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Chain A, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
Protein Classification
DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB1; RNAP_II_RPB1_N and RNAP_II_Rpb1_C domain-containing protein ( domain architecture ID 10119705 )
DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA; DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA; protein containing domains RNAP_II_RPB1_N, RNA_pol_Rpb1_6, and RNAP_II_Rpb1_C
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
15-853
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: 1434.63
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 15 K E VQFG LF SP E E V RA I SVA K I RF PET MDETQT r A K I GGLNDPR L G S IDRN LK CQTC QEG M N ECPGHFGHI D LAKPVFH V G 94
Cdd:cd02733 1 K R VQFG IL SP D E I RA M SVA E I EH PET YENGGG - P K L GGLNDPR M G T IDRN SR CQTC GGD M K ECPGHFGHI E LAKPVFH I G 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 95 F IA KI K K VCE CVC mhcgkllldehnelmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqpti 174
Cdd:cd02733 80 F LT KI L K ILR CVC ------------------------------------------------------------------- 92
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 175 rkdglklvgswkkdratgdadepe L R V LS T E EI L N IFK H IS VK D FTS LGF NEV FSRP E WMILT C LPVPPP P VRPS ISFNE 254
Cdd:cd02733 93 ------------------------ K R E LS A E RV L E IFK R IS DE D CRI LGF DPK FSRP D WMILT V LPVPPP A VRPS VVMDG 148
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 255 S Q R G EDDLT F KLADI L KAN IS L ETL E H NGAP H H A IEE A E S LLQFHVATYMDN D I A G Q PQA L QKSGRP V KSIR A RLKGKEG 334
Cdd:cd02733 149 S A R S EDDLT H KLADI I KAN NQ L KRQ E Q NGAP A H I IEE D E Q LLQFHVATYMDN E I P G L PQA T QKSGRP L KSIR Q RLKGKEG 228
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 335 RIRGNLMGKRVDFSARTVI SG DPNLELDQVGVP K SIA KT LT Y PE V VTP Y NIDRL TQ LVRNGPNE H PGAKY V IRD S G D RID 414
Cdd:cd02733 229 RIRGNLMGKRVDFSARTVI TP DPNLELDQVGVP R SIA MN LT F PE I VTP F NIDRL QE LVRNGPNE Y PGAKY I IRD D G E RID 308
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 415 LRY S K R A G D IQ LQYG WK VERH IM D N D P VLFNRQPSLHKMSMM A HRVKV I PYSTFRLNLSVT S PYNADFDGDEMNLHVPQS 494
Cdd:cd02733 309 LRY L K K A S D LH LQYG YI VERH LQ D G D V VLFNRQPSLHKMSMM G HRVKV L PYSTFRLNLSVT T PYNADFDGDEMNLHVPQS 388
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 495 E ETRAEL SQ L CA VP L QIVSPQSNKP C MGIVQDTL C G I RKLT L RDTF I E L DQV L N M L Y W V PDWDG V IP T PAI I KPKPLW S G 574
Cdd:cd02733 389 L ETRAEL KE L MM VP R QIVSPQSNKP V MGIVQDTL L G V RKLT K RDTF L E K DQV M N L L M W L PDWDG K IP Q PAI L KPKPLW T G 468
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 575 KQI L S VA IP NGIH L Q R FDEGT ---- TLL SP K D NGML I ID G QIIF G VVE KKTVG S S N GGLIHV VTR E K GP QVCAKLF GNIQ 650
Cdd:cd02733 469 KQI F S LI IP KINN L I R SSSHH dgdk KWI SP G D TKVI I EN G ELLS G ILC KKTVG A S S GGLIHV IWL E Y GP EAARDFI GNIQ 548
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 651 K VVN F WLLHNGFS T GIGDTIAD GP TM RE I T ETI AE AK KK V LDVTKE AQ ANL L TAKH G M TLRESFE DN V V R F LN E ARDKAG 730
Cdd:cd02733 549 R VVN N WLLHNGFS I GIGDTIAD KE TM KK I Q ETI KK AK RD V IKLIEK AQ NGE L EPQP G K TLRESFE NK V N R I LN K ARDKAG 628
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 731 RL A EVN L KDL NN V K Q MV M AGSKGSFINI A Q MS ACVGQQ S VEGKRI A FGF VD RTLPHF S KDDY S PES K GFVENSYLRGLTP 810
Cdd:cd02733 629 KS A QKS L SED NN F K A MV T AGSKGSFINI S Q II ACVGQQ N VEGKRI P FGF RR RTLPHF I KDDY G PES R GFVENSYLRGLTP 708
810 820 830 840
....*....|....*....|....*....|....*....|...
gi 359546325 811 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKA L ED I MV H YD 853
Cdd:cd02733 709 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKA M ED V MV K YD 751
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1035-1446
0e+00
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: 715.91
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1035 YRL T K Q AFDW V L SN IE AQ F L RS V VHPGEMVG VL AAQSIGEPATQMTLNTFHFAGV AS K K VT S GVPRLKEI L NVAKN M KTP 1114
Cdd:cd02584 1 YRL N K E AFDW I L GE IE TR F N RS L VHPGEMVG TI AAQSIGEPATQMTLNTFHFAGV SA K N VT L GVPRLKEI I NVAKN I KTP 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1115 SLTVYLEPG H A A D Q E Q AK L I R S AI EHTTLK S VT I A S EIYYDPDP RS TVI P ED E E IIQLH F SLL DE EA E qs F D QQ SPWLLR 1194
Cdd:cd02584 81 SLTVYLEPG F A K D E E K AK K I Q S RL EHTTLK D VT A A T EIYYDPDP QN TVI E ED K E FVESY F EFP DE DV E -- Q D RL SPWLLR 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1195 L ELDR AA M N DK D L T M G Q VGER IK QT FK N DL F VI W S E DN D EKL I IR C R VVRPKS l DA E TEA E E D HM LKKIE NT ML ENI TL R 1274
Cdd:cd02584 159 I ELDR KK M T DK K L S M E Q IAKK IK EE FK D DL N VI F S D DN A EKL V IR I R IINDDE - EK E EDS E D D VF LKKIE SN ML SDM TL K 237
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1275 G V E N I ER V VMMK - YDR KV PSP TGE YV K EP EWVLETDGVNL S EV MTV PG I DPTR IYT N SFID I M EVLGIEA G R A AL Y KE VY 1353
Cdd:cd02584 238 G I E G I RK V FIRE e NKK KV DIE TGE FK K RE EWVLETDGVNL R EV LSH PG V DPTR TTS N DIVE I F EVLGIEA A R K AL L KE LR 317
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1354 NVI AS DGSYVNYRH M ALL V DVMT TQ G G L TSV TRHG F NR SN TG A LMRCSFEETV E IL F EA G A SA E L DD CR GVSEN VI LGQ M 1433
Cdd:cd02584 318 NVI SF DGSYVNYRH L ALL C DVMT QR G H L MAI TRHG I NR QD TG P LMRCSFEETV D IL L EA A A FG E T DD LK GVSEN IM LGQ L 397
410
....*....|...
gi 359546325 1434 APIGTG A FD VMI D 1446
Cdd:cd02584 398 APIGTG C FD LLL D 410
RNA_pol_Rpb1_6
pfam04992 RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
873-1056
1.03e-90
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511
Cd Length: 188
Bit Score: 292.10
E-value: 1.03e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 873 M D A A H IEKQ SL DT IGG SDAAFEKRYR V D LLNTDHTLD P SL LE S G -- S EI L GD LKL Q V LLDEEY K QL VK DR KF LRE - V F VD 949
Cdd:pfam04992 1 L D G A F IEKQ KI DT LKL SDAAFEKRYR L D VMDEKSGFL P GY LE E G vi K EI A GD PEV Q Q LLDEEY E QL LE DR EL LRE i I F PT 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 950 G EANW P - LPVNI R RIIQNAQ QT FHID HT KPSDL TIKDIVL GV KD L QEN L L V L RG KNEIIQN AQ RD A VT LF CC LLRSRLA T 1028
Cdd:pfam04992 81 G DSKV P q LPVNI Q RIIQNAQ KI FHID DR KPSDL HPIYVIE GV RE L LDR L V V V RG DDPLSKE AQ EN A TL LF KI LLRSRLA S 160
170 180
....*....|....*....|....*...
gi 359546325 1029 R RVL Q EYRL T K Q AFDWVL SN IE AQ FL RS 1056
Cdd:pfam04992 161 K RVL E EYRL N K E AFDWVL GE IE SR FL QA 188
RNA_pol_Rpb1_R
pfam05001 RNA polymerase Rpb1 C-terminal repeat; The repetitive C-terminal domain (CTD) of Rpb1 (RNA ...
1698-1709
3.22e-03
RNA polymerase Rpb1 C-terminal repeat; The repetitive C-terminal domain (CTD) of Rpb1 (RNA polymerase Pol II) plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation.
Pssm-ID: 461513
Cd Length: 12
Bit Score: 36.34
E-value: 3.22e-03
Name
Accession
Description
Interval
E-value
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
15-853
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: 1434.63
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 15 K E VQFG LF SP E E V RA I SVA K I RF PET MDETQT r A K I GGLNDPR L G S IDRN LK CQTC QEG M N ECPGHFGHI D LAKPVFH V G 94
Cdd:cd02733 1 K R VQFG IL SP D E I RA M SVA E I EH PET YENGGG - P K L GGLNDPR M G T IDRN SR CQTC GGD M K ECPGHFGHI E LAKPVFH I G 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 95 F IA KI K K VCE CVC mhcgkllldehnelmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqpti 174
Cdd:cd02733 80 F LT KI L K ILR CVC ------------------------------------------------------------------- 92
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 175 rkdglklvgswkkdratgdadepe L R V LS T E EI L N IFK H IS VK D FTS LGF NEV FSRP E WMILT C LPVPPP P VRPS ISFNE 254
Cdd:cd02733 93 ------------------------ K R E LS A E RV L E IFK R IS DE D CRI LGF DPK FSRP D WMILT V LPVPPP A VRPS VVMDG 148
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 255 S Q R G EDDLT F KLADI L KAN IS L ETL E H NGAP H H A IEE A E S LLQFHVATYMDN D I A G Q PQA L QKSGRP V KSIR A RLKGKEG 334
Cdd:cd02733 149 S A R S EDDLT H KLADI I KAN NQ L KRQ E Q NGAP A H I IEE D E Q LLQFHVATYMDN E I P G L PQA T QKSGRP L KSIR Q RLKGKEG 228
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 335 RIRGNLMGKRVDFSARTVI SG DPNLELDQVGVP K SIA KT LT Y PE V VTP Y NIDRL TQ LVRNGPNE H PGAKY V IRD S G D RID 414
Cdd:cd02733 229 RIRGNLMGKRVDFSARTVI TP DPNLELDQVGVP R SIA MN LT F PE I VTP F NIDRL QE LVRNGPNE Y PGAKY I IRD D G E RID 308
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 415 LRY S K R A G D IQ LQYG WK VERH IM D N D P VLFNRQPSLHKMSMM A HRVKV I PYSTFRLNLSVT S PYNADFDGDEMNLHVPQS 494
Cdd:cd02733 309 LRY L K K A S D LH LQYG YI VERH LQ D G D V VLFNRQPSLHKMSMM G HRVKV L PYSTFRLNLSVT T PYNADFDGDEMNLHVPQS 388
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 495 E ETRAEL SQ L CA VP L QIVSPQSNKP C MGIVQDTL C G I RKLT L RDTF I E L DQV L N M L Y W V PDWDG V IP T PAI I KPKPLW S G 574
Cdd:cd02733 389 L ETRAEL KE L MM VP R QIVSPQSNKP V MGIVQDTL L G V RKLT K RDTF L E K DQV M N L L M W L PDWDG K IP Q PAI L KPKPLW T G 468
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 575 KQI L S VA IP NGIH L Q R FDEGT ---- TLL SP K D NGML I ID G QIIF G VVE KKTVG S S N GGLIHV VTR E K GP QVCAKLF GNIQ 650
Cdd:cd02733 469 KQI F S LI IP KINN L I R SSSHH dgdk KWI SP G D TKVI I EN G ELLS G ILC KKTVG A S S GGLIHV IWL E Y GP EAARDFI GNIQ 548
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 651 K VVN F WLLHNGFS T GIGDTIAD GP TM RE I T ETI AE AK KK V LDVTKE AQ ANL L TAKH G M TLRESFE DN V V R F LN E ARDKAG 730
Cdd:cd02733 549 R VVN N WLLHNGFS I GIGDTIAD KE TM KK I Q ETI KK AK RD V IKLIEK AQ NGE L EPQP G K TLRESFE NK V N R I LN K ARDKAG 628
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 731 RL A EVN L KDL NN V K Q MV M AGSKGSFINI A Q MS ACVGQQ S VEGKRI A FGF VD RTLPHF S KDDY S PES K GFVENSYLRGLTP 810
Cdd:cd02733 629 KS A QKS L SED NN F K A MV T AGSKGSFINI S Q II ACVGQQ N VEGKRI P FGF RR RTLPHF I KDDY G PES R GFVENSYLRGLTP 708
810 820 830 840
....*....|....*....|....*....|....*....|...
gi 359546325 811 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKA L ED I MV H YD 853
Cdd:cd02733 709 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKA M ED V MV K YD 751
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
14-874
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 938.51
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 14 VKEVQ FGL F SPEE V R AI SV A KI RFPE T M D ETQTRAK i GGL N DPRLG S ID RN L K C Q TC QEGMN ECPGHFGHI D LA K PV F HV 93
Cdd:PRK08566 9 IGSIK FGL L SPEE I R KM SV T KI ITAD T Y D DDGYPID - GGL M DPRLG V ID PG L R C K TC GGRAG ECPGHFGHI E LA R PV I HV 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 94 GF IAK I K K VCECV C MH CG K L L L D E h N E LMRQALAIKDS K KRFAAIWT L C K T ------- K MVC etdv P S eddptqlvsrgg 166
Cdd:PRK08566 88 GF AKL I Y K LLRAT C RE CG R L K L T E - E E IEEYLEKLERL K EWGSLADD L I K E vkkeaak R MVC ---- P H ------------ 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 167 CG NT Q PT I rkdglklvgsw K KDRA T G -- DADEPE L RV L STEE I LNIFKH I SVK D FTS LG F N EVFS RPEWM I LT C LPVPP P 244
Cdd:PRK08566 151 CG EK Q YK I ----------- K FEKP T T fy EERKEG L VK L TPSD I RERLEK I PDE D LEL LG I N PEVA RPEWM V LT V LPVPP V 219
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 245 P VRPSI SFNES QR G EDDLT F KL A DI LKA N IS L ETLEHN GAP HHA IE EAES LLQ F HV A TY M DN D I A G Q P Q A LQK SGRP V K S 324
Cdd:PRK08566 220 T VRPSI TLETG QR S EDDLT H KL V DI IRI N QR L KENIEA GAP QLI IE DLWE LLQ Y HV T TY F DN E I P G I P P A RHR SGRP L K T 299
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 325 IRA RLKGKEGR I RGNL M GKRV D FSARTVIS G DPNL ELDQ VGVP KS IAK T LT Y PE V VT PY NI DR L TQL V R NGP NE HPGA K Y 404
Cdd:PRK08566 300 LAQ RLKGKEGR F RGNL S GKRV N FSARTVIS P DPNL SINE VGVP EA IAK E LT V PE R VT EW NI EE L REY V L NGP EK HPGA N Y 379
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 405 VIR DS G D RI D L RYS - K RAGDIQ L QY GW K VERH IM D N D P VLFNRQPSLH K MS M MAHRV K V I P YS TFRLNL S V TS PYNADFD 483
Cdd:PRK08566 380 VIR PD G R RI K L TDK n K EELAEK L EP GW I VERH LI D G D I VLFNRQPSLH R MS I MAHRV R V L P GK TFRLNL A V CP PYNADFD 459
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 484 GDEMNLHVPQ S EE T RAE LSQ L CA V PLQ I V SP QSNK P CM G IV QD TLC G IRK LT LRD T FIELDQV L NM L YWVPDWDGVI P T P 563
Cdd:PRK08566 460 GDEMNLHVPQ T EE A RAE ARI L ML V QEH I L SP RYGG P II G GI QD HIS G AYL LT RKS T LFTKEEA L DL L RAAGIDELPE P E P 539
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 564 AI IKP KP L W S GKQI L S VAI P NGIH L QR ------- F DE GTTLLSPK D NGML I ID G QIIF GV VE KK TV G SSN G GLIHVVTR E 636
Cdd:PRK08566 540 AI ENG KP Y W T GKQI F S LFL P KDLN L EF kakicsg C DE CKKEDCEH D AYVV I KN G KLLE GV ID KK AI G AEQ G SILDRIVK E 619
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 637 K GP QVCAKLFGNIQKVVNFWLLHN GF S TGI G D TIADGPTMR EI T E T I A EA K K K V LDVTKEAQANL L TAKH G M TL R E SF E D 716
Cdd:PRK08566 620 Y GP ERARRFLDSVTRLAIRFIMLR GF T TGI D D EDIPEEAKE EI D E I I E EA E K R V EELIEAYENGE L EPLP G R TL E E TL E M 699
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 717 NVVRF L NE ARD K AG RL AE VN L KDL N NV kq MV MA -- G SK GS FI N IA QM S ACVGQQSV E G K RI AF G FV DRTLPHF SKD D YSP 794
Cdd:PRK08566 700 KIMQV L GK ARD E AG EI AE KY L GLD N PA -- VI MA rt G AR GS ML N LT QM A ACVGQQSV R G E RI RR G YR DRTLPHF KPG D LGA 777
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 795 E SK GFV EN SY LR GLTP Q EFFFHAMGGREGL I DTAV K T AET GY I QRRL VK AL E D IM V H YD N T T R NSL GN VI QF I YGEDG M D 874
Cdd:PRK08566 778 E AR GFV RS SY KS GLTP T EFFFHAMGGREGL V DTAV R T SQS GY M QRRL IN AL Q D LK V E YD G T V R DTR GN IV QF K YGEDG V D 857
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
14-876
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: 885.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 14 VKEVQ FGL F SPEE V R AI SV AKIRFPE T M D ETQTRAK i GGL N DPRLG S I DRN L K C Q TC QEGMN ECPGHFGHI D LA K PV F HV 93
Cdd:TIGR02390 4 IGSIK FGL L SPEE I R KM SV VEVVTAD T Y D DDGYPIE - GGL M DPRLG V I EPG L R C K TC GGKVG ECPGHFGHI E LA R PV V HV 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 94 GF IAK I K K VCECV C MH CG KLL L -- D E HNELMRQALAI K DSKKRF A ai W TL CK ------- TK M V C etdv P S eddptqlvsr 164
Cdd:TIGR02390 83 GF AKE I Y K ILRAT C RK CG RIT L te E E IEQYLEKINKL K EEGGDL A -- S TL IE kivkeaa KR M K C ---- P H ---------- 146
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 165 gg CG NT Q PT I rkdgl K LVGSWKKDRATGDA D EP elrv L STE EI LNIFKH I SVK D FTS LG F N EVFS RPEWM I LT C LPVPP P 244
Cdd:TIGR02390 147 -- CG EE Q KK I ----- K FEKPTYFYEEGKEG D VK ---- L TPS EI RERLEK I PDE D AEL LG I N PKVA RPEWM V LT V LPVPP V 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 245 P VRPSI SFNESQ R G EDDLT F KL A DI LKA N IS L ETLEHN GAP HHA IE EAES LLQ F HVATY M DN DIA G Q P Q A LQK SGRP V K S 324
Cdd:TIGR02390 216 T VRPSI TLETGE R S EDDLT H KL V DI IRI N QR L KENIEA GAP QLI IE DLWE LLQ Y HVATY F DN ELP G I P P A RHR SGRP L K T 295
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 325 IRA RLKGKEGR I RGNL M GKRV D FSARTVIS G DPN LELDQ VGVP KS IAK T LT Y PE V VTP Y NID R L TQL V R NGP NEH PGA K Y 404
Cdd:TIGR02390 296 LAQ RLKGKEGR F RGNL S GKRV N FSARTVIS P DPN ISINE VGVP EQ IAK E LT V PE R VTP W NID E L REY V L NGP DSW PGA N Y 375
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 405 VIR DS G D RI DL R YSKRAGDIQ - L QY GW K VERH IM D N D P VLFNRQPSLH K MSMM A H R VKV I P YS TFRLNL S V TS PYNADFD 483
Cdd:TIGR02390 376 VIR PD G R RI KI R DENKEELAE r L EP GW V VERH LI D G D I VLFNRQPSLH R MSMM G H K VKV L P GK TFRLNL A V CP PYNADFD 455
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 484 GDEMNLHVPQ S EE T RAE LSQ L CA V PLQ I VS P QSNK P CM G IVQ D TLC G IRK LT LRD T FIELDQ V LNM L Y w V PDWD G VI P T P 563
Cdd:TIGR02390 456 GDEMNLHVPQ T EE A RAE ARE L ML V EEH I LT P RYGG P II G GIH D YIS G AYL LT HKS T LFTKEE V QTI L G - V AGYF G DP P E P 534
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 564 AI I KPK PL W S GKQI L S VAI P NGIHLQ ------- RF D EGTTLLS P K D NGML I ID G QIIF GV VE KK TV G SSN G GLI H VVT RE 636
Cdd:TIGR02390 535 AI E KPK EY W T GKQI F S AFL P EDLNFE grakics GS D ACKKEEC P H D AYVV I KN G KLLK GV ID KK AI G AEK G KIL H RIV RE 614
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 637 K GP QVCAKLFGNIQKVVNFWLLHN GF S TGI G D TIADGPTMR EI T E T I AE A K K K V LDVTKEAQANL L TAKH G M T LR E SF E D 716
Cdd:TIGR02390 615 Y GP EAARRFLDSVTRLFIRFITLR GF T TGI D D IDIPKEAKE EI E E L I EK A E K R V DNLIERYRNGE L EPLP G R T VE E TL E M 694
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 717 NVVRF L NE ARD K AG RL AE VN L KDL N NVKQ M VMA G SK GS FI NI A QM S A C VGQQSV E G K RI AF G FVD RTLPHF S K D D YSPES 796
Cdd:TIGR02390 695 KIMEV L GK ARD E AG EV AE KY L DPE N HAVI M ART G AR GS LL NI T QM A A M VGQQSV R G G RI RR G YRN RTLPHF K K G D IGAKA 774
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 797 K GFV EN S YLR GL T P Q E F FFHA M GGREGL I DTAV K T AET GY I QRRL VK AL E D IM V H YD N T T R NSL GN V IQF I YGEDG M D AA 876
Cdd:TIGR02390 775 R GFV RS S FKK GL D P T E Y FFHA A GGREGL V DTAV R T SQS GY M QRRL IN AL Q D LY V E YD G T V R DTR GN L IQF K YGEDG V D PM 854
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1035-1446
0e+00
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: 715.91
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1035 YRL T K Q AFDW V L SN IE AQ F L RS V VHPGEMVG VL AAQSIGEPATQMTLNTFHFAGV AS K K VT S GVPRLKEI L NVAKN M KTP 1114
Cdd:cd02584 1 YRL N K E AFDW I L GE IE TR F N RS L VHPGEMVG TI AAQSIGEPATQMTLNTFHFAGV SA K N VT L GVPRLKEI I NVAKN I KTP 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1115 SLTVYLEPG H A A D Q E Q AK L I R S AI EHTTLK S VT I A S EIYYDPDP RS TVI P ED E E IIQLH F SLL DE EA E qs F D QQ SPWLLR 1194
Cdd:cd02584 81 SLTVYLEPG F A K D E E K AK K I Q S RL EHTTLK D VT A A T EIYYDPDP QN TVI E ED K E FVESY F EFP DE DV E -- Q D RL SPWLLR 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1195 L ELDR AA M N DK D L T M G Q VGER IK QT FK N DL F VI W S E DN D EKL I IR C R VVRPKS l DA E TEA E E D HM LKKIE NT ML ENI TL R 1274
Cdd:cd02584 159 I ELDR KK M T DK K L S M E Q IAKK IK EE FK D DL N VI F S D DN A EKL V IR I R IINDDE - EK E EDS E D D VF LKKIE SN ML SDM TL K 237
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1275 G V E N I ER V VMMK - YDR KV PSP TGE YV K EP EWVLETDGVNL S EV MTV PG I DPTR IYT N SFID I M EVLGIEA G R A AL Y KE VY 1353
Cdd:cd02584 238 G I E G I RK V FIRE e NKK KV DIE TGE FK K RE EWVLETDGVNL R EV LSH PG V DPTR TTS N DIVE I F EVLGIEA A R K AL L KE LR 317
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1354 NVI AS DGSYVNYRH M ALL V DVMT TQ G G L TSV TRHG F NR SN TG A LMRCSFEETV E IL F EA G A SA E L DD CR GVSEN VI LGQ M 1433
Cdd:cd02584 318 NVI SF DGSYVNYRH L ALL C DVMT QR G H L MAI TRHG I NR QD TG P LMRCSFEETV D IL L EA A A FG E T DD LK GVSEN IM LGQ L 397
410
....*....|...
gi 359546325 1434 APIGTG A FD VMI D 1446
Cdd:cd02584 398 APIGTG C FD LLL D 410
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
807-1397
0e+00
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: 617.83
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 807 GLTPQEFFFH A MGGREGLIDTAVKTAE T GY I QRRLVKALED IM V H YD N T T RNS L G NVI QF I YGEDG M D AAH IEKQ SLD TI 886
Cdd:pfam04998 1 GLTPQEFFFH T MGGREGLIDTAVKTAE S GY L QRRLVKALED LV V T YD D T V RNS G G EIV QF L YGEDG L D PLK IEKQ GRF TI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 887 GG SD AAF E KRYRV DLL NTDHT L DPSL L ESGS EIL GDLKLQ vlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqn 966
Cdd:pfam04998 81 EF SD LKL E DKFKN DLL DDLLL L SEFS L SYKK EIL VRDSKL ---------------------------------------- 120
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 967 aqqtfhidhtkpsdltikdivlgvkdlqenllvlr G KNEIIQN AQ RD A VT LF CC LL R S R L ATR RV LQ E YRLTKQ AF DWV L 1046
Cdd:pfam04998 121 ----------------------------------- G RDRLSKE AQ ER A TL LF EL LL K S G L ESK RV RS E LTCNSK AF VCL L 165
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1047 SNIEAQFLR S VVH PGE M VG VL AAQSIGEP A TQMTLNTFHFAGVASK K VT S GVPRLKEI L NV A KN M K T PSLTVYL EPGHAA 1126
Cdd:pfam04998 166 CYGRLLYQQ S LIN PGE A VG II AAQSIGEP G TQMTLNTFHFAGVASK N VT L GVPRLKEI I NV S KN I K S PSLTVYL FDEVGR 245
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1127 DQ E Q AK LIRS AIE HT TL K SV TIAS EI Y YDPDP RS T V I PE D EEIIQLH F SLL DE EAEQSFDQQSPW LL R L ELDRAAMND K D 1206
Cdd:pfam04998 246 EL E K AK KVYG AIE KV TL G SV VESG EI L YDPDP FN T P I IS D VKGVVKF F DII DE VTNEEEIDPETG LL I L VIRLLKILN K S 325
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1207 L ------- TMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDA E TEA EED HM L KKIENTM L E NITLRG VEN I 1279
Cdd:pfam04998 326 I kkvvkse VIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVD E LFM EED PK L AILVASL L G NITLRG IPG I 405
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1280 E R VVMMKY D RKVP sptgeyvk EP E WVLET D GVNL SE V MT VPG - I D PT RI YT N SFID I M E V LGIEA G R A AL YK E VY NV IAS 1358
Cdd:pfam04998 406 K R ILVNED D KGKV -------- EP D WVLET E GVNL LR V LL VPG f V D AG RI LS N DIHE I L E I LGIEA A R N AL LN E IR NV YRF 477
570 580 590
....*....|....*....|....*....|....*....
gi 359546325 1359 D G S Y V N Y RH MA L LV D V MT TQ G GLTSVT RHG F N RSNTG AL 1397
Cdd:pfam04998 478 Q G I Y I N D RH LE L IA D Q MT RK G YIMAIG RHG I N KAELS AL 516
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
232-532
1.76e-161
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 492.80
E-value: 1.76e-161
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 232 EWMILT C LPVPPP PV RPS ISFNESQRG EDDLT FK L A DI L K A N IS L ET L EHN GAP HHA I EEAES LLQ FH V A T YM DN D ia G Q 311
Cdd:smart00663 1 EWMILT V LPVPPP CL RPS VQLDGGRFA EDDLT HL L R DI I K R N NR L KR L LEL GAP SII I RNEKR LLQ EA V D T LI DN E -- G L 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 312 P Q A L QKSGRP V KS IRA RLKGKEGR I R G NL M GKRVDFSAR T VI SG DPNL E L DQ VGVPK S IA KT LT Y PE V VTP Y NID R L TQ L 391
Cdd:smart00663 79 P R A N QKSGRP L KS LSQ RLKGKEGR F R Q NL L GKRVDFSAR S VI TP DPNL K L NE VGVPK E IA LE LT F PE I VTP L NID K L RK L 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 392 VRNGP neh P GAKY V IR ds G DRID L RYS K RA - GDIQ L QY G WK VERH IM D N D P VLFNRQP S LH K MS MM AHRV K V IPYS T F RL 470
Cdd:smart00663 159 VRNGP --- N GAKY I IR -- G KKTN L KLA K KS k IANH L KI G DI VERH VI D G D V VLFNRQP T LH R MS IQ AHRV R V LEGK T I RL 233
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 359546325 471 N LS V T SPYNADFDGDEMNLHVPQS E E T RAE LSQ L CA VP LQ I V SP QSN KP CM G IV QD T L C G IR 532
Cdd:smart00663 234 N PL V C SPYNADFDGDEMNLHVPQS L E A RAE ARE L ML VP NN I L SP KNG KP II G PI QD M L L G LY 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
11-340
1.47e-142
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: 442.88
E-value: 1.47e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 11 L RTV KE V QFG LF SPEE V R AI SV AKIRF PET MDETQTRAKI GGL N D P R L G S ID RNLK C Q TC QEGMNE CPGHFGHI D LAKPV 90
Cdd:pfam04997 1 L KKI KE I QFG IA SPEE I R KW SV GEVTK PET YNYGSLKPEE GGL L D E R M G T ID KDYE C E TC GKKKKD CPGHFGHI E LAKPV 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 91 FH V GF IA K IK K VC ECVC MH C G KLLLD EHNE ---- LMRQA L AIKDS K KRFA AI WT LCK T K MV CE TDVPSE ddptqlvsr G G 166
Cdd:pfam04997 81 FH I GF FK K TL K IL ECVC KY C S KLLLD PGKP klfn KDKKR L GLENL K MGAK AI LE LCK K K DL CE HCGGKN --------- G V 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 167 CG NT QP TI RK D GLKL VGSW KK DR atgda D E P E LRV L ST E EI L N IFK H IS VK D FTS LGFN EVF SRPEWMILT C LPVPPP PV 246
Cdd:pfam04997 152 CG SQ QP VS RK E GLKL KAAI KK SK ----- E E E E KEI L NP E KV L K IFK R IS DE D VEI LGFN PSG SRPEWMILT V LPVPPP CI 226
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 247 RPS ISFNESQ R G EDDLT F KL A DI L K A N IS L ET L EHN GAP H H A I E E AES LLQ F HVAT YM DN D I A G Q P Q ALQKS G RP V KSI R 326
Cdd:pfam04997 227 RPS VQLDGGR R A EDDLT H KL R DI I K R N NR L KK L LEL GAP S H I I R E EWR LLQ E HVAT LF DN E I P G L P P ALQKS K RP L KSI S 306
330
....*....|....
gi 359546325 327 A RLKGKEGR I RGNL 340
Cdd:pfam04997 307 Q RLKGKEGR F RGNL 320
RNA_pol_Rpb1_6
pfam04992 RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
873-1056
1.03e-90
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511
Cd Length: 188
Bit Score: 292.10
E-value: 1.03e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 873 M D A A H IEKQ SL DT IGG SDAAFEKRYR V D LLNTDHTLD P SL LE S G -- S EI L GD LKL Q V LLDEEY K QL VK DR KF LRE - V F VD 949
Cdd:pfam04992 1 L D G A F IEKQ KI DT LKL SDAAFEKRYR L D VMDEKSGFL P GY LE E G vi K EI A GD PEV Q Q LLDEEY E QL LE DR EL LRE i I F PT 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 950 G EANW P - LPVNI R RIIQNAQ QT FHID HT KPSDL TIKDIVL GV KD L QEN L L V L RG KNEIIQN AQ RD A VT LF CC LLRSRLA T 1028
Cdd:pfam04992 81 G DSKV P q LPVNI Q RIIQNAQ KI FHID DR KPSDL HPIYVIE GV RE L LDR L V V V RG DDPLSKE AQ EN A TL LF KI LLRSRLA S 160
170 180
....*....|....*....|....*...
gi 359546325 1029 R RVL Q EYRL T K Q AFDWVL SN IE AQ FL RS 1056
Cdd:pfam04992 161 K RVL E EYRL N K E AFDWVL GE IE SR FL QA 188
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1032-1446
6.01e-90
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 298.30
E-value: 6.01e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1032 L Q E YR LT KQAFDWVLSNIEAQF LRS V V H PGE M VGV L AAQSIGEP A TQMT LN TFH F AGVA SKK VT S G V PRL K EI LNVA K NM 1111
Cdd:PRK04309 30 L E E RK LT EEEVEEIIEEVVREY LRS L V E PGE A VGV V AAQSIGEP G TQMT MR TFH Y AGVA EIN VT L G L PRL I EI VDAR K EP 109
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1112 K TP SL T V YL EPGH A A D Q E Q A KLIRSA IE H TTL KS vt I A SE I YY D PD prstvipe DEE II qlhfslldeeaeqsfdqqspw 1191
Cdd:PRK04309 110 S TP MM T I YL KDEY A Y D R E K A EEVARK IE A TTL EN -- L A KD I SV D LA -------- NMT II --------------------- 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1192 llr L ELD RAAMN D KD LT MGQ V G E R I KQTFKNDL fviws E DNDEK LII RCRVVRPKS L daeteaeedhm L K KI E N tm LE NI 1271
Cdd:PRK04309 159 --- I ELD EEMLE D RG LT VDD V K E A I EKKKGGEV ----- E IEGNT LII SPKEPSYRE L ----------- R K LA E K -- IR NI 217
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1272 TLR G VEN I E RV VMM K ydrkvpsptgeyv KEP E W V LE T D G V NL S EV MT V P G I D P TR IY TN SFID I M EVLGIEA G R A A LYK E 1351
Cdd:PRK04309 218 KIK G IKG I K RV IIR K ------------- EGD E Y V IY T E G S NL K EV LK V E G V D A TR TT TN NIHE I E EVLGIEA A R N A IIE E 284
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1352 VY N VIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA L M R CS FE E TV EI L FE A GASA E L D DCR GV S EN V I L G 1431
Cdd:PRK04309 285 IK N TLEEQ G LD V DI RH IM L VA D M MT WD G EVRQIG RHG VSGEKASV L A R AA FE V TV KH L LD A AVRG E V D ELK GV T EN I I V G 364
410
....*....|....*
gi 359546325 1432 Q MA P I GTG AFDVMI D 1446
Cdd:PRK04309 365 Q PI P L GTG DVELTM D 379
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1031-1446
3.77e-85
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: 283.87
E-value: 3.77e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1031 V LQEYRLT K QAF D WVLSNI E AQF LRS VVH PGE M VG VL AAQSIGEP A TQMT LN TFH F AGVA SKK VT S G V PRL K EI LNVA K N 1110
Cdd:TIGR02389 14 V KKREISD K EEL D EIIKRV E EEY LRS LID PGE A VG IV AAQSIGEP G TQMT MR TFH Y AGVA ELN VT L G L PRL I EI VDAR K T 93
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1111 MK TPS L T V YLE PGHAA D Q E Q A KLIRSA IE H T T L K sv TI A SE I YY D PDPRSTV I pedeeiiqlhfslldeeaeqsfdqqsp 1190
Cdd:TIGR02389 94 PS TPS M T I YLE DEYEK D R E K A EEVAKK IE A T K L E -- DV A KD I SI D LADMTVI I --------------------------- 144
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1191 wllrl ELD RAAMNDKDL T MGQ V GER IK QT f K NDLFVIWSE DN DE k LI I RCRVVRP K S L daeteaeed HM LK K ient MLE N 1270
Cdd:TIGR02389 145 ----- ELD EEQLKERGI T VDD V EKA IK KA - K LGKVIEIDM DN NT - IT I KPGNPSL K E L --------- RK LK E ---- KIK N 204
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1271 ITLR G VEN I E RVV MM K ydrkvpsptgeyv KEP E W V LE T D G V NL S EV MTVP G I D P TR IY TN SFID I M EVLGIEA G R A A LYK 1350
Cdd:TIGR02389 205 LHIK G IKG I K RVV IR K ------------- EGD E Y V IY T E G S NL K EV LKLE G V D K TR TT TN DIHE I A EVLGIEA A R N A IIE 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1351 E VYNVIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA L M R CS FE E TV EI L FE A GASA E L D DCR GV S EN V I L 1430
Cdd:TIGR02389 272 E IKRTLEEQ G LD V DI RH LM L VA D L MT WD G EVRQIG RHG ISGEKASV L A R AA FE V TV KH L LD A AIRG E V D ELK GV I EN I I V 351
410
....*....|....*.
gi 359546325 1431 GQ MA P I GTG AF D VMI D 1446
Cdd:TIGR02389 352 GQ PI P L GTG DV D LVM D 367
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
17-1180
8.60e-50
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: 194.22
E-value: 8.60e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 17 VQF GL F SPE EV R AI S VAKIRF PET MDETQTRAKIG GL NDP R - L G SID ------ RNL K -------- C QT C Q ---------- 71
Cdd:COG0086 10 IKI GL A SPE KI R SW S YGEVKK PET INYRTFKPERD GL FCE R i F G PCK dyecyc GKY K rmvykgvv C EK C G vevtlskvrr 89
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 72 E G M necpghf GHI D LA K PVFH VGFIA ---- K I K kvcecvcmhcgk LLLD ehnelmrqa LAIK D SKK -- R F AA - IWTLCKT 144
Cdd:COG0086 90 E R M ------- GHI E LA M PVFH IWGLK slps R I G ------------ LLLD --------- MSLR D LER vl Y F ES y VVIDPGD 141
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 145 KMVCETDVPS ED DPTQLVSRG G CGNTQPT ---- I RK dglk L V G SWKKDRATGDAD E PELRVL S TEEILNIF K HIS V KD ft 220
Cdd:COG0086 142 TPLEKGQLLT ED EYREILEEY G DEFVAKM gaea I KD ---- L L G RIDLEKESEELR E ELKETT S EQKRKKLI K RLK V VE -- 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 221 sl G F N E VFS RPEWMIL TC LPV P PP PV RP SISFNESQRGED DL TFKLADILKA N IS L ET L EHNG AP HHAIEEAESL LQ FH V 300
Cdd:COG0086 216 -- A F R E SGN RPEWMIL DV LPV I PP DL RP LVPLDGGRFATS DL NDLYRRVINR N NR L KR L LELK AP DIIVRNEKRM LQ EA V 293
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 301 ATYM DN DIA G QP q ALQKSG RP V KS IRAR LKGK E GR I R G NL M GKRVD F S A R T VI SGD P N L E L D Q V G V PK SI A KT L TY P EV v 380
Cdd:COG0086 294 DALF DN GRR G RA - VTGANK RP L KS LSDM LKGK Q GR F R Q NL L GKRVD Y S G R S VI VVG P E L K L H Q C G L PK KM A LE L FK P FI - 371
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 381 tp Y NIDRLTQ L VRN gpnehpgakyvirdsgdrid LRYS K RAGDIQLQYG W KVERHIMDND PVL F NR Q P S LH KMSMM A HRV 460
Cdd:COG0086 372 -- Y RKLEERG L ATT -------------------- IKSA K KMVEREEPEV W DILEEVIKEH PVL L NR A P T LH RLGIQ A FEP 429
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 461 KV I PYSTFR L NLS V TSPY NADFDGD E M NL HVP Q S E E TRA E LSQ L CAVPLQ I V SP QSN KP CMGIV QD TLC G IRK LT LRD -- 538
Cdd:COG0086 430 VL I EGKAIQ L HPL V CTAF NADFDGD Q M AV HVP L S L E AQL E ARL L MLSTNN I L SP ANG KP IIVPS QD MVL G LYY LT RER eg 509
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 539 ------ T F IELDQ VL NMLY wvpdw D G VIPTP A I IK PKPLWS G K Q ILSVAI pngihlqrfdeg TT L lspkdngmliid G QI 612
Cdd:COG0086 510 akgegm I F ADPEE VL RAYE ----- N G AVDLH A R IK VRITED G E Q VGKIVE ------------ TT V ------------ G RY 560
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 613 IFGVVEKKT V GSS N -------- GGL I HVVT R EK G PQVCAKLFGNIQ K VVNFWLLHN G F S T G IG D TIAD gptm R E IT E TIA 684
Cdd:COG0086 561 LVNEILPQE V PFY N qvinkkhi EVI I RQMY R RC G LKETVIFLDRLK K LGFKYATRA G I S I G LD D MVVP ---- K E KQ E IFE 636
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 685 EA K K K V LDVT K EAQAN L L T A khgmtl R E SFE d N V VRFLNE A RDKAGRLAEVNLKDL N NVKQ M VMA G SK GS FINIA Q MSAC 764
Cdd:COG0086 637 EA N K E V KEIE K QYAEG L I T E ------ P E RYN - K V IDGWTK A SLETESFLMAAFSSQ N TTYM M ADS G AR GS ADQLR Q LAGM 709
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 765 V G QQSVEGKR I afgfvdrtlphfskddyspeskgf V E N --- S YL R - GL TPQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ RR 840
Cdd:COG0086 710 R G LMAKPSGN I ------------------------ I E T pig S NF R e GL GVL E Y F ISTH G A R K GL A DTA L KTA DS GY LT RR 765
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 841 LV KALE D IM V hydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekry RVDLLN TD HTLDPSLLES G S E IL 920
Cdd:COG0086 766 LV DVAQ D VI V ----------------------------------------------- TEEDCG TD RGITVTAIKE G G E VI 798
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 921 GD L klqvlldeeykqlv K D R KFL R EVFV D geanwplpvnirriiqnaqqtfhidhtkpsdlt IK D IVL G VKDLQENL L VL 1000
Cdd:COG0086 799 EP L -------------- K E R ILG R VAAE D --------------------------------- VV D PGT G EVLVPAGT L ID 831
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1001 RGKN EII QN A QR D A V T lfccl L RS R L ATRR vlq EYRLTKQAFDWV L S nieaqf LRSV V HP GE M VGV L AAQSIGEP A TQ M T 1080
Cdd:COG0086 832 EEVA EII EE A GI D S V K ----- V RS V L TCET --- RGGVCAKCYGRD L A ------ RGHL V NI GE A VGV I AAQSIGEP G TQ L T 897
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1081 LN TFH FA G V AS ------- KKVTS G VPRLKEI L N V AK N ------ MKTPSLTVYLEPGHAADQ E QA K LIRSAIEHTTLKS V T 1147
Cdd:COG0086 898 MR TFH IG G A AS raaeess IEAKA G GIVRLNN L K V VV N eegkgv VVSRNSELVIVDDGGRRE E EY K VPYGGVLVVVGGG V V 977
1210 1220 1230
....*....|....*....|....*....|...
gi 359546325 1148 IASE I YYDP DP RSTV I P E DEEIIQLHFSLLDEE 1180
Cdd:COG0086 978 VGGG I VAEW DP HTPP I I E EVGGGVVFDDIVEGG 1010
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
807-1094
7.08e-11
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 67.71
E-value: 7.08e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 807 GLT PQ E FFFHAM G G R E GL I DTA VK TA ET GY IQ RRLV KALE D IM V H - Y D NT T RNSL gnviq FIYGE D GM D AAH I ekqsldt 885
Cdd:PRK02597 166 GLT VT E YVISSY G A R K GL V DTA LR TA DS GY LT RRLV DVSQ D VI V R e E D CG T TRGI ----- VVEAM D DG D RVL I ------- 233
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 886 iggsda AFEK R yrvdllntdhtldpsllesgse I LG dlklqvlldeeykqlvkd R KFLRE V FV - D GE anwplpvnirr I I 964
Cdd:PRK02597 234 ------ PLGD R ---------------------- L LG ------------------ R VLAED V VD p E GE ----------- V I 256
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 965 qn A QQTFH ID H tkps DL TI K divlgvkdlqenllvlrgknei I QN A QRDA V TL fccll RS R L --- A T R R V LQ eyrltk QA 1041
Cdd:PRK02597 257 -- A ERNTA ID P ---- DL AK K ---------------------- I EK A GVEE V MV ----- RS P L tce A A R S V CR ------ KC 297
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|...
gi 359546325 1042 FD W V L SNIE aqflrs V V HP GE M VG VL AAQSIGEP A TQ M T LN TFH FA GV ASKK V 1094
Cdd:PRK02597 298 YG W S L AHNH ------ L V DL GE A VG II AAQSIGEP G TQ L T MR TFH TG GV FTGE V 344
RNA_pol_Rpb1_R
pfam05001 RNA polymerase Rpb1 C-terminal repeat; The repetitive C-terminal domain (CTD) of Rpb1 (RNA ...
1698-1709
3.22e-03
RNA polymerase Rpb1 C-terminal repeat; The repetitive C-terminal domain (CTD) of Rpb1 (RNA polymerase Pol II) plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation.
Pssm-ID: 461513
Cd Length: 12
Bit Score: 36.34
E-value: 3.22e-03
Name
Accession
Description
Interval
E-value
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
15-853
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: 1434.63
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 15 K E VQFG LF SP E E V RA I SVA K I RF PET MDETQT r A K I GGLNDPR L G S IDRN LK CQTC QEG M N ECPGHFGHI D LAKPVFH V G 94
Cdd:cd02733 1 K R VQFG IL SP D E I RA M SVA E I EH PET YENGGG - P K L GGLNDPR M G T IDRN SR CQTC GGD M K ECPGHFGHI E LAKPVFH I G 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 95 F IA KI K K VCE CVC mhcgkllldehnelmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqpti 174
Cdd:cd02733 80 F LT KI L K ILR CVC ------------------------------------------------------------------- 92
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 175 rkdglklvgswkkdratgdadepe L R V LS T E EI L N IFK H IS VK D FTS LGF NEV FSRP E WMILT C LPVPPP P VRPS ISFNE 254
Cdd:cd02733 93 ------------------------ K R E LS A E RV L E IFK R IS DE D CRI LGF DPK FSRP D WMILT V LPVPPP A VRPS VVMDG 148
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 255 S Q R G EDDLT F KLADI L KAN IS L ETL E H NGAP H H A IEE A E S LLQFHVATYMDN D I A G Q PQA L QKSGRP V KSIR A RLKGKEG 334
Cdd:cd02733 149 S A R S EDDLT H KLADI I KAN NQ L KRQ E Q NGAP A H I IEE D E Q LLQFHVATYMDN E I P G L PQA T QKSGRP L KSIR Q RLKGKEG 228
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 335 RIRGNLMGKRVDFSARTVI SG DPNLELDQVGVP K SIA KT LT Y PE V VTP Y NIDRL TQ LVRNGPNE H PGAKY V IRD S G D RID 414
Cdd:cd02733 229 RIRGNLMGKRVDFSARTVI TP DPNLELDQVGVP R SIA MN LT F PE I VTP F NIDRL QE LVRNGPNE Y PGAKY I IRD D G E RID 308
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 415 LRY S K R A G D IQ LQYG WK VERH IM D N D P VLFNRQPSLHKMSMM A HRVKV I PYSTFRLNLSVT S PYNADFDGDEMNLHVPQS 494
Cdd:cd02733 309 LRY L K K A S D LH LQYG YI VERH LQ D G D V VLFNRQPSLHKMSMM G HRVKV L PYSTFRLNLSVT T PYNADFDGDEMNLHVPQS 388
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 495 E ETRAEL SQ L CA VP L QIVSPQSNKP C MGIVQDTL C G I RKLT L RDTF I E L DQV L N M L Y W V PDWDG V IP T PAI I KPKPLW S G 574
Cdd:cd02733 389 L ETRAEL KE L MM VP R QIVSPQSNKP V MGIVQDTL L G V RKLT K RDTF L E K DQV M N L L M W L PDWDG K IP Q PAI L KPKPLW T G 468
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 575 KQI L S VA IP NGIH L Q R FDEGT ---- TLL SP K D NGML I ID G QIIF G VVE KKTVG S S N GGLIHV VTR E K GP QVCAKLF GNIQ 650
Cdd:cd02733 469 KQI F S LI IP KINN L I R SSSHH dgdk KWI SP G D TKVI I EN G ELLS G ILC KKTVG A S S GGLIHV IWL E Y GP EAARDFI GNIQ 548
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 651 K VVN F WLLHNGFS T GIGDTIAD GP TM RE I T ETI AE AK KK V LDVTKE AQ ANL L TAKH G M TLRESFE DN V V R F LN E ARDKAG 730
Cdd:cd02733 549 R VVN N WLLHNGFS I GIGDTIAD KE TM KK I Q ETI KK AK RD V IKLIEK AQ NGE L EPQP G K TLRESFE NK V N R I LN K ARDKAG 628
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 731 RL A EVN L KDL NN V K Q MV M AGSKGSFINI A Q MS ACVGQQ S VEGKRI A FGF VD RTLPHF S KDDY S PES K GFVENSYLRGLTP 810
Cdd:cd02733 629 KS A QKS L SED NN F K A MV T AGSKGSFINI S Q II ACVGQQ N VEGKRI P FGF RR RTLPHF I KDDY G PES R GFVENSYLRGLTP 708
810 820 830 840
....*....|....*....|....*....|....*....|...
gi 359546325 811 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKA L ED I MV H YD 853
Cdd:cd02733 709 QEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKA M ED V MV K YD 751
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
11-876
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: 943.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 11 LRTV K EVQ FGL F SPEE V R AI SV AK I RF P E T M DE TQTRAK i GGL N DPRLG S I DRN L K C Q TC QEGMN ECPGHFGHI D LA K PV 90
Cdd:cd02582 1 PKRI K GIK FGL L SPEE I R KM SV VE I IT P D T Y DE DGYPIE - GGL M DPRLG V I EPG L R C K TC GNTAG ECPGHFGHI E LA R PV 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 91 F HVGF IAK I KKVCECV C MH CG KL LL -- D E HNELMRQALAI K D ---- SK KR FAA - IWTLC K TKM VC etdv P S eddptqlvs 163
Cdd:cd02582 80 I HVGF AKH I YDLLRAT C RS CG RI LL pe E E IEKYLERIRRL K E kwpe LV KR VIE k VKKKA K KRK VC ---- P H --------- 146
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 164 rgg CG NT Q PT I rkdglklvgsw K KDRA T G -- DAD E PELRV L STE EI LNIFKH I SVK D FTS LG FNEVFS RPEWM I LT C LPV 241
Cdd:cd02582 147 --- CG AP Q YK I ----------- K LEKP T T fy EEK E EGEVK L TPS EI RERLEK I PDE D LEL LG IDPKTA RPEWM V LT V LPV 212
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 242 PP PP VRPSI SFNESQ R G EDDLT F KL A DI LKA N IS L ETLEHN GAP HHA IE EAES LLQ F HV A TY M DN D I A G Q P Q A LQK SGRP 321
Cdd:cd02582 213 PP VT VRPSI TLETGE R S EDDLT H KL V DI IRI N QR L KENIEA GAP QLI IE DLWD LLQ Y HV T TY F DN E I P G I P P A RHR SGRP 292
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 322 V K SIRA RLKGKEGR I RGNL M GKRV D FSARTVIS G DPNL ELDQ VGVP KS IAK T LT Y PE V VT PY NI DRLTQ LV R NGP NEH PG 401
Cdd:cd02582 293 L K TLAQ RLKGKEGR F RGNL S GKRV N FSARTVIS P DPNL SINE VGVP ED IAK E LT V PE R VT EW NI EKMRK LV L NGP DKW PG 372
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 402 A K YVIR DS G D RI D LRY S - KRAGDIQ L QY GW K VERH IM D N D P VLFNRQPSLH K MS M MAHRV K V I P YS TFRLNL S V TS PYNA 480
Cdd:cd02582 373 A N YVIR PD G R RI R LRY V n REELAER L EP GW I VERH LI D G D I VLFNRQPSLH R MS I MAHRV R V L P GK TFRLNL A V CP PYNA 452
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 481 DFDGDEMNLHVPQSEE T RAE LSQ L CA V PLQ I V SP QSNK P CM G IV QD TLC G IRK LT LRD T FIELDQV L NM L YWV p DW DG VI 560
Cdd:cd02582 453 DFDGDEMNLHVPQSEE A RAE ARE L ML V QEH I L SP RYGG P II G GI QD YIS G AYL LT RKT T LFTKEEA L QL L SAA - GY DG LL 531
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 561 P T PAI IK PKPLW S GKQ IL S VAI P NGIHLQR ------- FD E GTTLLS P K D NGML I ID G QIIF GV VE KK TV G S - SN G G L I H V 632
Cdd:cd02582 532 P E PAI LE PKPLW T GKQ LF S LFL P KDLNFEG kakvcsg CS E CKDEDC P N D GYVV I KN G KLLE GV ID KK AI G A e QP G S L L H R 611
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 633 VTR E K G PQ V CAKLFGNIQKVVNFWLLHN GF ST GI G D TIADGPTMR EI T E T I A EA K KKV LDVTKEAQANL L TAKH G M TL R E 712
Cdd:cd02582 612 IAK E Y G NE V ARRFLDSVTRLAIRFIELR GF TI GI D D EDIPEEARK EI E E I I K EA E KKV YELIEQYKNGE L EPLP G R TL E E 691
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 713 SF E DNVVRF L NE ARD K AG RL A EVN L KDL NN VKQ M VMA G SK GS FI N IA QM S AC V GQQSV E G K RI AF G FVD RTLPHF SKD D Y 792
Cdd:cd02582 692 TL E MKIMQV L GK ARD E AG KV A SKY L DPF NN AVI M ART G AR GS ML N LT QM A AC L GQQSV R G E RI NR G YRN RTLPHF KPG D L 771
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 793 S PE SK GFV EN S YLR GL T P Q EFFFHAMGGREGL I DTAV K T AET GY I QRRL VK AL E D IM V H YD N T T R N S L GN V IQF I YGEDG 872
Cdd:cd02582 772 G PE AR GFV RS S FRD GL S P T EFFFHAMGGREGL V DTAV R T SQS GY M QRRL IN AL Q D LY V E YD G T V R D S R GN I IQF K YGEDG 851
....
gi 359546325 873 M D A A 876
Cdd:cd02582 852 V D P A 855
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
14-874
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 938.51
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 14 VKEVQ FGL F SPEE V R AI SV A KI RFPE T M D ETQTRAK i GGL N DPRLG S ID RN L K C Q TC QEGMN ECPGHFGHI D LA K PV F HV 93
Cdd:PRK08566 9 IGSIK FGL L SPEE I R KM SV T KI ITAD T Y D DDGYPID - GGL M DPRLG V ID PG L R C K TC GGRAG ECPGHFGHI E LA R PV I HV 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 94 GF IAK I K K VCECV C MH CG K L L L D E h N E LMRQALAIKDS K KRFAAIWT L C K T ------- K MVC etdv P S eddptqlvsrgg 166
Cdd:PRK08566 88 GF AKL I Y K LLRAT C RE CG R L K L T E - E E IEEYLEKLERL K EWGSLADD L I K E vkkeaak R MVC ---- P H ------------ 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 167 CG NT Q PT I rkdglklvgsw K KDRA T G -- DADEPE L RV L STEE I LNIFKH I SVK D FTS LG F N EVFS RPEWM I LT C LPVPP P 244
Cdd:PRK08566 151 CG EK Q YK I ----------- K FEKP T T fy EERKEG L VK L TPSD I RERLEK I PDE D LEL LG I N PEVA RPEWM V LT V LPVPP V 219
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 245 P VRPSI SFNES QR G EDDLT F KL A DI LKA N IS L ETLEHN GAP HHA IE EAES LLQ F HV A TY M DN D I A G Q P Q A LQK SGRP V K S 324
Cdd:PRK08566 220 T VRPSI TLETG QR S EDDLT H KL V DI IRI N QR L KENIEA GAP QLI IE DLWE LLQ Y HV T TY F DN E I P G I P P A RHR SGRP L K T 299
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 325 IRA RLKGKEGR I RGNL M GKRV D FSARTVIS G DPNL ELDQ VGVP KS IAK T LT Y PE V VT PY NI DR L TQL V R NGP NE HPGA K Y 404
Cdd:PRK08566 300 LAQ RLKGKEGR F RGNL S GKRV N FSARTVIS P DPNL SINE VGVP EA IAK E LT V PE R VT EW NI EE L REY V L NGP EK HPGA N Y 379
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 405 VIR DS G D RI D L RYS - K RAGDIQ L QY GW K VERH IM D N D P VLFNRQPSLH K MS M MAHRV K V I P YS TFRLNL S V TS PYNADFD 483
Cdd:PRK08566 380 VIR PD G R RI K L TDK n K EELAEK L EP GW I VERH LI D G D I VLFNRQPSLH R MS I MAHRV R V L P GK TFRLNL A V CP PYNADFD 459
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 484 GDEMNLHVPQ S EE T RAE LSQ L CA V PLQ I V SP QSNK P CM G IV QD TLC G IRK LT LRD T FIELDQV L NM L YWVPDWDGVI P T P 563
Cdd:PRK08566 460 GDEMNLHVPQ T EE A RAE ARI L ML V QEH I L SP RYGG P II G GI QD HIS G AYL LT RKS T LFTKEEA L DL L RAAGIDELPE P E P 539
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 564 AI IKP KP L W S GKQI L S VAI P NGIH L QR ------- F DE GTTLLSPK D NGML I ID G QIIF GV VE KK TV G SSN G GLIHVVTR E 636
Cdd:PRK08566 540 AI ENG KP Y W T GKQI F S LFL P KDLN L EF kakicsg C DE CKKEDCEH D AYVV I KN G KLLE GV ID KK AI G AEQ G SILDRIVK E 619
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 637 K GP QVCAKLFGNIQKVVNFWLLHN GF S TGI G D TIADGPTMR EI T E T I A EA K K K V LDVTKEAQANL L TAKH G M TL R E SF E D 716
Cdd:PRK08566 620 Y GP ERARRFLDSVTRLAIRFIMLR GF T TGI D D EDIPEEAKE EI D E I I E EA E K R V EELIEAYENGE L EPLP G R TL E E TL E M 699
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 717 NVVRF L NE ARD K AG RL AE VN L KDL N NV kq MV MA -- G SK GS FI N IA QM S ACVGQQSV E G K RI AF G FV DRTLPHF SKD D YSP 794
Cdd:PRK08566 700 KIMQV L GK ARD E AG EI AE KY L GLD N PA -- VI MA rt G AR GS ML N LT QM A ACVGQQSV R G E RI RR G YR DRTLPHF KPG D LGA 777
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 795 E SK GFV EN SY LR GLTP Q EFFFHAMGGREGL I DTAV K T AET GY I QRRL VK AL E D IM V H YD N T T R NSL GN VI QF I YGEDG M D 874
Cdd:PRK08566 778 E AR GFV RS SY KS GLTP T EFFFHAMGGREGL V DTAV R T SQS GY M QRRL IN AL Q D LK V E YD G T V R DTR GN IV QF K YGEDG V D 857
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
14-876
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: 885.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 14 VKEVQ FGL F SPEE V R AI SV AKIRFPE T M D ETQTRAK i GGL N DPRLG S I DRN L K C Q TC QEGMN ECPGHFGHI D LA K PV F HV 93
Cdd:TIGR02390 4 IGSIK FGL L SPEE I R KM SV VEVVTAD T Y D DDGYPIE - GGL M DPRLG V I EPG L R C K TC GGKVG ECPGHFGHI E LA R PV V HV 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 94 GF IAK I K K VCECV C MH CG KLL L -- D E HNELMRQALAI K DSKKRF A ai W TL CK ------- TK M V C etdv P S eddptqlvsr 164
Cdd:TIGR02390 83 GF AKE I Y K ILRAT C RK CG RIT L te E E IEQYLEKINKL K EEGGDL A -- S TL IE kivkeaa KR M K C ---- P H ---------- 146
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 165 gg CG NT Q PT I rkdgl K LVGSWKKDRATGDA D EP elrv L STE EI LNIFKH I SVK D FTS LG F N EVFS RPEWM I LT C LPVPP P 244
Cdd:TIGR02390 147 -- CG EE Q KK I ----- K FEKPTYFYEEGKEG D VK ---- L TPS EI RERLEK I PDE D AEL LG I N PKVA RPEWM V LT V LPVPP V 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 245 P VRPSI SFNESQ R G EDDLT F KL A DI LKA N IS L ETLEHN GAP HHA IE EAES LLQ F HVATY M DN DIA G Q P Q A LQK SGRP V K S 324
Cdd:TIGR02390 216 T VRPSI TLETGE R S EDDLT H KL V DI IRI N QR L KENIEA GAP QLI IE DLWE LLQ Y HVATY F DN ELP G I P P A RHR SGRP L K T 295
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 325 IRA RLKGKEGR I RGNL M GKRV D FSARTVIS G DPN LELDQ VGVP KS IAK T LT Y PE V VTP Y NID R L TQL V R NGP NEH PGA K Y 404
Cdd:TIGR02390 296 LAQ RLKGKEGR F RGNL S GKRV N FSARTVIS P DPN ISINE VGVP EQ IAK E LT V PE R VTP W NID E L REY V L NGP DSW PGA N Y 375
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 405 VIR DS G D RI DL R YSKRAGDIQ - L QY GW K VERH IM D N D P VLFNRQPSLH K MSMM A H R VKV I P YS TFRLNL S V TS PYNADFD 483
Cdd:TIGR02390 376 VIR PD G R RI KI R DENKEELAE r L EP GW V VERH LI D G D I VLFNRQPSLH R MSMM G H K VKV L P GK TFRLNL A V CP PYNADFD 455
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 484 GDEMNLHVPQ S EE T RAE LSQ L CA V PLQ I VS P QSNK P CM G IVQ D TLC G IRK LT LRD T FIELDQ V LNM L Y w V PDWD G VI P T P 563
Cdd:TIGR02390 456 GDEMNLHVPQ T EE A RAE ARE L ML V EEH I LT P RYGG P II G GIH D YIS G AYL LT HKS T LFTKEE V QTI L G - V AGYF G DP P E P 534
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 564 AI I KPK PL W S GKQI L S VAI P NGIHLQ ------- RF D EGTTLLS P K D NGML I ID G QIIF GV VE KK TV G SSN G GLI H VVT RE 636
Cdd:TIGR02390 535 AI E KPK EY W T GKQI F S AFL P EDLNFE grakics GS D ACKKEEC P H D AYVV I KN G KLLK GV ID KK AI G AEK G KIL H RIV RE 614
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 637 K GP QVCAKLFGNIQKVVNFWLLHN GF S TGI G D TIADGPTMR EI T E T I AE A K K K V LDVTKEAQANL L TAKH G M T LR E SF E D 716
Cdd:TIGR02390 615 Y GP EAARRFLDSVTRLFIRFITLR GF T TGI D D IDIPKEAKE EI E E L I EK A E K R V DNLIERYRNGE L EPLP G R T VE E TL E M 694
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 717 NVVRF L NE ARD K AG RL AE VN L KDL N NVKQ M VMA G SK GS FI NI A QM S A C VGQQSV E G K RI AF G FVD RTLPHF S K D D YSPES 796
Cdd:TIGR02390 695 KIMEV L GK ARD E AG EV AE KY L DPE N HAVI M ART G AR GS LL NI T QM A A M VGQQSV R G G RI RR G YRN RTLPHF K K G D IGAKA 774
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 797 K GFV EN S YLR GL T P Q E F FFHA M GGREGL I DTAV K T AET GY I QRRL VK AL E D IM V H YD N T T R NSL GN V IQF I YGEDG M D AA 876
Cdd:TIGR02390 775 R GFV RS S FKK GL D P T E Y FFHA A GGREGL V DTAV R T SQS GY M QRRL IN AL Q D LY V E YD G T V R DTR GN L IQF K YGEDG V D PM 854
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
10-1446
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 860.48
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 10 PLRTVKEVQ FGL F SP EEV R A I SV A K I RF PE TM DE TQTRAK i GGL N D P RLG S I DRNL KC Q TC QEGMNE CPGHFGHI D LA K P 89
Cdd:PRK14977 5 AVKAIDGII FGL I SP ADA R K I GF A E I TA PE AY DE DGLPVQ - GGL L D G RLG T I EPGQ KC L TC GNLAAN CPGHFGHI E LA E P 83
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 90 V F H VG FI AK IK KVCECV C MH C G KL L L DEHNELMRQAL aikdsk KRFA A IWTLCKT K MVCETDVPSED D PTQLVSRGG --- 166
Cdd:PRK14977 84 V I H IA FI DN IK DLLNST C HK C A KL K L PQEDLNVFKLI ------ EEAH A AARDIPE K RIDDEIIEEVR D QVKVYAKKA kec 157
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 167 -- CG NT Q - PTIRKDGLKLV gswkkdratg DAD E P E LRV L STE EI LN IF KH I SVK D FTSL GF NEVFS RPEW MI L TCLP VPP 243
Cdd:PRK14977 158 ph CG AP Q h ELEFEEPTIFI ---------- EKT E I E EHR L LPI EI RD IF EK I IDD D LELI GF DPKKA RPEW AV L QAFL VPP 227
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 244 PPV RPSI SFNESQ R G EDDLT FK L A DI L KAN IS L ETLEHN GAP HHAI E EAESL LQ F H VA T YM DN DI AG Q PQA LQ K - SGRP V 322
Cdd:PRK14977 228 LTA RPSI ILETGE R S EDDLT HI L V DI I KAN QK L KESKDA GAP PLIV E DEVDH LQ Y H TS T FF DN AT AG I PQA HH K g SGRP L 307
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 323 KS IRA RLKGKEGR I RGNL M GKRVDFSARTVIS G DP NLEL D Q VGVP KS IA KT LT Y PE V V TPY NI DRLTQ LV R NGP N E H PGA 402
Cdd:PRK14977 308 KS LFQ RLKGKEGR F RGNL I GKRVDFSARTVIS P DP MIDI D E VGVP EA IA MK LT I PE I V NEN NI EKMKE LV I NGP D E F PGA 387
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 403 KYVIRDS G DR I D L RYSKRA G DI ------- QL QY G WK VERH IM D N D P V L FNRQPSLHK M S MM AHRVKV I P YS TFRL NLS V T 475
Cdd:PRK14977 388 NAIRKGD G TK I R L DFLEDK G KD alreaae QL EI G DI VERH LA D G D I V I FNRQPSLHK L S IL AHRVKV L P GA TFRL HPA V C 467
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 476 S PYNADFDGDEMNLHVPQ S E ET RAE LSQ L CA V PLQIV SP QSNK P CM G IV QD TLCGIRKL T LR D TFIELDQVL N MLY w VPD 555
Cdd:PRK14977 468 P PYNADFDGDEMNLHVPQ I E DA RAE AIE L MG V KDNLI SP RTGG P II G AL QD FITAAYLI T KD D ALFDKNEAS N IAM - LAG 546
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 556 WDGVI P T PAI - I K PK P L W S GKQ IL S VAI P --- N GIHLQRFDE G TT ----- LLSPK D NGM LI ID G QI I F GV VEKKTV G SSN 626
Cdd:PRK14977 547 ITDPL P E PAI k T K DG P A W T GKQ LF S LFL P kdf N FEGIAKWSA G KA geakd PSCLG D GYV LI KE G EL I S GV IDDNII G ALV 626
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 627 GG --- LI HVVTREK G PQ V CAKLFGN I QKVVNFWL LH N GFS T G I GD T I ADGPTMR EI TET I AEA K KK V L D VTKEAQANLLT 703
Cdd:PRK14977 627 EE pes LI DRIAKDY G EA V AIEFLNK I LIIAKKEI LH Y GFS N G P GD L I IPDEAKQ EI EDD I QGM K DE V S D LIDQRKITRKI 706
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 704 AKH -------- GM TLR E SF E DNV V RF L NE ARDKAG RL A EVNLKDL N NV K Q M VMA G SK GS FI N I AQ MSACV GQQ SVE ---- 771
Cdd:PRK14977 707 TIY kgkeellr GM KEE E AL E ADI V NE L DK ARDKAG SS A NDCIDAD N AG K I M AKT G AR GS MA N L AQ IAGAL GQQ KRK trig 786
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 772 ---- G K R IAF G FV DR T L P HF SKD D YS P ESK GFV E N S Y LR GL TPQ EFFFHAMGGREGLID T A VK T AET GY I QRRL VK ALED 847
Cdd:PRK14977 787 fvlt G G R LHE G YK DR A L S HF QEG D DN P DAH GFV K N N Y RE GL NAA EFFFHAMGGREGLID K A RR T EDS GY F QRRL AN ALED 866
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 848 I MVH YD N T T R NSL G NV IQF IY GEDG mdaahiekqsldtiggsdaafekryrvdllntdht L DP SL L ES G S eilgdlklqv 927
Cdd:PRK14977 867 I RLE YD E T V R DPH G HI IQF KF GEDG ----------------------------------- I DP QK L DH G E ---------- 901
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 928 lldeeykqlvkdrkflrevfvdgeanwpl PV N IR RII QNA qqtfhidhtkpsdlti K DIVL G VKDLQENLLV L RGKNEII 1007
Cdd:PRK14977 902 ----------------------------- AF N LE RII EKQ ---------------- K IEDR G KGASKDEIEE L AKEYTKT 936
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1008 Q NA qrdavtlfccll RSRLATRRVLQEYR L TKQAFDWVLSNIEAQ F LRSV V H PG EMV G VLA AQSI G EP A TQMTL N TFH F A 1087
Cdd:PRK14977 937 F NA ------------ NLPKLLADAIHGAE L KEDELEAICAEGKEG F EKAK V E PG QAI G IIS AQSI A EP G TQMTL R TFH A A 1004
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1088 G VASKK VT S G VP R LK E ILNVAKNMK TP SLTV YL EPGHAA D Q E Q A KL I RSAIEHTTLKSVTIA S E I YY d PDPRSTVI P EDE 1167
Cdd:PRK14977 1005 G IKAMD VT H G LE R FI E LVDARAKPS TP TMDI YL DDECKE D I E K A IE I ARNLKELKVRALIAD S A I DN - ANEIKLIK P DKR 1083
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1168 eiiqlhfs L L DEEA eqsfdqq S P WLLRL E LDR A AMND K DLT M GQVGER I kqtfkndlfviwsedndekliircrvvrpk S 1247
Cdd:PRK14977 1084 -------- A L ENGC ------- I P MERFA E IEA A LAKG K KFE M ELEDDL I ------------------------------ I 1118
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1248 LD AETE A EE D H --- M L KK I E N TM L e NITLR GV EN IER -- V VMMKY D RK vpsptgeyvke P EW VLE T D G V NL SE V MTVPG I 1322
Cdd:PRK14977 1119 LD LVEA A DR D K pla T L IA I R N KI L - DKPVK GV PD IER aw V ELVEK D GR ----------- D EW IIQ T S G S NL AA V LEMKC I 1186
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1323 D PTRIY TN SFID I MEV LGIEA G R A A LYK E VYNVIASD G SY V NY R HMA L LV D V M TTQ G GLTSV ------ T RHGF NRSNTGA 1396
Cdd:PRK14977 1187 D IANTI TN DCFE I AGT LGIEA A R N A IFN E LASILEDQ G LE V DN R YIM L VA D I M CSR G TIEAI glqaag V RHGF AGEKDSP 1266
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|
gi 359546325 1397 L MRCS FE E T VEILFE A GASA E LDDCR G VSENV I L GQ MA PIG T G AF D VMI D 1446
Cdd:PRK14977 1267 L AKAA FE I T THTIAH A ALGG E IEKIK G ILDAL I M GQ NI PIG S G KV D LLM D 1316
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
22-857
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: 854.54
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 22 F SPE EVRAI S VAKIRFPETM D ETQTRAKIG G LN DPRLG SI D RNLK C Q TC QEGMNE C P GHFG H I D L AK PVFH V G FIAK I KK 101
Cdd:cd02583 1 L SPE DIIRL S EVEVTNRNLY D IETRKPLPY G VL DPRLG TS D KDGI C E TC GLNLAD C V GHFG Y I K L EL PVFH I G YFKA I IN 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 102 VCE C V C MH C GKL LL D E hn E LM R QA L ----- AIK D SKKR --- FAA I WTL CK TKMV C etdv P S eddptqlvsrgg CG NTQPT 173
Cdd:cd02583 81 ILQ C I C KT C SRV LL P E -- E EK R KF L krlrr PNL D NLQK kal KKK I LEK CK KVRK C ---- P H ------------ CG LLKKA 142
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 174 irkdglklvgswkkdratgdad EPE L RV L ste EI LN I FK H I SVK D FTS L GF N EVFS RPE WM ILT CL PVPP PPV RPS ISFN 253
Cdd:cd02583 143 ---------------------- QED L NP L --- KV LN L FK N I PPE D VEL L LM N PLAG RPE NL ILT RI PVPP LCI RPS VVMD 197
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 254 E SQ - RG EDDLT F KL AD I LKA N ISLETLEHN GA PHHA I E E AESL LQ FHV A T Y MDNDIA G Q P QA l QKSGR P VKSIRA RLKGK 332
Cdd:cd02583 198 E KS g TN EDDLT V KL SE I IFL N DVIKKHLEK GA KTQK I M E DWDF LQ LQC A L Y INSELP G L P LS - MQPKK P IRGFCQ RLKGK 276
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 333 E GR I RGNL M GKRVDFS A RTVIS G DPNL EL DQVGVP KSI AK T LTYPE V VT P YNI DR L TQ LV R NGP NE HPGA KY VI - RD S G D 411
Cdd:cd02583 277 Q GR F RGNL S GKRVDFS G RTVIS P DPNL RI DQVGVP EHV AK I LTYPE R VT R YNI EK L RK LV L NGP DV HPGA NF VI k RD G G K 356
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 412 RID L R Y SK R AGDIQ - L QY G WK VERH IM D N D P VLFNRQPSLH KM S M MAHR V KV I P YS TFR L N LS V TS PYNADFDGDEMNLH 490
Cdd:cd02583 357 KKF L K Y GN R RKIAR e L KI G DI VERH LE D G D I VLFNRQPSLH RL S I MAHR A KV M P WR TFR F N EC V CT PYNADFDGDEMNLH 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 491 VPQ S EE T RAE LSQ L CA V PLQI V S P QSNK P CMGIV QD T L CGIRK LT LR D T F IELD Q VLNMLYWVP D WDGV I -- P T PAI I KP 568
Cdd:cd02583 437 VPQ T EE A RAE ALE L MG V KNNL V T P RNGE P LIAAT QD F L TASYL LT SK D V F FDRA Q FCQLCSYML D GEIK I dl P P PAI L KP 516
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 569 KP LW S GKQI L S VAI ------ P NGIH L Q ---- RFDEGTTLLS P K D NGML I IDGQIIF G VVE K K T V GS SN - GG L IH V VT R EK 637
Cdd:cd02583 517 VE LW T GKQI F S LLL rpnkks P VLVN L E akek SYTKKSPDMC P N D GYVV I RNSELLC G RLD K S T L GS GS k NS L FY V LL R DY 596
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 638 GP QVC A KLFGNIQ K VVNF WL LHN GFS T GI G D TIADGPTMREIT E TIAEAKK K VLDVT K EAQANL L TAKH G M T LRESF E DN 717
Cdd:cd02583 597 GP EAA A AAMNRLA K LSSR WL SNR GFS I GI D D VTPSKELLKKKE E LVDNGYA K CDEYI K QYKKGK L ELQP G C T AEQTL E AK 676
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 718 VVRF L NEA R DK AG RLAEVN L KDL N NVKQ M VMA GSKGS F INI A QM S ACVGQQ SVE GKRI AF GF V DRTLPHF SKDDYS P ES K 797
Cdd:cd02583 677 ISGE L SKI R ED AG KACLKE L HKS N SPLI M ALC GSKGS N INI S QM I ACVGQQ IIS GKRI PN GF E DRTLPHF PRNSKT P AA K 756
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 798 GFV E NS YLR GLTP Q EFFFH A M G GREGL I DTAVKTAETGY I QRRL V KALED IM V H YD N T T R 857
Cdd:cd02583 757 GFV A NS FYS GLTP T EFFFH T M S GREGL V DTAVKTAETGY M QRRL M KALED LS V Q YD G T V R 816
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1035-1446
0e+00
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: 715.91
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1035 YRL T K Q AFDW V L SN IE AQ F L RS V VHPGEMVG VL AAQSIGEPATQMTLNTFHFAGV AS K K VT S GVPRLKEI L NVAKN M KTP 1114
Cdd:cd02584 1 YRL N K E AFDW I L GE IE TR F N RS L VHPGEMVG TI AAQSIGEPATQMTLNTFHFAGV SA K N VT L GVPRLKEI I NVAKN I KTP 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1115 SLTVYLEPG H A A D Q E Q AK L I R S AI EHTTLK S VT I A S EIYYDPDP RS TVI P ED E E IIQLH F SLL DE EA E qs F D QQ SPWLLR 1194
Cdd:cd02584 81 SLTVYLEPG F A K D E E K AK K I Q S RL EHTTLK D VT A A T EIYYDPDP QN TVI E ED K E FVESY F EFP DE DV E -- Q D RL SPWLLR 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1195 L ELDR AA M N DK D L T M G Q VGER IK QT FK N DL F VI W S E DN D EKL I IR C R VVRPKS l DA E TEA E E D HM LKKIE NT ML ENI TL R 1274
Cdd:cd02584 159 I ELDR KK M T DK K L S M E Q IAKK IK EE FK D DL N VI F S D DN A EKL V IR I R IINDDE - EK E EDS E D D VF LKKIE SN ML SDM TL K 237
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1275 G V E N I ER V VMMK - YDR KV PSP TGE YV K EP EWVLETDGVNL S EV MTV PG I DPTR IYT N SFID I M EVLGIEA G R A AL Y KE VY 1353
Cdd:cd02584 238 G I E G I RK V FIRE e NKK KV DIE TGE FK K RE EWVLETDGVNL R EV LSH PG V DPTR TTS N DIVE I F EVLGIEA A R K AL L KE LR 317
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1354 NVI AS DGSYVNYRH M ALL V DVMT TQ G G L TSV TRHG F NR SN TG A LMRCSFEETV E IL F EA G A SA E L DD CR GVSEN VI LGQ M 1433
Cdd:cd02584 318 NVI SF DGSYVNYRH L ALL C DVMT QR G H L MAI TRHG I NR QD TG P LMRCSFEETV D IL L EA A A FG E T DD LK GVSEN IM LGQ L 397
410
....*....|...
gi 359546325 1434 APIGTG A FD VMI D 1446
Cdd:cd02584 398 APIGTG C FD LLL D 410
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
22-853
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: 715.36
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 22 F SPEE V R AI SVAK IRF PET M D ETQTR A KI GG LN DPRLGSIDR NL KC Q TC QE G M N E CPGHFGHI D LAKPVFHVGFI A K IKK 101
Cdd:cd00399 1 M SPEE I R KW SVAK VIK PET I D NRTLK A ER GG KY DPRLGSIDR CE KC G TC GT G L N D CPGHFGHI E LAKPVFHVGFI K K VPS 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 102 VCE cvcmhcgkllldehnelmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglkl 181
Cdd:cd00399 81 FLG ----------------------------------------------------------------------------- 83
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 182 vgswkkdratgdadepelrvlsteeilnifkhisvkdftslgfnevfsr PEWMILTCLPVPPP PV RPS I sfnesqrgedd 261
Cdd:cd00399 84 ------------------------------------------------- PEWMILTCLPVPPP CL RPS V ----------- 103
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 262 ltfkladilkanisletlehngaphh A IEE AES LLQ F HV A TY M DN D IAGQPQ A l QKSGRP VK S IRA RLKGKEGR I RGNLM 341
Cdd:cd00399 104 -------------------------- I IEE RWR LLQ E HV D TY L DN G IAGQPQ T - QKSGRP LR S LAQ RLKGKEGR F RGNLM 156
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 342 GKRVDFS A R T VIS G DPNL E LDQVGVPKSIA K TL typevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskra 421
Cdd:cd00399 157 GKRVDFS G R S VIS P DPNL R LDQVGVPKSIA L TL ----------------------------------------------- 189
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 422 gdiqlqygwkverhim D N DPVLFNRQPSLHK M S M MAHRV K V I P Y STFRLN LS V T SPYNADFDGDEMNLHVPQSEE T RAE L 501
Cdd:cd00399 190 ---------------- D G DPVLFNRQPSLHK L S I MAHRV R V L P G STFRLN PL V C SPYNADFDGDEMNLHVPQSEE A RAE A 253
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 502 SQ L CA VP LQ I V SPQ SNK P CM G IV QDTL C G IRK LTL rdtfieldqvlnmlywvpdwdgviptpaiikpkplws GKQI L S V A 581
Cdd:cd00399 254 RE L ML VP NN I L SPQ NGE P LI G LS QDTL L G AYL LTL ------------------------------------- GKQI V S A A 296
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 582 I P N G ihlqrfdegttllspkdngmliidgqiifgvvekktvgssngg L I H V VTRE K GP QVC AKL FG N I Q K V VNFW L LHN G 661
Cdd:cd00399 297 L P G G ------------------------------------------- L L H T VTRE L GP EKA AKL LS N L Q R V GFVF L TTS G 333
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 662 FS T GIGD T I A DG PTMR E I TE T I A EAKKKV LD V TKEA QA N LLTA KH GMTL R ES F EDN VVR FLNEARDKAG RL A E VNL K --- 738
Cdd:cd00399 334 FS V GIGD V I D DG VIPE E K TE L I E EAKKKV DE V EEAF QA G LLTA QE GMTL E ES L EDN ILD FLNEARDKAG SA A S VNL D lvs 413
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 739 DL N NVKQ M V M A G S KGSFINI A QMSACVGQQSVEGKRI AF GF V DRTLPHFSKDDYSPE S KGF VE NS Y L R GLTP Q E F FFHAM 818
Cdd:cd00399 414 KF N SIYV M A M S G A KGSFINI R QMSACVGQQSVEGKRI PR GF S DRTLPHFSKDDYSPE A KGF IR NS F L E GLTP L E Y FFHAM 493
810 820 830
....*....|....*....|....*....|....*
gi 359546325 819 GGREGL I DTAVKTAE T GY I QRRLVKALED IM VHYD 853
Cdd:cd00399 494 GGREGL V DTAVKTAE S GY L QRRLVKALED LV VHYD 528
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
807-1397
0e+00
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: 617.83
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 807 GLTPQEFFFH A MGGREGLIDTAVKTAE T GY I QRRLVKALED IM V H YD N T T RNS L G NVI QF I YGEDG M D AAH IEKQ SLD TI 886
Cdd:pfam04998 1 GLTPQEFFFH T MGGREGLIDTAVKTAE S GY L QRRLVKALED LV V T YD D T V RNS G G EIV QF L YGEDG L D PLK IEKQ GRF TI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 887 GG SD AAF E KRYRV DLL NTDHT L DPSL L ESGS EIL GDLKLQ vlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqn 966
Cdd:pfam04998 81 EF SD LKL E DKFKN DLL DDLLL L SEFS L SYKK EIL VRDSKL ---------------------------------------- 120
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 967 aqqtfhidhtkpsdltikdivlgvkdlqenllvlr G KNEIIQN AQ RD A VT LF CC LL R S R L ATR RV LQ E YRLTKQ AF DWV L 1046
Cdd:pfam04998 121 ----------------------------------- G RDRLSKE AQ ER A TL LF EL LL K S G L ESK RV RS E LTCNSK AF VCL L 165
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1047 SNIEAQFLR S VVH PGE M VG VL AAQSIGEP A TQMTLNTFHFAGVASK K VT S GVPRLKEI L NV A KN M K T PSLTVYL EPGHAA 1126
Cdd:pfam04998 166 CYGRLLYQQ S LIN PGE A VG II AAQSIGEP G TQMTLNTFHFAGVASK N VT L GVPRLKEI I NV S KN I K S PSLTVYL FDEVGR 245
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1127 DQ E Q AK LIRS AIE HT TL K SV TIAS EI Y YDPDP RS T V I PE D EEIIQLH F SLL DE EAEQSFDQQSPW LL R L ELDRAAMND K D 1206
Cdd:pfam04998 246 EL E K AK KVYG AIE KV TL G SV VESG EI L YDPDP FN T P I IS D VKGVVKF F DII DE VTNEEEIDPETG LL I L VIRLLKILN K S 325
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1207 L ------- TMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDA E TEA EED HM L KKIENTM L E NITLRG VEN I 1279
Cdd:pfam04998 326 I kkvvkse VIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVD E LFM EED PK L AILVASL L G NITLRG IPG I 405
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1280 E R VVMMKY D RKVP sptgeyvk EP E WVLET D GVNL SE V MT VPG - I D PT RI YT N SFID I M E V LGIEA G R A AL YK E VY NV IAS 1358
Cdd:pfam04998 406 K R ILVNED D KGKV -------- EP D WVLET E GVNL LR V LL VPG f V D AG RI LS N DIHE I L E I LGIEA A R N AL LN E IR NV YRF 477
570 580 590
....*....|....*....|....*....|....*....
gi 359546325 1359 D G S Y V N Y RH MA L LV D V MT TQ G GLTSVT RHG F N RSNTG AL 1397
Cdd:pfam04998 478 Q G I Y I N D RH LE L IA D Q MT RK G YIMAIG RHG I N KAELS AL 516
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
18-853
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: 601.48
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 18 Q F GLF S P EE V R AI SV AK I RF P E T M D ETQ t RAKI GGL N DP R LG SI D RNLK C Q TC QEGMNE CPGHFGHI D L AK PV FHVG F IA 97
Cdd:cd01435 1 S F SFY S A EE I R KL SV KE I TN P V T F D SLG - HPVP GGL Y DP A LG PL D KDDI C S TC GLNYLN CPGHFGHI E L PL PV YNPL F FD 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 98 KIK K VCECV C MH C GKLLLD ehnelmrqalai K DSK K R F A A IWT L CKTKMVC E td VPSE D DPT qlvsrggcgntqptirkd 177
Cdd:cd01435 80 LLY K LLRGS C FY C HRFRIS ------------ K WEV K L F V A KLK L LDKGLLV E -- AAEL D FGY ------------------ 127
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 178 glklvgswkkdratgdadepel RVLSTEEI L --- N I F khisvkdftslgfnevfs RP ewmiltclpvppppvrps I SF NE 254
Cdd:cd01435 128 ---------------------- DMFFLDVL L vpp N R F ------------------ RP ------------------ P SF LG 149
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 255 SQRG E DDLTFK L AD ILK A N ISLET L --------------- EHNGAPHHAIEE A ESL LQ FH V ATYM D NDI A GQPQALQKS G 319
Cdd:cd01435 150 DKVF E NPQNVL L SK ILK D N QQIRD L lasmrqaesqskldl ISGKTNSEKLIN A WLQ LQ SA V NELF D STK A PKSGKKSPP G 229
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 320 rpvks I RAR L KG KEG RI R G N L MGKRV DFS AR T VIS G DP NL E LDQV G V P KSI AK T LT Y PE V VTP Y N IDR L T Q L V R NGP NEH 399
Cdd:cd01435 230 ----- I KQL L EK KEG LF R M N M MGKRV NYA AR S VIS P DP FI E TNEI G I P LVF AK K LT F PE P VTP F N VEE L R Q A V I NGP DVY 304
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 400 PGA KYVIRDS G DR I D L RYSK ------------- RAGDIQ L QY G - W KV E RH IM D N D P VL F NRQP S LHK M S M MAH R V K V I P Y 465
Cdd:cd01435 305 PGA NAIEDED G RL I L L SALS eerrkalakllll LSSAKL L LN G p K KV Y RH LL D G D V VL L NRQP T LHK P S I MAH K V R V L P G 384
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 466 S - T F RL NLSVTSP YNADFDGDEMNLH V PQSE ET RAE LSQLCAVPL Q IVS P QSN KP CM G IV QD TLCGIRK LT L RDTF IELD 544
Cdd:cd01435 385 E k T L RL HYANCKS YNADFDGDEMNLH F PQSE LA RAE AYYIASTDN Q YLV P TDG KP LR G LI QD HVVSGVL LT S RDTF FTRE 464
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 545 QVLNML Y -- WV P DWDG ------ VIPT PAI I KPKPLW S GKQ IL S VAIP N G I -- HLQRFDEGTTLLSP K DN G ---------- 604
Cdd:cd01435 465 EYQQLV Y aa LR P LFTS dkdgri KLLP PAI L KPKPLW T GKQ VI S TILK N L I pg NAPLLNLSGKKKTK K KV G ggkwgggsee 544
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 605 -- ML I ID G QIIF GV VE K KTV G S S NG GL I H V V TREK G PQVCA KL FGNIQKVVNFW L LHN GF ST GI G D TI adgptmre I T ET 682
Cdd:cd01435 545 sq VI I RN G ELLT GV LD K SQF G A S AY GL V H A V YELY G GETAG KL LSALGRLFTAY L QMR GF TC GI E D LL -------- L T PK 616
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 683 IA E AKK K V L DVT K EAQANL ltakhgmt LR E SFEDNVVRFLNEARDKA -- GR L a EVNLKD l NN VKQ MV MA G S KGS FI N IA Q 760
Cdd:cd01435 617 AD E KRR K I L RKA K KLGLEA -------- AA E FLGLKLNKVTSSIIKAC lp KG L - LKPFPE - NN LQL MV QS G A KGS MV N AS Q 686
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 761 M S ACV GQQ SV EG K R IAFGFVDR TLP H F SKD D Y SP ESK GF VENSY L R G LT PQE F FFH A M G GREGLIDTAVKT AET GY I QR R 840
Cdd:cd01435 687 I S CLL GQQ EL EG R R VPLMVSGK TLP S F PPY D T SP RAG GF ITDRF L T G IR PQE Y FFH C M A GREGLIDTAVKT SRS GY L QR C 766
890
....*....|...
gi 359546325 841 L V K A LE DIM V H YD 853
Cdd:cd01435 767 L I K H LE GLK V N YD 779
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
232-532
1.76e-161
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 492.80
E-value: 1.76e-161
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 232 EWMILT C LPVPPP PV RPS ISFNESQRG EDDLT FK L A DI L K A N IS L ET L EHN GAP HHA I EEAES LLQ FH V A T YM DN D ia G Q 311
Cdd:smart00663 1 EWMILT V LPVPPP CL RPS VQLDGGRFA EDDLT HL L R DI I K R N NR L KR L LEL GAP SII I RNEKR LLQ EA V D T LI DN E -- G L 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 312 P Q A L QKSGRP V KS IRA RLKGKEGR I R G NL M GKRVDFSAR T VI SG DPNL E L DQ VGVPK S IA KT LT Y PE V VTP Y NID R L TQ L 391
Cdd:smart00663 79 P R A N QKSGRP L KS LSQ RLKGKEGR F R Q NL L GKRVDFSAR S VI TP DPNL K L NE VGVPK E IA LE LT F PE I VTP L NID K L RK L 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 392 VRNGP neh P GAKY V IR ds G DRID L RYS K RA - GDIQ L QY G WK VERH IM D N D P VLFNRQP S LH K MS MM AHRV K V IPYS T F RL 470
Cdd:smart00663 159 VRNGP --- N GAKY I IR -- G KKTN L KLA K KS k IANH L KI G DI VERH VI D G D V VLFNRQP T LH R MS IQ AHRV R V LEGK T I RL 233
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 359546325 471 N LS V T SPYNADFDGDEMNLHVPQS E E T RAE LSQ L CA VP LQ I V SP QSN KP CM G IV QD T L C G IR 532
Cdd:smart00663 234 N PL V C SPYNADFDGDEMNLHVPQS L E A RAE ARE L ML VP NN I L SP KNG KP II G PI QD M L L G LY 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
11-340
1.47e-142
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: 442.88
E-value: 1.47e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 11 L RTV KE V QFG LF SPEE V R AI SV AKIRF PET MDETQTRAKI GGL N D P R L G S ID RNLK C Q TC QEGMNE CPGHFGHI D LAKPV 90
Cdd:pfam04997 1 L KKI KE I QFG IA SPEE I R KW SV GEVTK PET YNYGSLKPEE GGL L D E R M G T ID KDYE C E TC GKKKKD CPGHFGHI E LAKPV 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 91 FH V GF IA K IK K VC ECVC MH C G KLLLD EHNE ---- LMRQA L AIKDS K KRFA AI WT LCK T K MV CE TDVPSE ddptqlvsr G G 166
Cdd:pfam04997 81 FH I GF FK K TL K IL ECVC KY C S KLLLD PGKP klfn KDKKR L GLENL K MGAK AI LE LCK K K DL CE HCGGKN --------- G V 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 167 CG NT QP TI RK D GLKL VGSW KK DR atgda D E P E LRV L ST E EI L N IFK H IS VK D FTS LGFN EVF SRPEWMILT C LPVPPP PV 246
Cdd:pfam04997 152 CG SQ QP VS RK E GLKL KAAI KK SK ----- E E E E KEI L NP E KV L K IFK R IS DE D VEI LGFN PSG SRPEWMILT V LPVPPP CI 226
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 247 RPS ISFNESQ R G EDDLT F KL A DI L K A N IS L ET L EHN GAP H H A I E E AES LLQ F HVAT YM DN D I A G Q P Q ALQKS G RP V KSI R 326
Cdd:pfam04997 227 RPS VQLDGGR R A EDDLT H KL R DI I K R N NR L KK L LEL GAP S H I I R E EWR LLQ E HVAT LF DN E I P G L P P ALQKS K RP L KSI S 306
330
....*....|....
gi 359546325 327 A RLKGKEGR I RGNL 340
Cdd:pfam04997 307 Q RLKGKEGR F RGNL 320
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
342-507
6.23e-103
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: 326.18
E-value: 6.23e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 342 GKRVDFSARTVIS G DPNL E LD Q VGVP K S I AKTLT Y PE V VTPYNI D RL T QLV R NGPN EH PGA K Y V IR DS G D R I DLRY S KR A 421
Cdd:pfam00623 1 GKRVDFSARTVIS P DPNL K LD E VGVP I S F AKTLT F PE I VTPYNI K RL R QLV E NGPN VY PGA N Y I IR IN G A R R DLRY Q KR R 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 422 G D IQ L QY G WK VERH IM D N D P VLFNRQPSLH KM S M M A HRV K V I P YS TFRLNLSVT S PYNADFDGDEMNLHVPQSEE T RAE L 501
Cdd:pfam00623 81 L D KE L EI G DI VERH VI D G D V VLFNRQPSLH RL S I M G HRV R V L P GK TFRLNLSVT T PYNADFDGDEMNLHVPQSEE A RAE A 160
....*.
gi 359546325 502 SQ L CA V 507
Cdd:pfam00623 161 EE L ML V 166
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1031-1447
4.20e-92
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: 303.40
E-value: 4.20e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1031 VL Q E YR LT KQAFDWVLSNIEAQF LRS VVH PGE M VG VL AAQSIGEP A TQMTL N TFH F AGVA SKK VT S G V PRL K EI LNVA K N 1110
Cdd:cd06528 10 VL K E HG LT LSEAEEIIKEVLREY LRS LIE PGE A VG IV AAQSIGEP G TQMTL R TFH Y AGVA EIN VT L G L PRL I EI VDAR K E 89
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1111 MK TP SL T V YLE PGHAA D Q E Q A KLIRSA IE H TTL KS vt I A SE I YY D PDPRSTV I pedeeiiqlhfslldeeaeqsfdqqsp 1190
Cdd:cd06528 90 PS TP TM T I YLE EEYKY D R E K A EEVARK IE E TTL EN -- L A ED I SI D LFNMRIT I --------------------------- 140
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1191 wllrl ELD RAAMN D KDL T MGQ V GER I KQTF K NDL fviw S E DN D EK LI I rcrvvrpks L D AE TEAEED hm L K K IENTM L e N 1270
Cdd:cd06528 141 ----- ELD EEMLE D RGI T VDD V LKA I EKLK K GKV ---- G E EG D VT LI V --------- L K AE EPSIKE -- L R K LAEKI L - N 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1271 ITLR G VEN I E RV VMM K ydrkvpsptgeyv K E P E W V LE T D G V NL SE V MT V P G I DPTR IY TN SFID I M EVLGIEA G R A A LYK 1350
Cdd:cd06528 200 TKIK G IKG I K RV IVR K ------------- E E D E Y V IY T E G S NL KA V LK V E G V DPTR TT TN NIHE I E EVLGIEA A R N A IIN 266
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1351 E VYNVIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA L M R CS FE E TV EI L FE A GASA E L D DC RGV S EN V I L 1430
Cdd:cd06528 267 E IKRTLEEQ G LD V DI RH IM L VA D I MT YD G EVRQIG RHG IAGEKPSV L A R AA FE V TV KH L LD A AVRG E V D EL RGV I EN I I V 346
410
....*....|....*..
gi 359546325 1431 GQ MA P I GTG AFDVMI D E 1447
Cdd:cd06528 347 GQ PI P L GTG DVELTM D P 363
RNA_pol_Rpb1_6
pfam04992 RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
873-1056
1.03e-90
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511
Cd Length: 188
Bit Score: 292.10
E-value: 1.03e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 873 M D A A H IEKQ SL DT IGG SDAAFEKRYR V D LLNTDHTLD P SL LE S G -- S EI L GD LKL Q V LLDEEY K QL VK DR KF LRE - V F VD 949
Cdd:pfam04992 1 L D G A F IEKQ KI DT LKL SDAAFEKRYR L D VMDEKSGFL P GY LE E G vi K EI A GD PEV Q Q LLDEEY E QL LE DR EL LRE i I F PT 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 950 G EANW P - LPVNI R RIIQNAQ QT FHID HT KPSDL TIKDIVL GV KD L QEN L L V L RG KNEIIQN AQ RD A VT LF CC LLRSRLA T 1028
Cdd:pfam04992 81 G DSKV P q LPVNI Q RIIQNAQ KI FHID DR KPSDL HPIYVIE GV RE L LDR L V V V RG DDPLSKE AQ EN A TL LF KI LLRSRLA S 160
170 180
....*....|....*....|....*...
gi 359546325 1029 R RVL Q EYRL T K Q AFDWVL SN IE AQ FL RS 1056
Cdd:pfam04992 161 K RVL E EYRL N K E AFDWVL GE IE SR FL QA 188
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1032-1446
6.01e-90
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 298.30
E-value: 6.01e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1032 L Q E YR LT KQAFDWVLSNIEAQF LRS V V H PGE M VGV L AAQSIGEP A TQMT LN TFH F AGVA SKK VT S G V PRL K EI LNVA K NM 1111
Cdd:PRK04309 30 L E E RK LT EEEVEEIIEEVVREY LRS L V E PGE A VGV V AAQSIGEP G TQMT MR TFH Y AGVA EIN VT L G L PRL I EI VDAR K EP 109
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1112 K TP SL T V YL EPGH A A D Q E Q A KLIRSA IE H TTL KS vt I A SE I YY D PD prstvipe DEE II qlhfslldeeaeqsfdqqspw 1191
Cdd:PRK04309 110 S TP MM T I YL KDEY A Y D R E K A EEVARK IE A TTL EN -- L A KD I SV D LA -------- NMT II --------------------- 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1192 llr L ELD RAAMN D KD LT MGQ V G E R I KQTFKNDL fviws E DNDEK LII RCRVVRPKS L daeteaeedhm L K KI E N tm LE NI 1271
Cdd:PRK04309 159 --- I ELD EEMLE D RG LT VDD V K E A I EKKKGGEV ----- E IEGNT LII SPKEPSYRE L ----------- R K LA E K -- IR NI 217
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1272 TLR G VEN I E RV VMM K ydrkvpsptgeyv KEP E W V LE T D G V NL S EV MT V P G I D P TR IY TN SFID I M EVLGIEA G R A A LYK E 1351
Cdd:PRK04309 218 KIK G IKG I K RV IIR K ------------- EGD E Y V IY T E G S NL K EV LK V E G V D A TR TT TN NIHE I E EVLGIEA A R N A IIE E 284
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1352 VY N VIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA L M R CS FE E TV EI L FE A GASA E L D DCR GV S EN V I L G 1431
Cdd:PRK04309 285 IK N TLEEQ G LD V DI RH IM L VA D M MT WD G EVRQIG RHG VSGEKASV L A R AA FE V TV KH L LD A AVRG E V D ELK GV T EN I I V G 364
410
....*....|....*
gi 359546325 1432 Q MA P I GTG AFDVMI D 1446
Cdd:PRK04309 365 Q PI P L GTG DVELTM D 379
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
53-857
9.30e-90
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: 310.11
E-value: 9.30e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 53 LND PRLG SIDRNLK C Q TC qe G MNE --- C P GHFG H I D L AKPVF H VG FI AKIKKVCECV C MH C GK llldehnelmrqala IK 129
Cdd:cd10506 20 VTN PRLG LPNESGQ C T TC -- G AKD nkk C E GHFG V I K L PVTIY H PY FI SEVAQILNKI C PG C KS --------------- IK 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 130 DS KK R faaiwtlcktkmvcetd V P S E DD P T qlvsrggcgntqptirkdglklv GS W kk D RATG D ADEP E LR V -- LSTEEI 207
Cdd:cd10506 83 QK KK K ----------------- P P R E TL P P ----------------------- DY W -- D FIPK D GQQE E SC V tk NLPILS 120
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 208 L NIF K H I S v K DFTSLGFNEVFS R P E WMI L T CLPV ppppvrpsisfnesqrgeddltfkladilkanisletlehng A P H - 286
Cdd:cd10506 121 L AQV K K I L - K EIDPKLIAKGLP R Q E GLF L K CLPV ------------------------------------------ P P N c 157
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 287 H AIE E AES ll Q F HVATYMDN D I ag QPQ A LQ K S ---- G RPVK S IRARLK G KE g RIRGN L M GKR VDF S A R T V IS GDP N LEL D 362
Cdd:cd10506 158 H RVT E FTH -- G F STGSRLIF D E -- RTR A YK K L vdfi G TANE S AASKKS G LK - WMKDL L L GKR SGH S F R S V VV GDP Y LEL N 232
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 363 QV G V P KS IA KT LT YP E V V TPY N ID RL TQLV rngp NEHPGA K Y VI rds G D R idl R YSKRA G DI --- Q LQ Y G WKVE R HIM D N 439
Cdd:cd10506 233 EI G I P CE IA ER LT VS E R V SSW N RE RL QEYC ---- DLTLLL K G VI --- G V R --- R NGRLV G VR shn T LQ I G DVIH R PLV D G 302
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 440 D P VL F NR Q PS L H KM S MM A HR VKV I P Y - S TFRL N LSVT SP YNA DFDGD EMNLHV PQS EET RAEL SQ L C A V P L Q IV S P QS NK 518
Cdd:cd10506 303 D V VL V NR P PS I H QH S LI A LS VKV L P T n S VVSI N PLCC SP FRG DFDGD CLHGYI PQS LQA RAEL EE L V A L P K Q LI S S QS GQ 382
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 519 PCMGIV QD T L CGIRKL T L R DT F IELD Q VLNMLYWV P D wdg VI P T PAIIK ---- PK PLW S GKQ ILSVAI P ngihlqrfdeg 594
Cdd:cd10506 383 NLLSLT QD S L LAAHLM T E R GV F LDKA Q MQQLQMLC P S --- QL P P PAIIK spps NG PLW T GKQ LFQMLL P ----------- 448
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 595 T T L LSPKDNGMLI I DGQIIFGVVEKKTVGSSNG G LIHVVTREK GP QVCAKLFGNI Q KVVNF WL LHN GFS TGIG D -- TIA D 672
Cdd:cd10506 449 T D L DYSFPSNLVF I SDGELISSSGGSSWLRDSE G NLFSILVKH GP GKALDFLDSA Q GLLCE WL SMR GFS VSLS D ly LSS D 528
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 673 GPTMREIT E T I AEA kkkv L DVTKE A -- QAN LL TAKHGMT L RE S F E D N V V RFLN E ---- A R D K AGR L AE ------------ 734
Cdd:cd10506 529 SYSRQKMI E E I SLG ---- L REAEI A cn IKQ LL VDSRKDF L SG S G E E N D V SSDV E rviy E R Q K SAA L SQ asvsafkqvfrd 604
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 735 ------- VNL KD l N NVKQ M VM AGSKGS FINIA Q M S A C V G - Q Q S VEGKRIAF ------- GFVDRTL P HFSKD D Y ----- S P 794
Cdd:cd10506 605 iqnlvyk YAS KD - N SLLA M IK AGSKGS LLKLV Q Q S G C L G l Q L S LVKLSYRI prqlsca AWNSQKS P RVIEK D G secte S Y 683
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 359546325 795 ESK G F VE N S Y L R GL T P Q E F F F H AMGG R EGLID tav KT A ET - G YIQ R R L VKALE DI M V H YD N T T R 857
Cdd:cd10506 684 IPY G V VE S S F L D GL N P L E C F V H SITS R DSSFS --- SN A DL p G TLF R K L MFFMR DI Y V A YD G T V R 744
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1031-1446
3.77e-85
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: 283.87
E-value: 3.77e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1031 V LQEYRLT K QAF D WVLSNI E AQF LRS VVH PGE M VG VL AAQSIGEP A TQMT LN TFH F AGVA SKK VT S G V PRL K EI LNVA K N 1110
Cdd:TIGR02389 14 V KKREISD K EEL D EIIKRV E EEY LRS LID PGE A VG IV AAQSIGEP G TQMT MR TFH Y AGVA ELN VT L G L PRL I EI VDAR K T 93
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1111 MK TPS L T V YLE PGHAA D Q E Q A KLIRSA IE H T T L K sv TI A SE I YY D PDPRSTV I pedeeiiqlhfslldeeaeqsfdqqsp 1190
Cdd:TIGR02389 94 PS TPS M T I YLE DEYEK D R E K A EEVAKK IE A T K L E -- DV A KD I SI D LADMTVI I --------------------------- 144
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1191 wllrl ELD RAAMNDKDL T MGQ V GER IK QT f K NDLFVIWSE DN DE k LI I RCRVVRP K S L daeteaeed HM LK K ient MLE N 1270
Cdd:TIGR02389 145 ----- ELD EEQLKERGI T VDD V EKA IK KA - K LGKVIEIDM DN NT - IT I KPGNPSL K E L --------- RK LK E ---- KIK N 204
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1271 ITLR G VEN I E RVV MM K ydrkvpsptgeyv KEP E W V LE T D G V NL S EV MTVP G I D P TR IY TN SFID I M EVLGIEA G R A A LYK 1350
Cdd:TIGR02389 205 LHIK G IKG I K RVV IR K ------------- EGD E Y V IY T E G S NL K EV LKLE G V D K TR TT TN DIHE I A EVLGIEA A R N A IIE 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1351 E VYNVIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA L M R CS FE E TV EI L FE A GASA E L D DCR GV S EN V I L 1430
Cdd:TIGR02389 272 E IKRTLEEQ G LD V DI RH LM L VA D L MT WD G EVRQIG RHG ISGEKASV L A R AA FE V TV KH L LD A AIRG E V D ELK GV I EN I I V 351
410
....*....|....*.
gi 359546325 1431 GQ MA P I GTG AF D VMI D 1446
Cdd:TIGR02389 352 GQ PI P L GTG DV D LVM D 367
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1053-1441
1.65e-77
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: 259.07
E-value: 1.65e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1053 FL R SV V H PG EM VG VL AAQSIGEP A TQMTL N TFHFAGVAS KKV T S GVPR L KEI L N VA KN MK TP SL T VY LE PGH aa D QEQ A K 1132
Cdd:cd02736 2 YM R AK V E PG TA VG AI AAQSIGEP G TQMTL K TFHFAGVAS MNI T L GVPR I KEI I N AS KN IS TP II T AK LE NDR -- D EKS A R 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1133 LIRSA IE H T T L KS V TIAS E IY Y D PD PRSTV I PE D EE II Q lhfslldeeaeqsfdqqspwll R L E L DR aamndkdltmgqv 1212
Cdd:cd02736 80 IVKGR IE K T Y L GE V ASYI E EV Y S PD DCYIL I KL D KK II E ---------------------- K L Q L SK ------------- 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1213 gerikqtf K N DL F VI wsedndekliircrvvrpksldaeteaeed HM LK K ient M L ENITLR G VENIE R V V MM K YD rkvp 1292
Cdd:cd02736 125 -------- S N LY F LL ------------------------------ QS LK R ---- K L PDVVVS G IPEVK R A V IN K DK ---- 158
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1293 sptgeyv K EPEWV L ETD G VN L SE VM TV PG IDP TR IYT N SFIDIME VLGIEA G R AALYK E VYNVIA S D G SYVNY RH MA LL V 1372
Cdd:cd02736 159 ------- K KGKYK L LVE G YG L RA VM NT PG VIG TR TTS N HIMEVEK VLGIEA A R STIIN E IQYTMK S H G MSIDP RH IM LL A 231
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 359546325 1373 D V MT TQ G GLTSV TR H G FNRSNTGA LM RC SFE E T VEI LF E A GASAEL D DCR GVSE NV I L G QMA PIGTG A F 1441
Cdd:cd02736 232 D L MT FK G EVLGI TR F G IAKMKESV LM LA SFE K T TDH LF N A ALHGRK D SIE GVSE CI I M G KPM PIGTG L F 300
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1030-1452
1.21e-69
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 243.95
E-value: 1.21e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1030 RVLQEYR L TKQAFDWV L SN I EAQFL R SV V H P G E M VG VL AAQSIGEP A TQMT LN TFH F AGVA SKK VT S G V PRL K EI LNVA K 1109
Cdd:PRK14897 151 KAMKKKE L SDDEYEEI L RR I REEYE R AR V D P Y E A VG IV AAQSIGEP G TQMT MR TFH Y AGVA EMN VT L G L PRL I EI VDAR K 230
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1110 NMK TP SL T V YL EPGHAA D Q E QAKLIRSA IE H TTL KS V T - I ASE I yydpdprstvipedeeiiqlhfslldee AE Q S fdqq 1188
Cdd:PRK14897 231 KPS TP TM T I YL KKDYRE D E E KVREVAKK IE N TTL ID V A d I ITD I ---------------------------- AE M S ---- 278
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1189 spwl LRL ELD RAA M NDKDLTMGQVGER I - K Q TFK ND lfviws E DN D EKLIIRCRVVRP K S L DAET E A eedhmlkkientm 1267
Cdd:PRK14897 279 ---- VVV ELD EEK M KERLIEYDDILAA I s K L TFK TV ------ E ID D GIIRLKPQQPSF K K L YLLA E K ------------- 335
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1268 LENI T LR G VEN I E R VVMM K YD rkvpsptgeyv K E PE WV LE T D G V NL SE V MTVPGI DPTR I YTN SF I D I ME VLGIEA G R A A 1347
Cdd:PRK14897 336 VKSL T IK G IKG I K R AIAR K EN ----------- D E RR WV IY T Q G S NL KD V LEIDEV DPTR T YTN DI I E I AT VLGIEA A R N A 404
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1348 LYK E VYNVIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA L M R CS FE E T VEI L FE AG ASA E L D DCR GV S EN 1427
Cdd:PRK14897 405 IIH E AKRTLQEQ G LN V DI RH IM L VA D M MT FD G SVKAIG RHG ISGEKSSV L A R AA FE I T GKH L LR AG ILG E V D KLA GV A EN 484
410 420
....*....|....*....|....*
gi 359546325 1428 V I L GQ MAPI GTGA FDVMIDEESL VK 1452
Cdd:PRK14897 485 I I V GQ PITL GTGA VSLVYKGRKK VK 509
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
229-1439
1.83e-68
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: 253.43
E-value: 1.83e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 229 S RPEWM I L TCL PV P PP PV RP SISFNESQRGED DL TFKLADILKA N IS L ET L EHN GAP HHAIEEAESL LQ FH V ATYM DN DI 308
Cdd:TIGR02386 214 N RPEWM V L DVI PV I PP EL RP MVQLDGGRFATS DL NDLYRRVINR N NR L KR L LEL GAP EIIVRNEKRM LQ EA V DALF DN GR 293
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 309 A G Q P q ALQ K SG RP V KS IRAR LKGK E GR I R G NL M GKRVD F S A R T VI SGD P N L ELD Q V G V PK SI A KT L typev VT P YN I D RL 388
Cdd:TIGR02386 294 R G K P - VVG K NN RP L KS LSDM LKGK Q GR F R Q NL L GKRVD Y S G R S VI VVG P E L KMY Q C G L PK KM A LE L ----- FK P FI I K RL 367
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 389 TQL vrngpnehp GAKYV I RDSGDR I D lryskr AG D IQL qyg W K V ERHIMDND PVL F NR Q P S LH KMSMM A HRVKVIPYSTF 468
Cdd:TIGR02386 368 IDR --------- ELAAN I KSAKKM I E ------ QE D PEV --- W D V LEDVIKEH PVL L NR A P T LH RLGIQ A FEPVLVEGKAI 429
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 469 RL NLS V TSPY NADFDGD E M NL HVP Q S E E TR AE LSQ L CAVPLQ I VS P QSN KP CMGIV QD TLC G IRK LT LR dtfieldqvln 548
Cdd:TIGR02386 430 RL HPL V CTAF NADFDGD Q M AV HVP L S P E AQ AE ARA L MLASNN I LN P KDG KP IVTPS QD MVL G LYY LT TE ----------- 498
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 549 mlywvpdwdgvi PTP A IIKP K PLWSGKQIL s V A IP NG - I HL Q rfdegt T L LSPKDN G MLIID -- G QI IF G ---------- 615
Cdd:TIGR02386 499 ------------ KPG A KGEG K IFSNVDEAI - R A YD NG k V HL H ------ A L IGVRTS G EILET tv G RV IF N eilpegfpyi 559
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 616 ---- VVE KK TVG S sngg LI HVVTREK G PQVC A KLFGN I QKVVNFWLLHN G FSTGIG D TIA dg P TMRE it E TIA EA K K K V L 691
Cdd:TIGR02386 560 ndne PLS KK EIS S ---- LI DLLYEVH G IEET A EMLDK I KALGFKYATKS G TTISAS D IVV -- P DEKY -- E ILK EA D K E V A 631
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 692 DVT K EAQAN L L T akhgmtl R E SFEDN VV RFLN E AR DK AGRLAEVN LK D ---- L N NVKQ M VMA G SK G SFINIA Q MSACV G Q 767
Cdd:TIGR02386 632 KIQ K FYNKG L I T ------- D E ERYRK VV SIWS E TK DK VTDAMMKL LK K dtyk F N PIFM M ADS G AR G NISQFR Q LAGMR G L 704
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 768 QSVEGKR I A fgfvdr T LP hfskddyspeskgf VEN S YLR GLT PQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ RRLV KALE D 847
Cdd:TIGR02386 705 MAKPSGD I I ------ E LP -------------- IKS S FRE GLT VL E Y F ISTH G A R K GL A DTA L KTA DS GY LT RRLV DVAQ D 764
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 848 IM V HYD nttrnslgnviqfiygedgmdaahiekqsldtiggs D AAF E KRYR V dllntdhtld PSLL E SGS EI LGD L klqv 927
Cdd:TIGR02386 765 VV V REE ------------------------------------ D CGT E EGIE V ---------- EAIV E GKD EI IES L ---- 794
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 928 lldeeykqlv KDR KFL R EVFV D geanwplpvnirriiqnaqqtfhidhtkpsdlt IK D IVL G VKDLQE N L L VLRGKN E I I 1007
Cdd:TIGR02386 795 ---------- KDR IVG R YSAE D --------------------------------- VY D PDT G KLIAEA N T L ITEEIA E K I 831
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1008 Q N AQRDA V tlfcc LL RS R L ATRR vlq E YRLTKQAFDWV L SN ieaqfl RSV V HP GE M VGV L AAQSIGEP A TQ M T LN TFH FA 1087
Cdd:TIGR02386 832 E N SGIEK V ----- KV RS V L TCES --- E HGVCQKCYGRD L AT ------ GKL V EI GE A VGV I AAQSIGEP G TQ L T MR TFH TG 897
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1088 GVA SKK -- V T S G V PR L KE ILNV aknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdprst VI P E 1165
Cdd:TIGR02386 898 GVA GAS gd I T Q G L PR V KE LFEA ------------------------------------------------------ RT P K 923
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1166 D EEI I Q lhfslldeeaeqsfdqqspwllrl E L D raamndkdltm G Q V g E R I KQTF KN DLF V IWSED NDE K liircrvvrp 1245
Cdd:TIGR02386 924 D KAV I A ------------------------ E V D ----------- G T V - E I I EDIV KN KRV V VIKDE NDE E ---------- 957
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1246 ksldaeteaeedhmlkkientmlenitlrgveniervvmmkyd R K VPS P T G EYVK epew V LET D G V NLSEVM T VPG IDP T 1325
Cdd:TIGR02386 958 ------------------------------------------- K K YTI P F G AQLR ---- V KDG D S V SAGDKL T EGS IDP H 990
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1326 riytnsfi D IMEVL GI E A GRAA L Y KEV YN V IASD G SYV N YR H MALL V DV M T ----- T QG G LTS ------ VTR H G FN RS N T 1394
Cdd:TIGR02386 991 -------- D LLRIK GI Q A VQEY L V KEV QK V YRLQ G VEI N DK H IEVI V RQ M L rkvri T DS G DSN llpgel IDI H E FN EE N R 1062
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 359546325 1395 GA L MR --------------------------- C SF E ET VEI L FE A GASAEL D DCR G VS ENVI L G QMA P I GTG 1439
Cdd:TIGR02386 1063 KL L EQ gkkpasaipqllgitkaslntesflsa A SF Q ET TKV L TD A AIKGKV D YLL G LK ENVI I G NLI P A GTG 1134
RNA_pol_Rpb1_7
pfam04990 RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
1141-1274
5.83e-64
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).
Pssm-ID: 461510 [Multi-domain]
Cd Length: 136
Bit Score: 213.55
E-value: 5.83e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1141 TTL K SVT I A S EIYYDPDPR S TVI P ED E E IIQLH F SLL DE EA E q SF D Q QSPWLLR L ELDR AA M N DK D LTM GQ V G E R IK QT F 1220
Cdd:pfam04990 1 TTL R SVT A A T EIYYDPDPR N TVI E ED R E FVESY F EIP DE DV E - DL D R QSPWLLR I ELDR KK M L DK G LTM ED V A E K IK EE F 79
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 359546325 1221 K NDLFVI W S E DN D EKL I IR C R VVR --- P K SLDA E TE AE E D HM LK KI E NT ML ENI TLR 1274
Cdd:pfam04990 80 G NDLFVI F S D DN A EKL V IR I R IIN dek E K DEEQ E DK AE D D VF LK RL E AN ML DSL TLR 136
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1053-1444
5.28e-60
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: 208.97
E-value: 5.28e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1053 FL RS V V H PGE M VG V LAAQSIGEP A TQMTLNTFHFAG VASKK VT S G V PRL K EIL NV A - KN M KTPS L T VY L EP G HA A dq E Q A 1131
Cdd:cd02735 2 YM RS L V E PGE A VG L LAAQSIGEP S TQMTLNTFHFAG RGEMN VT L G I PRL R EIL MT A s KN I KTPS M T LP L KN G KS A -- E R A 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1132 KLIRSAIEHT TL K svtiaseiyydpdprstvipede EII qlhfslldeeaeqsfdqqspwllrleldraamnd KDLTMGQ 1211
Cdd:cd02735 80 ETLKKRLSRV TL S ----------------------- DVV ---------------------------------- EKVEVTE 102
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1212 VGER I KQT FK N d L FVI W S E dndek LI I RCRVVR PK S L daeteaeedh M L KKI E NT m LENITL R GVEN I E R VVMMKY D RK v 1291
Cdd:cd02735 103 ILKT I ERV FK K - L LGK W C E ----- VT I KLPLSS PK L L ---------- L L SIV E KL - ARKAVI R EIPG I T R CFVVEE D KG - 164
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1292 psptgeyv KEPEWVLE T D GVNL SEVMTVPG - I D PT RIYTN SFIDIMEVL GIEA G R A A LY KE VY NV IASD G SY V NY RH MA L 1370
Cdd:cd02735 165 -------- GKTKYLVI T E GVNL AALWKFSD i L D VN RIYTN DIHAMLNTY GIEA A R R A IV KE IS NV FKVY G IA V DP RH LS L 236
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 359546325 1371 LV D V MT TQ GG LTSVT R H G F n R S N T GA L MRC SFE E T VEI L FE A GASAEL D DCRGV S ENVIL G QMAPI GTG A FD VM 1444
Cdd:cd02735 237 IA D Y MT FE GG YRPFN R I G M - E S S T SP L QKM SFE T T LAF L KK A TLNGDI D NLSSP S SRLVV G KPVNG GTG L FD LL 309
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
18-1092
7.54e-59
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 225.57
E-value: 7.54e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 18 Q FG L F SPE EVRAI S VAKIRF PET MDETQTRAKIG GL NDPRLGSIDRNLK C ------------- Q TC QEGMNECP ------ 78
Cdd:PRK09603 1400 Q LT L A SPE KIHSW S YGEVKK PET INYRTLKPERD GL FCMKIFGPTKDYE C lcgkykkprfkdi G TC EKCGVAIT hskvrr 1479
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 79 GHF GHI D LA K PV F H VGFIAKIKK vcecvcm HC G K LL LDEHNE L M R ---- Q A LAI K DSKKRF aai WTLCK TK M V CET D VPS 154
Cdd:PRK09603 1480 FRM GHI E LA T PV A H IWYVNSLPS ------- RI G T LL GVKMKD L E R vlyy E A YIV K EPGEAA --- YDNEG TK L V MKY D ILN 1549
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 155 E DDPTQLVS R ---------- GG CGNTQPTIRK D GLK L VG S W K KDRATGDA D EPELRVLSTEEI lnifkhis V KD F TSL G f 224
Cdd:PRK09603 1550 E EQYQNISR R yedrgfvaqm GG EAIKDLLEEI D LIT L LQ S L K EEVKDTNS D AKKKKLIKRLKV -------- V ES F LNS G - 1620
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 225 nevf S RPEWM I LT C LPV P PP PV RP SISFNESQRGED D LTFKLADILKA N IS L ET L EHN GAP HHAIEEAESL LQ FH V ATYM 304
Cdd:PRK09603 1621 ---- N RPEWM M LT V LPV L PP DL RP LVALDGGKFAVS D VNELYRRVINR N QR L KR L MEL GAP EIIVRNEKRM LQ EA V DVLF 1696
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 305 DN dia G QPQALQ K SG -- RP V KS IRARL KGK E GR I R G NL M GKRVDFS A R T VI SGD PNL EL D QV G V PK SI A KT L TY P evvtp 382
Cdd:PRK09603 1697 DN --- G RSTNAV K GA nk RP L KS LSEII KGK Q GR F R Q NL L GKRVDFS G R S VI VVG PNL KM D EC G L PK NM A LE L FK P ----- 1768
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 383 ynidrltqlvrngpne H PGA K yv IRDS G DRID L RYS KR AGDIQLQYG W KVERH I MDND PVL F NR Q P S LHK M S MM A HRV K V 462
Cdd:PRK09603 1769 ---------------- H LLS K -- LEER G YATT L KQA KR MIEQKSNEV W ECLQE I TEGY PVL L NR A P T LHK Q S IQ A FHP K L 1830
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 463 I PYSTFR L NLS V T S PY NADFDGD E M NL HVP Q S E E TR AE LSQ L CAVPLQ I VS P Q S N K PCMGIV QD TLC G IRK L T L RDT --- 539
Cdd:PRK09603 1831 I DGKAIQ L HPL V C S AF NADFDGD Q M AV HVP L S Q E AI AE CKV L MLSSMN I LL P A S G K AVAIPS QD MVL G LYY L S L EKS gvk 1910
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 540 ----- F IELDQVLNML - YWVP D WDGV I PT pa IIKPKPLWS -- G KQ I LSVAI P NG I HLQRFDE gttllspkdngmliidgq 611
Cdd:PRK09603 1911 gehkl F SSVNEIITAI d TKEL D IHAK I RV -- LDQGNIIAT sa G RM I IKSIL P DF I PTDLWNR ------------------ 1970
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 612 iifg VVE KK TV G S sngg L IHV V TREK G PQVC A KLFG N IQKV vnfwllhn GF ---- ST GI GDTIA D GP T MREITETIAE AK 687
Cdd:PRK09603 1971 ---- PMK KK DI G V ---- L VDY V HKVG G IGIT A TFLD N LKTL -------- GF ryat KA GI SISME D II T PKDKQKMVEK AK 2034
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 688 KK V LDVTKEAQAN LLT AK hgmtlr E SF e DNVVRFLN E AR DK AGR ---- LAEVNLKDL N NVKQ M VMA G SK GS FIN I A Q M SA 763
Cdd:PRK09603 2035 VE V KKIQQQYDQG LLT DQ ------ E RY - NKIIDTWT E VN DK MSK emmt AIAKDKEGF N SIYM M ADS G AR GS AAQ I R Q L SA 2107
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 764 CV G Q qsvegkriafgfvdrtlph FS K D D Y S PESKGFVE N s YLR GL TPQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ R R L VK 843
Cdd:PRK09603 2108 MR G L ------------------- MT K P D G S IIETPIIS N - FKE GL NVL E Y F NSTH G A R K GL A DTA L KTA NA GY LT R K L ID 2167
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 844 ALEDIM V HY D NT trnslgnviqfiygedgmd AA H IEKQSL D TIG GS D -- AAF E K R YRVDL L NT D h TL DP slle SGS EIL g 921
Cdd:PRK09603 2168 VSQNVK V VS D DC ------------------- GT H EGIEIT D IAV GS E li EPL E E R IFGRV L LE D - VI DP ---- ITN EIL - 2222
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 922 d L KLQV L L DEE YKQL V K drkflrevfvdg EA N wplpvnirriiqnaqqtfhidhtkpsdlt IK D I VL gvkdlqenllvlr 1001
Cdd:PRK09603 2223 - L YADT L I DEE GAKK V V ------------ EA G ----------------------------- IK S I TI ------------- 2247
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1002 g KNEIIQN A QR d A V TLF C CL L R srlatrrv L Q E YRLTK qafdwvlsnieaqflrsvvh PGE M VGV L AAQSIGEP A TQ M TL 1081
Cdd:PRK09603 2248 - RTPVTCK A PK - G V CAK C YG L N -------- L G E GKMSY -------------------- PGE A VGV V AAQSIGEP G TQ L TL 2297
1130
....*....|.
gi 359546325 1082 N TFH FA G V AS K 1092
Cdd:PRK09603 2298 R TFH VG G T AS R 2308
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
269-1135
7.50e-57
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 217.82
E-value: 7.50e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 269 ILKA N IS L ET L EHN GAP HHAIEEAESL LQ FH V ATYM DN DIA G Q P q ALQKSG RP V KS IRAR LKGK E GR I R G NL M GKRVD F S 348
Cdd:PRK14906 350 VINR N NR L KR L LDL GAP EIIVNNEKRM LQ EA V DSLF DN GRR G R P - VTGPGN RP L KS LADM LKGK Q GR F R Q NL L GKRVD Y S 428
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 349 A R T VI SGD P N L E L D Q V G V P KSI A K tltyp E VVT P YNID RL TQ L vrngpnehpga K Y VI rdsgdri DLRYS KRA G D IQLQ Y 428
Cdd:PRK14906 429 G R S VI VVG P H L K L H Q C G L P SAM A L ----- E LFK P FVMK RL VE L ----------- E Y AA ------- NIKAA KRA V D RGAS Y 485
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 429 G W K V ERHIMDND PVL F NR Q P S LH KMSMM A HRVKVIPYSTFR L NLS V TSPY NADFDGD E M NL HVP Q S EETR AE LSQ L CAVP 508
Cdd:PRK14906 486 V W D V LEEVIQDH PVL L NR A P T LH RLGIQ A FEPVLVEGKAIK L HPL V CTAF NADFDGD Q M AV HVP L S TQAQ AE ARV L MLSS 565
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 509 LQ I V SP QSNK P CMGIV QD TLC G IRK LT - L RD ------- TF IEL D QV LN MLYWVP D W D gviptpai IKP K PLWSGKQILS V 580
Cdd:PRK14906 566 NN I K SP AHGR P LTVPT QD MII G VYY LT t E RD gfegegr TF ADF D DA LN AYDARA D L D -------- LQA K IVVRLSRDMT V 637
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 581 AIPN G I ----- HLQ R FD eg TT LLSPKD N GM L II D GQIIFGVVE KK TV G S sngg L IH - VVT R EKGPQ V CAK L F G niqkvvn 654
Cdd:PRK14906 638 RGSY G D leetk AGE R IE -- TT VGRIIF N QV L PE D YPYLNYKMV KK DI G R ---- L VN d CCN R YSTAE V EPI L D G ------- 704
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 655 fw LLHN GF S ---- T G IGDTIA D GPTMREIT E TI AEA KK KV LDVTKEAQANL L T akhgmtl RESFEDN VV RFLN EA RDKA G 730
Cdd:PRK14906 705 -- IKKT GF H yatr A G LTVSVY D ATIPDDKP E IL AEA DE KV AAIDEDYEDGF L S ------- ERERHKQ VV DIWT EA TEEV G 775
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 731 RLAEVNLKDL N NVKQ M VMA G SK G SFIN I A Q MSACV G QQSVEGKR I afgf V D R tlphfskddys P ESKG F V E nsylr GL TP 810
Cdd:PRK14906 776 EAMLAGFDED N PIYM M ADS G AR G NIKQ I R Q LAGMR G LMADMKGE I ---- I D L ----------- P IKAN F R E ----- GL SV 835
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 811 Q E F F FHAM G G R E GL I DTA VK TA ET GY IQ RRLV KALE D IM V hydnttrnslgnviqfiygedgmdaahiekqsldtiggsd 890
Cdd:PRK14906 836 L E Y F ISTH G A R K GL V DTA LR TA DS GY LT RRLV DVAQ D VI V ---------------------------------------- 875
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 891 aafekry R VDLLN TD HTLDPS L LESGSEILGD L KLQV LL DE eykql V K D rkflrevf VD GE AN wplpvnirriiqnaqqt 970
Cdd:PRK14906 876 ------- R EEDCG TD EGVTYP L VKPKGDVDTN L IGRC LL ED ----- V C D -------- PN GE VL ----------------- 918
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 971 fhidhtkpsd L TIK D IVLGVK DL QE nl LV LR G KNEII qnaqrdavtlfccl L R SRLATR rvl Q EY RLTKQAFD W V L SN ie 1050
Cdd:PRK14906 919 ---------- L SAG D YIESMD DL KR -- LV EA G VTKVQ -------------- I R TLMTCH --- A EY GVCQKCYG W D L AT -- 967
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1051 aqfl R SV V HP G EM VG VL AAQSIGEP A TQ M T LN TFH FA GVA SKKV T S G V PR LK E ILNVA K NMKTPS L TVYLEPGHAADQEQ 1130
Cdd:PRK14906 968 ---- R RP V NI G TA VG II AAQSIGEP G TQ L T MR TFH SG GVA GDDI T Q G L PR VA E LFEAR K PKGEAV L AEISGTLQITGDKT 1043
....*
gi 359546325 1131 A K LIR 1135
Cdd:PRK14906 1044 E K TLT 1048
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
510-669
5.93e-56
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: 191.69
E-value: 5.93e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 510 Q I V SPQ SN KP CM G IV QD TLC G IRK LT LR DTF IELDQ V LNM L YWVP dwdg V I P T PAI I KP - KPLW S GKQ IL S VAI PN G I HL 588
Cdd:pfam04983 1 N I L SPQ NG KP II G PS QD MVL G AYL LT RE DTF FDREE V MQL L MYGI ---- V L P H PAI L KP i KPLW T GKQ TF S RLL PN E I NP 76
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 589 QRF - DEGTTL L SPK D NGM LI ID G QI I F GV VE KKTVG S S N G G LIH VVTR E K GP QVC AK LFGNI QK VVNFW L LHN GFS T GI G 667
Cdd:pfam04983 77 KGK p KTNEED L CEN D SYV LI NN G EL I S GV ID KKTVG K S L G S LIH IIYK E Y GP EET AK FLDRL QK LGFRY L TKS GFS I GI D 156
..
gi 359546325 668 D T 669
Cdd:pfam04983 157 D I 158
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1077-1448
1.02e-55
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 210.52
E-value: 1.02e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1077 T QM T LN TFH F AGVA SKK VT S G V PR LK EI LNVA K NMK TP SL TV Y L EPGH A A D Q E Q A KLIRSA IE HT TL KS V tiaseiyydp 1156
Cdd:PRK14898 541 T HN T MR TFH Y AGVA EIN VT L G L PR MI EI VDAR K EPS TP IM TV H L KGEY A T D R E K A EEVAKK IE SL TL GD V ---------- 610
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1157 dpr S T V I PE D eeiiqlhfslldeeaeqs FDQ QS pwl LRL ELD RAAMN D KD LT MGQ V G E R I KQTFKNDL fviwse D NDEKL 1236
Cdd:PRK14898 611 --- A T S I AI D ------------------ LWT QS --- IKV ELD EETLA D RG LT IES V E E A I EKKLGVKI ------ D RKGTV 660
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1237 I ircrvvrpk S L DAE T EAEED h ML K K I EN tm LE NI T L R G VEN IERV VMM K YDRK vps PTG EYV kepewv L E T D G V NL S EV 1316
Cdd:PRK14898 661 L --------- Y L KPK T PSYKA - LR K R I PK -- IK NI V L K G IPG IERV LVK K EEHE --- NDE EYV ------ L Y T Q G S NL R EV 719
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1317 MTVP G I D PT R IY TN SF I D I M EVLGIEA G R A A LYK E VY N VIASD G SY V NY RH MA L LV D V MT TQ G GLTSVT RHG FNRSNTGA 1396
Cdd:PRK14898 720 FKIE G V D TS R TT TN NI I E I Q EVLGIEA A R N A IIN E MM N TLEQQ G LE V DI RH LM L VA D I MT AD G EVKPIG RHG VAGEKGSV 799
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|..
gi 359546325 1397 L M R CS FEETV EI L FE A GASA E L D DCR GV S ENVI L G QMAPI GTG AF D VM ID E E 1448
Cdd:PRK14898 800 L A R AA FEETV KH L YD A AEHG E V D KLK GV I ENVI V G KPIKL GTG CV D LR ID R E 851
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
295-850
2.12e-55
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: 205.83
E-value: 2.12e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 295 L LQ FH V ATYM DN DIA G Q P q ALQKSG RP V KS IRAR LKGK E GR I R G NL M GKRVD F S A R T VI SGD P N L E L D Q V G V PK SI A KT L 374
Cdd:cd01609 203 M LQ EA V DALI DN GRR G K P - VTGANN RP L KS LSDM LKGK Q GR F R Q NL L GKRVD Y S G R S VI VVG P E L K L H Q C G L PK EM A LE L 281
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 375 TY P E V vtpyn I DR L tqlvrngpn EHP G AKYV I RDSGDR I D l R YSKRA gdiqlqyg W KVERHIMDND PVL F NR Q P S LH KMS 454
Cdd:cd01609 282 FK P F V ----- I RE L --------- IER G LAPN I KSAKKM I E - R KDPEV -------- W DILEEVIKGH PVL L NR A P T LH RLG 338
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 455 MM A HRVKV I PYSTFR L NLS V TSPY NADFDGD E M NL HVP Q S E E TR AE LSQ L CAVPLQ I V SP Q S N KP CMGIV QD TLC G IRK L 534
Cdd:cd01609 339 IQ A FEPVL I EGKAIQ L HPL V CTAF NADFDGD Q M AV HVP L S L E AQ AE ARV L MLSSNN I L SP A S G KP IVTPS QD MVL G LYY L 418
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 535 T LRD tfieldqvlnmly WVPDWD G V I P T PA iikpkplws G KQ I LSVAI P N G I hlq R F degttllspkdngmliidgqi I F 614
Cdd:cd01609 419 T KER ------------- KGDKGE G I I E T TV --------- G RV I FNEIL P E G L --- P F --------------------- I N 452
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 615 GVVE KK TVGS sngg LI HVVTREK G PQVC A K L FGN I q K VVN F W llhng FS T -- GI GDT I A D GPTMR E IT E T I A EA KK KV LD 692
Cdd:cd01609 453 KTLK KK VLKK ---- LI NECYDRY G LEET A E L LDD I - K ELG F K ----- YA T rs GI SIS I D D IVVPP E KK E I I K EA EE KV KE 522
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 693 VT K EAQAN LLT AK hgmtlr E SFE d N V VRFLN E ARD K AGRLAEV NL K -- DL N NVKQ M VMA G SK GS FIN I A Q MSACV G - QQS 769
Cdd:cd01609 523 IE K QYEKG LLT EE ------ E RYN - K V IEIWT E VTE K VADAMMK NL D kd PF N PIYM M ADS G AR GS KSQ I R Q LAGMR G l MAK 595
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 770 VE GK R I afgfvdr T LP hfskddyspeskgf VENSYLR GLT PQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ RRLV KALE D IM 849
Cdd:cd01609 596 PS GK I I ------- E LP -------------- IKSNFRE GLT VL E Y F ISTH G A R K GL A DTA L KTA DS GY LT RRLV DVAQ D VI 654
.
gi 359546325 850 V 850
Cdd:cd01609 655 V 655
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1329-1440
7.47e-50
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: 174.14
E-value: 7.47e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1329 TN S FIDIM E V LGIEA G R AALYK E VYN V I AS D G SY V NY RH MA L LV DVMT TQ GGL TS VTR H GF NR S N T GA LMR C SFE E T VEI 1408
Cdd:cd00630 47 AA S IHEML E A LGIEA A R ETIIR E IQK V L AS Q G VS V DR RH IE L IA DVMT YS GGL RG VTR S GF RA S K T SP LMR A SFE K T TKH 126
90 100 110
....*....|....*....|....*....|..
gi 359546325 1409 L FE A G A SA E L D DCR GVSEN V ILG QM AP I GTG A 1440
Cdd:cd00630 127 L LD A A A AG E K D ELE GVSEN I ILG RP AP L GTG S 158
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
17-1180
8.60e-50
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: 194.22
E-value: 8.60e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 17 VQF GL F SPE EV R AI S VAKIRF PET MDETQTRAKIG GL NDP R - L G SID ------ RNL K -------- C QT C Q ---------- 71
Cdd:COG0086 10 IKI GL A SPE KI R SW S YGEVKK PET INYRTFKPERD GL FCE R i F G PCK dyecyc GKY K rmvykgvv C EK C G vevtlskvrr 89
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 72 E G M necpghf GHI D LA K PVFH VGFIA ---- K I K kvcecvcmhcgk LLLD ehnelmrqa LAIK D SKK -- R F AA - IWTLCKT 144
Cdd:COG0086 90 E R M ------- GHI E LA M PVFH IWGLK slps R I G ------------ LLLD --------- MSLR D LER vl Y F ES y VVIDPGD 141
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 145 KMVCETDVPS ED DPTQLVSRG G CGNTQPT ---- I RK dglk L V G SWKKDRATGDAD E PELRVL S TEEILNIF K HIS V KD ft 220
Cdd:COG0086 142 TPLEKGQLLT ED EYREILEEY G DEFVAKM gaea I KD ---- L L G RIDLEKESEELR E ELKETT S EQKRKKLI K RLK V VE -- 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 221 sl G F N E VFS RPEWMIL TC LPV P PP PV RP SISFNESQRGED DL TFKLADILKA N IS L ET L EHNG AP HHAIEEAESL LQ FH V 300
Cdd:COG0086 216 -- A F R E SGN RPEWMIL DV LPV I PP DL RP LVPLDGGRFATS DL NDLYRRVINR N NR L KR L LELK AP DIIVRNEKRM LQ EA V 293
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 301 ATYM DN DIA G QP q ALQKSG RP V KS IRAR LKGK E GR I R G NL M GKRVD F S A R T VI SGD P N L E L D Q V G V PK SI A KT L TY P EV v 380
Cdd:COG0086 294 DALF DN GRR G RA - VTGANK RP L KS LSDM LKGK Q GR F R Q NL L GKRVD Y S G R S VI VVG P E L K L H Q C G L PK KM A LE L FK P FI - 371
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 381 tp Y NIDRLTQ L VRN gpnehpgakyvirdsgdrid LRYS K RAGDIQLQYG W KVERHIMDND PVL F NR Q P S LH KMSMM A HRV 460
Cdd:COG0086 372 -- Y RKLEERG L ATT -------------------- IKSA K KMVEREEPEV W DILEEVIKEH PVL L NR A P T LH RLGIQ A FEP 429
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 461 KV I PYSTFR L NLS V TSPY NADFDGD E M NL HVP Q S E E TRA E LSQ L CAVPLQ I V SP QSN KP CMGIV QD TLC G IRK LT LRD -- 538
Cdd:COG0086 430 VL I EGKAIQ L HPL V CTAF NADFDGD Q M AV HVP L S L E AQL E ARL L MLSTNN I L SP ANG KP IIVPS QD MVL G LYY LT RER eg 509
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 539 ------ T F IELDQ VL NMLY wvpdw D G VIPTP A I IK PKPLWS G K Q ILSVAI pngihlqrfdeg TT L lspkdngmliid G QI 612
Cdd:COG0086 510 akgegm I F ADPEE VL RAYE ----- N G AVDLH A R IK VRITED G E Q VGKIVE ------------ TT V ------------ G RY 560
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 613 IFGVVEKKT V GSS N -------- GGL I HVVT R EK G PQVCAKLFGNIQ K VVNFWLLHN G F S T G IG D TIAD gptm R E IT E TIA 684
Cdd:COG0086 561 LVNEILPQE V PFY N qvinkkhi EVI I RQMY R RC G LKETVIFLDRLK K LGFKYATRA G I S I G LD D MVVP ---- K E KQ E IFE 636
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 685 EA K K K V LDVT K EAQAN L L T A khgmtl R E SFE d N V VRFLNE A RDKAGRLAEVNLKDL N NVKQ M VMA G SK GS FINIA Q MSAC 764
Cdd:COG0086 637 EA N K E V KEIE K QYAEG L I T E ------ P E RYN - K V IDGWTK A SLETESFLMAAFSSQ N TTYM M ADS G AR GS ADQLR Q LAGM 709
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 765 V G QQSVEGKR I afgfvdrtlphfskddyspeskgf V E N --- S YL R - GL TPQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ RR 840
Cdd:COG0086 710 R G LMAKPSGN I ------------------------ I E T pig S NF R e GL GVL E Y F ISTH G A R K GL A DTA L KTA DS GY LT RR 765
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 841 LV KALE D IM V hydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekry RVDLLN TD HTLDPSLLES G S E IL 920
Cdd:COG0086 766 LV DVAQ D VI V ----------------------------------------------- TEEDCG TD RGITVTAIKE G G E VI 798
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 921 GD L klqvlldeeykqlv K D R KFL R EVFV D geanwplpvnirriiqnaqqtfhidhtkpsdlt IK D IVL G VKDLQENL L VL 1000
Cdd:COG0086 799 EP L -------------- K E R ILG R VAAE D --------------------------------- VV D PGT G EVLVPAGT L ID 831
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1001 RGKN EII QN A QR D A V T lfccl L RS R L ATRR vlq EYRLTKQAFDWV L S nieaqf LRSV V HP GE M VGV L AAQSIGEP A TQ M T 1080
Cdd:COG0086 832 EEVA EII EE A GI D S V K ----- V RS V L TCET --- RGGVCAKCYGRD L A ------ RGHL V NI GE A VGV I AAQSIGEP G TQ L T 897
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1081 LN TFH FA G V AS ------- KKVTS G VPRLKEI L N V AK N ------ MKTPSLTVYLEPGHAADQ E QA K LIRSAIEHTTLKS V T 1147
Cdd:COG0086 898 MR TFH IG G A AS raaeess IEAKA G GIVRLNN L K V VV N eegkgv VVSRNSELVIVDDGGRRE E EY K VPYGGVLVVVGGG V V 977
1210 1220 1230
....*....|....*....|....*....|...
gi 359546325 1148 IASE I YYDP DP RSTV I P E DEEIIQLHFSLLDEE 1180
Cdd:COG0086 978 VGGG I VAEW DP HTPP I I E EVGGGVVFDDIVEGG 1010
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
12-1439
6.58e-44
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 176.74
E-value: 6.58e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 12 RTVK EV QFGLF SPE EVRAI S VAK I RFPE T MDETQTRAKI GGL ND P RL - G SID -------------- R NLK C QT C QEGMNE 76
Cdd:PRK14844 1446 QSFN EV SISIA SPE SIKRM S YGE I EDVS T ANYRTFKVEK GGL FC P KI f G PVN ddeclcgkykkrrh R GRI C EK C GVEVTS 1525
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 77 CP --- GHF GHI D LA K PV F H VG F IAKI - KKVCECVC M H cgkl L L D EH N E L MRQALAIK D S kkrfa AIWTLC K TKMVC E TDV 152
Cdd:PRK14844 1526 SK vrr ERM GHI E LA S PV A H IW F LKSL p SRIGALLD M S ---- L R D IE N I L YSDNYIVI D P ----- LVSPFE K GEIIS E KAY 1596
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 153 PSED D PTQLV S RGGCGNTQ p T IR KDGLK L - VGSWK KD - R ATGDADEP E L R VLSTEEI L N I fkhis V KD F TSL G fnevf S R 230
Cdd:PRK14844 1597 NEAK D SYGID S FVAMQGVE - A IR ELLTR L d LHEIR KD l R LELESVAS E I R RKKIIKR L R I ----- V EN F IKS G ----- N R 1665
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 231 PEWMILT CL P VP PP PV RP SI S FNESQRGED DL TFKLAD I LKA N IS L ET L EHNGA P HHA I EEAESL LQ FH V ATYM DN D iag 310
Cdd:PRK14844 1666 PEWMILT TI P IL PP DL RP LV S LESGRPAVS DL NHHYRT I INR N NR L RK L LSLNP P EIM I RNEKRM LQ EA V DSLF DN S --- 1742
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 311 QPQ AL QKSGRP V --- KSI RAR LKGK E GR I R G NL M GKRVD F S A R T VI SGD P N L E L D Q V G V PK SI A KT L TY P E V VTPYNIDR 387
Cdd:PRK14844 1743 RRN AL VNKAGA V gyk KSI SDM LKGK Q GR F R Q NL L GKRVD Y S G R S VI VVG P T L K L N Q C G L PK RM A LE L FK P F V YSKLKMYG 1822
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 388 LTQLVRN gpnehpg A KYV IR DSGDRI dlryskragdiqlqyg W KVERHIMDND PVL F NR Q P S LH KMSMM A HRVKV I PYST 467
Cdd:PRK14844 1823 MAPTIKF ------- A SKL IR AEKPEV ---------------- W DMLEEVIKEH PVL L NR A P T LH RLGIQ A FEPIL I EGKA 1879
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 468 FR L NLS V TSPY NADFDGD E M NL HVP Q S E E TRA E LSQ L CAVPLQIV SP QSNK P CMGIVQ D TLC GI RK LTL RD --------- 538
Cdd:PRK14844 1880 IQ L HPL V CTAF NADFDGD Q M AV HVP I S L E AQL E ARV L MMSTNNVL SP SNGR P IIVPSK D IVL GI YY LTL QE pkeddlpsf 1959
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 539 - T F I E LDQV L N mlywvpdw DG VIPTPAI IK PK plwsgkq ILSVAIPNGI H LQ rfdeg T TLLS P kdn G M LI I d G QI I ---- 613
Cdd:PRK14844 1960 g A F C E VEHS L S -------- DG TLHIHSS IK YR ------- MEYINSSGET H YK ----- T ICTT P --- G R LI L - W QI F pkhe 2015
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 614 --- F GVVEKKTVGSSNGGLIHV V T R EK G p Q VCAKL F GNIQK V VN F - WLLHN G F S TGIG D TI adgptmreitet I A E A K KK 689
Cdd:PRK14844 2016 nlg F DLINQVLTVKEITSIVDL V Y R NC G - Q SATVA F SDKLM V LG F e YATFS G V S FSRC D MV ------------ I P E T K AT 2082
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 690 VL D VTK - E AQANLLTAKH G MTL R ESFEDN V VRFLNEAR D ------- KA GRLAEV N L K d L N N V KQ MV MA G SK GS FINIA Q M 761
Cdd:PRK14844 2083 HV D HAR g E IKKFSMQYQD G LIT R SERYNK V IDEWSKCT D miandml KA ISIYDG N S K - Y N S V YM MV NS G AR GS TSQMK Q L 2161
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 762 SACV G QQSVEGKR I A fgfvdrtlphfskdd YS P ESKG F V E nsylr GL TPQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ RRL 841
Cdd:PRK14844 2162 AGMR G LMTKPSGE I I --------------- ET P IISN F R E ----- GL NVF E Y F NSTH G A R K GL A DTA L KTA NS GY LT RRL 2221
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 842 V KALED - I MVHY D NT T R N S L gn V IQFIY g E DGMDA A HI E KQS L DTIGGS D aafekryrvdllntdh TLD P SL lesg S E I L 920
Cdd:PRK14844 2222 V DVSQN c I VTKH D CK T K N G L -- V VRATV - E GSTIV A SL E SVV L GRTAAN D ---------------- IYN P VT ---- K E L L 2278
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 921 gd L K LQV L L DE EY kqlvkdrkf LREVFVD G eanwplpvnirriiqnaqqtfh I D HT K PSDLTIKD I VL GV kdlqenllvl 1000
Cdd:PRK14844 2279 -- V K AGE L I DE DK --------- VKQINIA G ---------------------- L D VV K IRSPLTCE I SP GV ---------- 2315
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1001 rgkneiiqnaqrdavtlf C C L LRS R - LAT RR vlqeyrltkqafdwvlsnieaqflrs V V HP GE M VGV L AAQS I GEP A TQ M 1079
Cdd:PRK14844 2316 ------------------ C S L CYG R d LAT GK -------------------------- I V SI GE A VGV I AAQS V GEP G TQ L 2351
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1080 T LN TFH FA GV ASKK V tsgvprlkeilnvaknmktpsltvylepghaadq E QAKL I R S AIEHTT L KS vtia S E I YY D PDPR 1159
Cdd:PRK14844 2352 T MR TFH IG GV MTRG V ---------------------------------- E SSNI I A S INAKIK L NN ---- S N I II D KNGN 2393
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1160 ST VI PEDE E II qlhfs L L D EEAEQSFDQQS P WLLR L EL D RAA --- MN DK ----- DL T MGQVG E RIKQTFKN DL F -- VIWS 1229
Cdd:PRK14844 2394 KI VI SRSC E VV ----- L I D SLGSEKLKHSV P YGAK L YV D EGG svk IG DK vaewd PY T LPIIT E KTGTVSYQ DL K dg ISIT 2468
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1230 E DN DE KLI I RCR VV ------------ RP K ----------- S L DAET EA --------------- EED H MLKK I EN T ML E NI 1271
Cdd:PRK14844 2469 E VM DE STG I SSK VV kdwklysgganl RP R ivllddngkvm T L ASGV EA cyfipigavlnvqdg QKV H AGDV I TR T PR E SV 2548
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1272 TL R GVE - NIE RV VMM k YDRKV P sptgeyv KE PEW V L E T DG - V NL SE -------- VMTV P --- G I D P TR ---------- IY 1328
Cdd:PRK14844 2549 KT R DIT g GLP RV IEL - FEARR P ------- KE HAI V S E I DG y V AF SE kdrrgkrs ILIK P vde Q I S P VE ylvsrskhvi VN 2620
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1329 TNS F I -------------- DI ME VLG I EA GRAALYK E VYN V IASD G SYVNYR H MALLVDV M TTQGGL T ------------ 1382
Cdd:PRK14844 2621 EGD F V rkgdllmdgdpdlh DI LR VLG L EA LAHYMIS E IQQ V YRLQ G VRIDNK H LEVILKQ M LQKVEI T dpgdtmylvges 2700
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1383 ---- S V T R HGFNR SN T G ALMRC ---------------------- SF E ET VEI L F EA GASAEL D DCR G VS ENVI L G QMA P I 1436
Cdd:PRK14844 2701 idkl E V D R ENDAM SN S G KRPAH ylpilqgitrasletssfisaa SF Q ET TKV L T EA AFCGKS D PLS G LK ENVI V G RLI P A 2780
...
gi 359546325 1437 GTG 1439
Cdd:PRK14844 2781 GTG 2783
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
693-800
8.06e-43
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: 152.13
E-value: 8.06e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 693 V T KEAQANL L TAKH GMTL R ESFE DNVVRF LN E ARD K AG RL A EVN L KDL N NVKQ M VMA G S KGS F INI A Q MSA C V GQQ S VEG 772
Cdd:pfam05000 1 I T DAERYGK L EDIW GMTL E ESFE ALINNI LN K ARD P AG NI A SKS L DPN N SIYM M ADS G A KGS I INI S Q IAG C R GQQ N VEG 80
90 100
....*....|....*....|....*...
gi 359546325 773 KRI A FGF VD RTLPHF S KDD YS PES K GFV 800
Cdd:pfam05000 81 KRI P FGF SG RTLPHF K KDD EG PES R GFV 108
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
317-1104
1.87e-39
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 161.00
E-value: 1.87e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 317 KSG RP V KS IRAR LKGK E GR I R G NL M GKRVD F S A R T VI SGD P N L E L D Q V G V PK SI A KT L TY P EV vtpyn IDR L TQL ----- 391
Cdd:PRK00566 309 PNN RP L KS LSDM LKGK Q GR F R Q NL L GKRVD Y S G R S VI VVG P E L K L H Q C G L PK KM A LE L FK P FI ----- MKK L VER glatt 383
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 392 VRN gpnehpg AK YVIRDSGDRI dlryskragdiqlqyg W K V ERHIMDND PVL F NR Q P S LH KMSMM A HRVKV I PYSTFR L N 471
Cdd:PRK00566 384 IKS ------- AK KMVEREDPEV ---------------- W D V LEEVIKEH PVL L NR A P T LH RLGIQ A FEPVL I EGKAIQ L H 440
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 472 LS V TSPY NADFDGD E M NL HVP Q S E E TR AE LSQ L CAVPLQ I V SP QSN KP cmg I V --- QD TLC G IRK LT L - R D ------- T F 540
Cdd:PRK00566 441 PL V CTAF NADFDGD Q M AV HVP L S L E AQ AE ARV L MLSSNN I L SP ANG KP --- I I vps QD MVL G LYY LT R e R E gakgegm V F 517
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 541 IELDQV L NMLY wvpdw D G VIPTP A I IK pkplwsgkqils V A I PNGIHLQ rfdeg TT L lspkdngmliid G QI IF G ----- 615
Cdd:PRK00566 518 SSPEEA L RAYE ----- N G EVDLH A R IK ------------ V R I TSKKLVE ----- TT V ------------ G RV IF N eilpe 563
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 616 ---- VVEK K TVGSSN - GGL I HV V T R EK G PQVCAKLFGN I q K VVN F - WLLHN G F S T GI G D TIA dg P TMRE it E T I A EA K K K 689
Cdd:PRK00566 564 glpf INVN K PLKKKE i SKI I NE V Y R RY G LKETVIFLDK I - K DLG F k YATRS G I S I GI D D IVI -- P PEKK -- E I I E EA E K E 638
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 690 V LDVT K EAQAN L L T AK hgmtlresf E -- DN V VRFLNE A R D KAGRLAEV NL K ---- DL N NVKQ M VMA G SK GS FIN I A Q MS a 763
Cdd:PRK00566 639 V AEIE K QYRRG L I T DG --------- E ry NK V IDIWSK A T D EVAKAMMK NL S kdqe SF N PIYM M ADS G AR GS ASQ I R Q LA - 708
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 764 cvgqqsve G K R iaf G FVDRT lphfskddyspe S KGFV E N ---- SYLR GLT PQ E F F FHAM G G R E GL I DTA V KTA ET GY IQ R 839
Cdd:PRK00566 709 -------- G M R --- G LMAKP ------------ S GEII E T piks NFRE GLT VL E Y F ISTH G A R K GL A DTA L KTA DS GY LT R 765
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 840 RLV KALE D IM V - HY D NT T RNSL g N V IQF I Y G ED gmdaahi EKQS L - DT I G G sdaafek R Y rvdl L NT D h TL DP S ---- LL 913
Cdd:PRK00566 766 RLV DVAQ D VI V r ED D CG T DRGI - E V TAI I E G GE ------- VIEP L e ER I L G ------- R V ---- L AE D - VV DP E tgev IV 825
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 914 ES G SE I l GDLKLQVLLDEEYKQ lvkdrkflrevfvdgeanwplp V N IR RII qnaqq T FHID H tkpsdltikdivl GV kdl 993
Cdd:PRK00566 826 PA G TL I - DEEIADKIEEAGIEE ---------------------- V K IR SVL ----- T CETR H ------------- GV --- 861
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 994 qenllvlrgkneiiqnaqrdavtlf C -- C LL R S r LAT RR vlqeyrltkqafdwvlsnieaqflrs V V HP GE M VGV L AAQS 1071
Cdd:PRK00566 862 ------------------------- C ak C YG R D - LAT GK -------------------------- L V NI GE A VGV I AAQS 889
810 820 830
....*....|....*....|....*....|...
gi 359546325 1072 IGEP A TQ M T LN TFH FA GV ask KV T S G V PR LK E I 1104
Cdd:PRK00566 890 IGEP G TQ L T MR TFH TG GV --- DI T G G L PR VA E L 919
rpoC1
CHL00018 RNA polymerase beta' subunit
230-538
4.28e-36
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 147.36
E-value: 4.28e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 230 R PEWM I L TC LPV P PP PV RP S I SFNESQRGED DL TFKLADILKA N IS L ET L E -- HNGA P HHAIEEAES LLQ FH V ATYM DN D 307
Cdd:CHL00018 260 E PEWM V L CL LPV L PP EL RP I I QLDGGKLMSS DL NELYRRVIYR N NT L TD L L tt SRST P GELVMCQKK LLQ EA V DALL DN G 339
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 308 I A GQP q ALQKSGR P V KS IRARLK GKEGR I R G NL M GKRVD F S A R T VI SGD P N L E L D Q V G V P KS IA KT L TY P E V vtpyn I DR 387
Cdd:CHL00018 340 I R GQP - MRDGHNK P Y KS FSDVIE GKEGR F R E NL L GKRVD Y S G R S VI VVG P S L S L H Q C G L P RE IA IE L FQ P F V ----- I RG 413
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 388 L T -- Q L VR N gpne HPG AK YV IR DSGDRI dlryskragdiqlqyg W KVERHI M DND PVL F NR Q P S LH KMSMM A HRVKVIPY 465
Cdd:CHL00018 414 L I rq H L AS N ---- IRA AK SK IR EKEPIV ---------------- W EILQEV M QGH PVL L NR A P T LH RLGIQ A FQPILVEG 473
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359546325 466 STFR L NLS V TSPY NADFDGD E M NL HVP Q S E E TR AE LSQ L CAVPLQIV SP QSNK P CMGIV QD T L C G IRK LT LRD 538
Cdd:CHL00018 474 RAIC L HPL V CKGF NADFDGD Q M AV HVP L S L E AQ AE ARL L MFSHMNLL SP AIGD P ISVPS QD M L L G LYV LT IGN 546
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
229-535
8.39e-34
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 139.88
E-value: 8.39e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 229 SRPEWM I L TCL PV P PP PV RP SISFNESQRGED DL TFKLADILKA N IS L ET L EHNG AP HHAIEEAESL LQ FH V ATYM DN DI 308
Cdd:PRK02625 240 SRPEWM V L DVI PV I PP DL RP MVQLDGGRFATS DL NDLYRRVINR N NR L AR L QEIL AP EIIVRNEKRM LQ EA V DALI DN GR 319
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 309 A G Q p QALQKSG RP V KS IRARLK GK E GR I R G NL M GKRVD F S A R T VI SGD P N L ELD Q V G V PK SI A K tltyp E VVT P YN I D RL 388
Cdd:PRK02625 320 R G R - TVVGANN RP L KS LSDIIE GK Q GR F R Q NL L GKRVD Y S G R S VI VVG P K L KMH Q C G L PK EM A I ----- E LFQ P FV I H RL 393
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 389 TQ lv RNGP N EHPG AK YV I RDSGDRI dlryskragdiqlqyg W K V ERHIMDND PVL F NR Q P S LH KMSMM A HRVKVIPYSTF 468
Cdd:PRK02625 394 IR -- QGIV N NIKA AK KL I QRADPEV ---------------- W Q V LEEVIEGH PVL L NR A P T LH RLGIQ A FEPILVEGRAI 455
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 359546325 469 R L NLS V TSPY NADFDGD E M NL HVP Q S E E TR AE LSQ L CAVPLQ I V SP QSNK P CMGIV QD TLC G IRK LT 535
Cdd:PRK02625 456 Q L HPL V CPAF NADFDGD Q M AV HVP L S L E AQ AE ARL L MLASNN I L SP ATGE P IVTPS QD MVL G CYY LT 522
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1061-1108
6.84e-24
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain]
Cd Length: 158
Bit Score: 99.80
E-value: 6.84e-24
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 359546325 1061 GE M VGVLAAQSIGEP A TQMTL N TFHFAGVAS KK VT S G V PRLKEILN V A 1108
Cdd:cd00630 1 GE A VGVLAAQSIGEP G TQMTL R TFHFAGVAS MN VT L G L PRLKEILN A A 48
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1058-1105
2.56e-14
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: 73.72
E-value: 2.56e-14
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 359546325 1058 V HP GE M VG VL AAQSIGEP A TQ M T LN TFH FA GVA S k KV T S G V PR LK E IL 1105
Cdd:cd02655 3 V EL GE A VG II AAQSIGEP G TQ L T MR TFH TG GVA T - DI T Q G L PR VE E LF 49
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
678-1094
7.45e-12
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: 70.65
E-value: 7.45e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 678 EITE T ia E AKK KV L D VTKEAQ anlltakhgmtlr E SFE D N VV RFLN eardkagrlaev NLKD LN N V KQ M VMA G SK G sfi N 757
Cdd:TIGR02388 83 EITE V -- E RFQ KV I D TWNGTN ------------- E ELK D E VV NNFR ------------ QTDP LN S V YM M AFS G AR G --- N 132
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 758 IA Q MSAC VG QQSV ---- E G KR I afgfvdr T LP hfskddyspeskgf VENSYLR GLT PQ E FFFHAM G G R E GL I DTA VK TA E 833
Cdd:TIGR02388 133 MS Q VRQL VG MRGL manp Q G EI I ------- D LP -------------- IKTNFRE GLT VT E YVISSY G A R K GL V DTA LR TA D 191
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 834 T GY IQ RRLV KALE D IM V HYD nttrnslgnviqfiygedgmdaahiekqsldtiggs D AAF E KRYR V dlln TDH T LDPSLL 913
Cdd:TIGR02388 192 S GY LT RRLV DVSQ D VI V REE ------------------------------------ D CGT E RSIV V ---- RAM T EGDKKI 231
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 914 ES G SEI LG D L KLQVL L DE E YKQL V K drkflrevfvdge A N WPLPVNIRRI I QN A qqtfhidhtkpsdltikdivlgvkdl 993
Cdd:TIGR02388 232 SL G DRL LG R L VAEDV L HP E GEVI V P ------------- K N TAIDPDLAKT I ET A -------------------------- 272
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 994 qenllvlr G KN E II qnaqrdavtlfccl L RS R L --- A T R R V LQ eyrltk QAFD W V L SN ieaqfl RSV V HP GE M VG VL AAQ 1070
Cdd:TIGR02388 273 -------- G IS E VV -------------- V RS P L tce A A R S V CR ------ KCYG W S L AH ------ AHL V DL GE A VG II AAQ 318
410 420
....*....|....*....|....
gi 359546325 1071 SIGEP A TQ M T LN TFH FA GV ASKK V 1094
Cdd:TIGR02388 319 SIGEP G TQ L T MR TFH TG GV FTGE V 342
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
807-1094
7.08e-11
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 67.71
E-value: 7.08e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 807 GLT PQ E FFFHAM G G R E GL I DTA VK TA ET GY IQ RRLV KALE D IM V H - Y D NT T RNSL gnviq FIYGE D GM D AAH I ekqsldt 885
Cdd:PRK02597 166 GLT VT E YVISSY G A R K GL V DTA LR TA DS GY LT RRLV DVSQ D VI V R e E D CG T TRGI ----- VVEAM D DG D RVL I ------- 233
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 886 iggsda AFEK R yrvdllntdhtldpsllesgse I LG dlklqvlldeeykqlvkd R KFLRE V FV - D GE anwplpvnirr I I 964
Cdd:PRK02597 234 ------ PLGD R ---------------------- L LG ------------------ R VLAED V VD p E GE ----------- V I 256
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 965 qn A QQTFH ID H tkps DL TI K divlgvkdlqenllvlrgknei I QN A QRDA V TL fccll RS R L --- A T R R V LQ eyrltk QA 1041
Cdd:PRK02597 257 -- A ERNTA ID P ---- DL AK K ---------------------- I EK A GVEE V MV ----- RS P L tce A A R S V CR ------ KC 297
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|...
gi 359546325 1042 FD W V L SNIE aqflrs V V HP GE M VG VL AAQSIGEP A TQ M T LN TFH FA GV ASKK V 1094
Cdd:PRK02597 298 YG W S L AHNH ------ L V DL GE A VG II AAQSIGEP G TQ L T MR TFH TG GV FTGE V 344
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1061-1445
1.60e-10
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: 65.14
E-value: 1.60e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1061 GE M VG V LAA QS I G EPA TQMT L NTFHFAG vaskkv T S GVPR LKE I L -- NVAKNM K TPSLT V Y L EP ----- G H AADQ E Q A K L 1133
Cdd:cd02737 1 GE P VG S LAA TA I S EPA YKAL L DPPQSLE ------ S S PLEL LKE V L ec RSKSKS K ENDRR V I L SL hlckc D H GFEY E R A A L 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1134 - IRSAI E HT TL KSVTIA S E I Y Y D P DPRSTVIP E DEEIIQ - LHFSLLDEEAEQ S FDQQ -- SPW LLRLE LD raamndkdltm 1209
Cdd:cd02737 75 e VKNHL E RV TL EDLATT S M I K Y S P QATEAIVG E IGDQLN t KKKGKKKAIFST S LKIT kf SPW VCHFH LD ----------- 143
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1210 g QVGERIKQTF kndlfviwsedndekliir C RVV rpk S LDA E TEAEEDHM L KKIENTM --- L ENITLR G V E N I ER V VMMK 1286
Cdd:cd02737 144 - KECQKLSDGP ------------------- C LTF --- S VSK E VSKSSEEL L DVLRDRI ipf L LETVIK G D E R I KS V NILW 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1287 Y D RKVP S PTGEYV K EP -- E W VLE tdg V NLS E ------------------- VM TV pg ID PT R IYTN S FID I ME VLGI E A GR 1345
Cdd:cd02737 201 E D SPST S WVKSVG K SS rg E L VLE --- V TVE E sckktrgnawnvvmdacip VM DL -- ID WE R SMPY S IQQ I KS VLGI D A AF 275
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359546325 1346 AALYKEVYNVIASD G SY V NYR H MA L LV D V MT TQ G GL tsvtr H G F N RSNTG A LM R ---------- CS F EETVEILFE A GAS 1415
Cdd:cd02737 276 EQFVQRLESAVSMT G KS V LRE H LL L VA D S MT YS G EF ----- V G L N AKGYK A QR R slkisapfte AC F SSPIKCFLK A AKK 350
410 420 430
....*....|....*....|....*....|.
gi 359546325 1416 AEL D DCR GV SENVIL G QM AP I GTG A - F DVMI 1445
Cdd:cd02737 351 GAS D SLS GV LDACAW G KE AP V GTG S k F EILW 381
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1061-1089
1.19e-08
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 60.34
E-value: 1.19e-08
10 20
....*....|....*....|....*....
gi 359546325 1061 GE M VG VL A A QSIGEP A TQ M TL N TFH FA GV 1089
Cdd:CHL00117 315 GE A VG II A G QSIGEP G TQ L TL R TFH TG GV 343
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1037-1081
9.59e-06
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 50.66
E-value: 9.59e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 359546325 1037 L T KQAFDWVLSNIEAQF L RSV V H P G E M VG VL AAQSIGEP A TQM T L 1081
Cdd:PRK14898 33 V T EEMVEEIIDEVVSAY L NAL V E P Y E A VG IV AAQSIGEP G TQM S L 77
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
1401-1465
1.53e-03
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 43.45
E-value: 1.53e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 359546325 1401 SF E ET VEI L F EA GASAEL D DC RG VS ENVI L G QMA P I GTG a F DVM i D EE SLVKYM P EQK I TEIEDG 1465
Cdd:PRK02597 1184 SF Q ET TRV L T EA AIEGKS D WL RG LK ENVI I G RLI P A GTG - F SGF - E EE LSAEAG P HPD I LAEDPA 1246
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1401-1439
1.78e-03
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 43.39
E-value: 1.78e-03
10 20 30
....*....|....*....|....*....|....*....
gi 359546325 1401 SF E ET VEI L FE A GASAEL D DCR G VS ENVILG QMA P I GTG 1439
Cdd:CHL00117 1278 SF Q ET TRV L AK A ALRGRI D WLK G LK ENVILG GLI P A GTG 1316
RNA_pol_Rpb1_R
pfam05001 RNA polymerase Rpb1 C-terminal repeat; The repetitive C-terminal domain (CTD) of Rpb1 (RNA ...
1698-1709
3.22e-03
RNA polymerase Rpb1 C-terminal repeat; The repetitive C-terminal domain (CTD) of Rpb1 (RNA polymerase Pol II) plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation.
Pssm-ID: 461513
Cd Length: 12
Bit Score: 36.34
E-value: 3.22e-03
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
