E ILVRDSKLG R DRLSKEAQ eratllfelll KS G LES KR VRS 152
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 988 CIDL - CHQIE CL TTE qllqfvrr INDR Y NRAVTE PG T AVG A IAAQSIGEPGTQMTL K TFHFAGVAS M N I T Q GVPR IV EII 1066
Cdd:pfam04998 153 ELTC n SKAFV CL LCY -------- GRLL Y QQSLIN PG E AVG I IAAQSIGEPGTQMTL N TFHFAGVAS K N V T L GVPR LK EII 224
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1067 N AT K T I ST P II T AE L ENCHSM E F -- A RQ V KAR IEK T TL AELSSYV E VVCG P YS --------------- CYLAIG V DM --- 1126
Cdd:pfam04998 225 N VS K N I KS P SL T VY L FDEVGR E L ek A KK V YGA IEK V TL GSVVESG E ILYD P DP fntpiisdvkgvvkf FDIIDE V TN eee 304
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1127 ------ AR I KLLG L HID L DTIVFSIL KS --------------- RMRVKPTQVEVVASQSR I VVRVEAT R TSTINAELARL 1185
Cdd:pfam04998 305 idpetg LL I LVIR L LKI L NKSIKKVV KS eviprsirnkvdegr DIAIGEITAFIIKISKK I RQDTGGL R RVDELFMEEDP 384
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1186 A L S ------ L Q N VVVA G L P N I N R AVIAV DD A - RQP P TYK L CI EG YG L RD V IATY G V V GK - R TR SN N I C EI YQT LGIEAAR 1257
Cdd:pfam04998 385 K L A ilvasl L G N ITLR G I P G I K R ILVNE DD K g KVE P DWV L ET EG VN L LR V LLVP G F V DA g R IL SN D I H EI LEI LGIEAAR 464
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|..
gi 281360912 1258 TIIMS EI TE V MEGH G MSVDW RH IM L L A S QMT AR G EVLG I T RHG LA K MRE S VF 1309
Cdd:pfam04998 465 NALLN EI RN V YRFQ G IYIND RH LE L I A D QMT RK G YIMA I G RHG IN K AEL S AL 516
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
998-1356
1.63e-97
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: 317.27
E-value: 1.63e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 998 LT TEQLLQFVRRINDR Y N R AVT EPG T AVG AI AAQSIGEPGTQMTL K TFH F AGVA SM N I T Q G V PR IV EI IN A T K TI STP II 1077
Cdd:cd06528 16 LT LSEAEEIIKEVLRE Y L R SLI EPG E AVG IV AAQSIGEPGTQMTL R TFH Y AGVA EI N V T L G L PR LI EI VD A R K EP STP TM 95
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1078 T AE LE NCH -- SM E F A RQ V KAR IE K TTL AE L SSYVEV vc GPYSCYLA I GV D MARIKLL G LHI D L dti V FSILKSRMRV K pt 1155
Cdd:cd06528 96 T IY LE EEY ky DR E K A EE V ARK IE E TTL EN L AEDISI -- DLFNMRIT I EL D EEMLEDR G ITV D D --- V LKAIEKLKKG K -- 168
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1156 qvev V ASQSRIVVR V EATRTST I N a EL AR LA LSLQ N VVVA G LPN I N R AVIAVDDAR qppt Y KLCI EG YG L RD V IATY GV V 1235
Cdd:cd06528 169 ---- V GEEGDVTLI V LKAEEPS I K - EL RK LA EKIL N TKIK G IKG I K R VIVRKEEDE ---- Y VIYT EG SN L KA V LKVE GV D 239
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1236 GK RT RS NNI C EI YQT LGIEAAR TI I MS EI TEVM E GH G MS VD W RHIML L A SQ MT AR GEV LG I T RHG L A KMRE SV FNL A S FE 1315
Cdd:cd06528 240 PT RT TT NNI H EI EEV LGIEAAR NA I IN EI KRTL E EQ G LD VD I RHIML V A DI MT YD GEV RQ I G RHG I A GEKP SV LAR A A FE 319
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 281360912 1316 K T AD HL F DAA YY G QT D AIN GV S E R II L G M P ACI GTG IFK L L 1356
Cdd:cd06528 320 V T VK HL L DAA VR G EV D ELR GV I E N II V G Q P IPL GTG DVE L T 360
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
998-1356
4.83e-96
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 314.09
E-value: 4.83e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 998 LT T E QLLQFVRRINDR Y N R AVT EPG T AVG AI AAQSIGEPGTQMT LK TFH F AGVA SM N I T Q G V PR IV EI IN A T K TI STP II 1077
Cdd:PRK04309 35 LT E E EVEEIIEEVVRE Y L R SLV EPG E AVG VV AAQSIGEPGTQMT MR TFH Y AGVA EI N V T L G L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1078 T AE L -- E NCHSM E F A RQ V KAR IE K TTL AE L SSYVE V vc GPYSCYLA I GV D MARIKLL G lh IDL D TIV f SILKSRMRV kpt 1155
Cdd:PRK04309 115 T IY L kd E YAYDR E K A EE V ARK IE A TTL EN L AKDIS V -- DLANMTII I EL D EEMLEDR G -- LTV D DVK - EAIEKKKGG --- 186
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1156 qv EV VASQSRIVVRVEATRTS tina EL AR LA LSLQ N VVVA G LPN I N R AV I AVDDAR qppt Y KLCI EG YG L RD V IATY GV V 1235
Cdd:PRK04309 187 -- EV EIEGNTLIISPKEPSYR ---- EL RK LA EKIR N IKIK G IKG I K R VI I RKEGDE ---- Y VIYT EG SN L KE V LKVE GV D 256
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1236 GK RT RS NNI C EI YQT LGIEAAR TI I MS EI TEVM E GH G MS VD W RHIML L A SQ MT AR GEV LG I T RHG LAKMRE SV FNL A S FE 1315
Cdd:PRK04309 257 AT RT TT NNI H EI EEV LGIEAAR NA I IE EI KNTL E EQ G LD VD I RHIML V A DM MT WD GEV RQ I G RHG VSGEKA SV LAR A A FE 336
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 281360912 1316 K T AD HL F DAA YY G QT D AIN GV S E R II L G M P ACI GTG IFK L L 1356
Cdd:PRK04309 337 V T VK HL L DAA VR G EV D ELK GV T E N II V G Q P IPL GTG DVE L T 377
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
12-355
3.62e-95
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: 309.22
E-value: 3.62e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 12 N KKI SHV QFGI SGAD EI QQEALVRIISKNL Y Q - AQRQ P VPY G V LD R RMG IST KD AM CETCG QGLNE C I GHFG YLD LA L PV 90
Cdd:pfam04997 1 L KKI KEI QFGI ASPE EI RKWSVGEVTKPET Y N y GSLK P EEG G L LD E RMG TID KD YE CETCG KKKKD C P GHFG HIE LA K PV 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 91 FHIG H F RS T IN IL QMI CK V C AHVM L K P EDRQ L YE K KLHNPNFSY L GKK A LHV qm L AKA KK VTK C P HCG SP NG GVKKGPGL 170
Cdd:pfam04997 81 FHIG F F KK T LK IL ECV CK Y C SKLL L D P GKPK L FN K DKKRLGLEN L KMG A KAI -- L ELC KK KDL C E HCG GK NG VCGSQQPV 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 171 LKILH dpykgrkmdslft SNMNEMLRSTQTNRDL nstlgnysta E E L T P LM VL DL F EQ I PQR DV AL LG MCSHDAH P KHL I 250
Cdd:pfam04997 159 SRKEG ------------- LKLKAAIKKSKEEEEK ---------- E I L N P EK VL KI F KR I SDE DV EI LG FNPSGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 251 V T RVF VPP A CIRPSV LSEVK a GTT EDDLT M K QSE I LLI N DVIQRHMAT G GKIEL I H E D W DF LQ L HVA LY F HS EI S G I - P I 329
Cdd:pfam04997 216 L T VLP VPP P CIRPSV QLDGG - RRA EDDLT H K LRD I IKR N NRLKKLLEL G APSHI I R E E W RL LQ E HVA TL F DN EI P G L p P A 294
330 340
....*....|....*....|....*.
gi 281360912 330 NMAP K KTTRG I V QRLKGK Q GRFR C NL 355
Cdd:pfam04997 295 LQKS K RPLKS I S QRLKGK E GRFR G NL 320
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
357-523
1.27e-91
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: 292.67
E-value: 1.27e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 357 GKRVDFS G RTVISPDPNL MINQ VGVP VRV AK I LT Y PE R V N P A NI RHM R E LV R NGP SMH PGANY VQ q R GSSFKKY L A Y GN R 436
Cdd:pfam00623 1 GKRVDFS A RTVISPDPNL KLDE VGVP ISF AK T LT F PE I V T P Y NI KRL R Q LV E NGP NVY PGANY II - R INGARRD L R Y QK R 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 437 e KVAQ EL KC GD V VERH LR DGD I VLFNRQPSLH KM SIM C HR AK V Q P QR TFR F N ECAC TPYNADFDGDEMNLH L PQ T EEARA 516
Cdd:pfam00623 80 - RLDK EL EI GD I VERH VI DGD V VLFNRQPSLH RL SIM G HR VR V L P GK TFR L N LSVT TPYNADFDGDEMNLH V PQ S EEARA 158
....*..
gi 281360912 517 EA LI LM G 523
Cdd:pfam00623 159 EA EE LM L 165
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
982-1356
5.31e-87
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: 288.10
E-value: 5.31e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 982 Q K RYEKCIDLCHQI E CLTT E Q L LQFVR R INDR Y N R AVTE PG T AVG AI AAQSIGEPGTQMT LK TFH F AGVA SM N I T Q G V PR 1061
Cdd:TIGR02389 4 E K LLKELEETVKKR E ISDK E E L DEIIK R VEEE Y L R SLID PG E AVG IV AAQSIGEPGTQMT MR TFH Y AGVA EL N V T L G L PR 83
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1062 IV EI IN A T KT I STP II T AE LE NCH -- SM E F A RQ V KAR IE K T T L AELSS yvevvcgpyscyl A I GV D M A RIKLL glh I D LD 1139
Cdd:TIGR02389 84 LI EI VD A R KT P STP SM T IY LE DEY ek DR E K A EE V AKK IE A T K L EDVAK ------------- D I SI D L A DMTVI --- I E LD 147
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1140 T ivf SI LK S R MRVKPTQVEVVASQSRIV V RVEATRTS TI NA -------- EL AR L ALSLQ N VVVA G LPN I N R A VI AVDDAR 1211
Cdd:TIGR02389 148 E --- EQ LK E R GITVDDVEKAIKKAKLGK V IEIDMDNN TI TI kpgnpslk EL RK L KEKIK N LHIK G IKG I K R V VI RKEGDE 224
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1212 qppt Y KLCI EG YG L RD V IATY GV VGK RT RS N N I C EI YQT LGIEAAR TI I MS EI TEVM E GH G MS VD W RH I ML L A SQ MT AR G 1291
Cdd:TIGR02389 225 ---- Y VIYT EG SN L KE V LKLE GV DKT RT TT N D I H EI AEV LGIEAAR NA I IE EI KRTL E EQ G LD VD I RH L ML V A DL MT WD G 300
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 281360912 1292 EV LG I T RHG LAKMRE SV FNL A S FE K T AD HL F DAA YY G QT D AIN GV S E R II L G M P ACI GTG IFK L L 1356
Cdd:TIGR02389 301 EV RQ I G RHG ISGEKA SV LAR A A FE V T VK HL L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L V 365
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
998-1356
1.12e-82
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 280.93
E-value: 1.12e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 998 L TTEQLLQFV RRI NDR Y N RA VTE P GT AVG AI AAQSIGEPGTQMT LK TFH F AGVA S MN I T Q G V PR IV EI IN A T K TI STP II 1077
Cdd:PRK14897 158 L SDDEYEEIL RRI REE Y E RA RVD P YE AVG IV AAQSIGEPGTQMT MR TFH Y AGVA E MN V T L G L PR LI EI VD A R K KP STP TM 237
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1078 T AE L EN -- CHSM E FA R Q V KAR IE K TTL AELSSYVEVVCG pyscy LAIG V DMARI K LLGLH I DL D T I VFS I L K srmrvkp T 1155
Cdd:PRK14897 238 T IY L KK dy REDE E KV R E V AKK IE N TTL IDVADIITDIAE ----- MSVV V ELDEE K MKERL I EY D D I LAA I S K ------- L 305
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1156 QVEV V ASQSR I V v R VEATRT S T in AE L AR LA LSLQNVVVA G LPN I N RA VIAVDDARQ pp TYKLCIE G YG L R DV IATYG V V 1235
Cdd:PRK14897 306 TFKT V EIDDG I I - R LKPQQP S F -- KK L YL LA EKVKSLTIK G IKG I K RA IARKENDER -- RWVIYTQ G SN L K DV LEIDE V D 380
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1236 GK RT RS N N I C EI YQT LGIEAAR TI I MS E ITEVMEGH G MS VD W RHIML L A SQ MT AR G E V LG I T RHG LAKMRE SV FNL A S FE 1315
Cdd:PRK14897 381 PT RT YT N D I I EI ATV LGIEAAR NA I IH E AKRTLQEQ G LN VD I RHIML V A DM MT FD G S V KA I G RHG ISGEKS SV LAR A A FE 460
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 281360912 1316 K T AD HL FD A AYY G QT D AIN GV S E R II L G M P ACI GTG IFK L L 1356
Cdd:PRK14897 461 I T GK HL LR A GIL G EV D KLA GV A E N II V G Q P ITL GTG AVS L V 501
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
998-1356
4.22e-82
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: 276.01
E-value: 4.22e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 998 L TT E QLLQFVRR I ND R Y NR AVTE PG TA VG A IAAQSIGEP G TQMTL K TFHFAGV ASM N I T Q GVPR IV EIIN AT K T I S TP II 1077
Cdd:cd02584 3 L NK E AFDWILGE I ET R F NR SLVH PG EM VG T IAAQSIGEP A TQMTL N TFHFAGV SAK N V T L GVPR LK EIIN VA K N I K TP SL 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1078 T AE LE N -- CHSM E F A RQVKA R I E K TTL AELSSYV E VVCG P ------------- YSC Y LAIGVDMARIKL L G --- L H I D LD 1139
Cdd:cd02584 83 T VY LE P gf AKDE E K A KKIQS R L E H TTL KDVTAAT E IYYD P dpqntvieedkef VES Y FEFPDEDVEQDR L S pwl L R I E LD 162
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1140 TIVF -------- S I L K SRMRVKPTQVE V VA S Q --- SRI V V R VEATRTSTINA E LARLALS L QN ----------------- 1191
Cdd:cd02584 163 RKKM tdkklsme Q I A K KIKEEFKDDLN V IF S D dna EKL V I R IRIINDDEEKE E DSEDDVF L KK iesnmlsdmtlkgiegi 242
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1192 - V V VAGLP N INRAV I AVDDARQPPTYK L CIE G YG LR D V IATY GV VGK RT R SN N I C EI YQT LGIEAAR TIIMS E ITE V MEG 1270
Cdd:cd02584 243 r K V FIREE N KKKVD I ETGEFKKREEWV L ETD G VN LR E V LSHP GV DPT RT T SN D I V EI FEV LGIEAAR KALLK E LRN V ISF 322
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1271 H G MS V DW RH IM LL ASQ MT A RG EVLG ITRHG LAKMRESVFNLA SFE K T A D H L FD AA YY G Q TD AIN GVSE R I I LG MP A C IGT 1350
Cdd:cd02584 323 D G SY V NY RH LA LL CDV MT Q RG HLMA ITRHG INRQDTGPLMRC SFE E T V D I L LE AA AF G E TD DLK GVSE N I M LG QL A P IGT 402
....*.
gi 281360912 1351 G I F K LL 1356
Cdd:cd02584 403 G C F D LL 408
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
63-1351
1.04e-80
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: 290.03
E-value: 1.04e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 63 K DAM CE T CG QGLN E CI --- GHF G YLD LA L PV F HI GH F RSTIN ---- I L QMIC K ------- VCAH V M L K P E D RQ L YE K KLH 128
Cdd:TIGR02386 63 K GVV CE R CG VEVT E SK vrr ERM G HIE LA A PV A HI WY F KGLPS rigl L L DITA K elesvly FENY V V L D P G D TK L DK K EVL 142
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 129 NPN f S Y LGKKALH vqmlakakkvtkcphcgsp NG G VKK G P G LLK I L h DPYKGRKM D SLF t SNMNEM LR STQTNRD lnstl 208
Cdd:TIGR02386 143 DET - E Y REVLKRY ------------------- GD G FRA G M G AEA I K - ELLEKIDL D KEI - EELKIQ LR ESKSDQK ----- 195
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 209 gnys TAEE L TP L MVLDL F EQ ipqrdvallgmcs HDAH P KHLIVTRVF V P P ACI RP S V LSEVKAGT T E D -- DL TMK qse IL 286
Cdd:TIGR02386 196 ---- RKKL L KR L EIVEA F KD ------------- SGNR P EWMVLDVIP V I P PEL RP M V QLDGGRFA T S D ln DL YRR --- VI 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 287 LI N DVIQ R HMAT G GKIELIHEDWDF LQ LH V ALY F HSEIS G I P INMAPKKTTRGIVQR LKGKQGRFR C NL S GKRVD F SGR T 366
Cdd:TIGR02386 256 NR N NRLK R LLEL G APEIIVRNEKRM LQ EA V DAL F DNGRR G K P VVGKNNRPLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S 335
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 367 VI SPD P N L MIN Q V G V P VRV A KI L TY P ervnpani RHMRE L VR ngpsm HPG A NYVQQR gssfkkylaygn REKVA QE L - KC 445
Cdd:TIGR02386 336 VI VVG P E L KMY Q C G L P KKM A LE L FK P -------- FIIKR L ID ----- REL A ANIKSA ------------ KKMIE QE D p EV 390
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 446 G DV V E RHLRDGD i VL F NR Q P S LH KMS I MCHRAKVQPQRTF R FNECA CT PY NADFDGD E M NL H L P QTE EA R AEA LI LM GNQ 525
Cdd:TIGR02386 391 W DV L E DVIKEHP - VL L NR A P T LH RLG I QAFEPVLVEGKAI R LHPLV CT AF NADFDGD Q M AV H V P LSP EA Q AEA RA LM LAS 469
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 526 S N LVT PK N G EILIAAT QD FIT G G Y L LT QKE -------- V F LTKE EA mqlaac FL A NEDSTM H IKLPPPALLKPRR L W T -- 595
Cdd:TIGR02386 470 N N ILN PK D G KPIVTPS QD MVL G L Y Y LT TEK pgakgegk I F SNVD EA ------ IR A YDNGKV H LHALIGVRTSGEI L E T tv 543
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 596 G KQM F sllmrpnddsqvrlnmvnkgrnytr N KD L CSNDSW I HIRN selmcg VMD K ATMG S GTKQC if Y LL ---------- 665
Cdd:TIGR02386 544 G RVI F ------------------------- N EI L PEGFPY I NDNE ------ PLS K KEIS S LIDLL -- Y EV hgieetaeml 590
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 666 -- LRDF G ESH ATK A mwrlariasyflqnr G FSFGI SD V tpsk KLLQH K ELL L NNGYAKCNEYIELLKA G TL qcqpgc T P E 743
Cdd:TIGR02386 591 dk IKAL G FKY ATK S --------------- G TTISA SD I ---- VVPDE K YEI L KEADKEVAKIQKFYNK G LI ------ T D E 645
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 744 E --- TLE S VMLRELSAIREQAA K TCFAELHPT N SALI MA L SG SK G sni NISQ MIACV G QQAISG K rv P N G fenralphfe 820
Cdd:TIGR02386 646 E ryr KVV S IWSETKDKVTDAMM K LLKKDTYKF N PIFM MA D SG AR G --- NISQ FRQLA G MRGLMA K -- P S G ---------- 710
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 821 rh SA I PAA rgf VQN SF YS GLT PT E F F FH T MAG R E GL V DTA V KTA ET GYL Q RRLV KCLE D L VV HYD -- GT VRNAV nem V DT 898
Cdd:TIGR02386 711 -- DI I ELP --- IKS SF RE GLT VL E Y F IS T HGA R K GL A DTA L KTA DS GYL T RRLV DVAQ D V VV REE dc GT EEGIE --- V EA 782
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 899 I YG G DGLDPV S MET R nkpvd L V HQ Y DNLRAQH P Q gkdrpl NAEEMS EA l E TL L r T P E F AE ARDDF --- K LD VR NHINTV S 975
Cdd:TIGR02386 783 I VE G KDEIIE S LKD R ----- I V GR Y SAEDVYD P D ------ TGKLIA EA - N TL I - T E E I AE KIENS gie K VK VR SVLTCE S 849
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 976 KR i G QL QK R Y E kc I DL C hqiecltteqllqfvrrindry NRAVT E P G T AVG A IAAQSIGEPGTQ M T LK TFH FA GVA S -- M 1053
Cdd:TIGR02386 850 EH - G VC QK C Y G -- R DL A ---------------------- TGKLV E I G E AVG V IAAQSIGEPGTQ L T MR TFH TG GVA G as G 904
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1054 N ITQG V PR IV E IIN atktistpiitaelenchsmef AR QV K ari E K TTL AE LSSY VE vvcgpyscylaigvdmarikllg 1133
Cdd:TIGR02386 905 D ITQG L PR VK E LFE ---------------------- AR TP K --- D K AVI AE VDGT VE ----------------------- 936
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1134 lhidldt I VFS I L K SRMR V K ptqvevvasqsr I VVRVEATRTS TI NAE l A R L ALSLQNV V V AG lpninraviavddarqp 1213
Cdd:TIGR02386 937 ------- I IED I V K NKRV V V ------------ I KDENDEEKKY TI PFG - A Q L RVKDGDS V S AG ----------------- 979
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1214 pt Y KL C i EG yglrdviatygvvgkrtr S NNICEIYQTL GI E A ARTIIMS E ITE V MEGH G MSVDWR HI MLLAS QM T ----- 1288
Cdd:TIGR02386 980 -- D KL T - EG ------------------ S IDPHDLLRIK GI Q A VQEYLVK E VQK V YRLQ G VEINDK HI EVIVR QM L rkvri 1038
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1289 ----------------------------------- A RGEV LGIT RHG L AK mr ES VFNL ASF EK T ADH L F DAA YY G QT D AI 1333
Cdd:TIGR02386 1039 tdsgdsnllpgelidihefneenrklleqgkkpas A IPQL LGIT KAS L NT -- ES FLSA ASF QE T TKV L T DAA IK G KV D YL 1116
1370 1380
....*....|....*....|
gi 281360912 1334 N G VS E RI I L G -- M PA ci GTG 1351
Cdd:TIGR02386 1117 L G LK E NV I I G nl I PA -- GTG 1134
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
53-889
3.61e-77
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: 271.97
E-value: 3.61e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 53 V LDR R M G ISTKDAM C E TCG - QGLNE C I GHFG YLD L ALPVF H IGHFRSTIN IL QM IC kvcahvmlkpedrqlyekklhnpn 131
Cdd:cd10506 20 V TNP R L G LPNESGQ C T TCG a KDNKK C E GHFG VIK L PVTIY H PYFISEVAQ IL NK IC ------------------------ 75
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 132 fsylgkkalhvqmlakakkvtkc P H C G S PNGGV KK G P GLL k ILH D PY kgrkm D SLFTSNMN E MLRS T QTNR dlnstlgny 211
Cdd:cd10506 76 ----------------------- P G C K S IKQKK KK P P RET - LPP D YW ----- D FIPKDGQQ E ESCV T KNLP --------- 117
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 212 stae E L TPLM V LDLFEQ I PQR dval L GMCSHDA h PKH L IVTRVF VPP A C I R PSVLSEVKAGTTED dltmkq SEILLINDV 291
Cdd:cd10506 118 ---- I L SLAQ V KKILKE I DPK ---- L IAKGLPR - QEG L FLKCLP VPP N C H R VTEFTHGFSTGSRL ------ IFDERTRAY 182
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 292 IQRHMAT G GKI E lihedwdflqlhvalyfhseisgipi NM A P KK TT rgivqrlk G K Q gr FRCN L S GKR VDF S G R T V ISP D 371
Cdd:cd10506 183 KKLVDFI G TAN E -------------------------- SA A S KK SG -------- L K W -- MKDL L L GKR SGH S F R S V VVG D 226
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 372 P N L MI N QV G V P VRV A KI LT YP ERV NPA N IRHMR E LVRN gpsm HPGANY V Q - Q R G ssfkkyla Y G N -- REKVAQE L KC GDV 448
Cdd:cd10506 227 P Y L EL N EI G I P CEI A ER LT VS ERV SSW N RERLQ E YCDL ---- TLLLKG V I g V R R -------- N G R lv GVRSHNT L QI GDV 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 449 VE R H L R DGD I VL F NR Q PS L H KM S IMCHRA KV Q P - QRTFRF N ECA C T P YNA DFDGD EMNLHL PQ TEE ARAE ALI L MGNQSN 527
Cdd:cd10506 295 IH R P L V DGD V VL V NR P PS I H QH S LIALSV KV L P t NSVVSI N PLC C S P FRG DFDGD CLHGYI PQ SLQ ARAE LEE L VALPKQ 374
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 528 L VTPKN G EI L IAA TQD FITGGY L L T QKE VFL T K EEAM QL aa CF L ANE dstmhi K LPPPA LL K -- P RR -- LWTGKQ M F SL L 603
Cdd:cd10506 375 L ISSQS G QN L LSL TQD SLLAAH L M T ERG VFL D K AQMQ QL -- QM L CPS ------ Q LPPPA II K sp P SN gp LWTGKQ L F QM L 446
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 604 MRPND D SQVRL N M V N kgrnytrnkdlcsndswih I RNS EL M c GVMDKATMGSGTKQCI F YL L LRD f G ESH A TKAMWRLAR 683
Cdd:cd10506 447 LPTDL D YSFPS N L V F ------------------- I SDG EL I - SSSGGSSWLRDSEGNL F SI L VKH - G PGK A LDFLDSAQG 505
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 684 IASYF L QN RGFS FGI SD VTP S KKLLQHKELL -- LNN G Y -- A KCNEY I EL L KAGTLQCQPGCTP EE TLE S VMLRELSAI R - 758
Cdd:cd10506 506 LLCEW L SM RGFS VSL SD LYL S SDSYSRQKMI ee ISL G L re A EIACN I KQ L LVDSRKDFLSGSG EE NDV S SDVERVIYE R q 585
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 759 --------- EQ A A K TC F AELHPT -------- NS A L I M ALS GSKGS NINIS Q MIA C V G Q Q -------- A I SGKRVPNGFEN 813
Cdd:cd10506 586 ksaalsqas VS A F K QV F RDIQNL vykyaskd NS L L A M IKA GSKGS LLKLV Q QSG C L G L Q lslvklsy R I PRQLSCAAWNS 665
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 814 RAL P HFER ------- H S A IP aa R G F V QN SF YS GL T P T E F F F H TMAG R EGLVD tav KT A ET - G Y L Q R R L VKCLE D LV V H YD 885
Cdd:cd10506 666 QKS P RVIE kdgsect E S Y IP -- Y G V V ES SF LD GL N P L E C F V H SITS R DSSFS --- SN A DL p G T L F R K L MFFMR D IY V A YD 740
....
gi 281360912 886 GTVR 889
Cdd:cd10506 741 GTVR 744
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
246-1352
2.78e-65
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 244.40
E-value: 2.78e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 246 P KHL I VTRVF V P P ACI RP S V ls EVKA G T - TED DL TMKQSEILLI N DVIQ R HMAT G GKIELIHEDWDF LQ LH V ALY F HSEI 324
Cdd:PRK14906 312 P ADM I LDVIP V I P PDL RP M V -- QLDG G R f ATS DL NDLYRRVINR N NRLK R LLDL G APEIIVNNEKRM LQ EA V DSL F DNGR 389
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 325 S G I P INMAPKKTTRGIVQR LKGKQGRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY P ER vnpanirh M R 404
Cdd:PRK14906 390 R G R P VTGPGNRPLKSLADM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P H L KLH Q C G L P SAM A LE L FK P FV -------- M K 461
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 405 E LV RNGPSMH - PG A NYVQQ RG S S F kkylaygnrekvaqelk CG DV V E RHLR D g DI VL F NR Q P S LH KMS I MCHRAKVQPQR 483
Cdd:PRK14906 462 R LV ELEYAAN i KA A KRAVD RG A S Y ----------------- VW DV L E EVIQ D - HP VL L NR A P T LH RLG I QAFEPVLVEGK 523
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 484 TFRFNECA CT PY NADFDGD E M NL H L P QTEE A R AEA LI LM GNQS N LVT P KN G EI L IAA TQD F I T G G Y L LT -------- QKE 555
Cdd:PRK14906 524 AIKLHPLV CT AF NADFDGD Q M AV H V P LSTQ A Q AEA RV LM LSSN N IKS P AH G RP L TVP TQD M I I G V Y Y LT terdgfeg EGR 603
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 556 V F LTKEE A MQ laa CFL A NE D STMHI K L pppallkprrlwtgkqmfsllmrpndds Q VRL NMVNKG R NYTRNKDLCSNDSW 635
Cdd:PRK14906 604 T F ADFDD A LN --- AYD A RA D LDLQA K I ---------------------------- V VRL SRDMTV R GSYGDLEETKAGER 652
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 636 I H ------ I R N SE L ------ MCGV M D K ATM G SGTKQ C I - F Y LL --------- LRDF G ESH AT K A mwrlariasyflqnr G 693
Cdd:PRK14906 653 I E ttvgri I F N QV L pedypy LNYK M V K KDI G RLVND C C n R Y ST aevepildg IKKT G FHY AT R A --------------- G 717
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 694 FSFGIS D V T pskk LLQH K ELL L NNGYA K CNEYI E LLKA G T L qcqpgc TPE E TLES V M -- LR E LSAIREQ A AKTC F A E LH P 771
Cdd:PRK14906 718 LTVSVY D A T ---- IPDD K PEI L AEADE K VAAID E DYED G F L ------ SER E RHKQ V V di WT E ATEEVGE A MLAG F D E DN P 787
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 772 T nsa LI MA L SG SK G SNIN I S Q MIACV G QQ A isgkr VPN G f E NRA LP hferhsaipaargf VQNS F YS GL TPT E F F FH T MA 851
Cdd:PRK14906 788 I --- YM MA D SG AR G NIKQ I R Q LAGMR G LM A ----- DMK G - E IID LP -------------- IKAN F RE GL SVL E Y F IS T HG 844
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 852 G R E GLVDTA VK TA ET GYL Q RRLV KCLE D LV V HYD -- GT VRNAVNEM V DTIYGG D G ldpvsmetrnkpv D L VHQYDNLRAQ 929
Cdd:PRK14906 845 A R K GLVDTA LR TA DS GYL T RRLV DVAQ D VI V REE dc GT DEGVTYPL V KPKGDV D T ------------- N L IGRCLLEDVC 911
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 930 H P Q G kdrplnaeemseal E T LL RTPEFA E AR DD F K LD V RNHINT V SK R - IGQLQKR Y EK C i DL C HQIECL T T eqllqfv R 1008
Cdd:PRK14906 912 D P N G -------------- E V LL SAGDYI E SM DD L K RL V EAGVTK V QI R t LMTCHAE Y GV C - QK C YGWDLA T R ------- R 969
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1009 RI N drynravte P GTAVG A IAAQSIGEPGTQ M T LK TFH FA GVA SMN ITQG V PR IV E IIN A T K TIS tpiitaelenchsme 1088
Cdd:PRK14906 970 PV N --------- I GTAVG I IAAQSIGEPGTQ L T MR TFH SG GVA GDD ITQG L PR VA E LFE A R K PKG --------------- 1025
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1089 farqvkariekttlaelssyv E V V CGPY S CY L A I GV D MAR i K L L GL H IDLDTIVFSILKS R MRVK P ----- TQ V E V VASQ 1163
Cdd:PRK14906 1026 --------------------- E A V LAEI S GT L Q I TG D KTE - K T L TI H DQDGNSREYVVSA R VQFM P gvedg VE V R V GQQI 1083
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1164 S R IV V RVEATRTS T - I N AE L ARLALSL Q N V V V AGLPN IN RAV I A V d D ARQ P ptyklciegyg LR D V IA T ygvvgkrtrsn 1242
Cdd:PRK14906 1084 T R GS V NPHDLLRL T d P N TT L RYIVSQV Q D V Y V SQGVD IN DKH I E V - I ARQ M ----------- LR K V AV T ----------- 1140
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1243 N ICEIYQTL G IEAA R TIIMSEITE - VM EG HGMS V dwrhimllasqmt ARGEV LGIT RHG LA K mr E S VFNL ASF EK T ADH L 1321
Cdd:PRK14906 1141 N PGDSDYLP G RQVN R YEFEDTANN l IL EG KQPP V ------------- GQPLL LGIT KAS LA T -- D S WLSA ASF QE T TKV L 1205
1130 1140 1150
....*....|....*....|....*....|.
gi 281360912 1322 F DAA YY G QT D AIN G VS E RI I L G M P ACI GTG I 1352
Cdd:PRK14906 1206 T DAA IE G KV D HLA G LK E NV I I G K P IPA GTG L 1236
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1013-1356
6.72e-64
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: 220.14
E-value: 6.72e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1013 R Y N R AVT EPG T AVG AI AAQSIGEP G TQMTL K TFHFAG VAS MN I T Q G V PR IV EI I - N A T K T I S TP II T AE L E N CH S M E F A R 1091
Cdd:cd02735 1 K Y M R SLV EPG E AVG LL AAQSIGEP S TQMTL N TFHFAG RGE MN V T L G I PR LR EI L m T A S K N I K TP SM T LP L K N GK S A E R A E 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1092 QV K A R IEKT TL AELSSY VEV V cgpysc YLAIGVDMARI KLLG LH idldt IVFS I LKSRMRV K PTQVEV V ASQ srivvrve 1171
Cdd:cd02735 81 TL K K R LSRV TL SDVVEK VEV T ------ EILKTIERVFK KLLG KW ----- CEVT I KLPLSSP K LLLLSI V EKL -------- 141
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1172 atrtstinaelarlals LQNV V VAGL P N I N R AVIAVD D ARQPPT Y KLCI EG YG L RDVIATYGVVG - K R TRS N N I CEIYQ T 1250
Cdd:cd02735 142 ----------------- ARKA V IREI P G I T R CFVVEE D KGGKTK Y LVIT EG VN L AALWKFSDILD v N R IYT N D I HAMLN T 204
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1251 L GIEAAR TI I MS EI TE V MEGH G MS VD W RH IM L L A SQ MT AR G EVLGIT R H G LAK m RE S VFNLA SFE K T ADH L FD A AYY G QT 1330
Cdd:cd02735 205 Y GIEAAR RA I VK EI SN V FKVY G IA VD P RH LS L I A DY MT FE G GYRPFN R I G MES - ST S PLQKM SFE T T LAF L KK A TLN G DI 283
330 340
....*....|....*....|....*.
gi 281360912 1331 D AINGV S E R IIL G M P ACI GTG I F K LL 1356
Cdd:cd02735 284 D NLSSP S S R LVV G K P VNG GTG L F D LL 309
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
344-1070
9.93e-64
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 238.04
E-value: 9.93e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 344 LKGKQGRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY P ervnpa N I rh M RE LV RN G psmhpgan YVQQR 423
Cdd:PRK00566 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KKM A LE L FK P ------ F I -- M KK LV ER G -------- LATTI 384
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 424 G S S f KK YL aygnr E KVAQ E ---- L K cg D V VER H L rdgdi VL F NR Q P S LH KMS I mch R A k VQ P Q ---- RTFRFNECA CT PY 495
Cdd:PRK00566 385 K S A - KK MV ----- E REDP E vwdv L E -- E V IKE H P ----- VL L NR A P T LH RLG I --- Q A - FE P V lieg KAIQLHPLV CT AF 447
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 496 NADFDGD E M NL H L P QTE EA R AEA LI LM GNQS N LVT P K NG EIL I AAT QD FIT G G Y L LT QKE -------- VF LTK EEA M q L A 567
Cdd:PRK00566 448 NADFDGD Q M AV H V P LSL EA Q AEA RV LM LSSN N ILS P A NG KPI I VPS QD MVL G L Y Y LT RER egakgegm VF SSP EEA L - R A 526
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 568 acf LA N EDSTM H -- IK LPPP all KPRRLW T -- G KQM F SLLM r P ND dsqvr L NMV N KGRNYTR n K DL csnd S W I h I RNSEL 643
Cdd:PRK00566 527 --- YE N GEVDL H ar IK VRIT --- SKKLVE T tv G RVI F NEIL - P EG ----- L PFI N VNKPLKK - K EI ---- S K I - I NEVYR 588
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 644 MC G V md K A T mgsgtkq C IF YLLLR D F G ESH AT KA mwrlariasyflqnr G F S F GI S D - V T P SK K llqh KE LL l NNGYAKC 722
Cdd:PRK00566 589 RY G L -- K E T ------- V IF LDKIK D L G FKY AT RS --------------- G I S I GI D D i V I P PE K ---- KE II - EEAEKEV 639
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 723 N E YIELLKA G TL qcqpgc T PE E TLES V M l REL S AIREQA AK TCFAE L ---- HPT N SALI MA L SG SK GS NIN I S Q M iacvg 798
Cdd:PRK00566 640 A E IEKQYRR G LI ------ T DG E RYNK V I - DIW S KATDEV AK AMMKN L skdq ESF N PIYM MA D SG AR GS ASQ I R Q L ----- 707
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 799 qqai S G K R ---- V P N G -- F E nralphferhsa I P aargf VQNS F YS GLT PT E F F FH T MAG R E GL V DTA V KTA ET GYL Q RR 872
Cdd:PRK00566 708 ---- A G M R glma K P S G ei I E ------------ T P ----- IKSN F RE GLT VL E Y F IS T HGA R K GL A DTA L KTA DS GYL T RR 766
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 873 LV KCLE D LV V HY D -- GT V R NA vn E MVDT I Y GG DGL dp VSM E T R nkpvd LVHQYDNLRAQH P QGKDRPLN A EEMS ealetl 950
Cdd:PRK00566 767 LV DVAQ D VI V RE D dc GT D R GI -- E VTAI I E GG EVI -- EPL E E R ----- ILGRVLAEDVVD P ETGEVIVP A GTLI ------ 831
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 951 lr TP E F A EARDDFKLD --- V R NHINTVSKR i G QLQ K R Y EK ci DL chqiecl T T eqllqfvrrindry NRA V t EP G T AVG A 1027
Cdd:PRK00566 832 -- DE E I A DKIEEAGIE evk I R SVLTCETRH - G VCA K C Y GR -- DL ------- A T -------------- GKL V - NI G E AVG V 884
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 281360912 1028 IAAQSIGEPGTQ M T LK TFH FA GV asm N IT Q G V PR IV E IIN A T K 1070
Cdd:PRK00566 885 IAAQSIGEPGTQ L T MR TFH TG GV --- D IT G G L PR VA E LFE A R K 924
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1038-1355
5.62e-63
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 232.09
E-value: 5.62e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1038 T QM T LK TFH F AGVA SM N I T Q G V PR IV EI IN A T K TI STPI I T AE L -- E NCHSM E F A RQ V KAR IE KT TL AELSSYVEVVCGP 1115
Cdd:PRK14898 541 T HN T MR TFH Y AGVA EI N V T L G L PR MI EI VD A R K EP STPI M T VH L kg E YATDR E K A EE V AKK IE SL TL GDVATSIAIDLWT 620
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1116 Y S cyla I G V DMARIK L LGLHIDLDTIVFS I l KSRMR VK p TQVE vvas QSRIVVRVE atr T STIN A ELA R LA l SLQ N V V VA 1195
Cdd:PRK14898 621 Q S ---- I K V ELDEET L ADRGLTIESVEEA I - EKKLG VK - IDRK ---- GTVLYLKPK --- T PSYK A LRK R IP - KIK N I V LK 686
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1196 G L P N I N R AVIAVDDARQPPT Y K L CIE G YG LR D V IATY GV VGK RT RS NNI C EI YQT LGIEAAR TI I MS E ITEVM E GH G MS V 1275
Cdd:PRK14898 687 G I P G I E R VLVKKEEHENDEE Y V L YTQ G SN LR E V FKIE GV DTS RT TT NNI I EI QEV LGIEAAR NA I IN E MMNTL E QQ G LE V 766
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1276 D W RH I ML L A SQ MTA R GEV LG I T RHG L A KMRE SV FNL A S FE K T AD HL F DAA YY G QT D AIN GV S E RI I L G M P ACI GTG IFK L 1355
Cdd:PRK14898 767 D I RH L ML V A DI MTA D GEV KP I G RHG V A GEKG SV LAR A A FE E T VK HL Y DAA EH G EV D KLK GV I E NV I V G K P IKL GTG CVD L 846
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
312-1210
8.54e-60
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: 225.42
E-value: 8.54e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 312 LQ LH V ALY F HSEIS G IPINM A P K KTTRGIVQR LKGKQGRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY 391
Cdd:COG0086 289 LQ EA V DAL F DNGRR G RAVTG A N K RPLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KKM A LE L FK 368
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 392 P ER vnpanirh M R E L VRN G psmhp G A NYV qqrg S S F KK YL aygnr E KVAQ E LK cg D VV E RHLR d GDI VL F NR Q P S LH KMS 471
Cdd:COG0086 369 P FI -------- Y R K L EER G ----- L A TTI ---- K S A KK MV ----- E REEP E VW -- D IL E EVIK - EHP VL L NR A P T LH RLG 423
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 472 I MCHRAKVQPQRTFRFNECA CT PY NADFDGD E M NL H L P QTE EA RA EA LI LM GNQS N LVT P K NG EIL I AAT QD FIT G G Y L L 551
Cdd:COG0086 424 I QAFEPVLIEGKAIQLHPLV CT AF NADFDGD Q M AV H V P LSL EA QL EA RL LM LSTN N ILS P A NG KPI I VPS QD MVL G L Y Y L 503
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 552 T QKE -------- V F LTK EE A mq L A A cf LA N EDSTM H iklppp A LL K P R RLWT G K Q MFSLLM ---- R pnddsq VRL N MV - N 618
Cdd:COG0086 504 T RER egakgegm I F ADP EE V -- L R A -- YE N GAVDL H ------ A RI K V R ITED G E Q VGKIVE ttvg R ------ YLV N EI l P 567
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 619 KGRNYT r N KDL cs N DSW I H -- IR NSELM CG V md K A T mgsgtkq C IF YLL L RDF G ESH AT K A mwrlariasyflqnr G F S F 696
Cdd:COG0086 568 QEVPFY - N QVI -- N KKH I E vi IR QMYRR CG L -- K E T ------- V IF LDR L KKL G FKY AT R A --------------- G I S I 620
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 697 G IS D VTPS K K llqh K ELLLNNGYAKCN E YIELLKA G TL qcqpgc T PE E TLES V ML r ELSAIREQAAKTCF A ELHPT N SAL 776
Cdd:COG0086 621 G LD D MVVP K E ---- K QEIFEEANKEVK E IEKQYAE G LI ------ T EP E RYNK V ID - GWTKASLETESFLM A AFSSQ N TTY 689
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 777 I MA L SG SK GS NINIS Q MIACV G QQ A isgkr V P N G -- F E NRAL phferh S AIPA argfvqnsfys GL TPT E F F FH T MAG R E 854
Cdd:COG0086 690 M MA D SG AR GS ADQLR Q LAGMR G LM A ----- K P S G ni I E TPIG ------ S NFRE ----------- GL GVL E Y F IS T HGA R K 747
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 855 GL V DTA V KTA ET GYL Q RRLV KCLE D LV V HYD -- GT V R NA vn EMVDTIY GG DGLD P VS -- MET R NKPV D L V H qydnlraqh 930
Cdd:COG0086 748 GL A DTA L KTA DS GYL T RRLV DVAQ D VI V TEE dc GT D R GI -- TVTAIKE GG EVIE P LK er ILG R VAAE D V V D --------- 816
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 931 pqgkdr P LNA E EMSE A LETL lr TP E F AE ARDD fkldvrnhintvs KR I GQLQK R YEKCIDLCHQIECLTTEQL L QFVRRI 1010
Cdd:COG0086 817 ------ P GTG E VLVP A GTLI -- DE E V AE IIEE ------------- AG I DSVKV R SVLTCETRGGVCAKCYGRD L ARGHLV 875
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1011 N D rynravtep G T AVG A IAAQSIGEPGTQ M T LK TFH FA G V AS M ---- NITQGVPRIVEII N AT K TISTPIITAELENCH S 1086
Cdd:COG0086 876 N I --------- G E AVG V IAAQSIGEPGTQ L T MR TFH IG G A AS R aaee SSIEAKAGGIVRL N NL K VVVNEEGKGVVVSRN S 946
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1087 MEFARQVKA R I E KTTLAELSSYVE VV C G PYSCYLA I GVDMARIKLLGLHIDLDTI VF SILKSRMRVKPTQV E VVASQ S RI 1166
Cdd:COG0086 947 ELVIVDDGG R R E EEYKVPYGGVLV VV G G GVVVGGG I VAEWDPHTPPIIEEVGGGV VF DDIVEGGVIVEKTD E ETGGL S IV 1026
890 900 910 920
....*....|....*....|....*....|....*....|....
gi 281360912 1167 V VRVE A T R TSTINAEL A RLA L SLQNVVVAGLPNINR A VIAVDDA 1210
Cdd:COG0086 1027 V EDDK A R R GGGKLLIR A LKL L DAVGLSLLLGGTDAA A AGVIIGG 1070
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
344-882
7.27e-54
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: 200.82
E-value: 7.27e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 344 LKGKQGRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY P ER vnpanirh M REL VRN G PSMHPG anyvqqr 423
Cdd:cd01609 236 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KEM A LE L FK P FV -------- I REL IER G LAPNIK ------- 300
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 424 gs S F KK YL aygnr E KVAQ E L kc G D VV E RHLR d G DI VL F NR Q P S LH KMS I MCHRAKVQPQRTFRFNECA CT PY NADFDGD E 503
Cdd:cd01609 301 -- S A KK MI ----- E RKDP E V -- W D IL E EVIK - G HP VL L NR A P T LH RLG I QAFEPVLIEGKAIQLHPLV CT AF NADFDGD Q 370
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 504 M NL H L P QTE EA R AEA LI LM GNQS N LVT P KN G EILIAAT QD FIT G G Y L LT q KE VFLT K E E AM qlaacflan EDS T mhiklp 583
Cdd:cd01609 371 M AV H V P LSL EA Q AEA RV LM LSSN N ILS P AS G KPIVTPS QD MVL G L Y Y LT - KE RKGD K G E GI --------- IET T ------ 434
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 584 ppallkprrlw T G KQM F SLLMRPN ddsqvr L NMV NK GRN ytr N K D L csndswihirn SE L MCGVM D K atmg S G TKQCIFY 663
Cdd:cd01609 435 ----------- V G RVI F NEILPEG ------ L PFI NK TLK --- K K V L ----------- KK L INECY D R ---- Y G LEETAEL 479
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 664 L - LLRDF G ESH AT KA mwrlariasyflqnr G F S FG I S D - V T P SK kllqh K ELLLNNGYA K CN E YIELLKA G T L qcqpgc T 741
Cdd:cd01609 480 L d DIKEL G FKY AT RS --------------- G I S IS I D D i V V P PE ----- K KEIIKEAEE K VK E IEKQYEK G L L ------ T 533
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 742 P EE TLES V m LRELSAIR E QA A KTCFAE L -- H P T N SALI MA L SG SK GS NIN I S Q MIACV G QQ A - I SGK RVP ngfenra LP h 818
Cdd:cd01609 534 E EE RYNK V - IEIWTEVT E KV A DAMMKN L dk D P F N PIYM MA D SG AR GS KSQ I R Q LAGMR G LM A k P SGK IIE ------- LP - 604
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281360912 819 ferhsaipaargf VQNS F YS GLT PT E F F FH T MAG R E GL V DTA V KTA ET GYL Q RRLV KCLE D LV V 882
Cdd:cd01609 605 ------------- IKSN F RE GLT VL E Y F IS T HGA R K GL A DTA L KTA DS GYL T RRLV DVAQ D VI V 655
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
246-1352
2.07e-52
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 203.70
E-value: 2.07e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 246 P KHL I V T RVFVP P ACI RP S V LS E v KAGTTED DL TMKQSE I LLI N DVIQRHMATGGKIEL I HEDWDF LQ LH V ALY F HSEIS 325
Cdd:PRK14844 1666 P EWM I L T TIPIL P PDL RP L V SL E - SGRPAVS DL NHHYRT I INR N NRLRKLLSLNPPEIM I RNEKRM LQ EA V DSL F DNSRR 1744
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 326 GIPI N M A - PKKTTRG I VQR LKGKQGRFR C NL S GKRVD F SGR T VI SPD P N L MI NQ V G V P V R V A KI L TY P ERVNPANIRH M R 404
Cdd:PRK14844 1745 NALV N K A g AVGYKKS I SDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P T L KL NQ C G L P K R M A LE L FK P FVYSKLKMYG M A 1824
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 405 ELVR ngpsmhpganyvqqrgss F KKY L AYGNREK V AQE L K cg D V VER H lrdgd I VL F NR Q P S LH KMS I MCHRAKVQPQRT 484
Cdd:PRK14844 1825 PTIK ------------------ F ASK L IRAEKPE V WDM L E -- E V IKE H ----- P VL L NR A P T LH RLG I QAFEPILIEGKA 1879
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 485 FRFNECA CT PY NADFDGD E M NL H L P QTE EA RA EA LI LM GNQS N LVT P K NG EIL I AATQ D FIT G G Y L LT QK E V flt KE EAM 564
Cdd:PRK14844 1880 IQLHPLV CT AF NADFDGD Q M AV H V P ISL EA QL EA RV LM MSTN N VLS P S NG RPI I VPSK D IVL G I Y Y LT LQ E P --- KE DDL 1956
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 565 QLAAC F LAN E ---- D S T M HI klpppallkprrlwtgkqmfsllmrp NDDSQV R LNMV N KGRN y T RN K DL C SNDS ---- W - 635
Cdd:PRK14844 1957 PSFGA F CEV E hsls D G T L HI -------------------------- HSSIKY R MEYI N SSGE - T HY K TI C TTPG rlil W q 2009
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 636 I HIRNSE L MCGVMDKA - T MGSG T K qc I FY L LL R DF G E S HATKAMWR L ARIASYFLQNR G F SF GIS D VTPSKKLLQ H KE ll 714
Cdd:PRK14844 2010 I FPKHEN L GFDLINQV l T VKEI T S -- I VD L VY R NC G Q S ATVAFSDK L MVLGFEYATFS G V SF SRC D MVIPETKAT H VD -- 2085
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 715 lnng Y A KCN eyiel L K AGTL Q C Q P G CTPEETLESVMLR E L S AIREQA A K ------ TCFAELHPT NS ALI M AL SG SK GS N i 788
Cdd:PRK14844 2086 ---- H A RGE ----- I K KFSM Q Y Q D G LITRSERYNKVID E W S KCTDMI A N dmlkai SIYDGNSKY NS VYM M VN SG AR GS T - 2155
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 789 ni SQM IACV G QQAISG K rv P N G f E NRAL P hferhsaipaargf VQNS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY 868
Cdd:PRK14844 2156 -- SQM KQLA G MRGLMT K -- P S G - E IIET P -------------- IISN F RE GL NVF E Y F NS T HGA R K GL A DTA L KTA NS GY 2216
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 869 L Q RRLV KCLED - L V VHY D GTVR N A ------------ V NEMVDTIY G ---- G D GLD PV SM E TRN K PVD L VHQ y D NLRAQHP 931
Cdd:PRK14844 2217 L T RRLV DVSQN c I V TKH D CKTK N G lvvratvegsti V ASLESVVL G rtaa N D IYN PV TK E LLV K AGE L IDE - D KVKQINI 2295
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 932 Q G K D rplnaeemseal ETLL R T P EFA E arddfkldvrnhint V S KRI gqlqkryek C i D LC HQIECL T TE qllqfvrrin 1011
Cdd:PRK14844 2296 A G L D ------------ VVKI R S P LTC E --------------- I S PGV --------- C - S LC YGRDLA T GK ---------- 2328
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1012 drynra VTEP G T AVG A IAAQS I GEPGTQ M T LK TFH FA GV asmn I T Q GV -- PR I VEI INA TKTISTPI I TAE l E N CHSMEF 1089
Cdd:PRK14844 2329 ------ IVSI G E AVG V IAAQS V GEPGTQ L T MR TFH IG GV ---- M T R GV es SN I IAS INA KIKLNNSN I IID - K N GNKIVI 2397
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1090 A R QVKA ---- RIEKTT L AELSS Y VEVVCGPYSCYLA IG VDM A RIKLLG L H I DLD --- T IVFSI LK SRMRVKPTQV E VVAS 1162
Cdd:PRK14844 2398 S R SCEV vlid SLGSEK L KHSVP Y GAKLYVDEGGSVK IG DKV A EWDPYT L P I ITE ktg T VSYQD LK DGISITEVMD E STGI 2477
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1163 Q S RI V ----------- V R ------------------ VEA TRTST I N A E L ----------------- A R LALSLQN v VVA G 1196
Cdd:PRK14844 2478 S S KV V kdwklysggan L R privllddngkvmtlasg VEA CYFIP I G A V L nvqdgqkvhagdvitrt P R ESVKTRD - ITG G 2556
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1197 LP N inra VI AVDD AR Q P PTYKLC -- I E GY --------- G L R DVI ----------------- ATYGV V -- G KRT R SNNIC - 1245
Cdd:PRK14844 2557 LP R ---- VI ELFE AR R P KEHAIV se I D GY vafsekdrr G K R SIL ikpvdeqispveylvsr SKHVI V ne G DFV R KGDLL m 2632
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1246 ------- E I YQT LG I EA ARTIIM SEI TE V MEGH G MSV D WR H IMLLAS QM TARG E VL ------------------------ 1294
Cdd:PRK14844 2633 dgdpdlh D I LRV LG L EA LAHYMI SEI QQ V YRLQ G VRI D NK H LEVILK QM LQKV E IT dpgdtmylvgesidklevdrenda 2712
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281360912 1295 ---------------- GITR HG L AK mr E S VFNL ASF EK T ADH L FD AA YY G QT D AIN G VS E RI I L G MPACI GTG I 1352
Cdd:PRK14844 2713 msnsgkrpahylpilq GITR AS L ET -- S S FISA ASF QE T TKV L TE AA FC G KS D PLS G LK E NV I V G RLIPA GTG L 2784
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
246-1052
5.33e-48
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 189.36
E-value: 5.33e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 246 P KHLIV T RVF V P P ACI RP S V - L SEV K AGTTE - DD L TMK qse ILLI N DVIQ R H M AT G GKIELIHEDWDF LQ LH V ALY F HSE 323
Cdd:PRK09603 1623 P EWMML T VLP V L P PDL RP L V a L DGG K FAVSD v NE L YRR --- VINR N QRLK R L M EL G APEIIVRNEKRM LQ EA V DVL F DNG 1699
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 324 I S GIPINM A P K KTTRGIVQRL KGKQGRFR C NL S GKRVDFSGR T VI SPD PNL MINQV G V P VRV A KI L TY P ervnpanirhm 403
Cdd:PRK09603 1700 R S TNAVKG A N K RPLKSLSEII KGKQGRFR Q NL L GKRVDFSGR S VI VVG PNL KMDEC G L P KNM A LE L FK P ----------- 1768
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 404 relvrngpsm H PGAN y VQQ RG ssfkk Y LAYGNRE K VAQ E L K CGD V V E -- RHLRD G DI VL F NR Q P S LHK M SI MCHRA K VQP 481
Cdd:PRK09603 1769 ---------- H LLSK - LEE RG ----- Y ATTLKQA K RMI E Q K SNE V W E cl QEITE G YP VL L NR A P T LHK Q SI QAFHP K LID 1832
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 482 QRTFRFNECA C TPY NADFDGD E M NL H L P QTE EA R AE ALI LM GNQS N LVT P KN G EILIAAT QD FIT G G Y L L T -------- Q 553
Cdd:PRK09603 1833 GKAIQLHPLV C SAF NADFDGD Q M AV H V P LSQ EA I AE CKV LM LSSM N ILL P AS G KAVAIPS QD MVL G L Y Y L S leksgvkg E 1912
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 554 KEV F LTKE E AM qlaacf L A NEDSTMH I KLPPPA L LKPRRLW T -- G KQMFSLLM r P N dds QVRLNMV N K grn YTRN KD LCS 631
Cdd:PRK09603 1913 HKL F SSVN E II ------ T A IDTKELD I HAKIRV L DQGNIIA T sa G RMIIKSIL - P D --- FIPTDLW N R --- PMKK KD IGV 1979
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 632 NDSWI H IRN selmc G VMDK AT mgsgtkqci F YLL L RDF G ESH ATKA mwrlariasyflqnr G F S FGIS D V - TP skkll QH 710
Cdd:PRK09603 1980 LVDYV H KVG ----- G IGIT AT --------- F LDN L KTL G FRY ATKA --------------- G I S ISME D I i TP ----- KD 2025
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 711 K ELLLNNGYAKCNEYIELLKA G T L QC Q PG -------- CTPEETLESV M LREL saire QAA K TC F aelhpt NS ALI MA L SG 782
Cdd:PRK09603 2026 K QKMVEKAKVEVKKIQQQYDQ G L L TD Q ER ynkiidtw TEVNDKMSKE M MTAI ----- AKD K EG F ------ NS IYM MA D SG 2094
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 783 SK GS NIN I S Q MI A CV G QQA isgkr V P N G fenralphferh S A I PAA rgf VQNS F YS GL TPT E F F FH T MAG R E GL V DTA V K 862
Cdd:PRK09603 2095 AR GS AAQ I R Q LS A MR G LMT ----- K P D G ------------ S I I ETP --- IISN F KE GL NVL E Y F NS T HGA R K GL A DTA L K 2154
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 863 TA ET GYL Q R R L VKCLEDL - VV HY D GTVRNAV n E MV D TIY G GDGLD P VSMETRNKPV -- D LVHQYD N l RAQHPQGK drp L N 939
Cdd:PRK09603 2155 TA NA GYL T R K L IDVSQNV k VV SD D CGTHEGI - E IT D IAV G SELIE P LEERIFGRVL le D VIDPIT N - EILLYADT --- L I 2229
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 940 A EE MSEAL ------ ETLL RTP EFAE A R ddfkldvrnhintvskrigql QKRYE KC ID L chqiecltteqllqfvrrin DR 1013
Cdd:PRK09603 2230 D EE GAKKV veagik SITI RTP VTCK A P --------------------- KGVCA KC YG L -------------------- NL 2268
810 820 830
....*....|....*....|....*....|....*....
gi 281360912 1014 YNRAVTE PG T AVG AI AAQSIGEPGTQ M TL K TFH FA G V AS 1052
Cdd:PRK09603 2269 GEGKMSY PG E AVG VV AAQSIGEPGTQ L TL R TFH VG G T AS 2307
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1022-1351
2.34e-46
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: 163.74
E-value: 2.34e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1022 G T AVG AI AAQSIGEPGTQMTL K TFHFAGVASMN I T Q G V PR IV EI I NA T ktistpiitaelenchsmefarqvkariektt 1101
Cdd:cd00630 1 G E AVG VL AAQSIGEPGTQMTL R TFHFAGVASMN V T L G L PR LK EI L NA A -------------------------------- 48
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1102 laelssyvevvcgpyscylaigvdmarikllglhidldtivfsilksrmrvkptqvevvasqsrivvrveatrtstinae 1181
Cdd:cd00630 --------------------------------------------------------------------------------
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1182 larlalslqnvvvaglpninraviavddarqpptyklciegyglrdviatygvvgkrtrsn N I C E IYQT LGIEAAR TI I M 1261
Cdd:cd00630 49 ------------------------------------------------------------- S I H E MLEA LGIEAAR ET I I 67
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1262 S EI TE V MEGH G M SVD W RHI M L L A SQ MT AR G EVL G I TR H G LAKMRE S VFNL ASFEKT AD HL F DAA YY G QT D AIN GVSE R II 1341
Cdd:cd00630 68 R EI QK V LASQ G V SVD R RHI E L I A DV MT YS G GLR G V TR S G FRASKT S PLMR ASFEKT TK HL L DAA AA G EK D ELE GVSE N II 147
330
....*....|
gi 281360912 1342 LG M PA CI GTG 1351
Cdd:cd00630 148 LG R PA PL GTG 157
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
527-701
3.68e-45
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: 160.49
E-value: 3.68e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 527 N LVT P K NG EIL I AAT QD FIT G G YLLT QKEV F LTK EE A MQL AA cflanedst MH I K LP P PA L LKP RR - LWTGKQ M FS L L MR 605
Cdd:pfam04983 1 N ILS P Q NG KPI I GPS QD MVL G A YLLT REDT F FDR EE V MQL LM --------- YG I V LP H PA I LKP IK p LWTGKQ T FS R L LP 71
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 606 pnddsqvrl N MV N - KG RNY T RNK DLC S NDS WIH I R N S EL MC GV M DK A T M G s GTKQCIFYLLLRDF G ESHAT K AMW RL ARI 684
Cdd:pfam04983 72 --------- N EI N p KG KPK T NEE DLC E NDS YVL I N N G EL IS GV I DK K T V G - KSLGSLIHIIYKEY G PEETA K FLD RL QKL 141
170
....*....|....*..
gi 281360912 685 ASYF L QNR GFS F GI S D V 701
Cdd:pfam04983 142 GFRY L TKS GFS I GI D D I 158
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
730-832
7.03e-36
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: 131.72
E-value: 7.03e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 730 KA G T L QCQP G C T P EE TL E SVMLRE L SAI R EQ A AKTCFAE L H P T NS ALI MA L SG S KGS N INISQ MIA C V GQQ AIS GKR V P N 809
Cdd:pfam05000 6 RY G K L EDIW G M T L EE SF E ALINNI L NKA R DP A GNIASKS L D P N NS IYM MA D SG A KGS I INISQ IAG C R GQQ NVE GKR I P F 85
90 100
....*....|....*....|...
gi 281360912 810 GF EN R A LPHF ERHSAI P AA RGFV 832
Cdd:pfam05000 86 GF SG R T LPHF KKDDEG P ES RGFV 108
rpoC1
CHL00018 RNA polymerase beta' subunit
344-552
3.83e-33
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 137.73
E-value: 3.83e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 344 LK GK Q GRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY P ERV npanirhm R E L V R NGPSMHPG A -- NYVQ 421
Cdd:CHL00018 360 IE GK E GRFR E NL L GKRVD Y SGR S VI VVG P S L SLH Q C G L P REI A IE L FQ P FVI -------- R G L I R QHLASNIR A ak SKIR 431
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 422 QRGSSFKKY L aygnr EK V A Q elkcgdvverhlrd G DI VL F NR Q P S LH KMS I MCHRAKVQPQ R TFRFNECA C TPY NADFDG 501
Cdd:CHL00018 432 EKEPIVWEI L ----- QE V M Q -------------- G HP VL L NR A P T LH RLG I QAFQPILVEG R AICLHPLV C KGF NADFDG 492
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 281360912 502 D E M NL H L P QTE EA R AEA LI LM GNQS NL VT P KN G EILIAAT QD FIT G G Y L LT 552
Cdd:CHL00018 493 D Q M AV H V P LSL EA Q AEA RL LM FSHM NL LS P AI G DPISVPS QD MLL G L Y V LT 543
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
330-552
1.72e-30
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 129.10
E-value: 1.72e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 330 N MA P K K TTRG I VQ rlk GKQGRFR C NL S GKRVD F SGR T VI SPD P N L MIN Q V G V P VRV A KI L TY P ERVN panirhmr E L V R N 409
Cdd:PRK02625 328 N NR P L K SLSD I IE --- GKQGRFR Q NL L GKRVD Y SGR S VI VVG P K L KMH Q C G L P KEM A IE L FQ P FVIH -------- R L I R Q 396
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 410 G P smhpg A N YVQQ rgssf K K Y L AYGNREK V A Q E L K cg D V V E R H lrdgd I VL F NR Q P S LH KMS I MCHRAKVQPQ R TFRFNE 489
Cdd:PRK02625 397 G I ----- V N NIKA ----- A K K L IQRADPE V W Q V L E -- E V I E G H ----- P VL L NR A P T LH RLG I QAFEPILVEG R AIQLHP 459
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 281360912 490 CA C TPY NADFDGD E M NL H L P QTE EA R AEA LI LM GNQS N LVT P KN GE ILIAAT QD FIT G G Y L LT 552
Cdd:PRK02625 460 LV C PAF NADFDGD Q M AV H V P LSL EA Q AEA RL LM LASN N ILS P AT GE PIVTPS QD MVL G C Y Y LT 522
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
761-1059
2.67e-23
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: 108.01
E-value: 2.67e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 761 AAKTC F AELH P T NS ALI MA L SG SK G sni N I SQ MIAC VG QQAISGK rv P N G f E NRA LP hferhsaipaargf VQNS F YS GL 840
Cdd:TIGR02388 107 EVVNN F RQTD P L NS VYM MA F SG AR G --- N M SQ VRQL VG MRGLMAN -- P Q G - E IID LP -------------- IKTN F RE GL 166
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 841 T P TE FFFHTMAG R E GLVDTA VK TA ET GYL Q RRLV KCLE D LV V HYD -- GT V R N - A V NE M VD tiyg GD GLDPVSMETRNKP V 917
Cdd:TIGR02388 167 T V TE YVISSYGA R K GLVDTA LR TA DS GYL T RRLV DVSQ D VI V REE dc GT E R S i V V RA M TE ---- GD KKISLGDRLLGRL V 242
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 918 -- D LV H QYDNLRAQHPQGK D RP L n A EEMSE A L -- E TLL R T P EFA EA R ddfkldvrnhi NT V SKRIGQLQKRYEKCI DL ch 993
Cdd:TIGR02388 243 ae D VL H PEGEVIVPKNTAI D PD L - A KTIET A G is E VVV R S P LTC EA A ----------- RS V CRKCYGWSLAHAHLV DL -- 308
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281360912 994 qiecltteqllqfvrrindrynravtep G T AVG A IAAQSIGEPGTQ M T LK TFH FA GV ASMNITQG V 1059
Cdd:TIGR02388 309 ---------------------------- G E AVG I IAAQSIGEPGTQ L T MR TFH TG GV FTGEVARQ V 346
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
760-1050
9.45e-23
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 106.23
E-value: 9.45e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 760 QAAKTC F AELH P T NS ALI MA L SG SK G sni N I SQ MIAC VG QQAISGK rv P N G f E NRA LP hferhsaipaargf VQNS F YS G 839
Cdd:PRK02597 107 DEVVKN F RQND P L NS VYM MA F SG AR G --- N M SQ VRQL VG MRGLMAN -- P Q G - E IID LP -------------- IKTN F RE G 166
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 840 LT P TE FFFHTMAG R E GLVDTA VK TA ET GYL Q RRLV KCLE D LV V HYD -- GT V R NA vne M V DTIYG GD GL d PVSMET R -- NK 915
Cdd:PRK02597 167 LT V TE YVISSYGA R K GLVDTA LR TA DS GYL T RRLV DVSQ D VI V REE dc GT T R GI --- V V EAMDD GD RV - LIPLGD R ll GR 242
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 916 PV -- D L V HQYDNLR A QHPQGK D RP L n A EEMSE A L -- E TLL R T P EFA EA rddfkldvrnhintv SKRIGQ lqkrye KC I -- 989
Cdd:PRK02597 243 VL ae D V V DPEGEVI A ERNTAI D PD L - A KKIEK A G ve E VMV R S P LTC EA --------------- ARSVCR ------ KC Y gw 300
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281360912 990 D L C H qiecltteqllqfvrrindry N RA V t EP G T AVG A IAAQSIGEPGTQ M T LK TFH FA GV 1050
Cdd:PRK02597 301 S L A H --------------------- N HL V - DL G E AVG I IAAQSIGEPGTQ L T MR TFH TG GV 339
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1020-1070
1.26e-18
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: 85.66
E-value: 1.26e-18
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 281360912 1020 E P G T AVG A IAAQSIGEPGTQ M T LK TFH FA GVA S m N ITQG V PR IV E IIN A T K 1070
Cdd:cd02655 4 E L G E AVG I IAAQSIGEPGTQ L T MR TFH TG GVA T - D ITQG L PR VE E LFE A R K 53
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
771-1059
6.99e-17
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 86.92
E-value: 6.99e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 771 P T N SALI M AL SG SK G sni N I SQ MIAC VG -------- Q - Q A I S gkrvpngfenra LP hferhsaipaargf V Q NS F YS GL T 841
Cdd:CHL00117 124 P L N PVYM M SF SG AR G --- N A SQ VHQL VG mrglmsdp Q g Q I I D ------------ LP -------------- I Q SN F RE GL S 174
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 842 P TE FFFHTMAG R E G L VDTAV K TA ET GYL Q RRLV KCLEDL VV H - Y D - GT V R ---- NAV N E M ------ VD T IY G GDGL D PVS 909
Cdd:CHL00117 175 L TE YIISCYGA R K G V VDTAV R TA DA GYL T RRLV EVVQHI VV R e T D c GT T R gisv SPR N G M mieril IQ T LI G RVLA D DIY 254
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 910 ME ----- TRN KPVD -- L VHQYDNL RAQ H pqgkdrplnaeemseale TLL R T P efaearddfk L DV R N hintv SKR I G QL q 982
Cdd:CHL00117 255 IG srcia TRN QDIG ig L ANRFITF RAQ P ------------------ ISI R S P ---------- L TC R S ----- TSW I C QL - 300
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 983 kryekcidlchqie C ltteqllqfvrrindr Y NRAVT ----- E P G T AVG A IA A QSIGEPGTQ M TL K TFH FA GV ASMNITQ 1057
Cdd:CHL00117 301 -------------- C ---------------- Y GWSLA hgdlv E L G E AVG I IA G QSIGEPGTQ L TL R TFH TG GV FTGGTAE 350
..
gi 281360912 1058 G V 1059
Cdd:CHL00117 351 Q V 352
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1237-1356
7.25e-12
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: 68.99
E-value: 7.25e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281360912 1237 K R TRSNN I CE I YQT LGI E AA RTIIMSEITEVMEGH G M SV DWR H IM L L A SQ MT AR GE VL G ITRH G LAKM R E S V ----- F NL 1311
Cdd:cd02737 255 E R SMPYS I QQ I KSV LGI D AA FEQFVQRLESAVSMT G K SV LRE H LL L V A DS MT YS GE FV G LNAK G YKAQ R R S L kisap F TE 334
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 281360912 1312 A S F EKTADHLFD AA YY G QT D AIN GV SERIIL G MP A CI GTG - I F KL L 1356
Cdd:cd02737 335 A C F SSPIKCFLK AA KK G AS D SLS GV LDACAW G KE A PV GTG s K F EI L 380
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
998-1042
2.47e-07
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 55.28
E-value: 2.47e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 281360912 998 L T T E QLLQFVRRINDR Y NR A VT EP GT AVG AI AAQSIGEPGTQM T L 1042
Cdd:PRK14898 33 V T E E MVEEIIDEVVSA Y LN A LV EP YE AVG IV AAQSIGEPGTQM 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
