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DNA-directed RNA polymerase subunit [Caenorhabditis elegans]
Protein Classification
DNA-directed RNA polymerase III subunit RPC1 ( domain architecture ID 10118853 )
DNA-directed RNA polymerase III subunit RPC1 is the largest and is a catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
26-887
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: 1523.24
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 26 E FMRQTAH V PIF N NK LY EDVEG K lq P AN YG P LDP KM G V S T K T G T C S TCGL G L T DCVGHFGY FD L DV PVFHIG F FK LT I QL 105
Cdd:cd02583 4 E DIIRLSE V EVT N RN LY DIETR K -- P LP YG V LDP RL G T S D K D G I C E TCGL N L A DCVGHFGY IK L EL PVFHIG Y FK AI I NI 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 106 LQCICK N CS SI LL TP E QH R V F SRQVMN PNLD Y L HR KAL H K R I VAA CKK GST C S HCGL kngt V KKA vgavlkiafaspvsv 185
Cdd:cd02583 82 LQCICK T CS RV LL PE E EK R K F LKRLRR PNLD N L QK KAL K K K I LEK CKK VRK C P HCGL ---- L KKA --------------- 142
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 186 delgkfatmfssn QE V gdhvrkmkftl LNPL F V QK LF S NI KEG D IPV L MVRS g EEKH P ND L L LTR M PVPP V CIRPSVV SE 265
Cdd:cd02583 143 ------------- QE D ----------- LNPL K V LN LF K NI PPE D VEL L LMNP - LAGR P EN L I LTR I PVPP L CIRPSVV MD 197
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 266 V K A GT T EDD V T M KL M EI MLT NDV L KKH KRD GA PSKTLF E T W EH LQ I QCALYINSE MS GLP PD MQPK RAM R A F T QRLKGKQ 345
Cdd:cd02583 198 E K S GT N EDD L T V KL S EI IFL NDV I KKH LEK GA KTQKIM E D W DF LQ L QCALYINSE LP GLP LS MQPK KPI R G F C QRLKGKQ 277
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 346 GRFRGNL C GKRVDFSGRTVISPDPNLRIDQVGVP I HVA MT LT F PE I V NAS NIEK M R Q LV I NG S DVHPGAN YLVEKKT G N K 425
Cdd:cd02583 278 GRFRGNL S GKRVDFSGRTVISPDPNLRIDQVGVP E HVA KI LT Y PE R V TRY NIEK L R K LV L NG P DVHPGAN FVIKRDG G K K 357
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 426 K L LKYG K R DEL A KN L RM GD TI ERHL D D N D V VLFNRQPSLH KI SIM S HRAKVMP G RTFRFNEC A CTPYNADFDGDEMNLH L 505
Cdd:cd02583 358 K F LKYG N R RKI A RE L KI GD IV ERHL E D G D I VLFNRQPSLH RL SIM A HRAKVMP W RTFRFNEC V CTPYNADFDGDEMNLH V 437
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 506 PQT Y EA K AEA S ELM N VKNNL I TPR S GEPL V AA I QDF I T GG YLLT H KD T F LP RA EVYRFAAALI D AS akkq T KI RI PPPAI 585
Cdd:cd02583 438 PQT E EA R AEA L ELM G VKNNL V TPR N GEPL I AA T QDF L T AS YLLT S KD V F FD RA QFCQLCSYML D GE ---- I KI DL PPPAI 513
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 586 RR PVELWTGKQ LIE L II RP D K G S D V SL NL T AK N KSYT - GNLEL C SK D S YV I IRNS V LL A G C LDKS L LGS S SK VNI FY M L M 664
Cdd:cd02583 514 LK PVELWTGKQ IFS L LL RP N K K S P V LV NL E AK E KSYT k KSPDM C PN D G YV V IRNS E LL C G R LDKS T LGS G SK NSL FY V L L 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 665 RDYG ED AA VD AM W RLA RMAPVF LSNRGFSIGI G DV R PS EQ LL RE K GQ LVDNGY S KC SQ YIK ELEE GKL KA QPGCT E E E TL 744
Cdd:cd02583 594 RDYG PE AA AA AM N RLA KLSSRW LSNRGFSIGI D DV T PS KE LL KK K EE LVDNGY A KC DE YIK QYKK GKL EL QPGCT A E Q TL 673
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 745 E SI I LR ELS T IR DH AG QV CL RN L S K Y N A PL T MA V CGSKGS F INISQMIACVGQQ A ISG H R P P D GFE E R S LPHF E R KK KTP 824
Cdd:cd02583 674 E AK I SG ELS K IR ED AG KA CL KE L H K S N S PL I MA L CGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF P R NS KTP 753
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 25145495 825 E AKGFVANSFYSGLTPTEFFFHTM G GREGLVDTAVKTAETGYMQRRL V K C LEDL CAS YDGTVR 887
Cdd:cd02583 754 A AKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SVQ YDGTVR 816
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1034-1374
2.02e-176
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: 526.02
E-value: 2.02e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1034 K VA RA IT EPGTAVGAIAA T SIGEP S TQMTLKTFHFAGVASMNIT Q GVPRIKEIINA V K T ISTPIITA A L LDPY DE SL AR R 1113
Cdd:cd02736 1 K YM RA KV EPGTAVGAIAA Q SIGEP G TQMTLKTFHFAGVASMNIT L GVPRIKEIINA S K N ISTPIITA K L ENDR DE KS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1114 VK A RIEKT T LGE ICD YIEEVY L PDD YFL L V KL NS K R I RL LQL evcmesisyaiatskvcpqmrgckivahgktmmairpp 1193
Cdd:cd02736 81 VK G RIEKT Y LGE VAS YIEEVY S PDD CYI L I KL DK K I I EK LQL -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1194 st SK LSKTMTM Q I LK YS L AN VVV K GIP S V N R C VI HA D E KKG d F Y S LLVEG TDF R S V LSSV GV DPRK T NF N NALV V AD VLG 1273
Cdd:cd02736 123 -- SK SNLYFLL Q S LK RK L PD VVV S GIP E V K R A VI NK D K KKG - K Y K LLVEG YGL R A V MNTP GV IGTR T TS N HIME V EK VLG 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1274 IEAARS C IINEI IA TM DA HG IGL D R RH V MLLAD V MT YR GEVLGITR N G LV KMK D SVL L LASFEKT M DHLF E AA FFSQR D V 1353
Cdd:cd02736 200 IEAARS T IINEI QY TM KS HG MSI D P RH I MLLAD L MT FK GEVLGITR F G IA KMK E SVL M LASFEKT T DHLF N AA LHGRK D S 279
330 340
....*....|....*....|.
gi 25145495 1354 I H GVSECIIMG T PM TV GTG T F 1374
Cdd:cd02736 280 I E GVSECIIMG K PM PI GTG L F 300
rpoC2 super family
cl33332 RNA polymerase beta'' subunit; Reviewed
837-1080
2.90e-11
RNA polymerase beta'' subunit; Reviewed
CHL00117 :Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 68.43
E-value: 2.90e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 837 GL TP TE FFFHTM G G R E G L VDTAV K TA ET GY MQ RRLV KCLEDL ------ C asyd GT V R S ----- SV G DV IE FVF g EDG L D p 905
Cdd:CHL00117 172 GL SL TE YIISCY G A R K G V VDTAV R TA DA GY LT RRLV EVVQHI vvretd C ---- GT T R G isvsp RN G MM IE RIL - IQT L I - 245
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 906 ammeakd G S V V dfthvleh A KN I QTTKE ------ Q P I PVDKLDEVLKAEI Q KKF kgkyvhfadklseyitqte I K ----- 974
Cdd:CHL00117 246 ------- G R V L -------- A DD I YIGSR ciatrn Q D I GIGLANRFITFRA Q PIS ------------------- I R spltc 291
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 975 K S KK W qngkahcgnhetadlktkesck IC knleayktsllanscltkt QLC -------- SFI EL cyykvaraitep G T AV 1046
Cdd:CHL00117 292 R S TS W ---------------------- IC ------------------- QLC ygwslahg DLV EL ------------ G E AV 318
250 260 270
....*....|....*....|....*....|....
gi 25145495 1047 G A IA AT SIGEP S TQ M TL K TFH FA GV ASMNITQG V 1080
Cdd:CHL00117 319 G I IA GQ SIGEP G TQ L TL R TFH TG GV FTGGTAEQ V 352
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
26-887
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: 1523.24
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 26 E FMRQTAH V PIF N NK LY EDVEG K lq P AN YG P LDP KM G V S T K T G T C S TCGL G L T DCVGHFGY FD L DV PVFHIG F FK LT I QL 105
Cdd:cd02583 4 E DIIRLSE V EVT N RN LY DIETR K -- P LP YG V LDP RL G T S D K D G I C E TCGL N L A DCVGHFGY IK L EL PVFHIG Y FK AI I NI 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 106 LQCICK N CS SI LL TP E QH R V F SRQVMN PNLD Y L HR KAL H K R I VAA CKK GST C S HCGL kngt V KKA vgavlkiafaspvsv 185
Cdd:cd02583 82 LQCICK T CS RV LL PE E EK R K F LKRLRR PNLD N L QK KAL K K K I LEK CKK VRK C P HCGL ---- L KKA --------------- 142
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 186 delgkfatmfssn QE V gdhvrkmkftl LNPL F V QK LF S NI KEG D IPV L MVRS g EEKH P ND L L LTR M PVPP V CIRPSVV SE 265
Cdd:cd02583 143 ------------- QE D ----------- LNPL K V LN LF K NI PPE D VEL L LMNP - LAGR P EN L I LTR I PVPP L CIRPSVV MD 197
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 266 V K A GT T EDD V T M KL M EI MLT NDV L KKH KRD GA PSKTLF E T W EH LQ I QCALYINSE MS GLP PD MQPK RAM R A F T QRLKGKQ 345
Cdd:cd02583 198 E K S GT N EDD L T V KL S EI IFL NDV I KKH LEK GA KTQKIM E D W DF LQ L QCALYINSE LP GLP LS MQPK KPI R G F C QRLKGKQ 277
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 346 GRFRGNL C GKRVDFSGRTVISPDPNLRIDQVGVP I HVA MT LT F PE I V NAS NIEK M R Q LV I NG S DVHPGAN YLVEKKT G N K 425
Cdd:cd02583 278 GRFRGNL S GKRVDFSGRTVISPDPNLRIDQVGVP E HVA KI LT Y PE R V TRY NIEK L R K LV L NG P DVHPGAN FVIKRDG G K K 357
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 426 K L LKYG K R DEL A KN L RM GD TI ERHL D D N D V VLFNRQPSLH KI SIM S HRAKVMP G RTFRFNEC A CTPYNADFDGDEMNLH L 505
Cdd:cd02583 358 K F LKYG N R RKI A RE L KI GD IV ERHL E D G D I VLFNRQPSLH RL SIM A HRAKVMP W RTFRFNEC V CTPYNADFDGDEMNLH V 437
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 506 PQT Y EA K AEA S ELM N VKNNL I TPR S GEPL V AA I QDF I T GG YLLT H KD T F LP RA EVYRFAAALI D AS akkq T KI RI PPPAI 585
Cdd:cd02583 438 PQT E EA R AEA L ELM G VKNNL V TPR N GEPL I AA T QDF L T AS YLLT S KD V F FD RA QFCQLCSYML D GE ---- I KI DL PPPAI 513
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 586 RR PVELWTGKQ LIE L II RP D K G S D V SL NL T AK N KSYT - GNLEL C SK D S YV I IRNS V LL A G C LDKS L LGS S SK VNI FY M L M 664
Cdd:cd02583 514 LK PVELWTGKQ IFS L LL RP N K K S P V LV NL E AK E KSYT k KSPDM C PN D G YV V IRNS E LL C G R LDKS T LGS G SK NSL FY V L L 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 665 RDYG ED AA VD AM W RLA RMAPVF LSNRGFSIGI G DV R PS EQ LL RE K GQ LVDNGY S KC SQ YIK ELEE GKL KA QPGCT E E E TL 744
Cdd:cd02583 594 RDYG PE AA AA AM N RLA KLSSRW LSNRGFSIGI D DV T PS KE LL KK K EE LVDNGY A KC DE YIK QYKK GKL EL QPGCT A E Q TL 673
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 745 E SI I LR ELS T IR DH AG QV CL RN L S K Y N A PL T MA V CGSKGS F INISQMIACVGQQ A ISG H R P P D GFE E R S LPHF E R KK KTP 824
Cdd:cd02583 674 E AK I SG ELS K IR ED AG KA CL KE L H K S N S PL I MA L CGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF P R NS KTP 753
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 25145495 825 E AKGFVANSFYSGLTPTEFFFHTM G GREGLVDTAVKTAETGYMQRRL V K C LEDL CAS YDGTVR 887
Cdd:cd02583 754 A AKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SVQ YDGTVR 816
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
14-923
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 906.54
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 K VV G - V KF APGDC E FM R QTAHVP I FNNKL Y E D ---- VE G klqpany G PL DP KM GV STKTGT C S TCG LGLTD C V GHFG YFD 88
Cdd:PRK08566 7 K RI G s I KF GLLSP E EI R KMSVTK I ITADT Y D D dgyp ID G ------- G LM DP RL GV IDPGLR C K TCG GRAGE C P GHFG HIE 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 89 L DV PV F H I GF F KL TIQ LL QCI C KN C SSIL LT P E QHRVFSRQVMNPNLDYLHRKA L H K RIVAACK K GST C S HCG L K N gtvk 168
Cdd:PRK08566 80 L AR PV I H V GF A KL IYK LL RAT C RE C GRLK LT E E EIEEYLEKLERLKEWGSLADD L I K EVKKEAA K RMV C P HCG E K Q ---- 155
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 169 kavgav L KI A F AS P vsvdelgkfa T M F SSNQEV G DH vrkm K ftl L N P LFVQKLFSN I KEG D IPV L MVRS g E EKH P NDLL L 248
Cdd:PRK08566 156 ------ Y KI K F EK P ---------- T T F YEERKE G LV ---- K --- L T P SDIRERLEK I PDE D LEL L GINP - E VAR P EWMV L 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 249 T RM PVPPV CI RPS VVS E vk A G - TT EDD V T M KL ME I MLT N DV LK KHKRD GAP SKTLFET WE H LQ IQCAL Y INS E MS G L PP - 326
Cdd:PRK08566 212 T VL PVPPV TV RPS ITL E -- T G q RS EDD L T H KL VD I IRI N QR LK ENIEA GAP QLIIEDL WE L LQ YHVTT Y FDN E IP G I PP a 289
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 327 DMQPK R AMRAFT QRLKGK Q GRFRGNL C GKRV D FS G RTVISPDPNL R I DQ VGVP IHV A MT LT F PE I V NAS NIE KM R QL V I N 406
Cdd:PRK08566 290 RHRSG R PLKTLA QRLKGK E GRFRGNL S GKRV N FS A RTVISPDPNL S I NE VGVP EAI A KE LT V PE R V TEW NIE EL R EY V L N 369
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 407 G SDV HPGANY LV e KKT G NKKL L KYGKRD ELA KN L RM G DTI ERHL D D N D V VLFNRQPSLH KI SIM S HR AK V M PG R TFR F N E 486
Cdd:PRK08566 370 G PEK HPGANY VI - RPD G RRIK L TDKNKE ELA EK L EP G WIV ERHL I D G D I VLFNRQPSLH RM SIM A HR VR V L PG K TFR L N L 448
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 487 CA C T PYNADFDGDEMNLH L PQT Y EA K AEA SE LM N V KNNLIT PR S G E P LVAA IQD F I T G G YLLT H K D T FLPRA E VYR faaa 566
Cdd:PRK08566 449 AV C P PYNADFDGDEMNLH V PQT E EA R AEA RI LM L V QEHILS PR Y G G P IIGG IQD H I S G A YLLT R K S T LFTKE E ALD ---- 524
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 567 L ID A S ak KQTKIRI P P PAI RRPVEL WTGKQ LIE L II r P D kgs D VS L NLT AK N -- KSYTGNL E L C SK D S YV I I R N SV LL A G 644
Cdd:PRK08566 525 L LR A A -- GIDELPE P E PAI ENGKPY WTGKQ IFS L FL - P K --- D LN L EFK AK I cs GCDECKK E D C EH D A YV V I K N GK LL E G 598
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 645 CL DK SLL G SSSK v N I FYMLMRD YG EDA A VDAMWRLA R M A PV F LSN RGF SI GI G D VRPS E QLLR E KGQLVDNGYSKCSQY I 724
Cdd:PRK08566 599 VI DK KAI G AEQG - S I LDRIVKE YG PER A RRFLDSVT R L A IR F IML RGF TT GI D D EDIP E EAKE E IDEIIEEAEKRVEEL I 677
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 725 KEL E E G K L KAQ PG C T E EETLE SI I LRE L STI RD H AG QVCLRN L SKY N APLT MA VC G SK GS FI N IS QM I ACVGQQ AIS G H R 804
Cdd:PRK08566 678 EAY E N G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG EIAEKY L GLD N PAVI MA RT G AR GS ML N LT QM A ACVGQQ SVR G E R 757
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 805 PPD G FEE R S LPHF ERKKKTP EA K GFV AN S FY SGLTPTEFFFH T MGGREGLVDTAV K T AET GYMQRRL VKC L E DL CAS YDG 884
Cdd:PRK08566 758 IRR G YRD R T LPHF KPGDLGA EA R GFV RS S YK SGLTPTEFFFH A MGGREGLVDTAV R T SQS GYMQRRL INA L Q DL KVE YDG 837
890 900 910
....*....|....*....|....*....|....*....
gi 25145495 885 TVR SSV G DVIE F VF GEDG L DP am M EAKD G SV VD FTHVL E 923
Cdd:PRK08566 838 TVR DTR G NIVQ F KY GEDG V DP -- M KSDH G KP VD VDRII E 874
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
14-917
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: 859.02
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 K VVGV KF APGDC E FM R QTAH V PIFNNKL Y E D v E G kl Q P ANY G PL DP KM GV STKTGT C S TCG LGLTD C V GHFG YFD L DV PV 93
Cdd:TIGR02390 3 K IGSI KF GLLSP E EI R KMSV V EVVTADT Y D D - D G -- Y P IEG G LM DP RL GV IEPGLR C K TCG GKVGE C P GHFG HIE L AR PV 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 94 F H I GF F K LTIQL L QCI C KN C SS I L LT P E QHRVFSRQV mnpn LDYLHR ----- KA L HKR IV AACK K GST C S HCG LKN gtvk 168
Cdd:TIGR02390 80 V H V GF A K EIYKI L RAT C RK C GR I T LT E E EIEQYLEKI ---- NKLKEE ggdla ST L IEK IV KEAA K RMK C P HCG EEQ ---- 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 169 kavgav L KI A F AS P VSVD E L GK fatmfssnqe V GD h V R kmkftl L N P LFVQKLFSN I KEG D IPV L MVRS g EEKH P NDLL L 248
Cdd:TIGR02390 152 ------ K KI K F EK P TYFY E E GK ---------- E GD - V K ------ L T P SEIRERLEK I PDE D AEL L GINP - KVAR P EWMV L 207
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 249 T RM PVPPV CI RPS VVS E v KAGTT EDD V T M KL ME I MLT N DV LK KHKRD GAP SKTLFET WE H LQ IQC A L Y INS E MS G L PP - D 327
Cdd:TIGR02390 208 T VL PVPPV TV RPS ITL E - TGERS EDD L T H KL VD I IRI N QR LK ENIEA GAP QLIIEDL WE L LQ YHV A T Y FDN E LP G I PP a R 286
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 328 MQPK R AMRAFT QRLKGK Q GRFRGNL C GKRV D FS G RTVISPDPN LR I DQ VGVP IHV A MT LT F PE I V NAS NI EKM R QL V I NG 407
Cdd:TIGR02390 287 HRSG R PLKTLA QRLKGK E GRFRGNL S GKRV N FS A RTVISPDPN IS I NE VGVP EQI A KE LT V PE R V TPW NI DEL R EY V L NG 366
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 408 S D VH PGANY LV e KKT G NKKLLKYGKRD ELA KN L RM G DTI ERHL D D N D V VLFNRQPSLH KI S I M S H RA KV M PG R TFR F N EC 487
Cdd:TIGR02390 367 P D SW PGANY VI - RPD G RRIKIRDENKE ELA ER L EP G WVV ERHL I D G D I VLFNRQPSLH RM S M M G H KV KV L PG K TFR L N LA 445
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 488 A C T PYNADFDGDEMNLH L PQT Y EA K AEA S ELM N V KNNLI TPR S G E P LVAA I Q D F I T G G YLLTHK D T FLPRA EV YR faaal 567
Cdd:TIGR02390 446 V C P PYNADFDGDEMNLH V PQT E EA R AEA R ELM L V EEHIL TPR Y G G P IIGG I H D Y I S G A YLLTHK S T LFTKE EV QT ----- 520
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 568 I DAS A KKQTKI ri P P PAI RR P V E L WTGKQ LIELII r P D kgs D VSLNLT AK NK S Y -- TGNL E L C SK D S YV I I R N SV LL A G C 645
Cdd:TIGR02390 521 I LGV A GYFGDP -- P E PAI EK P K E Y WTGKQ IFSAFL - P E --- D LNFEGR AK IC S G sd ACKK E E C PH D A YV V I K N GK LL K G V 594
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 646 L DK SLL G SS s K VN I FYMLM R D YG ED AA VDAMWRLA R MAPV F LSN RGF SI GI G D VRPSEQLLR E KGQ L VDNGYSKCSQY I K 725
Cdd:TIGR02390 595 I DK KAI G AE - K GK I LHRIV R E YG PE AA RRFLDSVT R LFIR F ITL RGF TT GI D D IDIPKEAKE E IEE L IEKAEKRVDNL I E 673
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 726 ELEE G K L KAQ PG C T E EETLE SI I LRE L STI RD H AG Q V CLRN L SKY N APLT MA VC G SK GS FI NI S QM I A C VGQQ AIS G H R P 805
Cdd:TIGR02390 674 RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG E V AEKY L DPE N HAVI MA RT G AR GS LL NI T QM A A M VGQQ SVR G G R I 753
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 806 PD G FEE R S LPHF ERKKKTPE A K GFV AN SF YS GL T PTE F FFH TM GGREGLVDTAV K T AET GYMQRRL VKC L E DL CAS YDGT 885
Cdd:TIGR02390 754 RR G YRN R T LPHF KKGDIGAK A R GFV RS SF KK GL D PTE Y FFH AA GGREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE YDGT 833
890 900 910
....*....|....*....|....*....|..
gi 25145495 886 VR SSV G DV I E F VF GEDG L DP am M EAKD G SV VD 917
Cdd:TIGR02390 834 VR DTR G NL I Q F KY GEDG V DP -- M KSDH G KP VD 863
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1034-1374
2.02e-176
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: 526.02
E-value: 2.02e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1034 K VA RA IT EPGTAVGAIAA T SIGEP S TQMTLKTFHFAGVASMNIT Q GVPRIKEIINA V K T ISTPIITA A L LDPY DE SL AR R 1113
Cdd:cd02736 1 K YM RA KV EPGTAVGAIAA Q SIGEP G TQMTLKTFHFAGVASMNIT L GVPRIKEIINA S K N ISTPIITA K L ENDR DE KS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1114 VK A RIEKT T LGE ICD YIEEVY L PDD YFL L V KL NS K R I RL LQL evcmesisyaiatskvcpqmrgckivahgktmmairpp 1193
Cdd:cd02736 81 VK G RIEKT Y LGE VAS YIEEVY S PDD CYI L I KL DK K I I EK LQL -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1194 st SK LSKTMTM Q I LK YS L AN VVV K GIP S V N R C VI HA D E KKG d F Y S LLVEG TDF R S V LSSV GV DPRK T NF N NALV V AD VLG 1273
Cdd:cd02736 123 -- SK SNLYFLL Q S LK RK L PD VVV S GIP E V K R A VI NK D K KKG - K Y K LLVEG YGL R A V MNTP GV IGTR T TS N HIME V EK VLG 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1274 IEAARS C IINEI IA TM DA HG IGL D R RH V MLLAD V MT YR GEVLGITR N G LV KMK D SVL L LASFEKT M DHLF E AA FFSQR D V 1353
Cdd:cd02736 200 IEAARS T IINEI QY TM KS HG MSI D P RH I MLLAD L MT FK GEVLGITR F G IA KMK E SVL M LASFEKT T DHLF N AA LHGRK D S 279
330 340
....*....|....*....|.
gi 25145495 1354 I H GVSECIIMG T PM TV GTG T F 1374
Cdd:cd02736 280 I E GVSECIIMG K PM PI GTG L F 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
244-546
4.31e-151
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 459.29
E-value: 4.31e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 244 NDLL LT RM PVPP V C I RPSV VSEVKA g TT EDD V T MK L ME I MLT N DV LK KHKRD GAPS KTLFETWEH LQ IQCALY I NS E ms G 323
Cdd:smart00663 1 EWMI LT VL PVPP P C L RPSV QLDGGR - FA EDD L T HL L RD I IKR N NR LK RLLEL GAPS IIIRNEKRL LQ EAVDTL I DN E -- G 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 324 LP PDM Q PK - R AMRAFT QRLKGK Q GRFR G NL C GKRVDFS G R T VI S PDPNL RIDQ VGVP IHV A MT LTFPEIV NAS NI E K M R Q 402
Cdd:smart00663 78 LP RAN Q KS g R PLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLNE VGVP KEI A LE LTFPEIV TPL NI D K L R K 157
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 403 LV I NG sdv HP GA N Y LVE kkt G N K KL LK YG K RDEL A KN L RM GD TI ERH LD D N DVVLFNRQP S LH KI SI MS HR AK V MP G R T F 482
Cdd:smart00663 158 LV R NG --- PN GA K Y IIR --- G K K TN LK LA K KSKI A NH L KI GD IV ERH VI D G DVVLFNRQP T LH RM SI QA HR VR V LE G K T I 231
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25145495 483 R F N ECA C T PYNADFDGDEMNLH L PQ TY EA K AEA S ELM N V K NN LIT P RS G E P LVAA IQD FIT G G Y 546
Cdd:smart00663 232 R L N PLV C S PYNADFDGDEMNLH V PQ SL EA R AEA R ELM L V P NN ILS P KN G K P IIGP IQD MLL G L Y 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
14-352
1.32e-124
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: 389.73
E-value: 1.32e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 K VVGVK F APGDC E FM R QTAHVPIFNNKL Y ED ve G K L Q P ANY G P LD PK MG VST K TGT C S TCG LGLT DC V GHFG YFD L DV PV 93
Cdd:pfam04997 3 K IKEIQ F GIASP E EI R KWSVGEVTKPET Y NY -- G S L K P EEG G L LD ER MG TID K DYE C E TCG KKKK DC P GHFG HIE L AK PV 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 94 FHIGFFK L T IQL L Q C I CK N CS SI LL T P EQHRV F SRQVMNPN L DY L hr K ALH K R I VAA CKK GST C S HCG L KNG TVKK avga 173
Cdd:pfam04997 81 FHIGFFK K T LKI L E C V CK Y CS KL LL D P GKPKL F NKDKKRLG L EN L -- K MGA K A I LEL CKK KDL C E HCG G KNG VCGS ---- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 174 vlkiaf AS PVS VD E LG K FATMFSSNQ E VGDH vrkmkf TL LNP LF V Q K L F SN I KEG D IPV L MVRS g EEKH P NDLL LT RM PV 253
Cdd:pfam04997 155 ------ QQ PVS RK E GL K LKAAIKKSK E EEEK ------ EI LNP EK V L K I F KR I SDE D VEI L GFNP - SGSR P EWMI LT VL PV 221
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 254 PP V CIRPSV VSEVK a GTT EDD V T M KL ME I MLT N DV LKK HKRD GAPS KTLF E T W EH LQ IQC A LYINS E MS GLPP DM Q - P KR 332
Cdd:pfam04997 222 PP P CIRPSV QLDGG - RRA EDD L T H KL RD I IKR N NR LKK LLEL GAPS HIIR E E W RL LQ EHV A TLFDN E IP GLPP AL Q k S KR 300
330 340
....*....|....*....|
gi 25145495 333 AMRAFT QRLKGK Q GRFRGNL 352
Cdd:pfam04997 301 PLKSIS QRLKGK E GRFRGNL 320
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
837-1330
4.56e-105
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: 343.95
E-value: 4.56e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 837 GLTP T EFFFHTMGGREGL V DTAVKTAE T GY M QRRLVK C LEDL CAS YD G TVR S S V G DVIE F VF GEDGLDP AMM E AKDGSVV 916
Cdd:pfam04998 1 GLTP Q EFFFHTMGGREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G EIVQ F LY GEDGLDP LKI E KQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 917 D F thvleha KNIQTTKE qp IPV D K LD EV L KAEI qkk F KGK Y VHFADKLSEYITQTEIK K SKK w QNGKAHCGNHETAD L KT 996
Cdd:pfam04998 81 E F ------- SDLKLEDK -- FKN D L LD DL L LLSE --- F SLS Y KKEILVRDSKLGRDRLS K EAQ - ERATLLFELLLKSG L ES 147
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 997 K ESCK icknle AYKTSLL A NS CL tktqlcsfie LCY Y -- KVARAITE PG T AVG A IAA T SIGEP S TQMTL K TFHFAGVAS M 1074
Cdd:pfam04998 148 K RVRS ------ ELTCNSK A FV CL ---------- LCY G rl LYQQSLIN PG E AVG I IAA Q SIGEP G TQMTL N TFHFAGVAS K 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1075 N I T Q GVPR I KEIIN AV K T I ST P II T AA L L D PYDES L ARR -- V KAR IEK T TLG EICDYI E EV Y L PD DY ------------- 1139
Cdd:pfam04998 212 N V T L GVPR L KEIIN VS K N I KS P SL T VY L F D EVGRE L EKA kk V YGA IEK V TLG SVVESG E IL Y D PD PF ntpiisdvkgvvk 291
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1140 ----------------- FL L VK L NSKRIRL L QLEVCMESI S YA I A ------------------ T SKVCPQMRGCKIVAH G 1184
Cdd:pfam04998 292 ffdiidevtneeeidpe TG L LI L VIRLLKI L NKSIKKVVK S EV I P rsirnkvdegrdiaigei T AFIIKISKKIRQDTG G 371
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1185 K ----- TM M AIR P PSTS klsktmtmq ILKYS L A N VVVK GIP SVN R CVI -- HADE K KGDFYS L LV EG TDFRS VL SSV G - VD 1256
Cdd:pfam04998 372 L rrvde LF M EED P KLAI --------- LVASL L G N ITLR GIP GIK R ILV ne DDKG K VEPDWV L ET EG VNLLR VL LVP G f VD 442
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25145495 1257 PRKTNF N NALVVADV LGIEAAR SCII NEI IATMDAH GI GLDR RH VM L L AD V MT YR G EVLG I T R N G LV K MKD S V L 1330
Cdd:pfam04998 443 AGRILS N DIHEILEI LGIEAAR NALL NEI RNVYRFQ GI YIND RH LE L I AD Q MT RK G YIMA I G R H G IN K AEL S A L 516
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1019-1383
1.75e-91
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 301.38
E-value: 1.75e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1019 LT KTQLCSF IE LCYYKVA R AIT EPG T AVG AI AA T SIGEP S TQMT LK TFH F AGVA SM N I T Q G V PR IK EI IN A V K TI STP II 1098
Cdd:PRK04309 35 LT EEEVEEI IE EVVREYL R SLV EPG E AVG VV AA Q SIGEP G TQMT MR TFH Y AGVA EI N V T L G L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1099 T AA L L D P Y -- D ESL A RR V KAR IE K TTL GEICDY I E ev YLPDDYFLLVK L NSKR ir L LQLEVCMESISY AI ATS K vcpqmr 1176
Cdd:PRK04309 115 T IY L K D E Y ay D REK A EE V ARK IE A TTL ENLAKD I S -- VDLANMTIIIE L DEEM -- L EDRGLTVDDVKE AI EKK K ------ 184
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1177 G CKIVAH G K T M - MAIRP PS TSK L S K tmtmqi L KYSLA N VVV KGI PSVN R CV I had E K K GD F Y SLLV EG TDFRS VL SSV GV 1255
Cdd:PRK04309 185 G GEVEIE G N T L i ISPKE PS YRE L R K ------ L AEKIR N IKI KGI KGIK R VI I --- R K E GD E Y VIYT EG SNLKE VL KVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1256 D PRK T NF NN ALVVAD VLGIEAAR SC II N EI IA T MDAH G IGL D R RH V ML L AD V MT YR GEV LG I T R N G LVKM K D SVL LL A S F 1335
Cdd:PRK04309 256 D ATR T TT NN IHEIEE VLGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML V AD M MT WD GEV RQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 25145495 1336 E K T MD HL FE AA FFSQR D VIH GV S E C II M G T P MTV GTG TFK L MQKYDKK 1383
Cdd:PRK04309 336 E V T VK HL LD AA VRGEV D ELK GV T E N II V G Q P IPL GTG DVE L TMDPPLR 383
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1037-1376
2.47e-84
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: 280.79
E-value: 2.47e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1037 R AITE PG T AVG AI AA T SIGEP S TQMT LK TFH F AGVA SM N I T Q G V PR IK EI IN A V KT I STP II T AA L L D P Y -- D ESL A RR V 1114
Cdd:TIGR02389 38 R SLID PG E AVG IV AA Q SIGEP G TQMT MR TFH Y AGVA EL N V T L G L PR LI EI VD A R KT P STP SM T IY L E D E Y ek D REK A EE V 117
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1115 KAR IE K T T L GEICDY I EEVYL pd D YFLLVK L NSKRI -- R LLQLEVCMES I SY A IATSKVCPQ M RGCK I VAHGKT mmairp 1192
Cdd:TIGR02389 118 AKK IE A T K L EDVAKD I SIDLA -- D MTVIIE L DEEQL ke R GITVDDVEKA I KK A KLGKVIEID M DNNT I TIKPGN ------ 189
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1193 PS TSK L S K tmtmqi LK YSLA N VVV KGI PSVN R C VI had E K K GD F Y SLLV EG TDFRS VL SSV GVD PRK T NF N NALVV A D VL 1272
Cdd:TIGR02389 190 PS LKE L R K ------ LK EKIK N LHI KGI KGIK R V VI --- R K E GD E Y VIYT EG SNLKE VL KLE GVD KTR T TT N DIHEI A E VL 260
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1273 GIEAAR SC II N EI IA T MDAH G IGL D R RH V ML L AD V MT YR GEV LG I T R N G LVKM K D SVL LL A S FE K T MD HL FE AA FFSQR D 1352
Cdd:TIGR02389 261 GIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML V AD L MT WD GEV RQ I G R H G ISGE K A SVL AR A A FE V T VK HL LD AA IRGEV D 340
330 340
....*....|....*....|....
gi 25145495 1353 VIH GV S E C II M G T P MTV GTG TFK L 1376
Cdd:TIGR02389 341 ELK GV I E N II V G Q P IPL GTG DVD L 364
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
331-1073
9.36e-56
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: 212.71
E-value: 9.36e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 331 KR AMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P E I vnasniek M R Q L VIN G - SD 409
Cdd:COG0086 311 KR PLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KKM A LE L FK P F I -------- Y R K L EER G l AT 382
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 410 VHPG A NYL VE KK tgnkkllkygk RD E LAKN L R mg DT I ER H lddnd V VL F NR Q P S LH KIS I MSHRAKVMP G RTFRFNECA C 489
Cdd:COG0086 383 TIKS A KKM VE RE ----------- EP E VWDI L E -- EV I KE H ----- P VL L NR A P T LH RLG I QAFEPVLIE G KAIQLHPLV C 444
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 490 T PY NADFDGD E M NL H L P QTY EA KA EA SE LM NVK NN LIT P RS G E P LVAAI QD FIT G G Y L LT HKDTFLPR -------- A EV Y 561
Cdd:COG0086 445 T AF NADFDGD Q M AV H V P LSL EA QL EA RL LM LST NN ILS P AN G K P IIVPS QD MVL G L Y Y LT REREGAKG egmifadp E EV L 524
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 562 R - FAAALI D AS A KKQTK I RIPPPAIRRP VE LWT G KQ L IEL I IR pdkgsdvslnlta KNKSYT g N LELCS K DSY VIIR NSV 640
Cdd:COG0086 525 R a YENGAV D LH A RIKVR I TEDGEQVGKI VE TTV G RY L VNE I LP ------------- QEVPFY - N QVINK K HIE VIIR QMY 590
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 641 LLA G CLDKS llgssskvn IF YMLMRDY G EDA A VD A mwrlarmapvflsnr G F SIG IG D V rpse QLLR EK GQLVDNGYSKC 720
Cdd:COG0086 591 RRC G LKETV --------- IF LDRLKKL G FKY A TR A --------------- G I SIG LD D M ---- VVPK EK QEIFEEANKEV 642
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 721 SQYI K ELE EG KL kaqpgc TE E E TLESI I L r ELSTIRDHAGQVCLRNL S KY N APLT MA VC G SK GS FINIS Q MIACV G QQ A i 800
Cdd:COG0086 643 KEIE K QYA EG LI ------ TE P E RYNKV I D - GWTKASLETESFLMAAF S SQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A - 714
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 801 sghr P P D G -- F E erslphferkkk TP eakgf VANS F YS GL TPT E F F FH T M G G R E GL V DTA V KTA ET GY MQ RRLV KCLE D L 878
Cdd:COG0086 715 ---- K P S G ni I E ------------ TP ----- IGSN F RE GL GVL E Y F IS T H G A R K GL A DTA L KTA DS GY LT RRLV DVAQ D V 773
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 879 ------ C ASYD G TVRSSV --- G D VIE FVF gedgldpamm E AKD G S V vdfth VL E HAKNIQ T TKEQPIPVDKL DE VLKAE I 949
Cdd:COG0086 774 ivteed C GTDR G ITVTAI keg G E VIE PLK ---------- E RIL G R V ----- AA E DVVDPG T GEVLVPAGTLI DE EVAEI I 838
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 950 Q kkfkgkyvhfadklseyitqteikkskkwqngkahcgnh E TADLKT K ESCKIC knleayktsllans C L T KTQL C S fie 1029
Cdd:COG0086 839 E --------------------------------------- E AGIDSV K VRSVLT -------------- C E T RGGV C A --- 862
730 740 750 760
....*....|....*....|....*....|....*....|....*.
gi 25145495 1030 L CY YK -- VARAITEP G T AVG A IAA T SIGEP S TQ M T LK TFH FA G V AS 1073
Cdd:COG0086 863 K CY GR dl ARGHLVNI G E AVG V IAA Q SIGEP G TQ L T MR TFH IG G A AS 908
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
837-1080
2.90e-11
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 68.43
E-value: 2.90e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 837 GL TP TE FFFHTM G G R E G L VDTAV K TA ET GY MQ RRLV KCLEDL ------ C asyd GT V R S ----- SV G DV IE FVF g EDG L D p 905
Cdd:CHL00117 172 GL SL TE YIISCY G A R K G V VDTAV R TA DA GY LT RRLV EVVQHI vvretd C ---- GT T R G isvsp RN G MM IE RIL - IQT L I - 245
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 906 ammeakd G S V V dfthvleh A KN I QTTKE ------ Q P I PVDKLDEVLKAEI Q KKF kgkyvhfadklseyitqte I K ----- 974
Cdd:CHL00117 246 ------- G R V L -------- A DD I YIGSR ciatrn Q D I GIGLANRFITFRA Q PIS ------------------- I R spltc 291
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 975 K S KK W qngkahcgnhetadlktkesck IC knleayktsllanscltkt QLC -------- SFI EL cyykvaraitep G T AV 1046
Cdd:CHL00117 292 R S TS W ---------------------- IC ------------------- QLC ygwslahg DLV EL ------------ G E AV 318
250 260 270
....*....|....*....|....*....|....
gi 25145495 1047 G A IA AT SIGEP S TQ M TL K TFH FA GV ASMNITQG V 1080
Cdd:CHL00117 319 G I IA GQ SIGEP G TQ L TL R TFH TG GV FTGGTAEQ V 352
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
26-887
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: 1523.24
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 26 E FMRQTAH V PIF N NK LY EDVEG K lq P AN YG P LDP KM G V S T K T G T C S TCGL G L T DCVGHFGY FD L DV PVFHIG F FK LT I QL 105
Cdd:cd02583 4 E DIIRLSE V EVT N RN LY DIETR K -- P LP YG V LDP RL G T S D K D G I C E TCGL N L A DCVGHFGY IK L EL PVFHIG Y FK AI I NI 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 106 LQCICK N CS SI LL TP E QH R V F SRQVMN PNLD Y L HR KAL H K R I VAA CKK GST C S HCGL kngt V KKA vgavlkiafaspvsv 185
Cdd:cd02583 82 LQCICK T CS RV LL PE E EK R K F LKRLRR PNLD N L QK KAL K K K I LEK CKK VRK C P HCGL ---- L KKA --------------- 142
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 186 delgkfatmfssn QE V gdhvrkmkftl LNPL F V QK LF S NI KEG D IPV L MVRS g EEKH P ND L L LTR M PVPP V CIRPSVV SE 265
Cdd:cd02583 143 ------------- QE D ----------- LNPL K V LN LF K NI PPE D VEL L LMNP - LAGR P EN L I LTR I PVPP L CIRPSVV MD 197
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 266 V K A GT T EDD V T M KL M EI MLT NDV L KKH KRD GA PSKTLF E T W EH LQ I QCALYINSE MS GLP PD MQPK RAM R A F T QRLKGKQ 345
Cdd:cd02583 198 E K S GT N EDD L T V KL S EI IFL NDV I KKH LEK GA KTQKIM E D W DF LQ L QCALYINSE LP GLP LS MQPK KPI R G F C QRLKGKQ 277
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 346 GRFRGNL C GKRVDFSGRTVISPDPNLRIDQVGVP I HVA MT LT F PE I V NAS NIEK M R Q LV I NG S DVHPGAN YLVEKKT G N K 425
Cdd:cd02583 278 GRFRGNL S GKRVDFSGRTVISPDPNLRIDQVGVP E HVA KI LT Y PE R V TRY NIEK L R K LV L NG P DVHPGAN FVIKRDG G K K 357
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 426 K L LKYG K R DEL A KN L RM GD TI ERHL D D N D V VLFNRQPSLH KI SIM S HRAKVMP G RTFRFNEC A CTPYNADFDGDEMNLH L 505
Cdd:cd02583 358 K F LKYG N R RKI A RE L KI GD IV ERHL E D G D I VLFNRQPSLH RL SIM A HRAKVMP W RTFRFNEC V CTPYNADFDGDEMNLH V 437
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 506 PQT Y EA K AEA S ELM N VKNNL I TPR S GEPL V AA I QDF I T GG YLLT H KD T F LP RA EVYRFAAALI D AS akkq T KI RI PPPAI 585
Cdd:cd02583 438 PQT E EA R AEA L ELM G VKNNL V TPR N GEPL I AA T QDF L T AS YLLT S KD V F FD RA QFCQLCSYML D GE ---- I KI DL PPPAI 513
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 586 RR PVELWTGKQ LIE L II RP D K G S D V SL NL T AK N KSYT - GNLEL C SK D S YV I IRNS V LL A G C LDKS L LGS S SK VNI FY M L M 664
Cdd:cd02583 514 LK PVELWTGKQ IFS L LL RP N K K S P V LV NL E AK E KSYT k KSPDM C PN D G YV V IRNS E LL C G R LDKS T LGS G SK NSL FY V L L 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 665 RDYG ED AA VD AM W RLA RMAPVF LSNRGFSIGI G DV R PS EQ LL RE K GQ LVDNGY S KC SQ YIK ELEE GKL KA QPGCT E E E TL 744
Cdd:cd02583 594 RDYG PE AA AA AM N RLA KLSSRW LSNRGFSIGI D DV T PS KE LL KK K EE LVDNGY A KC DE YIK QYKK GKL EL QPGCT A E Q TL 673
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 745 E SI I LR ELS T IR DH AG QV CL RN L S K Y N A PL T MA V CGSKGS F INISQMIACVGQQ A ISG H R P P D GFE E R S LPHF E R KK KTP 824
Cdd:cd02583 674 E AK I SG ELS K IR ED AG KA CL KE L H K S N S PL I MA L CGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF P R NS KTP 753
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 25145495 825 E AKGFVANSFYSGLTPTEFFFHTM G GREGLVDTAVKTAETGYMQRRL V K C LEDL CAS YDGTVR 887
Cdd:cd02583 754 A AKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SVQ YDGTVR 816
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
14-907
0e+00
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain]
Cd Length: 861
Bit Score: 925.88
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 KVV G V KF APGDC E FM R QTAH V P I FNNKL Y ED ---- V EG klqpany G PL DP KM GV STKTGT C S TCG LGLTD C V GHFG YFD L 89
Cdd:cd02582 3 RIK G I KF GLLSP E EI R KMSV V E I ITPDT Y DE dgyp I EG ------- G LM DP RL GV IEPGLR C K TCG NTAGE C P GHFG HIE L 75
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 90 DV PV F H I GF F K LTIQ LL QCI C KN C SS ILL TP E QHRVFSRQVMN - PNLDYLHR K ALHKRIVAAC KK GST C S HCG LK ngtvk 168
Cdd:cd02582 76 AR PV I H V GF A K HIYD LL RAT C RS C GR ILL PE E EIEKYLERIRR l KEKWPELV K RVIEKVKKKA KK RKV C P HCG AP ----- 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 169 kavga VL KI AFAS P VSVD E LGK fatmfssnqev GDH V R kmkftl L N P LFVQKLFSN I KEG D IPV L MVRS g EEKH P NDLL L 248
Cdd:cd02582 151 ----- QY KI KLEK P TTFY E EKE ----------- EGE V K ------ L T P SEIRERLEK I PDE D LEL L GIDP - KTAR P EWMV L 207
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 249 T RM PVPPV CI RPS VVS E vk A G - TT EDD V T M KL ME I MLT N DV LK KHKRD GAP SKTLFET W EH LQ IQCAL Y INS E MS G L PP - 326
Cdd:cd02582 208 T VL PVPPV TV RPS ITL E -- T G e RS EDD L T H KL VD I IRI N QR LK ENIEA GAP QLIIEDL W DL LQ YHVTT Y FDN E IP G I PP a 285
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 327 DMQPK R AMRAFT QRLKGK Q GRFRGNL C GKRV D FS G RTVISPDPNL R I DQ VGVP IHV A MT LT F PE I V NAS NIEKMR Q LV I N 406
Cdd:cd02582 286 RHRSG R PLKTLA QRLKGK E GRFRGNL S GKRV N FS A RTVISPDPNL S I NE VGVP EDI A KE LT V PE R V TEW NIEKMR K LV L N 365
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 407 G S D VH PGANY LV e KKT G NKKL L K Y GK R D ELA KN L RM G DTI ERHL D D N D V VLFNRQPSLH KI SIM S HR AK V M PG R TFR F N E 486
Cdd:cd02582 366 G P D KW PGANY VI - RPD G RRIR L R Y VN R E ELA ER L EP G WIV ERHL I D G D I VLFNRQPSLH RM SIM A HR VR V L PG K TFR L N L 444
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 487 CA C T PYNADFDGDEMNLH L PQ TY EA K AEA S ELM N V KNNLIT PR S G E P LVAA IQD F I T G G YLLT H K D T FLPRA E VYRFAA A 566
Cdd:cd02582 445 AV C P PYNADFDGDEMNLH V PQ SE EA R AEA R ELM L V QEHILS PR Y G G P IIGG IQD Y I S G A YLLT R K T T LFTKE E ALQLLS A 524
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 567 lidas A KKQTKI ri P P PAI RR P VE LWTGKQL IE L II r P D kgsdv S LN LTA K N K SYT G NL ---- E L C SK D S YV I I R N SV LL 642
Cdd:cd02582 525 ----- A GYDGLL -- P E PAI LE P KP LWTGKQL FS L FL - P K ----- D LN FEG K A K VCS G CS eckd E D C PN D G YV V I K N GK LL 591
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 643 A G CL DK SLL G SSSKVNIFYMLMRD YG EDA A VDAMWRLA R M A PV F LSN RGF S IGI G D VRPS E QLLR E KGQLVDNGYS K CSQ 722
Cdd:cd02582 592 E G VI DK KAI G AEQPGSLLHRIAKE YG NEV A RRFLDSVT R L A IR F IEL RGF T IGI D D EDIP E EARK E IEEIIKEAEK K VYE 671
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 723 Y I KELEE G K L KAQ PG C T E EETLE SI I LRE L STI RD H AG Q V CLRN L SKY N APLT MA VC G SK GS FI N IS QM I AC V GQQ AIS G 802
Cdd:cd02582 672 L I EQYKN G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG K V ASKY L DPF N NAVI MA RT G AR GS ML N LT QM A AC L GQQ SVR G 751
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 803 H R PPD G FEE R S LPHF ERKKKT PEA K GFV AN SF YS GL T PTEFFFH T MGGREGLVDTAV K T AET GYMQRRL VKC L E DL CAS Y 882
Cdd:cd02582 752 E R INR G YRN R T LPHF KPGDLG PEA R GFV RS SF RD GL S PTEFFFH A MGGREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE Y 831
890 900
....*....|....*....|....*
gi 25145495 883 DGTVR S S V G DV I E F VF GEDG L DPA M 907
Cdd:cd02582 832 DGTVR D S R G NI I Q F KY GEDG V DPA K 856
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
14-923
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 906.54
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 K VV G - V KF APGDC E FM R QTAHVP I FNNKL Y E D ---- VE G klqpany G PL DP KM GV STKTGT C S TCG LGLTD C V GHFG YFD 88
Cdd:PRK08566 7 K RI G s I KF GLLSP E EI R KMSVTK I ITADT Y D D dgyp ID G ------- G LM DP RL GV IDPGLR C K TCG GRAGE C P GHFG HIE 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 89 L DV PV F H I GF F KL TIQ LL QCI C KN C SSIL LT P E QHRVFSRQVMNPNLDYLHRKA L H K RIVAACK K GST C S HCG L K N gtvk 168
Cdd:PRK08566 80 L AR PV I H V GF A KL IYK LL RAT C RE C GRLK LT E E EIEEYLEKLERLKEWGSLADD L I K EVKKEAA K RMV C P HCG E K Q ---- 155
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 169 kavgav L KI A F AS P vsvdelgkfa T M F SSNQEV G DH vrkm K ftl L N P LFVQKLFSN I KEG D IPV L MVRS g E EKH P NDLL L 248
Cdd:PRK08566 156 ------ Y KI K F EK P ---------- T T F YEERKE G LV ---- K --- L T P SDIRERLEK I PDE D LEL L GINP - E VAR P EWMV L 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 249 T RM PVPPV CI RPS VVS E vk A G - TT EDD V T M KL ME I MLT N DV LK KHKRD GAP SKTLFET WE H LQ IQCAL Y INS E MS G L PP - 326
Cdd:PRK08566 212 T VL PVPPV TV RPS ITL E -- T G q RS EDD L T H KL VD I IRI N QR LK ENIEA GAP QLIIEDL WE L LQ YHVTT Y FDN E IP G I PP a 289
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 327 DMQPK R AMRAFT QRLKGK Q GRFRGNL C GKRV D FS G RTVISPDPNL R I DQ VGVP IHV A MT LT F PE I V NAS NIE KM R QL V I N 406
Cdd:PRK08566 290 RHRSG R PLKTLA QRLKGK E GRFRGNL S GKRV N FS A RTVISPDPNL S I NE VGVP EAI A KE LT V PE R V TEW NIE EL R EY V L N 369
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 407 G SDV HPGANY LV e KKT G NKKL L KYGKRD ELA KN L RM G DTI ERHL D D N D V VLFNRQPSLH KI SIM S HR AK V M PG R TFR F N E 486
Cdd:PRK08566 370 G PEK HPGANY VI - RPD G RRIK L TDKNKE ELA EK L EP G WIV ERHL I D G D I VLFNRQPSLH RM SIM A HR VR V L PG K TFR L N L 448
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 487 CA C T PYNADFDGDEMNLH L PQT Y EA K AEA SE LM N V KNNLIT PR S G E P LVAA IQD F I T G G YLLT H K D T FLPRA E VYR faaa 566
Cdd:PRK08566 449 AV C P PYNADFDGDEMNLH V PQT E EA R AEA RI LM L V QEHILS PR Y G G P IIGG IQD H I S G A YLLT R K S T LFTKE E ALD ---- 524
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 567 L ID A S ak KQTKIRI P P PAI RRPVEL WTGKQ LIE L II r P D kgs D VS L NLT AK N -- KSYTGNL E L C SK D S YV I I R N SV LL A G 644
Cdd:PRK08566 525 L LR A A -- GIDELPE P E PAI ENGKPY WTGKQ IFS L FL - P K --- D LN L EFK AK I cs GCDECKK E D C EH D A YV V I K N GK LL E G 598
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 645 CL DK SLL G SSSK v N I FYMLMRD YG EDA A VDAMWRLA R M A PV F LSN RGF SI GI G D VRPS E QLLR E KGQLVDNGYSKCSQY I 724
Cdd:PRK08566 599 VI DK KAI G AEQG - S I LDRIVKE YG PER A RRFLDSVT R L A IR F IML RGF TT GI D D EDIP E EAKE E IDEIIEEAEKRVEEL I 677
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 725 KEL E E G K L KAQ PG C T E EETLE SI I LRE L STI RD H AG QVCLRN L SKY N APLT MA VC G SK GS FI N IS QM I ACVGQQ AIS G H R 804
Cdd:PRK08566 678 EAY E N G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG EIAEKY L GLD N PAVI MA RT G AR GS ML N LT QM A ACVGQQ SVR G E R 757
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 805 PPD G FEE R S LPHF ERKKKTP EA K GFV AN S FY SGLTPTEFFFH T MGGREGLVDTAV K T AET GYMQRRL VKC L E DL CAS YDG 884
Cdd:PRK08566 758 IRR G YRD R T LPHF KPGDLGA EA R GFV RS S YK SGLTPTEFFFH A MGGREGLVDTAV R T SQS GYMQRRL INA L Q DL KVE YDG 837
890 900 910
....*....|....*....|....*....|....*....
gi 25145495 885 TVR SSV G DVIE F VF GEDG L DP am M EAKD G SV VD FTHVL E 923
Cdd:PRK08566 838 TVR DTR G NIVQ F KY GEDG V DP -- M KSDH G KP VD VDRII E 874
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
51-1384
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 887.45
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 51 P ANY G P LD PKM G VSTKTGT C S TCG LGLTD C V GHFG YFD L DV PV F HI G F FKLTIQ LL QCI C KN C SSIL L TP E Q -------- 122
Cdd:PRK14977 42 P VQG G L LD GRL G TIEPGQK C L TCG NLAAN C P GHFG HIE L AE PV I HI A F IDNIKD LL NST C HK C AKLK L PQ E D lnvfklie 121
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 123 ----- H R VFSRQVMN pnl D YLHRKALHKRI V A A c KK GST C S HCG lkngtvkkav GAVLKIA F AS P vsvdelgkfa T M F SS 197
Cdd:PRK14977 122 eahaa A R DIPEKRID --- D EIIEEVRDQVK V Y A - KK AKE C P HCG ---------- APQHELE F EE P ---------- T I F IE 177
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 198 NQ E VGD H vrkmkft L L N P LFVQKL F SN I KEG D I p V L MVRSGEEKH P NDLL L TRMP VPP VCI RPS VVS E VKA g TT EDD V T M 277
Cdd:PRK14977 178 KT E IEE H ------- R L L P IEIRDI F EK I IDD D L - E L IGFDPKKAR P EWAV L QAFL VPP LTA RPS IIL E TGE - RS EDD L T H 248
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 278 K L ME I MLT N DV LK KH K RD GAP SKTLFETWE HLQ IQCALYINSEMS G L P PDMQ -- PK R AMRAFT QRLKGK Q GRFRGNL C GK 355
Cdd:PRK14977 249 I L VD I IKA N QK LK ES K DA GAP PLIVEDEVD HLQ YHTSTFFDNATA G I P QAHH kg SG R PLKSLF QRLKGK E GRFRGNL I GK 328
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 356 RVDFS G RTVISPDP NLR ID Q VGVP IHV AM T LT F PEIVN AS NIEKM RQ LVING S D VH PGAN YLV e K KT G N K KL L KYGKR -- 433
Cdd:PRK14977 329 RVDFS A RTVISPDP MID ID E VGVP EAI AM K LT I PEIVN EN NIEKM KE LVING P D EF PGAN AIR - K GD G T K IR L DFLED kg 407
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 434 ---- D E L A KN L RM GD TI ERHL D D N D V V L FNRQPSLHK I SI MS HR A KV M PG R TFR FNECA C T PYNADFDGDEMNLH L PQ TY 509
Cdd:PRK14977 408 kdal R E A A EQ L EI GD IV ERHL A D G D I V I FNRQPSLHK L SI LA HR V KV L PG A TFR LHPAV C P PYNADFDGDEMNLH V PQ IE 487
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 510 E A K AEA S ELM N VK N NLI T PR S G E P LVA A I QDFIT GG YL L T HK D TFLPRA E VYRF A -- A ALI D A sakkqtkir I P P PAI R - 586
Cdd:PRK14977 488 D A R AEA I ELM G VK D NLI S PR T G G P IIG A L QDFIT AA YL I T KD D ALFDKN E ASNI A ml A GIT D P --------- L P E PAI K t 558
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 587 RPVEL WTGKQL IE L IIRP D KGSDVSLNLT A KNKSYTGNLE l C SK D S YV I I RNSV L LA G CL D KSLL G SSSK -- VNIFYMLM 664
Cdd:PRK14977 559 KDGPA WTGKQL FS L FLPK D FNFEGIAKWS A GKAGEAKDPS - C LG D G YV L I KEGE L IS G VI D DNII G ALVE ep ESLIDRIA 637
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 665 R DYGE DA A VDAMWRLARM A PVFLSNR GFS I G I GD VRPSEQLLR E KGQLVDNGYSKC S QY I KE -------- LEE GK LKAQP 736
Cdd:PRK14977 638 K DYGE AV A IEFLNKILII A KKEILHY GFS N G P GD LIIPDEAKQ E IEDDIQGMKDEV S DL I DQ rkitrkit IYK GK EELLR 717
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 737 G CT EEE T LE SI I LR EL STI RD H AG QVCLRNLSKY NA PLT MA VC G SK GS FI N IS Q MIACV GQQ AI -------- S G H R PPD G 808
Cdd:PRK14977 718 G MK EEE A LE AD I VN EL DKA RD K AG SSANDCIDAD NA GKI MA KT G AR GS MA N LA Q IAGAL GQQ KR ktrigfvl T G G R LHE G 797
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 809 FEE R S L P HF ERKKKT P E A K GFV A N SFYS GL TPT EFFFH T MGGREGL V D T A VK T AET GY M QRRL VKC LED LCAS YD G TVR S 888
Cdd:PRK14977 798 YKD R A L S HF QEGDDN P D A H GFV K N NYRE GL NAA EFFFH A MGGREGL I D K A RR T EDS GY F QRRL ANA LED IRLE YD E TVR D 877
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 889 SV G DV I E F V FGEDG L DP AMME ak D G SVVDFTHVL E HA K NIQTT K E qp IPV D KLD E VL K aeiq KKF K GKYVHFADK L SEY I 968
Cdd:PRK14977 878 PH G HI I Q F K FGEDG I DP QKLD -- H G EAFNLERII E KQ K IEDRG K G -- ASK D EIE E LA K ---- EYT K TFNANLPKL L ADA I 949
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 969 TQT E I K KS kkwqngkahcgnhetadl KTKES C K ic KNL E AYK tsllanscltktqlcsfielcyykva R A IT EPG T A V G A 1048
Cdd:PRK14977 950 HGA E L K ED ------------------ ELEAI C A -- EGK E GFE -------------------------- K A KV EPG Q A I G I 983
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1049 I A A T SI G EP S TQMTL K TFH F AG VAS M NI T Q G VP R IK E IIN A VKTI STP IITAA L L D PYD E SLARRVK - AR IE K TT lg EIC 1127
Cdd:PRK14977 984 I S A Q SI A EP G TQMTL R TFH A AG IKA M DV T H G LE R FI E LVD A RAKP STP TMDIY L D D ECK E DIEKAIE i AR NL K EL -- KVR 1061
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1128 DY I EEVYL pd D YFLLV KL NSKRI R L L QLE - VC ME SISYAI - A TS K vcp QMRG c KIVAHGKTMMAIRPPSTSKLSKTM T MQ 1205
Cdd:PRK14977 1062 AL I ADSAI -- D NANEI KL IKPDK R A L ENG c IP ME RFAEIE a A LA K --- GKKF - EMELEDDLIILDLVEAADRDKPLA T LI 1135
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1206 ILKYSLANVV VKG I P SVN R CVIHAD EK K G - D FYSLLVE G TDFRS VL SSVGV D PRK T NF N NALVV A DV LGIEAAR SC I I NE 1284
Cdd:PRK14977 1136 AIRNKILDKP VKG V P DIE R AWVELV EK D G r D EWIIQTS G SNLAA VL EMKCI D IAN T IT N DCFEI A GT LGIEAAR NA I F NE 1215
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1285 IIATMDAH G IGL D R R HV ML L AD V M TY RG EVLG I ------ T R N G LVKM KDS V L LL A S FE K T MDHLFE AA FFSQRDV I H G VS 1358
Cdd:PRK14977 1216 LASILEDQ G LEV D N R YI ML V AD I M CS RG TIEA I glqaag V R H G FAGE KDS P L AK A A FE I T THTIAH AA LGGEIEK I K G IL 1295
1370 1380
....*....|....*....|....*.
gi 25145495 1359 ECI IMG TPMTV G T G TFK L MQKYDK KA 1384
Cdd:PRK14977 1296 DAL IMG QNIPI G S G KVD L LMDFSG KA 1321
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
14-917
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: 859.02
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 K VVGV KF APGDC E FM R QTAH V PIFNNKL Y E D v E G kl Q P ANY G PL DP KM GV STKTGT C S TCG LGLTD C V GHFG YFD L DV PV 93
Cdd:TIGR02390 3 K IGSI KF GLLSP E EI R KMSV V EVVTADT Y D D - D G -- Y P IEG G LM DP RL GV IEPGLR C K TCG GKVGE C P GHFG HIE L AR PV 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 94 F H I GF F K LTIQL L QCI C KN C SS I L LT P E QHRVFSRQV mnpn LDYLHR ----- KA L HKR IV AACK K GST C S HCG LKN gtvk 168
Cdd:TIGR02390 80 V H V GF A K EIYKI L RAT C RK C GR I T LT E E EIEQYLEKI ---- NKLKEE ggdla ST L IEK IV KEAA K RMK C P HCG EEQ ---- 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 169 kavgav L KI A F AS P VSVD E L GK fatmfssnqe V GD h V R kmkftl L N P LFVQKLFSN I KEG D IPV L MVRS g EEKH P NDLL L 248
Cdd:TIGR02390 152 ------ K KI K F EK P TYFY E E GK ---------- E GD - V K ------ L T P SEIRERLEK I PDE D AEL L GINP - KVAR P EWMV L 207
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 249 T RM PVPPV CI RPS VVS E v KAGTT EDD V T M KL ME I MLT N DV LK KHKRD GAP SKTLFET WE H LQ IQC A L Y INS E MS G L PP - D 327
Cdd:TIGR02390 208 T VL PVPPV TV RPS ITL E - TGERS EDD L T H KL VD I IRI N QR LK ENIEA GAP QLIIEDL WE L LQ YHV A T Y FDN E LP G I PP a R 286
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 328 MQPK R AMRAFT QRLKGK Q GRFRGNL C GKRV D FS G RTVISPDPN LR I DQ VGVP IHV A MT LT F PE I V NAS NI EKM R QL V I NG 407
Cdd:TIGR02390 287 HRSG R PLKTLA QRLKGK E GRFRGNL S GKRV N FS A RTVISPDPN IS I NE VGVP EQI A KE LT V PE R V TPW NI DEL R EY V L NG 366
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 408 S D VH PGANY LV e KKT G NKKLLKYGKRD ELA KN L RM G DTI ERHL D D N D V VLFNRQPSLH KI S I M S H RA KV M PG R TFR F N EC 487
Cdd:TIGR02390 367 P D SW PGANY VI - RPD G RRIKIRDENKE ELA ER L EP G WVV ERHL I D G D I VLFNRQPSLH RM S M M G H KV KV L PG K TFR L N LA 445
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 488 A C T PYNADFDGDEMNLH L PQT Y EA K AEA S ELM N V KNNLI TPR S G E P LVAA I Q D F I T G G YLLTHK D T FLPRA EV YR faaal 567
Cdd:TIGR02390 446 V C P PYNADFDGDEMNLH V PQT E EA R AEA R ELM L V EEHIL TPR Y G G P IIGG I H D Y I S G A YLLTHK S T LFTKE EV QT ----- 520
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 568 I DAS A KKQTKI ri P P PAI RR P V E L WTGKQ LIELII r P D kgs D VSLNLT AK NK S Y -- TGNL E L C SK D S YV I I R N SV LL A G C 645
Cdd:TIGR02390 521 I LGV A GYFGDP -- P E PAI EK P K E Y WTGKQ IFSAFL - P E --- D LNFEGR AK IC S G sd ACKK E E C PH D A YV V I K N GK LL K G V 594
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 646 L DK SLL G SS s K VN I FYMLM R D YG ED AA VDAMWRLA R MAPV F LSN RGF SI GI G D VRPSEQLLR E KGQ L VDNGYSKCSQY I K 725
Cdd:TIGR02390 595 I DK KAI G AE - K GK I LHRIV R E YG PE AA RRFLDSVT R LFIR F ITL RGF TT GI D D IDIPKEAKE E IEE L IEKAEKRVDNL I E 673
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 726 ELEE G K L KAQ PG C T E EETLE SI I LRE L STI RD H AG Q V CLRN L SKY N APLT MA VC G SK GS FI NI S QM I A C VGQQ AIS G H R P 805
Cdd:TIGR02390 674 RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG E V AEKY L DPE N HAVI MA RT G AR GS LL NI T QM A A M VGQQ SVR G G R I 753
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 806 PD G FEE R S LPHF ERKKKTPE A K GFV AN SF YS GL T PTE F FFH TM GGREGLVDTAV K T AET GYMQRRL VKC L E DL CAS YDGT 885
Cdd:TIGR02390 754 RR G YRN R T LPHF KKGDIGAK A R GFV RS SF KK GL D PTE Y FFH AA GGREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE YDGT 833
890 900 910
....*....|....*....|....*....|..
gi 25145495 886 VR SSV G DV I E F VF GEDG L DP am M EAKD G SV VD 917
Cdd:TIGR02390 834 VR DTR G NL I Q F KY GEDG V DP -- M KSDH G KP VD 863
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
43-883
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: 835.65
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 43 E DV E GKLQ P ANY G PL DP K MG VSTKTGT C S TCG LGLTD C V GHFG YFD L DV PVFHIGF FKLTIQL L Q C I CK ncss IL L TP E Q 122
Cdd:cd02733 25 E TY E NGGG P KLG G LN DP R MG TIDRNSR C Q TCG GDMKE C P GHFG HIE L AK PVFHIGF LTKILKI L R C V CK ---- RE L SA E R 100
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 123 - HRV F srqvmnpnldylhrkalh KRI vaackkgstcshcglkngtvkkavgavlkiafaspv S VDEL gkfatmfssnqev 201
Cdd:cd02733 101 v LEI F ------------------ KRI ------------------------------------ S DEDC ------------- 113
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 202 gdhv R KMK F tll N P L F vqklfsnikegdipvlmvrsgee KH P NDLL LT RM PVPP VCI RPSVV SE vka G TT -- EDD V T M KL 279
Cdd:cd02733 114 ---- R ILG F --- D P K F ----------------------- SR P DWMI LT VL PVPP PAV RPSVV MD --- G SA rs EDD L T H KL 160
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 280 ME I MLT N DV LK KHKRD GAP SKTLF E TWEH LQ IQC A L Y INS E MS GLP PDM Q PK - R AMRAFT QRLKGK Q GR F RGNL C GKRVD 358
Cdd:cd02733 161 AD I IKA N NQ LK RQEQN GAP AHIIE E DEQL LQ FHV A T Y MDN E IP GLP QAT Q KS g R PLKSIR QRLKGK E GR I RGNL M GKRVD 240
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 359 FS G RTVI S PDPNL RI DQVGVP IHV AM T LTFPEIV NAS NI EKMRQ LV I NG SDVH PGA N Y LV e KKT G NKKL L K Y G K RD e LAK 438
Cdd:cd02733 241 FS A RTVI T PDPNL EL DQVGVP RSI AM N LTFPEIV TPF NI DRLQE LV R NG PNEY PGA K Y II - RDD G ERID L R Y L K KA - SDL 318
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 439 N L RM G DTI ERHL D D N DVVLFNRQPSLHK I S I M S HR A KV M P GR TFR F N ECAC TPYNADFDGDEMNLH L PQ TY E AK AE AS EL 518
Cdd:cd02733 319 H L QY G YIV ERHL Q D G DVVLFNRQPSLHK M S M M G HR V KV L P YS TFR L N LSVT TPYNADFDGDEMNLH V PQ SL E TR AE LK EL 398
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 519 M N V KNNLIT P R S GE P LVAAI QD FIT G GYL LT HK DTFL PRAE V YRFAAA L I D asakkq TKIR IP P PAI RR P VE LWTGKQ LI 598
Cdd:cd02733 399 M M V PRQIVS P Q S NK P VMGIV QD TLL G VRK LT KR DTFL EKDQ V MNLLMW L P D ------ WDGK IP Q PAI LK P KP LWTGKQ IF 472
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 599 E LII r P D kgsd VSLNLTAKNKSYTGNLELCSK D SY VII R N SV LL A G C L D K SLL G S SS K v NIFYMLMRD YG ED AA V D AMWR 678
Cdd:cd02733 473 S LII - P K ---- INNLIRSSSHHDGDKKWISPG D TK VII E N GE LL S G I L C K KTV G A SS G - GLIHVIWLE YG PE AA R D FIGN 546
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 679 LA R MAPVF L SNR GFSIGIGD VRPSEQLLREKGQLVDNGYSKCSQY I KELEE G K L KA QPG C T EE E TL E SIIL R E L STI RD H 758
Cdd:cd02733 547 IQ R VVNNW L LHN GFSIGIGD TIADKETMKKIQETIKKAKRDVIKL I EKAQN G E L EP QPG K T LR E SF E NKVN R I L NKA RD K 626
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 759 AG QVCLRN LS KY N APLT M AVC GSKGSFINISQ M IACVGQQ AIS G H R P P D GF EE R S LPHF ERKKKT PE AK GFV A NS FYS GL 838
Cdd:cd02733 627 AG KSAQKS LS ED N NFKA M VTA GSKGSFINISQ I IACVGQQ NVE G K R I P F GF RR R T LPHF IKDDYG PE SR GFV E NS YLR GL 706
810 820 830 840
....*....|....*....|....*....|....*....|....*
gi 25145495 839 TP T EFFFH T MGGREGL V DTAVKTAETGY M QRRLVK CL ED LCAS YD 883
Cdd:cd02733 707 TP Q EFFFH A MGGREGL I DTAVKTAETGY I QRRLVK AM ED VMVK YD 751
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
26-883
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: 577.08
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 26 E FM R QTAHVPIFNNKLYEDV eg K L QPANY G PL DP KM G VSTKTGT C S TCG L GL T DC V GHFG YFD L DV PVFH I GF F K LTIQL 105
Cdd:cd00399 4 E EI R KWSVAKVIKPETIDNR -- T L KAERG G KY DP RL G SIDRCEK C G TCG T GL N DC P GHFG HIE L AK PVFH V GF I K KVPSF 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 106 L Q cickncssilltpeqhrvfsrqvmnpnldylhrkalhkrivaackkgstcshcglkngtvkkavgavlkiafaspvsv 185
Cdd:cd00399 82 L G ------------------------------------------------------------------------------ 83
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 186 delgkfatmfssnqevgdhvrkmkftllnplfvqklfsnikegdipvlmvrsgeekh P NDLL LT RM PVPP V C I RPSV VS E 265
Cdd:cd00399 84 --------------------------------------------------------- P EWMI LT CL PVPP P C L RPSV II E 106
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 266 vkagtteddvtmklmeimltndvlkkhkrdgapsktlf E T W EH LQ IQCAL Y INSEMS G L P PDMQPK R AM R AFT QRLKGK Q 345
Cdd:cd00399 107 -------------------------------------- E R W RL LQ EHVDT Y LDNGIA G Q P QTQKSG R PL R SLA QRLKGK E 148
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 346 GRFRGNL C GKRVDFSGR T VISPDPNLR I DQVGVP IHV A M TL tfpeivnasniekmrqlvingsdvhpganylvekktgnk 425
Cdd:cd00399 149 GRFRGNL M GKRVDFSGR S VISPDPNLR L DQVGVP KSI A L TL --------------------------------------- 189
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 426 kllkygkrdelaknlrmgdtierhld D N D V VLFNRQPSLHK I SIM S HR AK V M PG R TFR F N ECA C T PYNADFDGDEMNLH L 505
Cdd:cd00399 190 -------------------------- D G D P VLFNRQPSLHK L SIM A HR VR V L PG S TFR L N PLV C S PYNADFDGDEMNLH V 243
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 506 PQ TY EA K AEA S ELM N V K NN LIT P RS GEPL VAAI QD FIT G G YLLT hkdtflpraevyrfaaalidasakkqtkiripppai 585
Cdd:cd00399 244 PQ SE EA R AEA R ELM L V P NN ILS P QN GEPL IGLS QD TLL G A YLLT ------------------------------------ 287
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 586 rrpvelw T GKQ LI eliirpdkgsdvslnltaknksytgnlelcskdsyviirn S VL L A G cldksllgssskv NIFYMLM R 665
Cdd:cd00399 288 ------- L GKQ IV ---------------------------------------- S AA L P G ------------- GLLHTVT R 307
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 666 DY G EDA A VDAMWR L A R MAP VFL SNR GFS I GIGDV RPSEQLLR EK GQ L VDNGYS K CSQYIKELEE G K L K AQ P G C T E EE T LE 745
Cdd:cd00399 308 EL G PEK A AKLLSN L Q R VGF VFL TTS GFS V GIGDV IDDGVIPE EK TE L IEEAKK K VDEVEEAFQA G L L T AQ E G M T L EE S LE 387
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 746 SI IL RE L STI RD H AG QVCLR NL --- SK Y N APLT MA VC G S KGSFINI S QM I ACVGQQ AIS G H R P P D GF EE R S LPHF ERKKK 822
Cdd:cd00399 388 DN IL DF L NEA RD K AG SAASV NL dlv SK F N SIYV MA MS G A KGSFINI R QM S ACVGQQ SVE G K R I P R GF SD R T LPHF SKDDY 467
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 25145495 823 T PEAKGF VA NSF YS GLTP T E F FFH T MGGREGLVDTAVKTAE T GY M QRRLVK C LEDL CAS YD 883
Cdd:cd00399 468 S PEAKGF IR NSF LE GLTP L E Y FFH A MGGREGLVDTAVKTAE S GY L QRRLVK A LEDL VVH YD 528
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
58-883
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: 576.06
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 58 DP KM G VST K TGT CSTCGL GLTD C V GHFG YFD L DV PV FHIG FF K L TIQ LL QCI C KN C ssilltpeqhrvfsrqvmnpnldy 137
Cdd:cd01435 37 DP AL G PLD K DDI CSTCGL NYLN C P GHFG HIE L PL PV YNPL FF D L LYK LL RGS C FY C ------------------------ 92
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 138 l HR KALH K R ivaackkgstcshcglkng T VK KA V GAVLKIAFASP V SVD EL GKFAT MF ssnqevgdhvrkmkftllnplf 217
Cdd:cd01435 93 - HR FRIS K W ------------------- E VK LF V AKLKLLDKGLL V EAA EL DFGYD MF ---------------------- 130
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 218 vqkl F snikegdipvlmvrsgeekhpndll L TRMP VPP VCI RP sv V S EVKAGTT E DDVTMK L ME I MLT N DVLKK ------ 291
Cdd:cd01435 131 ---- F ------------------------- L DVLL VPP NRF RP -- P S FLGDKVF E NPQNVL L SK I LKD N QQIRD llasmr 179
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 292 --------- HKRDGAP S KT L FET W eh LQ I Q C A -- LYIN S EMSGLPPDMQ P K r AMR aft Q R L KG K Q G R FR G N LC GKRV DFS 360
Cdd:cd01435 180 qaesqskld LISGKTN S EK L INA W -- LQ L Q S A vn ELFD S TKAPKSGKKS P P - GIK --- Q L L EK K E G L FR M N MM GKRV NYA 253
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 361 G R T VISPDP NLRIDQV G V P IHV A MT LTFPE I V NAS N I E KM RQ L VING S DV H PGAN Y l V E KKT G NKK LL KYG --- K R DE LA 437
Cdd:cd01435 254 A R S VISPDP FIETNEI G I P LVF A KK LTFPE P V TPF N V E EL RQ A VING P DV Y PGAN A - I E DED G RLI LL SAL see R R KA LA 332
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 438 K N L RM ---------- GDTIE RHL D D N DVVL F NRQP S LHK I SIM S H RAK V M PG - R T F R FNECA C TP YNADFDGDEMNLH L P 506
Cdd:cd01435 333 K L L LL lssaklllng PKKVY RHL L D G DVVL L NRQP T LHK P SIM A H KVR V L PG e K T L R LHYAN C KS YNADFDGDEMNLH F P 412
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 507 Q TYE A K AEA SELMNVK N NLIT P RS G E PL VAA IQD FITG G Y LLT HK DTF LP R A E ---- VY rfa AAL IDASAK - K QTK I RIP 581
Cdd:cd01435 413 Q SEL A R AEA YYIASTD N QYLV P TD G K PL RGL IQD HVVS G V LLT SR DTF FT R E E yqql VY --- AAL RPLFTS d K DGR I KLL 489
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 582 PPAI RR P VE LWTGKQ L I EL I --- IR P DKGSDVS L NLTA K N K SYT G NLELC -- S KD S Y VIIRN SV LL A G C LDKS LL G S S SK 656
Cdd:cd01435 490 PPAI LK P KP LWTGKQ V I ST I lkn LI P GNAPLLN L SGKK K T K KKV G GGKWG gg S EE S Q VIIRN GE LL T G V LDKS QF G A S AY 569
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 657 -- V NIF Y M L mrd YG EDA A VDAMWR L A R MAPVF L SN RGF SI GI G D -- VR P SEQLL R E K G qlvdngyskcsqy IKELEEGK L 732
Cdd:cd01435 570 gl V HAV Y E L --- YG GET A GKLLSA L G R LFTAY L QM RGF TC GI E D ll LT P KADEK R R K I ------------- LRKAKKLG L 633
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 733 K A Q pgcte E E T L ESIILREL S T I RD hagq V CL - RN L S K --- Y N APLT M AVC G S KGS FI N I SQ MIACV GQQ AIS G H R P P DG 808
Cdd:cd01435 634 E A A ----- A E F L GLKLNKVT S S I IK ---- A CL p KG L L K pfp E N NLQL M VQS G A KGS MV N A SQ ISCLL GQQ ELE G R R V P LM 704
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 25145495 809 FEERS LP H F ERKKKT P E A K GF VANS F YS G LT P T E F FFH T M G GREGL V DTAVKT AET GY M QR R L V K C LE D L CAS YD 883
Cdd:cd01435 705 VSGKT LP S F PPYDTS P R A G GF ITDR F LT G IR P Q E Y FFH C M A GREGL I DTAVKT SRS GY L QR C L I K H LE G L KVN YD 779
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1034-1374
2.02e-176
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: 526.02
E-value: 2.02e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1034 K VA RA IT EPGTAVGAIAA T SIGEP S TQMTLKTFHFAGVASMNIT Q GVPRIKEIINA V K T ISTPIITA A L LDPY DE SL AR R 1113
Cdd:cd02736 1 K YM RA KV EPGTAVGAIAA Q SIGEP G TQMTLKTFHFAGVASMNIT L GVPRIKEIINA S K N ISTPIITA K L ENDR DE KS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1114 VK A RIEKT T LGE ICD YIEEVY L PDD YFL L V KL NS K R I RL LQL evcmesisyaiatskvcpqmrgckivahgktmmairpp 1193
Cdd:cd02736 81 VK G RIEKT Y LGE VAS YIEEVY S PDD CYI L I KL DK K I I EK LQL -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1194 st SK LSKTMTM Q I LK YS L AN VVV K GIP S V N R C VI HA D E KKG d F Y S LLVEG TDF R S V LSSV GV DPRK T NF N NALV V AD VLG 1273
Cdd:cd02736 123 -- SK SNLYFLL Q S LK RK L PD VVV S GIP E V K R A VI NK D K KKG - K Y K LLVEG YGL R A V MNTP GV IGTR T TS N HIME V EK VLG 199
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1274 IEAARS C IINEI IA TM DA HG IGL D R RH V MLLAD V MT YR GEVLGITR N G LV KMK D SVL L LASFEKT M DHLF E AA FFSQR D V 1353
Cdd:cd02736 200 IEAARS T IINEI QY TM KS HG MSI D P RH I MLLAD L MT FK GEVLGITR F G IA KMK E SVL M LASFEKT T DHLF N AA LHGRK D S 279
330 340
....*....|....*....|.
gi 25145495 1354 I H GVSECIIMG T PM TV GTG T F 1374
Cdd:cd02736 280 I E GVSECIIMG K PM PI GTG L F 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
244-546
4.31e-151
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 459.29
E-value: 4.31e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 244 NDLL LT RM PVPP V C I RPSV VSEVKA g TT EDD V T MK L ME I MLT N DV LK KHKRD GAPS KTLFETWEH LQ IQCALY I NS E ms G 323
Cdd:smart00663 1 EWMI LT VL PVPP P C L RPSV QLDGGR - FA EDD L T HL L RD I IKR N NR LK RLLEL GAPS IIIRNEKRL LQ EAVDTL I DN E -- G 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 324 LP PDM Q PK - R AMRAFT QRLKGK Q GRFR G NL C GKRVDFS G R T VI S PDPNL RIDQ VGVP IHV A MT LTFPEIV NAS NI E K M R Q 402
Cdd:smart00663 78 LP RAN Q KS g R PLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLNE VGVP KEI A LE LTFPEIV TPL NI D K L R K 157
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 403 LV I NG sdv HP GA N Y LVE kkt G N K KL LK YG K RDEL A KN L RM GD TI ERH LD D N DVVLFNRQP S LH KI SI MS HR AK V MP G R T F 482
Cdd:smart00663 158 LV R NG --- PN GA K Y IIR --- G K K TN LK LA K KSKI A NH L KI GD IV ERH VI D G DVVLFNRQP T LH RM SI QA HR VR V LE G K T I 231
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25145495 483 R F N ECA C T PYNADFDGDEMNLH L PQ TY EA K AEA S ELM N V K NN LIT P RS G E P LVAA IQD FIT G G Y 546
Cdd:smart00663 232 R L N PLV C S PYNADFDGDEMNLH V PQ SL EA R AEA R ELM L V P NN ILS P KN G K P IIGP IQD MLL G L Y 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
14-352
1.32e-124
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: 389.73
E-value: 1.32e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 14 K VVGVK F APGDC E FM R QTAHVPIFNNKL Y ED ve G K L Q P ANY G P LD PK MG VST K TGT C S TCG LGLT DC V GHFG YFD L DV PV 93
Cdd:pfam04997 3 K IKEIQ F GIASP E EI R KWSVGEVTKPET Y NY -- G S L K P EEG G L LD ER MG TID K DYE C E TCG KKKK DC P GHFG HIE L AK PV 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 94 FHIGFFK L T IQL L Q C I CK N CS SI LL T P EQHRV F SRQVMNPN L DY L hr K ALH K R I VAA CKK GST C S HCG L KNG TVKK avga 173
Cdd:pfam04997 81 FHIGFFK K T LKI L E C V CK Y CS KL LL D P GKPKL F NKDKKRLG L EN L -- K MGA K A I LEL CKK KDL C E HCG G KNG VCGS ---- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 174 vlkiaf AS PVS VD E LG K FATMFSSNQ E VGDH vrkmkf TL LNP LF V Q K L F SN I KEG D IPV L MVRS g EEKH P NDLL LT RM PV 253
Cdd:pfam04997 155 ------ QQ PVS RK E GL K LKAAIKKSK E EEEK ------ EI LNP EK V L K I F KR I SDE D VEI L GFNP - SGSR P EWMI LT VL PV 221
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 254 PP V CIRPSV VSEVK a GTT EDD V T M KL ME I MLT N DV LKK HKRD GAPS KTLF E T W EH LQ IQC A LYINS E MS GLPP DM Q - P KR 332
Cdd:pfam04997 222 PP P CIRPSV QLDGG - RRA EDD L T H KL RD I IKR N NR LKK LLEL GAPS HIIR E E W RL LQ EHV A TLFDN E IP GLPP AL Q k S KR 300
330 340
....*....|....*....|
gi 25145495 333 AMRAFT QRLKGK Q GRFRGNL 352
Cdd:pfam04997 301 PLKSIS QRLKGK E GRFRGNL 320
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
837-1330
4.56e-105
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: 343.95
E-value: 4.56e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 837 GLTP T EFFFHTMGGREGL V DTAVKTAE T GY M QRRLVK C LEDL CAS YD G TVR S S V G DVIE F VF GEDGLDP AMM E AKDGSVV 916
Cdd:pfam04998 1 GLTP Q EFFFHTMGGREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G EIVQ F LY GEDGLDP LKI E KQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 917 D F thvleha KNIQTTKE qp IPV D K LD EV L KAEI qkk F KGK Y VHFADKLSEYITQTEIK K SKK w QNGKAHCGNHETAD L KT 996
Cdd:pfam04998 81 E F ------- SDLKLEDK -- FKN D L LD DL L LLSE --- F SLS Y KKEILVRDSKLGRDRLS K EAQ - ERATLLFELLLKSG L ES 147
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 997 K ESCK icknle AYKTSLL A NS CL tktqlcsfie LCY Y -- KVARAITE PG T AVG A IAA T SIGEP S TQMTL K TFHFAGVAS M 1074
Cdd:pfam04998 148 K RVRS ------ ELTCNSK A FV CL ---------- LCY G rl LYQQSLIN PG E AVG I IAA Q SIGEP G TQMTL N TFHFAGVAS K 211
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1075 N I T Q GVPR I KEIIN AV K T I ST P II T AA L L D PYDES L ARR -- V KAR IEK T TLG EICDYI E EV Y L PD DY ------------- 1139
Cdd:pfam04998 212 N V T L GVPR L KEIIN VS K N I KS P SL T VY L F D EVGRE L EKA kk V YGA IEK V TLG SVVESG E IL Y D PD PF ntpiisdvkgvvk 291
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1140 ----------------- FL L VK L NSKRIRL L QLEVCMESI S YA I A ------------------ T SKVCPQMRGCKIVAH G 1184
Cdd:pfam04998 292 ffdiidevtneeeidpe TG L LI L VIRLLKI L NKSIKKVVK S EV I P rsirnkvdegrdiaigei T AFIIKISKKIRQDTG G 371
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1185 K ----- TM M AIR P PSTS klsktmtmq ILKYS L A N VVVK GIP SVN R CVI -- HADE K KGDFYS L LV EG TDFRS VL SSV G - VD 1256
Cdd:pfam04998 372 L rrvde LF M EED P KLAI --------- LVASL L G N ITLR GIP GIK R ILV ne DDKG K VEPDWV L ET EG VNLLR VL LVP G f VD 442
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25145495 1257 PRKTNF N NALVVADV LGIEAAR SCII NEI IATMDAH GI GLDR RH VM L L AD V MT YR G EVLG I T R N G LV K MKD S V L 1330
Cdd:pfam04998 443 AGRILS N DIHEILEI LGIEAAR NALL NEI RNVYRFQ GI YIND RH LE L I AD Q MT RK G YIMA I G R H G IN K AEL S A L 516
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
354-521
1.69e-98
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: 311.93
E-value: 1.69e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 354 GKRVDFS G RTVISPDPNL RI D Q VGVPI HV A M TLTFPEIV NAS NI EKM RQLV I NG SD V H PGANY l VEKKT G NKKL L K Y G KR 433
Cdd:pfam00623 1 GKRVDFS A RTVISPDPNL KL D E VGVPI SF A K TLTFPEIV TPY NI KRL RQLV E NG PN V Y PGANY - IIRIN G ARRD L R Y Q KR 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 434 d E L A K N L RM GD TI ERH LD D N DVVLFNRQPSLH KI SIM S HR AK V M PG R TFR F N ECAC TPYNADFDGDEMNLH L PQ TY EA K A 513
Cdd:pfam00623 80 - R L D K E L EI GD IV ERH VI D G DVVLFNRQPSLH RL SIM G HR VR V L PG K TFR L N LSVT TPYNADFDGDEMNLH V PQ SE EA R A 158
....*...
gi 25145495 514 EA S ELM N V 521
Cdd:pfam00623 159 EA E ELM L V 166
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1019-1380
7.61e-97
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain]
Cd Length: 363
Bit Score: 315.34
E-value: 7.61e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1019 LT KTQLCSF I ELCYYKVA R AIT EPG T AVG AI AA T SIGEP S TQMTL K TFH F AGVA SM N I T Q G V PR IK EI IN A V K TI STP II 1098
Cdd:cd06528 16 LT LSEAEEI I KEVLREYL R SLI EPG E AVG IV AA Q SIGEP G TQMTL R TFH Y AGVA EI N V T L G L PR LI EI VD A R K EP STP TM 95
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1099 T AA L LD -- P YD ESL A RR V KAR IE K TTL GEICDY I EEVY lp DDYFLLVK L NSKRIRLLQLE vc MESISY AI ATS K vcpqm R 1176
Cdd:cd06528 96 T IY L EE ey K YD REK A EE V ARK IE E TTL ENLAED I SIDL -- FNMRITIE L DEEMLEDRGIT -- VDDVLK AI EKL K ----- K 166
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1177 G CKIVAHGK T MMAIRP -- PS TSK L S K tmtmqi L KYSLA N VVV KGI PSVN R CVI had E K KG D F Y SLLV EG TDFRS VL SSV G 1254
Cdd:cd06528 167 G KVGEEGDV T LIVLKA ee PS IKE L R K ------ L AEKIL N TKI KGI KGIK R VIV --- R K EE D E Y VIYT EG SNLKA VL KVE G 237
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1255 VDP RK T NF NN ALVVAD VLGIEAAR SC IINEI IA T MDAH G IGL D R RH V ML L AD V MTY R GEV LG I T R N G LVKM K D SVL LL A S 1334
Cdd:cd06528 238 VDP TR T TT NN IHEIEE VLGIEAAR NA IINEI KR T LEEQ G LDV D I RH I ML V AD I MTY D GEV RQ I G R H G IAGE K P SVL AR A A 317
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 25145495 1335 FE K T MD HL FE AA FFSQR D VIH GV S E C II M G T P MTV GTG TFK L MQKY 1380
Cdd:cd06528 318 FE V T VK HL LD AA VRGEV D ELR GV I E N II V G Q P IPL GTG DVE L TMDP 363
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1019-1383
1.75e-91
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 301.38
E-value: 1.75e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1019 LT KTQLCSF IE LCYYKVA R AIT EPG T AVG AI AA T SIGEP S TQMT LK TFH F AGVA SM N I T Q G V PR IK EI IN A V K TI STP II 1098
Cdd:PRK04309 35 LT EEEVEEI IE EVVREYL R SLV EPG E AVG VV AA Q SIGEP G TQMT MR TFH Y AGVA EI N V T L G L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1099 T AA L L D P Y -- D ESL A RR V KAR IE K TTL GEICDY I E ev YLPDDYFLLVK L NSKR ir L LQLEVCMESISY AI ATS K vcpqmr 1176
Cdd:PRK04309 115 T IY L K D E Y ay D REK A EE V ARK IE A TTL ENLAKD I S -- VDLANMTIIIE L DEEM -- L EDRGLTVDDVKE AI EKK K ------ 184
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1177 G CKIVAH G K T M - MAIRP PS TSK L S K tmtmqi L KYSLA N VVV KGI PSVN R CV I had E K K GD F Y SLLV EG TDFRS VL SSV GV 1255
Cdd:PRK04309 185 G GEVEIE G N T L i ISPKE PS YRE L R K ------ L AEKIR N IKI KGI KGIK R VI I --- R K E GD E Y VIYT EG SNLKE VL KVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1256 D PRK T NF NN ALVVAD VLGIEAAR SC II N EI IA T MDAH G IGL D R RH V ML L AD V MT YR GEV LG I T R N G LVKM K D SVL LL A S F 1335
Cdd:PRK04309 256 D ATR T TT NN IHEIEE VLGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML V AD M MT WD GEV RQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 25145495 1336 E K T MD HL FE AA FFSQR D VIH GV S E C II M G T P MTV GTG TFK L MQKYDKK 1383
Cdd:PRK04309 336 E V T VK HL LD AA VRGEV D ELK GV T E N II V G Q P IPL GTG DVE L TMDPPLR 383
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
58-887
2.44e-84
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: 292.77
E-value: 2.44e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 58 D P KM G VSTKT G T C S TCG LGLTD - C V GHFG YFD L D V PVF H IG F FKLTI Q L L QC IC KN C S SI ll TPEQHRV f S R QVMN P NL - 135
Cdd:cd10506 22 N P RL G LPNES G Q C T TCG AKDNK k C E GHFG VIK L P V TIY H PY F ISEVA Q I L NK IC PG C K SI -- KQKKKKP - P R ETLP P DY w 98
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 136 D YLHRKALHK rivaackkg ST C SHCG L KN gtvkkavg AV L KIAFASPVSV D el G K F atmfssnqevgdhvrkmkftllnp 215
Cdd:cd10506 99 D FIPKDGQQE --------- ES C VTKN L PI -------- LS L AQVKKILKEI D -- P K L ------------------------ 135
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 216 lfvqklfsn I KE G DIP vlmvrsgeekh PND L L L TRM PVPP V C I R psv V S E VKA G TTE ddv TMK L MEIML T NDVL K K hkrd 295
Cdd:cd10506 136 --------- I AK G LPR ----------- QEG L F L KCL PVPP N C H R --- V T E FTH G FST --- GSR L IFDER T RAYK K L ---- 185
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 296 gapsktlfetwehlqiqc ALY I NSEMSGLPPDMQPKRA M RA ftqrlkgkqgrfrg N L C GKR VDF S G R T V ISP DP N L RIDQ 375
Cdd:cd10506 186 ------------------ VDF I GTANESAASKKSGLKW M KD -------------- L L L GKR SGH S F R S V VVG DP Y L ELNE 233
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 376 V G V P IHV A MT LT FP E I V NAS N I E KMRQLV ings D VHPGANYLVEKKTGNKKLLKYGKRD elakn L RM GD T I E R H L D D N DV 455
Cdd:cd10506 234 I G I P CEI A ER LT VS E R V SSW N R E RLQEYC ---- D LTLLLKGVIGVRRNGRLVGVRSHNT ----- L QI GD V I H R P L V D G DV 304
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 456 VL F NR Q PS L H KI S IMSHRA KV M P - GRTFRF N ECA C T P YNA DFDGD EMNLHL PQ TYE A K AE AS EL MNVKNN LI TPR SG EP L 534
Cdd:cd10506 305 VL V NR P PS I H QH S LIALSV KV L P t NSVVSI N PLC C S P FRG DFDGD CLHGYI PQ SLQ A R AE LE EL VALPKQ LI SSQ SG QN L 384
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 535 VAAI QD FITGGY L L T HKDT FL PR A EV yrfaaali DASAKKQTKIRI PP PA I RR P VE --- LWTGKQL IELIIRP D kgsdvs 611
Cdd:cd10506 385 LSLT QD SLLAAH L M T ERGV FL DK A QM -------- QQLQMLCPSQLP PP AI I KS P PS ngp LWTGKQL FQMLLPT D ------ 450
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 612 lnltakn KS Y TGNLE L cskdsy V I I RNSV L LA g CLDK S LLGSS S KV N I F YM L MR d Y G EDA A V D AMWRLARMAPVF LS N RG 691
Cdd:cd10506 451 ------- LD Y SFPSN L ------ V F I SDGE L IS - SSGG S SWLRD S EG N L F SI L VK - H G PGK A L D FLDSAQGLLCEW LS M RG 515
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 692 FS IGIG D VRP S EQLLREKGQLVDNGY ---- SKCSQY IK E L EEGKL K AQPGCTE EE TLE S IILRELSTI R DH --------- 758
Cdd:cd10506 516 FS VSLS D LYL S SDSYSRQKMIEEISL glre AEIACN IK Q L LVDSR K DFLSGSG EE NDV S SDVERVIYE R QK saalsqasv 595
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 759 - A GQVCL R NL -------- SK Y N AP L T M AVC GSKGS FINIS Q MIA C V G Q Q -------- A I SGHRPPDGFEERSL P HFER K K 821
Cdd:cd10506 596 s A FKQVF R DI qnlvykya SK D N SL L A M IKA GSKGS LLKLV Q QSG C L G L Q lslvklsy R I PRQLSCAAWNSQKS P RVIE K D 675
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 25145495 822 KT ----- PEAK G F V AN SF YS GL T P T E F F F H TMGG R EGLVD tav KT A ET - G YMQ R R L VKCLE D LCAS YDGTVR 887
Cdd:cd10506 676 GS ectes YIPY G V V ES SF LD GL N P L E C F V H SITS R DSSFS --- SN A DL p G TLF R K L MFFMR D IYVA YDGTVR 744
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1037-1376
2.47e-84
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: 280.79
E-value: 2.47e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1037 R AITE PG T AVG AI AA T SIGEP S TQMT LK TFH F AGVA SM N I T Q G V PR IK EI IN A V KT I STP II T AA L L D P Y -- D ESL A RR V 1114
Cdd:TIGR02389 38 R SLID PG E AVG IV AA Q SIGEP G TQMT MR TFH Y AGVA EL N V T L G L PR LI EI VD A R KT P STP SM T IY L E D E Y ek D REK A EE V 117
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1115 KAR IE K T T L GEICDY I EEVYL pd D YFLLVK L NSKRI -- R LLQLEVCMES I SY A IATSKVCPQ M RGCK I VAHGKT mmairp 1192
Cdd:TIGR02389 118 AKK IE A T K L EDVAKD I SIDLA -- D MTVIIE L DEEQL ke R GITVDDVEKA I KK A KLGKVIEID M DNNT I TIKPGN ------ 189
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1193 PS TSK L S K tmtmqi LK YSLA N VVV KGI PSVN R C VI had E K K GD F Y SLLV EG TDFRS VL SSV GVD PRK T NF N NALVV A D VL 1272
Cdd:TIGR02389 190 PS LKE L R K ------ LK EKIK N LHI KGI KGIK R V VI --- R K E GD E Y VIYT EG SNLKE VL KLE GVD KTR T TT N DIHEI A E VL 260
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1273 GIEAAR SC II N EI IA T MDAH G IGL D R RH V ML L AD V MT YR GEV LG I T R N G LVKM K D SVL LL A S FE K T MD HL FE AA FFSQR D 1352
Cdd:TIGR02389 261 GIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML V AD L MT WD GEV RQ I G R H G ISGE K A SVL AR A A FE V T VK HL LD AA IRGEV D 340
330 340
....*....|....*....|....
gi 25145495 1353 VIH GV S E C II M G T P MTV GTG TFK L 1376
Cdd:TIGR02389 341 ELK GV I E N II V G Q P IPL GTG DVD L 364
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1028-1377
9.88e-82
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain]
Cd Length: 410
Bit Score: 274.85
E-value: 9.88e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1028 IE LCYY kva R AITE PG TA VG A IAA T SIGEP S TQMTL K TFHFAGV ASM N I T Q GVPR I KEIIN AV K T I S TP II T AA L LDPY - 1106
Cdd:cd02584 15 IE TRFN --- R SLVH PG EM VG T IAA Q SIGEP A TQMTL N TFHFAGV SAK N V T L GVPR L KEIIN VA K N I K TP SL T VY L EPGF a 91
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1107 - DE SL A RRVKA R I E K TTL GEICDYI E EV Y L PD -------------- D YF ---------------- L LVK L N sk R IRLLQL 1155
Cdd:cd02584 92 k DE EK A KKIQS R L E H TTL KDVTAAT E IY Y D PD pqntvieedkefve S YF efpdedveqdrlspwl L RIE L D -- R KKMTDK 169
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1156 EVC ME S I SYA I A tskvcp QMRGCKIVAH ------ G K TMMA IR PPSTSKL s K TMTMQILKYS ------- L ANVVV KGI PSV 1222
Cdd:cd02584 170 KLS ME Q I AKK I K ------ EEFKDDLNVI fsddna E K LVIR IR IINDDEE - K EEDSEDDVFL kkiesnm L SDMTL KGI EGI 242
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1223 NRCV I HADE KK ------ G D F ----- YS L LVE G TDF R S VLS SV GVDP RK T NF N NALVVAD VLGIEAAR SCIIN E IIATMDA 1291
Cdd:cd02584 243 RKVF I REEN KK kvdiet G E F kkree WV L ETD G VNL R E VLS HP GVDP TR T TS N DIVEIFE VLGIEAAR KALLK E LRNVISF 322
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1292 H G IGLDR RH VM LL A DVMT Y RG EVLG ITR N G LVKMKDSV L LLA SFE K T M D H L F EAA F F SQR D VIH GVSE C I IM G TPMTV GT 1371
Cdd:cd02584 323 D G SYVNY RH LA LL C DVMT Q RG HLMA ITR H G INRQDTGP L MRC SFE E T V D I L L EAA A F GET D DLK GVSE N I ML G QLAPI GT 402
....*.
gi 25145495 1372 G T F K L M 1377
Cdd:cd02584 403 G C F D L L 408
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
242-1373
3.31e-78
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: 282.71
E-value: 3.31e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 242 H P NDLL L TRM PV P P VCI RP S V VSEVKAGT T E D -- D VTMK lme IMLT N DV LK KHKRD GAP SKTLFETWEH LQ IQC - AL YI N 318
Cdd:TIGR02386 215 R P EWMV L DVI PV I P PEL RP M V QLDGGRFA T S D ln D LYRR --- VINR N NR LK RLLEL GAP EIIVRNEKRM LQ EAV d AL FD N 291
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 319 SE m S G L P PDMQPK R AMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P E I vnasnie 398
Cdd:TIGR02386 292 GR - R G K P VVGKNN R PLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KMY Q C G L P KKM A LE L FK P F I ------- 363
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 399 k MRQ L V ingsdvhpganylvekktgnkkllkygk RD ELA K N LRMG - DT IE R hl D D ND V ------------ VL F NR Q P S LH 465
Cdd:TIGR02386 364 - IKR L I ---------------------------- DR ELA A N IKSA k KM IE Q -- E D PE V wdvledvikehp VL L NR A P T LH 412
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 466 KIS I MSHRAKVMP G RTF R FNECA CT PY NADFDGD E M NL H L P QTY EA K AEA SE LM NVK NN LIT P RS G E P L V AAI QD FIT G G 545
Cdd:TIGR02386 413 RLG I QAFEPVLVE G KAI R LHPLV CT AF NADFDGD Q M AV H V P LSP EA Q AEA RA LM LAS NN ILN P KD G K P I V TPS QD MVL G L 492
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 546 Y L LT -------- HKDT F LPRA E VY R faaalidas A KKQT K IR ipppa IRRPVELW T GKQLI E LII rpdk G SDVSLNLTAK 617
Cdd:TIGR02386 493 Y Y LT tekpgakg EGKI F SNVD E AI R --------- A YDNG K VH ----- LHALIGVR T SGEIL E TTV ---- G RVIFNEILPE 554
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 618 NKS Y TGNL E LC SK D sy V I irn S V L LAGCLDKS llg SSSKVNIFYMLMRDY G edaavdam WRL A RMA pvflsnr G FS I GIG 697
Cdd:TIGR02386 555 GFP Y INDN E PL SK K -- E I --- S S L IDLLYEVH --- GIEETAEMLDKIKAL G -------- FKY A TKS ------- G TT I SAS 611
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 698 D VRPSE qllr EK GQLVDNGYSKCSQYI K ELEE G KL kaqpgc T E EE TLESII lr EL - S TIR D --- H A GQVC L R - NLS K Y N A 772
Cdd:TIGR02386 612 D IVVPD ---- EK YEILKEADKEVAKIQ K FYNK G LI ------ T D EE RYRKVV -- SI w S ETK D kvt D A MMKL L K k DTY K F N P 679
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 773 PLT MA VC G SK G SFINIS Q MIACV G QQ A isghr P P D G feerslphfe RKKKT P eakgf VAN SF YS GLT PT E F F FH T M G G R E 852
Cdd:TIGR02386 680 IFM MA DS G AR G NISQFR Q LAGMR G LM A ----- K P S G ---------- DIIEL P ----- IKS SF RE GLT VL E Y F IS T H G A R K 739
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 853 GL V DTA V KTA ET GY MQ RRLV KCLE D LCASYD -- GT VRS svgdv IE F vfgedgld P A MM E A KD gsvvdft HVL E HA K niqt 930
Cdd:TIGR02386 740 GL A DTA L KTA DS GY LT RRLV DVAQ D VVVREE dc GT EEG ----- IE V -------- E A IV E G KD ------- EII E SL K ---- 795
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 931 tkeqpipv D KL - DEVLKAEIQKKFK GK YVHF A DK L sey IT QTEIK K skkwqngkahcgnhet ADLKTK E SC K I cknleay 1009
Cdd:TIGR02386 796 -------- D RI v GRYSAEDVYDPDT GK LIAE A NT L --- IT EEIAE K ---------------- IENSGI E KV K V ------- 841
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1010 k T S L L an S C LTKTQL C S fie L CY - YKV A RAI - T E P G T AVG A IAA T SIGEP S TQ M T LK TFH FA GVA S -- MN ITQG V PR I KE 1085
Cdd:TIGR02386 842 - R S V L -- T C ESEHGV C Q --- K CY g RDL A TGK l V E I G E AVG V IAA Q SIGEP G TQ L T MR TFH TG GVA G as GD ITQG L PR V KE 915
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1086 IIN avktistpiitaalldpydesl AR RV K ari E K TTLG E ICDYI E evylpddy FLLVKLNS KR IRLLQL E VCM E s IS Y A 1165
Cdd:TIGR02386 916 LFE ---------------------- AR TP K --- D K AVIA E VDGTV E -------- IIEDIVKN KR VVVIKD E NDE E - KK Y T 961
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1166 I ATSKVCPQMR G CKIV A HG K - T MMA I R P pstsklsktmt MQI L KY ---- SLANVV VK GIPS V N R cvihade KK G dfysll 1240
Cdd:TIGR02386 962 I PFGAQLRVKD G DSVS A GD K l T EGS I D P ----------- HDL L RI kgiq AVQEYL VK EVQK V Y R ------- LQ G ------ 1017
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1241 VE GT D ------ F R SV L SS V GV - D PRKT N F nnal VVADVLG I E aarsc II NE IIATMDAH G IGL drrhvmlladv MTYRGE 1313
Cdd:TIGR02386 1018 VE IN D khievi V R QM L RK V RI t D SGDS N L ---- LPGELID I H ----- EF NE ENRKLLEQ G KKP ----------- ASAIPQ 1077
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1314 V LGIT RNG L vk MKD S V L LL ASF EK T MDH L FE AA FFSQR D VIH G VS E CI I M G TPMTV GTG T 1373
Cdd:TIGR02386 1078 L LGIT KAS L -- NTE S F L SA ASF QE T TKV L TD AA IKGKV D YLL G LK E NV I I G NLIPA GTG L 1135
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1037-1383
1.21e-75
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 260.90
E-value: 1.21e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1037 RA ITE P GT AVG AI AA T SIGEP S TQMT LK TFH F AGVA S MN I T Q G V PR IK EI IN A V K TI STP II T A a L L DP --- Y DE SLA R R 1113
Cdd:PRK14897 176 RA RVD P YE AVG IV AA Q SIGEP G TQMT MR TFH Y AGVA E MN V T L G L PR LI EI VD A R K KP STP TM T I - Y L KK dyr E DE EKV R E 254
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1114 V KAR IE K TTL GEIC D Y I EEV ylp DDYFLL V K L NSKRI -- RL LQLEVCMES I syaiatskvc PQMRGCKIVAHGKTMMAIR 1191
Cdd:PRK14897 255 V AKK IE N TTL IDVA D I I TDI --- AEMSVV V E L DEEKM ke RL IEYDDILAA I ---------- SKLTFKTVEIDDGIIRLKP 321
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1192 P - PS TS KL sktmtm QI L KYSLANVVV KGI PSVN R CVIHADEKKGD f YSLLVE G TDFRS VL SSVG VDP RK T NF N NALVV A D 1270
Cdd:PRK14897 322 Q q PS FK KL ------ YL L AEKVKSLTI KGI KGIK R AIARKENDERR - WVIYTQ G SNLKD VL EIDE VDP TR T YT N DIIEI A T 394
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1271 VLGIEAAR SC II N E IIA T MDAH G IGL D R RH V ML L AD V MT YR G E V LG I T R N G LVKM K D SVL LL A S FE K T MD HL FE A AFFSQ 1350
Cdd:PRK14897 395 VLGIEAAR NA II H E AKR T LQEQ G LNV D I RH I ML V AD M MT FD G S V KA I G R H G ISGE K S SVL AR A A FE I T GK HL LR A GILGE 474
330 340 350
....*....|....*....|....*....|...
gi 25145495 1351 R D VIH GV S E C II M G T P M T V GTG TFK L MQ K YD KK 1383
Cdd:PRK14897 475 V D KLA GV A E N II V G Q P I T L GTG AVS L VY K GR KK 507
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
240-1098
5.33e-64
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 240.16
E-value: 5.33e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 240 EKH P N D LL L TRM PV P P VCI RP S V vs EVKA G T - TED D VTMKLMEIMLT N DV LK KHKRD GAP SKTLFETWEH LQ IQCALYIN 318
Cdd:PRK14906 309 GND P A D MI L DVI PV I P PDL RP M V -- QLDG G R f ATS D LNDLYRRVINR N NR LK RLLDL GAP EIIVNNEKRM LQ EAVDSLFD 386
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 319 SEMS G L P PDMQPK R AMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P EI vnasnie 398
Cdd:PRK14906 387 NGRR G R P VTGPGN R PLKSLADM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P H L KLH Q C G L P SAM A LE L FK P FV ------- 459
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 399 k M RQ LV ings DVHPG AN ylvekktgnkkl L K YG KR DELAKNLRMG D TI E RHLD D N d V VL F NR Q P S LH KIS I MSHRAKVMP 478
Cdd:PRK14906 460 - M KR LV ---- ELEYA AN ------------ I K AA KR AVDRGASYVW D VL E EVIQ D H - P VL L NR A P T LH RLG I QAFEPVLVE 521
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 479 G RTFRFNECA CT PY NADFDGD E M NL H L P QTYE A K AEA SE LM NVK NN LIT P RS G E PL VAAI QD F I T G G Y L LT - HK D T F LPR 557
Cdd:PRK14906 522 G KAIKLHPLV CT AF NADFDGD Q M AV H V P LSTQ A Q AEA RV LM LSS NN IKS P AH G R PL TVPT QD M I I G V Y Y LT t ER D G F EGE 601
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 558 AEVY - R F AA AL -- I DA S A KKQTKIR I pppairrpvelwtgkqlieliirpdkgs D V S L NLTAKNKSYT G N LE LCSKDSYV 634
Cdd:PRK14906 602 GRTF a D F DD AL na Y DA R A DLDLQAK I ---------------------------- V V R L SRDMTVRGSY G D LE ETKAGERI 653
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 635 ------ II R N S VL ------ L AGCLD K SLL G S sskvnifym L MR D ygedaa VDAMWRL A RMA P VF -- LSNR GF -------- 692
Cdd:PRK14906 654 ettvgr II F N Q VL pedypy L NYKMV K KDI G R --------- L VN D ------ CCNRYST A EVE P IL dg IKKT GF hyatragl 718
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 693 SIGIG D VRPSE qllr E K GQLVDNGYS K CSQYIKEL E E G K L kaqpgc T E E E TLESII l RELSTIRDHA G QVC L RNLSKY N A 772
Cdd:PRK14906 719 TVSVY D ATIPD ---- D K PEILAEADE K VAAIDEDY E D G F L ------ S E R E RHKQVV - DIWTEATEEV G EAM L AGFDED N P 787
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 773 PLT MA VC G SK G SFIN I S Q MIACV G QQ A isghr PPD G f E ERS LP hferkkktpeakgf VANS F YS GL TPT E F F FH T M G G R E 852
Cdd:PRK14906 788 IYM MA DS G AR G NIKQ I R Q LAGMR G LM A ----- DMK G - E IID LP -------------- IKAN F RE GL SVL E Y F IS T H G A R K 847
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 853 GLVDTA VK TA ET GY MQ RRLV KCLE D L ------ C ASYD G T --- VRSSV GDV IEFVF G ---- ED GL DP ammeak D G svvdft 919
Cdd:PRK14906 848 GLVDTA LR TA DS GY LT RRLV DVAQ D V ivreed C GTDE G V typ LVKPK GDV DTNLI G rcll ED VC DP ------ N G ------ 915
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 920 hvlehakniqttkeqpipvdkld EVL KA eiqkkf K G K Y VHFA D K L seyitqteikks K KWQNGKA hcgnh ETADLK T KES 999
Cdd:PRK14906 916 ----------------------- EVL LS ------ A G D Y IESM D D L ------------ K RLVEAGV ----- TKVQIR T LMT 949
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1000 C K icknleayktsllanscl TKTQL C sfi EL CY --- YKVA R AIT e P GTAVG A IAA T SIGEP S TQ M T LK TFH FA GVA SMN I 1076
Cdd:PRK14906 950 C H ------------------ AEYGV C --- QK CY gwd LATR R PVN - I GTAVG I IAA Q SIGEP G TQ L T MR TFH SG GVA GDD I 1007
890 900
....*....|....*....|..
gi 25145495 1077 TQG V PR IK E IIN A V K TISTPII 1098
Cdd:PRK14906 1008 TQG L PR VA E LFE A R K PKGEAVL 1029
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1034-1377
9.85e-64
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain]
Cd Length: 309
Bit Score: 219.37
E-value: 9.85e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1034 K VA R AIT EPG T AVG AI AA T SIGEPSTQMTL K TFHFAG VAS MN I T Q G V PR IK EI I - N A V K T I S TP II T AA L LDPYDESL A R 1112
Cdd:cd02735 1 K YM R SLV EPG E AVG LL AA Q SIGEPSTQMTL N TFHFAG RGE MN V T L G I PR LR EI L m T A S K N I K TP SM T LP L KNGKSAER A E 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1113 RV K A R IEKT TL GEICDYI E EVY lpddyf L L VKLNSKRIR LL Q l EV C MES I SYAIATS K V cpqmrgckivahgktmmairp 1192
Cdd:cd02735 81 TL K K R LSRV TL SDVVEKV E VTE ------ I L KTIERVFKK LL G - KW C EVT I KLPLSSP K L --------------------- 132
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1193 pstsklskt MTMQ I LKYSLANV V VKG IP SVN RC VIHADE K K G DFYS L LVEGTDFRSV L SSVG -- V D PRKTNF N NALVVAD 1270
Cdd:cd02735 133 --------- LLLS I VEKLARKA V IRE IP GIT RC FVVEED K G G KTKY L VITEGVNLAA L WKFS di L D VNRIYT N DIHAMLN 203
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1271 VL GIEAAR SC I IN EI IATMDAH GI GL D R RH VM L L AD V MT YR G EVLGIT R N G LVK m KD S V L LLA SFE K T MDH L FE A AFFSQ 1350
Cdd:cd02735 204 TY GIEAAR RA I VK EI SNVFKVY GI AV D P RH LS L I AD Y MT FE G GYRPFN R I G MES - ST S P L QKM SFE T T LAF L KK A TLNGD 282
330 340
....*....|....*....|....*..
gi 25145495 1351 R D VIHGV S ECIIM G T P MTV GTG T F K L M 1377
Cdd:cd02735 283 I D NLSSP S SRLVV G K P VNG GTG L F D L L 309
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1059-1377
1.41e-61
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 227.85
E-value: 1.41e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1059 T QM T LK TFH F AGVA SM N I T Q G V PR IK EI IN A V K TI STPI I T AA L LDP Y -- D ESL A RR V KAR IE KT TLG EICDY I EEVYLP 1136
Cdd:PRK14898 541 T HN T MR TFH Y AGVA EI N V T L G L PR MI EI VD A R K EP STPI M T VH L KGE Y at D REK A EE V AKK IE SL TLG DVATS I AIDLWT 620
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1137 DD yf LL V K L NSKRIRLLQ L E vc M ES ISY AI a TS K V cpqmr G C KI VAH G KTM - MAIRP PS TSK L S K TMT mqilky SLA N V V 1215
Cdd:PRK14898 621 QS -- IK V E L DEETLADRG L T -- I ES VEE AI - EK K L ----- G V KI DRK G TVL y LKPKT PS YKA L R K RIP ------ KIK N I V 684
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1216 V KGIP SVN R CVIHAD E KKG D F - Y S L LVE G TDF R S V LSSV GVD PRK T NF NN ALVVAD VLGIEAAR SC IINE IIA T MDAH G I 1294
Cdd:PRK14898 685 L KGIP GIE R VLVKKE E HEN D E e Y V L YTQ G SNL R E V FKIE GVD TSR T TT NN IIEIQE VLGIEAAR NA IINE MMN T LEQQ G L 764
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1295 GL D R RH V ML L AD V MT YR GEV LG I T R N G LVKM K D SVL LL A S FE K T MD HL FE AA FFSQR D VIH GV S E CI I M G T P MTV GTG TF 1374
Cdd:PRK14898 765 EV D I RH L ML V AD I MT AD GEV KP I G R H G VAGE K G SVL AR A A FE E T VK HL YD AA EHGEV D KLK GV I E NV I V G K P IKL GTG CV 844
...
gi 25145495 1375 K L M 1377
Cdd:PRK14898 845 D L R 847
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
331-1091
2.93e-60
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 226.87
E-value: 2.93e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 331 K R AMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P E I vnasniek M RQ LV ingsdv 410
Cdd:PRK00566 311 N R PLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KKM A LE L FK P F I -------- M KK LV ------ 376
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 411 hpganylvekktgnkkllkygk RDE LA KNL ---- R M gdt I ER ------- H L DD --- NDV VL F NR Q P S LH KIS I MSHRAKV 476
Cdd:PRK00566 377 ---------------------- ERG LA TTI ksak K M --- V ER edpevwd V L EE vik EHP VL L NR A P T LH RLG I QAFEPVL 431
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 477 MP G RTFRFNECA CT PY NADFDGD E M NL H L P QTY EA K AEA SE LM NVK NN LIT P RS G E P LVAAI QD FIT G G Y L LT h KDTFLP 556
Cdd:PRK00566 432 IE G KAIQLHPLV CT AF NADFDGD Q M AV H V P LSL EA Q AEA RV LM LSS NN ILS P AN G K P IIVPS QD MVL G L Y Y LT - REREGA 510
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 557 RA E VYR F AA --- AL IDASAKK --- QTK I RIPPPAIRR p VE LWT G KQLIEL I I r P dkgsdvslnlta KNKSY tgnlelcsk 630
Cdd:PRK00566 511 KG E GMV F SS pee AL RAYENGE vdl HAR I KVRITSKKL - VE TTV G RVIFNE I L - P ------------ EGLPF --------- 567
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 631 dsyv I IR N SV llagc L D K SLLG ssskv N I FYMLM R D YG EDAA V --- D AMWR L A - RM A pv FL S nr G F SIGI G D VRPSE qll 706
Cdd:PRK00566 568 ---- I NV N KP ----- L K K KEIS ----- K I INEVY R R YG LKET V ifl D KIKD L G f KY A -- TR S -- G I SIGI D D IVIPP --- 626
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 707 r EK GQLVDNGYSKCSQYI K ELEE G KL kaqpgc T EE E TLESI I l REL S TIR D HAGQVCLR NLSK YNAPL ---- T MA VC G SK 782
Cdd:PRK00566 627 - EK KEIIEEAEKEVAEIE K QYRR G LI ------ T DG E RYNKV I - DIW S KAT D EVAKAMMK NLSK DQESF npiy M MA DS G AR 698
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 783 GS FIN I S Q miacvgqqa IS G H R ---- P P D G -- F E erslphferkkk TP eakgf VANS F YS GLT PT E F F FH T M G G R E GL V D 856
Cdd:PRK00566 699 GS ASQ I R Q --------- LA G M R glma K P S G ei I E ------------ TP ----- IKSN F RE GLT VL E Y F IS T H G A R K GL A D 752
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 857 TA V KTA ET GY MQ RRLV KCLE D L ------ C ASYD G TVRSSV --- G D VIE ---- FVF G ---- ED GL DP ammea KD G S V V dft 919
Cdd:PRK00566 753 TA L KTA DS GY LT RRLV DVAQ D V ivredd C GTDR G IEVTAI ieg G E VIE plee RIL G rvla ED VV DP ----- ET G E V I --- 824
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 920 hvlehakniqttkeqp I P VDK L - DE VL kaeiqkkfkgkyvhf ADK LS E Y - I TQTE I K kskkwqngkahcgnhetadlktk 997
Cdd:PRK00566 825 ---------------- V P AGT L i DE EI --------------- ADK IE E A g I EEVK I R ----------------------- 850
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 998 esckicknleaykt S L L an S C L T KTQL C S fie L CY YK - V A RA - ITEP G T AVG A IAA T SIGEP S TQ M T LK TFH FA GV asm N 1075
Cdd:PRK00566 851 -------------- S V L -- T C E T RHGV C A --- K CY GR d L A TG k LVNI G E AVG V IAA Q SIGEP G TQ L T MR TFH TG GV --- D 908
810
....*....|....*.
gi 25145495 1076 IT Q G V PR IK E IIN A V K 1091
Cdd:PRK00566 909 IT G G L PR VA E LFE A R K 924
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
331-872
2.47e-58
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: 214.30
E-value: 2.47e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 331 K R AMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P EI vnasniek M R Q L VIN G sdv 410
Cdd:cd01609 226 N R PLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KEM A LE L FK P FV -------- I R E L IER G --- 294
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 411 hpgany L VEKKTGN KK LLK y G K RD E LAKN L R mg DT I ER H lddnd V VL F NR Q P S LH KIS I MSHRAKVMP G RTFRFNECA CT 490
Cdd:cd01609 295 ------ L APNIKSA KK MIE - R K DP E VWDI L E -- EV I KG H ----- P VL L NR A P T LH RLG I QAFEPVLIE G KAIQLHPLV CT 360
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 491 PY NADFDGD E M NL H L P QTY EA K AEA SE LM NVK NN LIT P R SG E P L V AAI QD FIT G G Y L LT HKDT flpraev YRFAAAL I DA 570
Cdd:cd01609 361 AF NADFDGD Q M AV H V P LSL EA Q AEA RV LM LSS NN ILS P A SG K P I V TPS QD MVL G L Y Y LT KERK ------- GDKGEGI I ET 433
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 571 SAKKQTKIR I P P PAIRRPVELWTG K Q L IE LI irpdkgsdvslnltak N KS Y tgnl ELCSKDSYVII rnsvllagc LD K sl 650
Cdd:cd01609 434 TVGRVIFNE I L P EGLPFINKTLKK K V L KK LI ---------------- N EC Y ---- DRYGLEETAEL --------- LD D -- 482
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 651 lgssskvnifyml MRDY G EDA A VDA mwrlarmapvflsnr G F SI G I G D VRPSE qllr EK GQLVDNGYS K CSQYI K EL E E G 730
Cdd:cd01609 483 ------------- IKEL G FKY A TRS --------------- G I SI S I D D IVVPP ---- EK KEIIKEAEE K VKEIE K QY E K G 530
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 731 K L kaqpgc TEEE TLESI I lr E L - STIRDHAGQVCLR NL S K Y -- N APLT MA VC G SK GS FIN I S Q MIACV G QQ A isghr P P D 807
Cdd:cd01609 531 L L ------ TEEE RYNKV I -- E I w TEVTEKVADAMMK NL D K D pf N PIYM MA DS G AR GS KSQ I R Q LAGMR G LM A ----- K P S 597
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 25145495 808 G -- F E ers LP hferkkktpeakgf VANS F YS GLT PT E F F FH T M G G R E GL V DTA V KTA ET GY MQ RRLV 872
Cdd:cd01609 598 G ki I E --- LP -------------- IKSN F RE GLT VL E Y F IS T H G A R K GL A DTA L KTA DS GY LT RRLV 647
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
331-1073
9.36e-56
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: 212.71
E-value: 9.36e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 331 KR AMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P E I vnasniek M R Q L VIN G - SD 409
Cdd:COG0086 311 KR PLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLH Q C G L P KKM A LE L FK P F I -------- Y R K L EER G l AT 382
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 410 VHPG A NYL VE KK tgnkkllkygk RD E LAKN L R mg DT I ER H lddnd V VL F NR Q P S LH KIS I MSHRAKVMP G RTFRFNECA C 489
Cdd:COG0086 383 TIKS A KKM VE RE ----------- EP E VWDI L E -- EV I KE H ----- P VL L NR A P T LH RLG I QAFEPVLIE G KAIQLHPLV C 444
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 490 T PY NADFDGD E M NL H L P QTY EA KA EA SE LM NVK NN LIT P RS G E P LVAAI QD FIT G G Y L LT HKDTFLPR -------- A EV Y 561
Cdd:COG0086 445 T AF NADFDGD Q M AV H V P LSL EA QL EA RL LM LST NN ILS P AN G K P IIVPS QD MVL G L Y Y LT REREGAKG egmifadp E EV L 524
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 562 R - FAAALI D AS A KKQTK I RIPPPAIRRP VE LWT G KQ L IEL I IR pdkgsdvslnlta KNKSYT g N LELCS K DSY VIIR NSV 640
Cdd:COG0086 525 R a YENGAV D LH A RIKVR I TEDGEQVGKI VE TTV G RY L VNE I LP ------------- QEVPFY - N QVINK K HIE VIIR QMY 590
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 641 LLA G CLDKS llgssskvn IF YMLMRDY G EDA A VD A mwrlarmapvflsnr G F SIG IG D V rpse QLLR EK GQLVDNGYSKC 720
Cdd:COG0086 591 RRC G LKETV --------- IF LDRLKKL G FKY A TR A --------------- G I SIG LD D M ---- VVPK EK QEIFEEANKEV 642
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 721 SQYI K ELE EG KL kaqpgc TE E E TLESI I L r ELSTIRDHAGQVCLRNL S KY N APLT MA VC G SK GS FINIS Q MIACV G QQ A i 800
Cdd:COG0086 643 KEIE K QYA EG LI ------ TE P E RYNKV I D - GWTKASLETESFLMAAF S SQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A - 714
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 801 sghr P P D G -- F E erslphferkkk TP eakgf VANS F YS GL TPT E F F FH T M G G R E GL V DTA V KTA ET GY MQ RRLV KCLE D L 878
Cdd:COG0086 715 ---- K P S G ni I E ------------ TP ----- IGSN F RE GL GVL E Y F IS T H G A R K GL A DTA L KTA DS GY LT RRLV DVAQ D V 773
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 879 ------ C ASYD G TVRSSV --- G D VIE FVF gedgldpamm E AKD G S V vdfth VL E HAKNIQ T TKEQPIPVDKL DE VLKAE I 949
Cdd:COG0086 774 ivteed C GTDR G ITVTAI keg G E VIE PLK ---------- E RIL G R V ----- AA E DVVDPG T GEVLVPAGTLI DE EVAEI I 838
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 950 Q kkfkgkyvhfadklseyitqteikkskkwqngkahcgnh E TADLKT K ESCKIC knleayktsllans C L T KTQL C S fie 1029
Cdd:COG0086 839 E --------------------------------------- E AGIDSV K VRSVLT -------------- C E T RGGV C A --- 862
730 740 750 760
....*....|....*....|....*....|....*....|....*.
gi 25145495 1030 L CY YK -- VARAITEP G T AVG A IAA T SIGEP S TQ M T LK TFH FA G V AS 1073
Cdd:COG0086 863 K CY GR dl ARGHLVNI G E AVG V IAA Q SIGEP G TQ L T MR TFH IG G A AS 908
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
243-1073
2.02e-55
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 213.63
E-value: 2.02e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 243 P NDLL LT RM PV P P VCI RP S V V se VKA G T - TED DV TMKLMEIMLT N DV LK KHKRD GAP SKTLFETWEH LQ IQC - A L YI N SE 320
Cdd:PRK09603 1623 P EWMM LT VL PV L P PDL RP L V A -- LDG G K f AVS DV NELYRRVINR N QR LK RLMEL GAP EIIVRNEKRM LQ EAV d V L FD N GR 1700
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 321 MSGLPPDMQ p KR AMRAFTQRL KGKQGRFR G NL C GKRVDFSGR T VI SPD PNL RI D QV G V P IHV A MT L TF P EIV na S NI E K - 399
Cdd:PRK09603 1701 STNAVKGAN - KR PLKSLSEII KGKQGRFR Q NL L GKRVDFSGR S VI VVG PNL KM D EC G L P KNM A LE L FK P HLL -- S KL E E r 1777
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 400 ----- MR Q lvingsdvhpg A NYLV E K K T gnkkllkygkr D E LAKN L R mg DTI E RH lddnd V VL F NR Q P S LHK I SI MSHRA 474
Cdd:PRK09603 1778 gyatt LK Q ----------- A KRMI E Q K S ----------- N E VWEC L Q -- EIT E GY ----- P VL L NR A P T LHK Q SI QAFHP 1828
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 475 K VMP G RTFRFNECA C TPY NADFDGD E M NL H L P QTY EA K AE ASE LM NVKN N LIT P R SG EPLVAAI QD FIT G G Y L L T ----- 549
Cdd:PRK09603 1829 K LID G KAIQLHPLV C SAF NADFDGD Q M AV H V P LSQ EA I AE CKV LM LSSM N ILL P A SG KAVAIPS QD MVL G L Y Y L S leksg 1908
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 550 ---- HK d T F lpr AE V YRFAA A LIDASAKKQT KIR IPPP ai RRPVELWT G KQL I EL I I r PD K gsd VSLN L T aknksytg N L 625
Cdd:PRK09603 1909 vkge HK - L F --- SS V NEIIT A IDTKELDIHA KIR VLDQ -- GNIIATSA G RMI I KS I L - PD F --- IPTD L W -------- N R 1970
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 626 ELCS KD SY V IIRNSVLLA G cldksl L G SSSK vni F YMLMRDY G EDA A VD A mwrlarmapvflsnr G F SI GIG D VRPSE ql 705
Cdd:PRK09603 1971 PMKK KD IG V LVDYVHKVG G ------ I G ITAT --- F LDNLKTL G FRY A TK A --------------- G I SI SME D IITPK -- 2024
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 706 lr E K GQL V DNGYSKCSQYIKELEE G K L kaqpgc T EE E TLES II l RELSTIR D HAGQVCLRNLS K ---- Y N APLT MA VC G S 781
Cdd:PRK09603 2025 -- D K QKM V EKAKVEVKKIQQQYDQ G L L ------ T DQ E RYNK II - DTWTEVN D KMSKEMMTAIA K dkeg F N SIYM MA DS G A 2095
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 782 K GS FIN I S Q MI A CV G QQA isghr P PDG feerslphfe RKKK TP eakgf VANS F YS GL TPT E F F FH T M G G R E GL V DTA V KT 861
Cdd:PRK09603 2096 R GS AAQ I R Q LS A MR G LMT ----- K PDG ---------- SIIE TP ----- IISN F KE GL NVL E Y F NS T H G A R K GL A DTA L KT 2155
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 862 A ET GY MQ R R L ------ VK CLE D L C ASYD G T vrssvg DVIEFVF G EDGLD P a MM E AKD G S V V dfthvleh AKNIQ ttke Q P 935
Cdd:PRK09603 2156 A NA GY LT R K L idvsqn VK VVS D D C GTHE G I ------ EITDIAV G SELIE P - LE E RIF G R V L -------- LEDVI ---- D P 2216
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 936 I P vdkl D E V L KAE iqkkfkgkyvhfadkl SEY I TQTEI KK SKK wqngkahc GNHETADLK T KES CK IC K NLE A Y ktslla 1015
Cdd:PRK09603 2217 I T ---- N E I L LYA ---------------- DTL I DEEGA KK VVE -------- AGIKSITIR T PVT CK AP K GVC A K ------ 2262
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*...
gi 25145495 1016 nscltktql C SFIE L CYY K V arai TE PG T AVG AI AA T SIGEP S TQ M TL K TFH FA G V AS 1073
Cdd:PRK09603 2263 --------- C YGLN L GEG K M ---- SY PG E AVG VV AA Q SIGEP G TQ L TL R TFH VG G T AS 2307
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
235-1097
4.63e-50
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 196.00
E-value: 4.63e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 235 VR SG EE kh P NDLL LT RM P VP P VCI RP s V VS EVKAGTTED D VTMKLME I MLT N DV L K K HKRDGA P SKTLFETWEH LQ IQC - 313
Cdd:PRK14844 1660 IK SG NR -- P EWMI LT TI P IL P PDL RP - L VS LESGRPAVS D LNHHYRT I INR N NR L R K LLSLNP P EIMIRNEKRM LQ EAV d 1736
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 314 A L YI NS EMSG L PPDMQPKRAMRAFTQR LKGKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P EI vn 393
Cdd:PRK14844 1737 S L FD NS RRNA L VNKAGAVGYKKSISDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P T L KLN Q C G L P KRM A LE L FK P FV -- 1814
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 394 asniekmrqlvingsdvhpgan Y LVE K KT G NKKLL K YGKRDEL A KNLRMG D TI E RHLDDND V V L f NR Q P S LH KIS I MSHR 473
Cdd:PRK14844 1815 ---------------------- Y SKL K MY G MAPTI K FASKLIR A EKPEVW D ML E EVIKEHP V L L - NR A P T LH RLG I QAFE 1871
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 474 AKVMP G RTFRFNECA CT PY NADFDGD E M NL H L P QTY EA KA EA SE LM NVK NN LIT P RS G E P LVAAIQ D FIT G G Y L LT --- H 550
Cdd:PRK14844 1872 PILIE G KAIQLHPLV CT AF NADFDGD Q M AV H V P ISL EA QL EA RV LM MST NN VLS P SN G R P IIVPSK D IVL G I Y Y LT lqe P 1951
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 551 K DTF LP RAEVY - RFAAA L I D ASAKKQTK I RIPPPA I RRPV E LW ------ T GKQ LI ELI I R P d K GSDVSLN L T aknksytg 623
Cdd:PRK14844 1952 K EDD LP SFGAF c EVEHS L S D GTLHIHSS I KYRMEY I NSSG E TH yktict T PGR LI LWQ I F P - K HENLGFD L I -------- 2022
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 624 nlelcskdsyviir N S VL lagcldk SLLGSS S K V NIF Y mlm R DY G ED A A V DAMWR L ARMAPVFLSNR G F S IGIG D VRPS E 703
Cdd:PRK14844 2023 -------------- N Q VL ------- TVKEIT S I V DLV Y --- R NC G QS A T V AFSDK L MVLGFEYATFS G V S FSRC D MVIP E 2078
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 704 Q llre K GQL VD NGYSKCSQYIKELEE G KL kaqpgc T EE E TLESI I l R E L S TIR D HAGQVC L RNL ------ SKYN APLT M A 777
Cdd:PRK14844 2079 T ---- K ATH VD HARGEIKKFSMQYQD G LI ------ T RS E RYNKV I - D E W S KCT D MIANDM L KAI siydgn SKYN SVYM M V 2147
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 778 VC G SK GS fin I SQM IACV G QQAIS gh RP P D G feerslphfe RKKK TP eakgf VANS F YS GL TPT E F F FH T M G G R E GL V DT 857
Cdd:PRK14844 2148 NS G AR GS --- T SQM KQLA G MRGLM -- TK P S G ---------- EIIE TP ----- IISN F RE GL NVF E Y F NS T H G A R K GL A DT 2207
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 858 A V KTA ET GY MQ RRLV KCLEDL ------ C ASYD G - T VR SS V gdviefvfg E DGLDP A MM E akdg SVV dfthvlehakn IQT 930
Cdd:PRK14844 2208 A L KTA NS GY LT RRLV DVSQNC ivtkhd C KTKN G l V VR AT V --------- E GSTIV A SL E ---- SVV ----------- LGR 2263
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 931 T KEQP I -- PV D K ld E V L K aeiqkkfkgkyvhfad K LS E Y I TQTEI K kskkwqng KAHCGNHETADLKTKES C K I CKN lea 1008
Cdd:PRK14844 2264 T AAND I yn PV T K -- E L L V ---------------- K AG E L I DEDKV K -------- QINIAGLDVVKIRSPLT C E I SPG --- 2314
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1009 yktsllanscltktq L CS fie LCY YK -- VARA I TEP G T AVG A IAA T S I GEP S TQ M T LK TFH FA GV asmn I T Q GV prik E I 1086
Cdd:PRK14844 2315 --------------- V CS --- LCY GR dl ATGK I VSI G E AVG V IAA Q S V GEP G TQ L T MR TFH IG GV ---- M T R GV ---- E S 2368
890
....*....|.
gi 25145495 1087 I N AVKT I STP I 1097
Cdd:PRK14844 2369 S N IIAS I NAK I 2379
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
524-699
2.57e-47
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: 166.65
E-value: 2.57e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 524 N LIT P RS G E P LVAAI QD FIT G G YLLT HK DTF LP R A EV YRFA aalidasakk QTK I RI P P PAI RR P V - E LWTGKQ LIELII 602
Cdd:pfam04983 1 N ILS P QN G K P IIGPS QD MVL G A YLLT RE DTF FD R E EV MQLL ---------- MYG I VL P H PAI LK P I k P LWTGKQ TFSRLL 70
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 603 RPD kgsdvs L N L ta K N K SY T GNLE LC SK DSYV I I R N SV L LA G CL DK SLL G s S S KVNIFYMLMRD YG EDAAVDAMW RL ARM 682
Cdd:pfam04983 71 PNE ------ I N P -- K G K PK T NEED LC EN DSYV L I N N GE L IS G VI DK KTV G - K S LGSLIHIIYKE YG PEETAKFLD RL QKL 141
170
....*....|....*..
gi 25145495 683 APVF L SNR GFSIGI G D V 699
Cdd:pfam04983 142 GFRY L TKS GFSIGI D D I 158
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1043-1373
3.85e-45
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: 160.28
E-value: 3.85e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1043 G T AVG AI AA T SIGEP S TQMTL K TFHFAGVASMN I T Q G V PR I KEI I NA V ktistpiitaall DPYD eslarrvkariektt 1122
Cdd:cd00630 1 G E AVG VL AA Q SIGEP G TQMTL R TFHFAGVASMN V T L G L PR L KEI L NA A ------------- SIHE --------------- 52
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1123 lgeicdy IE E V ylpddyfllvklnskrirllqlevcmesisyaiatskvcpqmrgckivahgktmmairppstsklsktm 1202
Cdd:cd00630 53 ------- ML E A --------------------------------------------------------------------- 56
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1203 tmqilkyslanvvvkgipsvnrcvihadekkgdfysllvegtdfrsvlssvgvdprktnfnnalvvadv LGIEAAR SC II 1282
Cdd:cd00630 57 --------------------------------------------------------------------- LGIEAAR ET II 67
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1283 N EI IATMDAH G IGL DRRH VM L L ADVMTY R G EVL G I TR N G LVKM K D S V L LL ASFEKT MD HL FE AA FFSQR D VIH GVSE C II 1362
Cdd:cd00630 68 R EI QKVLASQ G VSV DRRH IE L I ADVMTY S G GLR G V TR S G FRAS K T S P L MR ASFEKT TK HL LD AA AAGEK D ELE GVSE N II 147
330
....*....|.
gi 25145495 1363 M G T P MTV GTG T 1373
Cdd:cd00630 148 L G R P APL GTG S 158
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
724-830
2.09e-38
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: 139.04
E-value: 2.09e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 724 I KEL E E - GKL KAQP G C T E EE TL E SI I LRE L STI RD H AG QVCLRN L SKY N APLT MA VC G S KGS F INISQ MIA C V GQQ AIS G 802
Cdd:pfam05000 1 I TDA E R y GKL EDIW G M T L EE SF E AL I NNI L NKA RD P AG NIASKS L DPN N SIYM MA DS G A KGS I INISQ IAG C R GQQ NVE G 80
90 100
....*....|....*....|....*...
gi 25145495 803 H R P P D GF EE R S LPHF ERKKKT PE AK GFV 830
Cdd:pfam05000 81 K R I P F GF SG R T LPHF KKDDEG PE SR GFV 108
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
332-549
3.13e-37
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 149.90
E-value: 3.13e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 332 R AMRAFTQRLK GKQGRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF P EIVN asniekmr Q L VIN G sdvh 411
Cdd:PRK02625 330 R PLKSLSDIIE GKQGRFR Q NL L GKRVD Y SGR S VI VVG P K L KMH Q C G L P KEM A IE L FQ P FVIH -------- R L IRQ G ---- 397
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 412 pgany L V EKKTGN KKL LK yg KR D ELAKNL r MGDT IE R H lddnd V VL F NR Q P S LH KIS I MSHRAKVMP GR TFRFNECA C TP 491
Cdd:PRK02625 398 ----- I V NNIKAA KKL IQ -- RA D PEVWQV - LEEV IE G H ----- P VL L NR A P T LH RLG I QAFEPILVE GR AIQLHPLV C PA 464
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 25145495 492 Y NADFDGD E M NL H L P QTY EA K AEA SE LM NVK NN LIT P RS GEP L V AAI QD FIT G G Y L LT 549
Cdd:PRK02625 465 F NADFDGD Q M AV H V P LSL EA Q AEA RL LM LAS NN ILS P AT GEP I V TPS QD MVL G C Y Y LT 522
rpoC1
CHL00018 RNA polymerase beta' subunit
311-549
6.64e-34
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 140.04
E-value: 6.64e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 311 I Q C A L -- YINSEMS G L P PDMQPKRAMRA F TQRLK GK Q GRFR G NL C GKRVD F SGR T VI SPD P N L RID Q V G V P IHV A MT L TF 388
Cdd:CHL00018 328 L Q E A V da LLDNGIR G Q P MRDGHNKPYKS F SDVIE GK E GRFR E NL L GKRVD Y SGR S VI VVG P S L SLH Q C G L P REI A IE L FQ 407
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 389 P EIVN ------- ASNI E kmrqlvingsdvhp G A NYLVEK K tg NKKLLK ygkrdelaknlrmgdt I ERHLDDNDV VL F NR Q 461
Cdd:CHL00018 408 P FVIR glirqhl ASNI R -------------- A A KSKIRE K -- EPIVWE ---------------- I LQEVMQGHP VL L NR A 455
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 462 P S LH KIS I MSHRAKVMP GR TFRFNECA C TPY NADFDGD E M NL H L P QTY EA K AEA SE LM NVKN NL IT P RS G E P LVAAI QD F 541
Cdd:CHL00018 456 P T LH RLG I QAFQPILVE GR AICLHPLV C KGF NADFDGD Q M AV H V P LSL EA Q AEA RL LM FSHM NL LS P AI G D P ISVPS QD M 535
....*...
gi 25145495 542 IT G G Y L LT 549
Cdd:CHL00018 536 LL G L Y V LT 543
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
686-1080
4.16e-17
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: 87.60
E-value: 4.16e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 686 FLSNR G F SI GIG D -- V R P SE Q L L R E KGQ lvdngyskcsqyi KE LEEGKLKAQP G - C TE E E TLESI I LRELS T IRDHAGQ V 762
Cdd:TIGR02388 42 YATRA G V SI SVD D lk V P P AK Q D L L E AAE ------------- KE IRATEERYRR G e I TE V E RFQKV I DTWNG T NEELKDE V 108
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 763 C -- L R NLSKY N APLT MA VC G SK G sfi N I SQ MIAC VG QQAISGH rp P D G f E ERS LP hferkkktpeakgf VANS F YS GLT P 840
Cdd:TIGR02388 109 V nn F R QTDPL N SVYM MA FS G AR G --- N M SQ VRQL VG MRGLMAN -- P Q G - E IID LP -------------- IKTN F RE GLT V 168
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 841 TE FFFHTM G G R E GLVDTA VK TA ET GY MQ RRLV KCLE D lcasydgtvrssvgd VI efvfgedgldpammeakdgsvvdfth 920
Cdd:TIGR02388 169 TE YVISSY G A R K GLVDTA LR TA DS GY LT RRLV DVSQ D --------------- VI -------------------------- 207
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 921 vleh AKNIQTTK E QP I P V DKLD E vlkaeiqkkf KG K YVHFA D K L SEYITQTEIKKSKK wqngkahcgn HETADLK T KESC 1000
Cdd:TIGR02388 208 ---- VREEDCGT E RS I V V RAMT E ---------- GD K KISLG D R L LGRLVAEDVLHPEG ---------- EVIVPKN T AIDP 263
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1001 KIC K NL E AYKT S - LLAN S C LT KTQLC S FIEL CY - YKV A R A - ITEP G T AVG A IAA T SIGEP S TQ M T LK TFH FA GV ASMNIT 1077
Cdd:TIGR02388 264 DLA K TI E TAGI S e VVVR S P LT CEAAR S VCRK CY g WSL A H A h LVDL G E AVG I IAA Q SIGEP G TQ L T MR TFH TG GV FTGEVA 343
...
gi 25145495 1078 QG V 1080
Cdd:TIGR02388 344 RQ V 346
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1039-1091
8.02e-17
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: 80.65
E-value: 8.02e-17
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 25145495 1039 IT E P G T AVG A IAA T SIGEP S TQ M T LK TFH FA GVA S m N ITQG V PR IK E IIN A V K 1091
Cdd:cd02655 2 LV E L G E AVG I IAA Q SIGEP G TQ L T MR TFH TG GVA T - D ITQG L PR VE E LFE A R K 53
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
771-1071
6.80e-14
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 76.96
E-value: 6.80e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 771 N A PL T ---- MA VC G SK G sfi N I SQ MIAC VG QQAISGH rp P D G f E ERS LP hferk K KT peakgfvan S F YS GLT P TE FFFH 846
Cdd:PRK02597 116 N D PL N svym MA FS G AR G --- N M SQ VRQL VG MRGLMAN -- P Q G - E IID LP ----- I KT --------- N F RE GLT V TE YVIS 175
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 847 TM G G R E GLVDTA VK TA ET GY MQ RRLV KCLE D L ------ C asyd GT V R SS V gdvief V FGE D GL D PAMMEAK D --- G S V VD 917
Cdd:PRK02597 176 SY G A R K GLVDTA LR TA DS GY LT RRLV DVSQ D V ivreed C ---- GT T R GI V ------ V EAM D DG D RVLIPLG D rll G R V LA 245
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 918 f TH V LEHAKNIQTTKEQP I pvdkl D EV L KAE I Q K kfkgkyvhfadklseyitqteikkskkwqngkahcgnhetadlktk 997
Cdd:PRK02597 246 - ED V VDPEGEVIAERNTA I ----- D PD L AKK I E K ---------------------------------------------- 273
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 25145495 998 esckicknle A YKTSLLAN S C LT KTQLC S FIEL CY - YKV A RA - ITEP G T AVG A IAA T SIGEP S TQ M T LK TFH FA GV 1071
Cdd:PRK02597 274 ---------- A GVEEVMVR S P LT CEAAR S VCRK CY g WSL A HN h LVDL G E AVG I IAA Q SIGEP G TQ L T MR TFH TG GV 339
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
837-1080
2.90e-11
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 68.43
E-value: 2.90e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 837 GL TP TE FFFHTM G G R E G L VDTAV K TA ET GY MQ RRLV KCLEDL ------ C asyd GT V R S ----- SV G DV IE FVF g EDG L D p 905
Cdd:CHL00117 172 GL SL TE YIISCY G A R K G V VDTAV R TA DA GY LT RRLV EVVQHI vvretd C ---- GT T R G isvsp RN G MM IE RIL - IQT L I - 245
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 906 ammeakd G S V V dfthvleh A KN I QTTKE ------ Q P I PVDKLDEVLKAEI Q KKF kgkyvhfadklseyitqte I K ----- 974
Cdd:CHL00117 246 ------- G R V L -------- A DD I YIGSR ciatrn Q D I GIGLANRFITFRA Q PIS ------------------- I R spltc 291
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 975 K S KK W qngkahcgnhetadlktkesck IC knleayktsllanscltkt QLC -------- SFI EL cyykvaraitep G T AV 1046
Cdd:CHL00117 292 R S TS W ---------------------- IC ------------------- QLC ygwslahg DLV EL ------------ G E AV 318
250 260 270
....*....|....*....|....*....|....
gi 25145495 1047 G A IA AT SIGEP S TQ M TL K TFH FA GV ASMNITQG V 1080
Cdd:CHL00117 319 G I IA GQ SIGEP G TQ L TL R TFH TG GV FTGGTAEQ V 352
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1043-1377
8.69e-11
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: 65.52
E-value: 8.69e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1043 G TA VG AI AAT S I G EP STQMT L KT fhfagv ASMNITQGVPRI KE IINA - V K TI S TPIITAAL L DPYDESL --------- A R 1112
Cdd:cd02737 1 G EP VG SL AAT A I S EP AYKAL L DP ------ PQSLESSPLELL KE VLEC r S K SK S KENDRRVI L SLHLCKC dhgfeyera A L 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1113 R VK ARI E KT TL GEICDYIEEV Y L P DDYFLL V KLNSKRIRLLQLEVCMESI S YAIATS K VC P --- QMRGC K IVAHGKTMMA 1189
Cdd:cd02737 75 E VK NHL E RV TL EDLATTSMIK Y S P QATEAI V GEIGDQLNTKKKGKKKAIF S TSLKIT K FS P wvc HFHLD K ECQKLSDGPC 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1190 IR ------- PP S TSK L SKTMTMQ I LK y S L ANV V V KG --- I P SVN rcvihadekkgdfys L L V E GTDFR S VLS SVG VDP R - 1258
Cdd:cd02737 155 LT fsvskev SK S SEE L LDVLRDR I IP - F L LET V I KG der I K SVN --------------- I L W E DSPST S WVK SVG KSS R g 218
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1259 --------------- KT N FN N ALV ---------------------- VAD VLGI E AA RSCIINEIIATMDAH G IGLD R R H V 1301
Cdd:cd02737 219 elvlevtveesckkt RG N AW N VVM dacipvmdlidwersmpysiqq IKS VLGI D AA FEQFVQRLESAVSMT G KSVL R E H L 298
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25145495 1302 M L L AD V MTY R GE VL G ITRN G LVKMKD S V ----- LLL A S F EKTMDHLFE AA FFSQR D VIH GV SECIIM G TPMT VGTG T - F K 1375
Cdd:cd02737 299 L L V AD S MTY S GE FV G LNAK G YKAQRR S L kisap FTE A C F SSPIKCFLK AA KKGAS D SLS GV LDACAW G KEAP VGTG S k F E 378
..
gi 25145495 1376 LM 1377
Cdd:cd02737 379 IL 380
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
1314-1387
5.56e-04
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 44.91
E-value: 5.56e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25145495 1314 V LGITR NGL vk MK DS VLLL ASF EK T MDH L F EA AFFSQR D VIHGVS E CIIM G TPMT VGTG TF K lmqky D KK A VL K 1387
Cdd:PRK09603 2816 L LGITR AAI -- GS DS IISA ASF QE T TKV L T EA SIAMKK D FLEDLK E NVVL G RMIP VGTG MY K ----- N KK I VL R 2882
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
