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DNA-directed RNA polymerase III subunit RPC1 isoform X1 [Eumetopias jubatus]
Protein Classification
DNA-directed RNA polymerase III subunit RPC1 ( domain architecture ID 10118853 )
DNA-directed RNA polymerase III subunit RPC1 is the largest and is a catalytic core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
24-891
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: 1670.39
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 24 SPE EMRQQAHIQ V VSK NLY SQDNHH a PL L YGVLD H R M GTS E KD RP CETCG K NLADC L GH Y GYI D LELP C FH V GYF R A V I G 103
Cdd:cd02583 2 SPE DIIRLSEVE V TNR NLY DIETRK - PL P YGVLD P R L GTS D KD GI CETCG L NLADC V GH F GYI K LELP V FH I GYF K A I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 104 ILQ M ICKTC CHIM L SQ EEK KQ FL DY L K RP G L TY LQK RG LKKKI SD KC R K KNI C HY CG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C PH CG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 184 kvvdpvvsnflqsfetaiehnkevep LL GR AQE N LNPL V VLNLFK R IP A EDV P LLLMNP E AG K P SD LILTR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL K VLNLFK N IP P EDV E LLLMNP L AG R P EN LILTR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RIS GAKTQ M IMEDWDFLQLQCALYINSEL S G I PL N M A PKK WT RGF V Q 343
Cdd:cd02583 192 PSVV M D E KSGTNEDDLT V KL S EIIFLNDVIKKH LEK GAKTQ K IMEDWDFLQLQCALYINSEL P G L PL S M Q PKK PI RGF C Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV R NGP E VHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGP D VHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 R HTQM K R FLKYGNR E K M A Q ELK Y GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L AKV K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R AKV M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDRA KA CQ IIASI L vgk D EK IK VH L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDRA QF CQ LCSYM L --- D GE IK ID L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C V ND S YV T I Q NSEL MS G SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 PPP A ILKPV E LWTGKQIFS LL LRP NKKS PV LV NL EA K E K S Y TK K SP D M C P ND G YV V I R NSEL LC G RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 664 FY I LLRD W G QNE AA D AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K Y EL LNA GY K KCDEYI EALNT GKL QQ QPGCT 743
Cdd:cd02583 589 FY V LLRD Y G PEA AA A AM N RLA K L SSRW LSNRGFSIGI D DVTP SKE LLK K K E EL VDN GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 744 AE E TLEA L I LK ELS V IR DH AG S ACL R EL D KSNSPL T MALCGSKGS F INISQMIACVGQQ A ISG S R V P D GFE N R S LPHF EK 823
Cdd:cd02583 669 AE Q TLEA K I SG ELS K IR ED AG K ACL K EL H KSNSPL I MALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1570460116 824 H SK L PAAKGFVANSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1051-1390
0e+00
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: 567.62
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1051 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DK D D D ADY AR L 1130
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK N ISTPIITA K L EN D R D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1131 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysicmsklrvkpgdvavhgeavvcvtpren 1210
Cdd:cd02736 81 VKGRIEKT Y LGE VAS YIEEV YS PDDC Y IL I KL DKKI I EK L Q L -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1211 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek YKLLVEG DN LRAVM A T H GV K GTRTTSN NTY EVEK T LGI 1290
Cdd:cd02736 123 SKS NL Y FL LQ S LK RK LP D VVV S GIPEV K RAVI NK D KKK GK -- YKLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1291 EAAR T TIINEIQYTM VN HGMSID R RH V MLL S DLMT Y KGEVLGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1370
Cdd:cd02736 201 EAAR S TIINEIQYTM KS HGMSID P RH I MLL A DLMT F KGEVLGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 1570460116 1371 C GVSECIIMG I PM N IGTGLF 1390
Cdd:cd02736 281 E GVSECIIMG K PM P IGTGLF 300
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
24-891
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: 1670.39
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 24 SPE EMRQQAHIQ V VSK NLY SQDNHH a PL L YGVLD H R M GTS E KD RP CETCG K NLADC L GH Y GYI D LELP C FH V GYF R A V I G 103
Cdd:cd02583 2 SPE DIIRLSEVE V TNR NLY DIETRK - PL P YGVLD P R L GTS D KD GI CETCG L NLADC V GH F GYI K LELP V FH I GYF K A I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 104 ILQ M ICKTC CHIM L SQ EEK KQ FL DY L K RP G L TY LQK RG LKKKI SD KC R K KNI C HY CG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C PH CG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 184 kvvdpvvsnflqsfetaiehnkevep LL GR AQE N LNPL V VLNLFK R IP A EDV P LLLMNP E AG K P SD LILTR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL K VLNLFK N IP P EDV E LLLMNP L AG R P EN LILTR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RIS GAKTQ M IMEDWDFLQLQCALYINSEL S G I PL N M A PKK WT RGF V Q 343
Cdd:cd02583 192 PSVV M D E KSGTNEDDLT V KL S EIIFLNDVIKKH LEK GAKTQ K IMEDWDFLQLQCALYINSEL P G L PL S M Q PKK PI RGF C Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV R NGP E VHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGP D VHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 R HTQM K R FLKYGNR E K M A Q ELK Y GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L AKV K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R AKV M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDRA KA CQ IIASI L vgk D EK IK VH L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDRA QF CQ LCSYM L --- D GE IK ID L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C V ND S YV T I Q NSEL MS G SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 PPP A ILKPV E LWTGKQIFS LL LRP NKKS PV LV NL EA K E K S Y TK K SP D M C P ND G YV V I R NSEL LC G RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 664 FY I LLRD W G QNE AA D AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K Y EL LNA GY K KCDEYI EALNT GKL QQ QPGCT 743
Cdd:cd02583 589 FY V LLRD Y G PEA AA A AM N RLA K L SSRW LSNRGFSIGI D DVTP SKE LLK K K E EL VDN GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 744 AE E TLEA L I LK ELS V IR DH AG S ACL R EL D KSNSPL T MALCGSKGS F INISQMIACVGQQ A ISG S R V P D GFE N R S LPHF EK 823
Cdd:cd02583 669 AE Q TLEA K I SG ELS K IR ED AG K ACL K EL H KSNSPL I MALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1570460116 824 H SK L PAAKGFVANSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
7-930
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 955.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 7 RETDVA K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D N hh A P LLY G VL D H R M G TSEKDRP C E TCG KNLAD C L GH Y G Y I 86
Cdd:PRK08566 1 SMMMIP K R I GS I K FG LL SPEE I R KMSVTKIITADT Y DD D G -- Y P IDG G LM D P R L G VIDPGLR C K TCG GRAGE C P GH F G H I 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 87 D L EL P CF HVG YFRAVIGI L QMI C KT C CHIM L SQ EE KKQF L DY L K R PGLTYLQKRG L K K KISDKCR K KNI C HY CG A fngtv 166
Cdd:PRK08566 79 E L AR P VI HVG FAKLIYKL L RAT C RE C GRLK L TE EE IEEY L EK L E R LKEWGSLADD L I K EVKKEAA K RMV C PH CG E ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 167 K K cgl L KI IH EK yktnkkvvd P V vsnflqsfe T AI E HN KE VE pllgraq EN L N P LVVLNLFKR IP A ED VP LL LM NPE AGK 246
Cdd:PRK08566 154 K Q --- Y KI KF EK --------- P T --------- T FY E ER KE GL ------- VK L T P SDIRERLEK IP D ED LE LL GI NPE VAR 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 247 P SDLI LT R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRIS GA K t Q M I M ED - W DF LQ LQCAL Y INS E 324
Cdd:PRK08566 206 P EWMV LT V L P VPP VTV RPS IT -- L ET G q RS EDDLT H KL VD II RI N QRL K ENIEA GA P - Q L I I ED l W EL LQ YHVTT Y FDN E 282
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 325 LS GIP lnma P ----- KKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT F PE K V NKA 399
Cdd:PRK08566 283 IP GIP ---- P arhrs GRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EAI AK E LT V PE R V TEW 358
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 400 NI NF LR KL V R NGPE V HPGAN FI qq RHTQMK R F - L KYG N R E KM A QE L KY G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA 478
Cdd:PRK08566 359 NI EE LR EY V L NGPE K HPGAN YV -- IRPDGR R I k L TDK N K E EL A EK L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RV 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 479 K V K P HR TFR F N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLVT PR N G E P L I AA IQD FLT GAYLLT L K D T F 558
Cdd:PRK08566 437 R V L P GK TFR L N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RI LM LVQEHILS PR Y G G P I I GG IQD HIS GAYLLT R K S T L 516
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 559 F DRAK A CQIIASILVGKDE kikvh L P P P T I LKPVTL WTGKQIFS VI L r P S D D N PVR anl RT K GKQY C GKGED - L C VN D S Y 637
Cdd:PRK08566 517 F TKEE A LDLLRAAGIDELP ----- E P E P A I ENGKPY WTGKQIFS LF L - P K D L N LEF --- KA K ICSG C DECKK e D C EH D A Y 587
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 638 V T I Q N SE L MS G SM DK GTL G SG s KNN I FYILLRDW G QNE A ADAMSRLA RLA PVYLSN RGF SI GI G D VT - P GQGLLKAK y E L 716
Cdd:PRK08566 588 V V I K N GK L LE G VI DK KAI G AE - QGS I LDRIVKEY G PER A RRFLDSVT RLA IRFIML RGF TT GI D D ED i P EEAKEEID - E I 665
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 717 LNAGY K KCD E Y IEA LNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE L DKS N SPLT MA LC G SK GS FI N IS QM I 796
Cdd:PRK08566 666 IEEAE K RVE E L IEA YEN 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 745
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 797 ACVGQQ AIS G S R VPD G FEN R S LPHF EKHSKLPA A K GFV AN S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GYMQRRL V 876
Cdd:PRK08566 746 ACVGQQ SVR G E R IRR G YRD R T LPHF KPGDLGAE A R GFV RS S YK SGLTPTEFFFH A M G GREGLVDTAV R T SQS GYMQRRL I 825
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 1570460116 877 KS L E DL CSQ YD L TVR SST G D I I QF I YG G DG L DP AAMEG k DE P LEFK R VLDNIKA 930
Cdd:PRK08566 826 NA L Q DL KVE YD G TVR DTR G N I V QF K YG E DG V DP MKSDH - GK P VDVD R IIERVLG 878
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-925
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 885.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 13 KKI SH I C FG MK SPEE M R QQAHIQ VV SKNL Y SQ D NH ha P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P C 92
Cdd:TIGR02390 2 KKI GS I K FG LL SPEE I R KMSVVE VV TADT Y DD D GY -- P IEG G LM D P R L G VI E PGLR C K TCG GKVGE C P GH F G H I E L AR P V 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 93 F HVG YFRAVIG IL QMI C KT C CH I M L SQ EE KK Q F L D - YL K RPGLTYLQKRG L KK KI SDKCR K KNI C HY CG A fngtvkkc GL 171
Cdd:TIGR02390 80 V HVG FAKEIYK IL RAT C RK C GR I T L TE EE IE Q Y L E k IN K LKEEGGDLAST L IE KI VKEAA K RMK C PH CG E -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 172 L KI IH EK yktnkkvvd P vv SN F LQ sfetaiehnkevep LLGRAQEN L N P LVVLNLFKR IP A ED VP LL LM NP EAGK P SDLI 251
Cdd:TIGR02390 152 K KI KF EK --------- P -- TY F YE -------------- EGKEGDVK L T P SEIRERLEK IP D ED AE LL GI NP KVAR P EWMV 206
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 252 LT R L L VPP LCI RPS VV sd L KS G T - N EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I MED W DF LQ LQC A L Y INS EL S GIP - 329
Cdd:TIGR02390 207 LT V L P VPP VTV RPS IT -- L ET G E r S EDDLT H KL VD II RI N QRL K ENIEA GA PQLI I EDL W EL LQ YHV A T Y FDN EL P GIP p 284
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 330 LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT F PE K V NKA NI NF LR KL V R 409
Cdd:TIGR02390 285 ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PE R V TPW NI DE LR EY V L 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 410 NGP EVH PGAN FIQQ rh TQMK R F - LKYG N R E KM A QE L KY G DI VERHLIDGD V VLFNRQPSLH KL S I M A H LA KV K P HR TFR F 488
Cdd:TIGR02390 365 NGP DSW PGAN YVIR -- PDGR R I k IRDE N K E EL A ER L EP G WV VERHLIDGD I VLFNRQPSLH RM S M M G H KV KV L P GK TFR L 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 489 N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLV TPR N G E P L I AA I Q D FLT GAYLLT L K D T F F DRAKACQ I I 568
Cdd:TIGR02390 443 N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RE LM LVEEHIL TPR Y G G P I I GG I H D YIS GAYLLT H K S T L F TKEEVQT I L 522
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 569 ASI lvgkde KIKVHL P P P T I L KP VTL WTGKQIFS VI L r P S D D N PVRANLRTK G KQY C G K G E dl C VN D S YV T I Q N SE L MS G 648
Cdd:TIGR02390 523 GVA ------ GYFGDP P E P A I E KP KEY WTGKQIFS AF L - P E D L N FEGRAKICS G SDA C K K E E -- C PH D A YV V I K N GK L LK G 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 649 SM DK GTL G S g S K NN I FYILL R DW G QNE A ADAMSRLA RL APVYLSN RGF SI GI G D VTPGQGLLKAKY EL LNAGY K KC D EY I 728
Cdd:TIGR02390 594 VI DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT RL FIRFITL RGF TT GI D D IDIPKEAKEEIE EL IEKAE K RV D NL I 672
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 729 E ALNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE LD KS N SPLT MA LC G SK GS FI NI S QM I A C VGQQ AIS G S R 808
Cdd:TIGR02390 673 E RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG EVAEKY LD PE N HAVI MA RT G AR GS LL NI T QM A A M VGQQ SVR G G R 752
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 809 VPD G FE NR S LPHF E K HSKLPA A K GFV AN SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GYMQRRL VKS L E DL CSQ YD L 888
Cdd:TIGR02390 753 IRR G YR NR T LPHF K K GDIGAK A R GFV RS SF KK GL D PTE Y FFH AAG GREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE YD G 832
890 900 910
....*....|....*....|....*....|....*...
gi 1570460116 889 TVR SST G DI IQF I YG G DG L DP AAME - GK de P LEF K RVL 925
Cdd:TIGR02390 833 TVR DTR G NL IQF K YG E DG V DP MKSD h GK -- P VDV K KIF 868
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1051-1390
0e+00
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: 567.62
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1051 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DK D D D ADY AR L 1130
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK N ISTPIITA K L EN D R D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1131 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysicmsklrvkpgdvavhgeavvcvtpren 1210
Cdd:cd02736 81 VKGRIEKT Y LGE VAS YIEEV YS PDDC Y IL I KL DKKI I EK L Q L -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1211 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek YKLLVEG DN LRAVM A T H GV K GTRTTSN NTY EVEK T LGI 1290
Cdd:cd02736 123 SKS NL Y FL LQ S LK RK LP D VVV S GIPEV K RAVI NK D KKK GK -- YKLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1291 EAAR T TIINEIQYTM VN HGMSID R RH V MLL S DLMT Y KGEVLGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1370
Cdd:cd02736 201 EAAR S TIINEIQYTM KS HGMSID P RH I MLL A DLMT F KGEVLGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 1570460116 1371 C GVSECIIMG I PM N IGTGLF 1390
Cdd:cd02736 281 E GVSECIIMG K PM P IGTGLF 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
248-550
5.81e-150
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 456.60
E-value: 5.81e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 248 SDL ILT R L L VPP L C I RPSV VS D L k SGTN EDDLT MK L TE II FL N DVI K KHRIS GA KTQM I MEDWDF LQ LQCALY I NS E l SG 327
Cdd:smart00663 1 EWM ILT V L P VPP P C L RPSV QL D G - GRFA EDDLT HL L RD II KR N NRL K RLLEL GA PSII I RNEKRL LQ EAVDTL I DN E - GL 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 328 IPL N MAPKKWTRGFV QRLKGK Q GRFR G NL S GKRVDFS G R T VI S PDPNL RID EV A VP VHV A KI LTFPE K V NKA NI NF LRKL 407
Cdd:smart00663 79 PRA N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLN EV G VP KEI A LE LTFPE I V TPL NI DK LRKL 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 408 VRNGP evh P GA NF I QQ rht QM K RF LK YGNRE K M A QE LK Y GDIVERH L IDGDVVLFNRQP S LH KL SI M AH LAK V KPHR T F R 487
Cdd:smart00663 159 VRNGP --- N GA KY I IR --- GK K TN LK LAKKS K I A NH LK I GDIVERH V IDGDVVLFNRQP T LH RM SI Q AH RVR V LEGK T I R 232
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1570460116 488 F N EC VC T PYNADFDGDEMNLH L PQ TE EA K AEA LV LM GTKA N LVT P R NG E P L I AA IQD F L T G A Y 550
Cdd:smart00663 233 L N PL VC S PYNADFDGDEMNLH V PQ SL EA R AEA RE LM LVPN N ILS P K NG K P I I GP IQD M L L G L Y 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
12-356
7.69e-131
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: 406.68
E-value: 7.69e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 12 A KKI SH I C FG MK SPEE M R QQAHIQ V VSKNL Y S q DNHHA P LLY G V LD H RMGT SE KD RP CETCGK NLA DC L GH Y G Y I D L EL P 91
Cdd:pfam04997 1 L KKI KE I Q FG IA SPEE I R KWSVGE V TKPET Y N - YGSLK P EEG G L LD E RMGT ID KD YE CETCGK KKK DC P GH F G H I E L AK P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 92 C FH V G Y F RAVIG IL QMI CK T C CHIM L SQEEK K Q F LDYL KR P GL TY L QKR gl K K K I SDK C R KK NI C HY CG AF NG TVKK cgl 171
Cdd:pfam04997 80 V FH I G F F KKTLK IL ECV CK Y C SKLL L DPGKP K L F NKDK KR L GL EN L KMG -- A K A I LEL C K KK DL C EH CG GK NG VCGS --- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 172 lkiihekyktnkkv VD PV VSNFLQSFET AI EHN KE V E pllgr AQ E N LNP LV VL NL FKRI PA EDV PL L LM NP EAGK P SDL I 251
Cdd:pfam04997 155 -------------- QQ PV SRKEGLKLKA AI KKS KE E E ----- EK E I LNP EK VL KI FKRI SD EDV EI L GF NP SGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 252 LT R L L VPP L CIRPSV VS D LK s GTN EDDLT M KL TE II FL N DVI KK HRIS GA KTQM I M E D W DF LQ LQC A LYINS E LS G I P L - 330
Cdd:pfam04997 216 LT V L P VPP P CIRPSV QL D GG - RRA EDDLT H KL RD II KR N NRL KK LLEL GA PSHI I R E E W RL LQ EHV A TLFDN E IP G L P P a 294
330 340
....*....|....*....|....*.
gi 1570460116 331 NMAP K KWTRGFV QRLKGK Q GRFRGNL 356
Cdd:pfam04997 295 LQKS K RPLKSIS QRLKGK E GRFRGNL 320
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
841-1346
1.55e-114
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: 370.15
E-value: 1.55e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 841 GLTP T EFFFHTM A GREGL V DTAVKTAE T GY M QRRLVK S LEDL CSQ YD L TVR S S T G D I I QF I YG G DGLDP AAM E GKD e PLE 920
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G E I V QF L YG E DGLDP LKI E KQG - RFT 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 921 FKRVLDNIKAV F PCQ sepa L SKNE L V L ttesimkkteflccq DS F LQEI K NFVKGVSE K IKKT R DKYGINDNG T TEVA L S 1000
Cdd:pfam04998 80 IEFSDLKLEDK F KND ---- L LDDL L L L --------------- SE F SLSY K KEILVRDS K LGRD R LSKEAQERA T LLFE L L 140
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1001 FPD G lgcpqrarvpqpdphtwflf L QPRVLYQLDRITPTQIEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL 1080
Cdd:pfam04998 141 LKS G -------------------- L ESKRVRSELTCNSKAFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1081 K TFHFAGVAS M N I TLGVPR I KEIIN A SK A I ST P II T AQ L -- DKDDDADY A RL V K G R IEK TL LG EIS E YI E ---------- 1148
Cdd:pfam04998 201 N TFHFAGVAS K N V TLGVPR L KEIIN V SK N I KS P SL T VY L fd EVGRELEK A KK V Y G A IEK VT LG SVV E SG E ilydpdpfnt 280
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1149 -------------------- EVFLP D DCFI L VK L SLERIRL L RLEVNAETVRYS I CM S k L R V K pg DVAVHGE A VVCV T PR 1208
Cdd:pfam04998 281 piisdvkgvvkffdiidevt NEEEI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I PR S - I R N K -- VDEGRDI A IGEI T AF 357
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1209 ENSK S SMYY ------- VLQF L KED ------------ L PKVVVQ GIP EVS R AVIHI D E q S GK EK -- YK L LV EG D NL RA V MA 1267
Cdd:pfam04998 358 IIKI S KKIR qdtgglr RVDE L FME edpklailvasl L GNITLR GIP GIK R ILVNE D D - K GK VE pd WV L ET EG V NL LR V LL 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1268 TH G - V KGT R TT SN NTY E VEKT LGIEAAR TTII NEI QYTMVNH G MS I DR RH VM L LS D L MT Y KG EVLG I T R F G LA K MKE S V L 1346
Cdd:pfam04998 437 VP G f V DAG R IL SN DIH E ILEI LGIEAAR NALL NEI RNVYRFQ G IY I ND RH LE L IA D Q MT R KG YIMA I G R H G IN K AEL S A L 516
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1036-1393
5.80e-97
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 316.79
E-value: 5.80e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1036 I T PTQI E KFL E TCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II 1115
Cdd:PRK04309 35 L T EEEV E EII E EVVRE Y L R SLV EPG E AVG VVA AQSIGEPGTQMT MR TFH Y AGVA EI N V TLG L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1116 T AQ L DKD -- D D ADY A RL V KGR IE K T L L GEISEY I E ev FLPDDCF I LVK L SL E RI -- R L L RLEVNA E TVR ysicmskl RV K 1191
Cdd:PRK04309 115 T IY L KDE ya Y D REK A EE V ARK IE A T T L ENLAKD I S -- VDLANMT I IIE L DE E ML ed R G L TVDDVK E AIE -------- KK K 184
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1192 P G D V AVH G EAVV c VT P R E N S kssm Y YV L QF L K E DLPKVVVQ GI PEVS R AV I HIDE qsgk EK Y KLLV EG D NL RA V MATH GV 1271
Cdd:PRK04309 185 G G E V EIE G NTLI - IS P K E P S ---- Y RE L RK L A E KIRNIKIK GI KGIK R VI I RKEG ---- DE Y VIYT EG S NL KE V LKVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1272 KG TRTT S NN TY E V E KT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS D L MT YK GEV LG I T R F G LAKM K E SVL ML A S F 1351
Cdd:PRK04309 256 DA TRTT T NN IH E I E EV LGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML VA D M MT WD GEV RQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 1570460116 1352 E K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L L 1393
Cdd:PRK04309 336 E V T VK HL L DAA VR G EV D ELK GV T E N II V G Q P IPL GTG DVE L T 377
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1040-1395
1.06e-85
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 284.64
E-value: 1.06e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1040 QIEKFLETCRDK Y M R AQME PG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L 1119
Cdd:TIGR02389 24 ELDEIIKRVEEE Y L R SLID PG E AVG IVA AQSIGEPGTQMT MR TFH Y AGVA EL N V TLG L PR LI EI VD A R K TP STP SM T IY L 103
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1120 DKDD -- D ADY A RL V KGR IE K T L L GEISEY I E evflpddcfil VK L SLERI rll RL E VNA E TVRYS - I CMSKL ----- RV K 1191
Cdd:TIGR02389 104 EDEY ek D REK A EE V AKK IE A T K L EDVAKD I S ----------- ID L ADMTV --- II E LDE E QLKER g I TVDDV ekaik KA K 169
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1192 P G D V AV -- HGEAVVCVT P REN S kssm YYV L QF LKE DLPKVVVQ GI PEVS R A VI hide QSGKEK Y KLLV EG D NL RA V MATH 1269
Cdd:TIGR02389 170 L G K V IE id MDNNTITIK P GNP S ---- LKE L RK LKE KIKNLHIK GI KGIK R V VI ---- RKEGDE Y VIYT EG S NL KE V LKLE 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1270 GV KG TRTT S N NTY E VEKT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS DLMT YK GEV LG I T R F G LAKM K E SVL ML A 1349
Cdd:TIGR02389 242 GV DK TRTT T N DIH E IAEV LGIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML VA DLMT WD GEV RQ I G R H G ISGE K A SVL AR A 321
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 1570460116 1350 S FE K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L LHK 1395
Cdd:TIGR02389 322 A FE V T VK HL L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L VMD 367
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
345-1150
1.75e-48
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: 189.60
E-value: 1.75e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - RKL VRN G pevhp G A NF I QQ 423
Cdd:COG0086 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A LE L FK P --------- F I y RKL EER G ----- L A TT I KS 386
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 rhtq M K RFL kygnr E KMAQ E LK yg DI V E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:COG0086 387 ---- A K KMV ----- E REEP E VW -- DI L E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 504 E M NL H L P QTE EA KA EA LV LM GTKA N LVT P R NG E P L I AAI QD FLT G A Y L LT LKD -------- T F F D RAKACQIIASIL V GK 575
Cdd:COG0086 455 Q M AV H V P LSL EA QL EA RL LM LSTN N ILS P A NG K P I I VPS QD MVL G L Y Y LT RER egakgegm I F A D PEEVLRAYENGA V DL 534
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 576 DEK IKV HLPPPTILKPVTLW T -- G KQIFSV IL r P SD dnpvranlrtkgkqycgkgedlcvndsy V TIQ N SE lmsgs MD K G 653
Cdd:COG0086 535 HAR IKV RITEDGEQVGKIVE T tv G RYLVNE IL - P QE ---------------------------- V PFY N QV ----- IN K K 580
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 654 TLG sgskn N I FYILL R DW G QN E AADAMS RL AR L APV Y LSNR G F SIG IG D - V T P gqgll K A K Y E LLNAGY K KCD E YIEALN 732
Cdd:COG0086 581 HIE ----- V I IRQMY R RC G LK E TVIFLD RL KK L GFK Y ATRA G I SIG LD D m V V P ----- K E K Q E IFEEAN K EVK E IEKQYA 650
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 733 T G KL qqqpgc T AE E TLEAL I L kelsv IRDH A G ---- S ACLRELDKS N SPLT MA LC G SK GS FINIS Q MIACV G QQ A isgsr 808
Cdd:COG0086 651 E G LI ------ T EP E RYNKV I D ----- GWTK A S lete S FLMAAFSSQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A ----- 714
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 809 V P D G -- F E NR slphfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV KSLE D L csqy 886
Cdd:COG0086 715 K P S G ni I E TP ----------------- IGSN F RE GL GVL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV DVAQ D V ---- 773
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 887 dltvrsstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E f K R V L DNIK A --- V F P CQS E PALSKNE L V lt T E SIMKKT E f 958
Cdd:COG0086 774 ---------- I VTEEDC G td R G IT v T A IK EG GE vi EPL K - E R I L GRVA A edv V D P GTG E VLVPAGT L I -- D E EVAEII E - 839
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 959 lccqdsflqeiknfvk GVSEKIK K T R dkygindngttevalsfpdglgcpqrarvpqpdphtwflflqprvlyqldri TP 1038
Cdd:COG0086 840 ---------------- EAGIDSV K V R ---------------------------------------------------- SV 851
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1039 TQI E KFLET C RDK Y M R -- A QMEP --- G S AVG ALC AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS KA ISTP 1113
Cdd:COG0086 852 LTC E TRGGV C AKC Y G R dl A RGHL vni G E AVG VIA AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA KA GGIV 924
810 820 830
....*....|....*....|....*....|....*..
gi 1570460116 1114 IITAQLDKDDDADYARL V KGRI E KTLLGEISEYI EE V 1150
Cdd:COG0086 925 RLNNLKVVVNEEGKGVV V SRNS E LVIVDDGGRRE EE Y 961
Name
Accession
Description
Interval
E-value
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
24-891
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: 1670.39
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 24 SPE EMRQQAHIQ V VSK NLY SQDNHH a PL L YGVLD H R M GTS E KD RP CETCG K NLADC L GH Y GYI D LELP C FH V GYF R A V I G 103
Cdd:cd02583 2 SPE DIIRLSEVE V TNR NLY DIETRK - PL P YGVLD P R L GTS D KD GI CETCG L NLADC V GH F GYI K LELP V FH I GYF K A I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 104 ILQ M ICKTC CHIM L SQ EEK KQ FL DY L K RP G L TY LQK RG LKKKI SD KC R K KNI C HY CG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C PH CG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 184 kvvdpvvsnflqsfetaiehnkevep LL GR AQE N LNPL V VLNLFK R IP A EDV P LLLMNP E AG K P SD LILTR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL K VLNLFK N IP P EDV E LLLMNP L AG R P EN LILTR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RIS GAKTQ M IMEDWDFLQLQCALYINSEL S G I PL N M A PKK WT RGF V Q 343
Cdd:cd02583 192 PSVV M D E KSGTNEDDLT V KL S EIIFLNDVIKKH LEK GAKTQ K IMEDWDFLQLQCALYINSEL P G L PL S M Q PKK PI RGF C Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV R NGP E VHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGP D VHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 R HTQM K R FLKYGNR E K M A Q ELK Y GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L AKV K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R AKV M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDRA KA CQ IIASI L vgk D EK IK VH L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDRA QF CQ LCSYM L --- D GE IK ID L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C V ND S YV T I Q NSEL MS G SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 PPP A ILKPV E LWTGKQIFS LL LRP NKKS PV LV NL EA K E K S Y TK K SP D M C P ND G YV V I R NSEL LC G RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 664 FY I LLRD W G QNE AA D AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K Y EL LNA GY K KCDEYI EALNT GKL QQ QPGCT 743
Cdd:cd02583 589 FY V LLRD Y G PEA AA A AM N RLA K L SSRW LSNRGFSIGI D DVTP SKE LLK K K E EL VDN GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 744 AE E TLEA L I LK ELS V IR DH AG S ACL R EL D KSNSPL T MALCGSKGS F INISQMIACVGQQ A ISG S R V P D GFE N R S LPHF EK 823
Cdd:cd02583 669 AE Q TLEA K I SG ELS K IR ED AG K ACL K EL H KSNSPL I MALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1570460116 824 H SK L PAAKGFVANSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
12-910
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: 967.87
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 12 A K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D N hh A P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P 91
Cdd:cd02582 1 P K R I KG I K FG LL SPEE I R KMSVVEIITPDT Y DE D G -- Y P IEG G LM D P R L G VI E PGLR C K TCG NTAGE C P GH F G H I E L AR P 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 92 CF HVG YFRAVIGI L QMI C KT C CH I M L SQ EE KKQF L DYLK R - PGLTYLQKRGLKK K ISD K CR K KNI C HY CGA fngtvkkc G 170
Cdd:cd02582 79 VI HVG FAKHIYDL L RAT C RS C GR I L L PE EE IEKY L ERIR R l KEKWPELVKRVIE K VKK K AK K RKV C PH CGA -------- P 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 171 LL KI IH EK yktnkkvvdpv VSN F LQSF E ta IEHN K evepllgraqen L N P LVVLNLFKR IP A ED VP LL LMN P EAGK P SDL 250
Cdd:cd02582 151 QY KI KL EK ----------- PTT F YEEK E -- EGEV K ------------ L T P SEIRERLEK IP D ED LE LL GID P KTAR P EWM 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 251 I LT R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I MED WD F LQ LQCAL Y INS E LS GIP 329
Cdd:cd02582 206 V LT V L P VPP VTV RPS IT -- L ET G e RS EDDLT H KL VD II RI N QRL K ENIEA GA PQLI I EDL WD L LQ YHVTT Y FDN E IP GIP 283
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 330 ln M A PKKWT R --- GFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT F PE K V NKA NI NFL RK 406
Cdd:cd02582 284 -- P A RHRSG R plk TLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EDI AK E LT V PE R V TEW NI EKM RK 361
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 407 LV R NGP EVH PGAN FIQQRHTQMK R f L K Y G NRE KM A QE L KY G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LAK V K P HR TF 486
Cdd:cd02582 362 LV L NGP DKW PGAN YVIRPDGRRI R - L R Y V NRE EL A ER L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RVR V L P GK TF 440
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 487 R F N EC VC T PYNADFDGDEMNLH L PQ T EEA K AEA LV LM GTKANLVT PR N G E P L I AA IQD FLT GAYLLT L K D T F F DRAK A C Q 566
Cdd:cd02582 441 R L N LA VC P PYNADFDGDEMNLH V PQ S EEA R AEA RE LM LVQEHILS PR Y G G P I I GG IQD YIS GAYLLT R K T T L F TKEE A L Q 520
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 567 IIASI lvgkde KIKVH LP P P T IL K P VT LWTGKQ I FS VI L r P S D D N PVR anl RT K GKQY C GKGE D - L C V ND S YV T I Q N SE L 645
Cdd:cd02582 521 LLSAA ------ GYDGL LP E P A IL E P KP LWTGKQ L FS LF L - P K D L N FEG --- KA K VCSG C SECK D e D C P ND G YV V I K N GK L 590
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 646 MS G SM DK GTL G SGSKNNIFYILLRDW G QNE A ADAMSRLA RLA PVYLSN RGF S IGI G D VTPGQGLL K AKY E LLNAGY KK CD 725
Cdd:cd02582 591 LE G VI DK KAI G AEQPGSLLHRIAKEY G NEV A RRFLDSVT RLA IRFIEL RGF T IGI D D EDIPEEAR K EIE E IIKEAE KK VY 670
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 726 E Y IE ALNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE LD KS N SPLT MA LC G SK GS FI N IS QM I AC V GQQ AIS 805
Cdd:cd02582 671 E L IE QYKN G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG KVASKY LD PF N NAVI MA RT G AR GS ML N LT QM A AC L GQQ SVR 750
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 806 G S R VPD G FE NR S LPHF EKHSKL P A A K GFV AN SF YS GL T PTEFFFH T M A GREGLVDTAV K T AET GYMQRRL VKS L E DL CSQ 885
Cdd:cd02582 751 G E R INR G YR NR T LPHF KPGDLG P E A R GFV RS SF RD GL S PTEFFFH A M G GREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE 830
890 900
....*....|....*....|....*
gi 1570460116 886 YD L TVR S S T G D IIQF I YG G DG L DPA 910
Cdd:cd02582 831 YD G TVR D S R G N IIQF K YG E DG V DPA 855
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
7-930
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 955.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 7 RETDVA K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D N hh A P LLY G VL D H R M G TSEKDRP C E TCG KNLAD C L GH Y G Y I 86
Cdd:PRK08566 1 SMMMIP K R I GS I K FG LL SPEE I R KMSVTKIITADT Y DD D G -- Y P IDG G LM D P R L G VIDPGLR C K TCG GRAGE C P GH F G H I 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 87 D L EL P CF HVG YFRAVIGI L QMI C KT C CHIM L SQ EE KKQF L DY L K R PGLTYLQKRG L K K KISDKCR K KNI C HY CG A fngtv 166
Cdd:PRK08566 79 E L AR P VI HVG FAKLIYKL L RAT C RE C GRLK L TE EE IEEY L EK L E R LKEWGSLADD L I K EVKKEAA K RMV C PH CG E ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 167 K K cgl L KI IH EK yktnkkvvd P V vsnflqsfe T AI E HN KE VE pllgraq EN L N P LVVLNLFKR IP A ED VP LL LM NPE AGK 246
Cdd:PRK08566 154 K Q --- Y KI KF EK --------- P T --------- T FY E ER KE GL ------- VK L T P SDIRERLEK IP D ED LE LL GI NPE VAR 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 247 P SDLI LT R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRIS GA K t Q M I M ED - W DF LQ LQCAL Y INS E 324
Cdd:PRK08566 206 P EWMV LT V L P VPP VTV RPS IT -- L ET G q RS EDDLT H KL VD II RI N QRL K ENIEA GA P - Q L I I ED l W EL LQ YHVTT Y FDN E 282
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 325 LS GIP lnma P ----- KKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT F PE K V NKA 399
Cdd:PRK08566 283 IP GIP ---- P arhrs GRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EAI AK E LT V PE R V TEW 358
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 400 NI NF LR KL V R NGPE V HPGAN FI qq RHTQMK R F - L KYG N R E KM A QE L KY G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA 478
Cdd:PRK08566 359 NI EE LR EY V L NGPE K HPGAN YV -- IRPDGR R I k L TDK N K E EL A EK L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RV 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 479 K V K P HR TFR F N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLVT PR N G E P L I AA IQD FLT GAYLLT L K D T F 558
Cdd:PRK08566 437 R V L P GK TFR L N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RI LM LVQEHILS PR Y G G P I I GG IQD HIS GAYLLT R K S T L 516
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 559 F DRAK A CQIIASILVGKDE kikvh L P P P T I LKPVTL WTGKQIFS VI L r P S D D N PVR anl RT K GKQY C GKGED - L C VN D S Y 637
Cdd:PRK08566 517 F TKEE A LDLLRAAGIDELP ----- E P E P A I ENGKPY WTGKQIFS LF L - P K D L N LEF --- KA K ICSG C DECKK e D C EH D A Y 587
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 638 V T I Q N SE L MS G SM DK GTL G SG s KNN I FYILLRDW G QNE A ADAMSRLA RLA PVYLSN RGF SI GI G D VT - P GQGLLKAK y E L 716
Cdd:PRK08566 588 V V I K N GK L LE G VI DK KAI G AE - QGS I LDRIVKEY G PER A RRFLDSVT RLA IRFIML RGF TT GI D D ED i P EEAKEEID - E I 665
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 717 LNAGY K KCD E Y IEA LNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE L DKS N SPLT MA LC G SK GS FI N IS QM I 796
Cdd:PRK08566 666 IEEAE K RVE E L IEA YEN 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 745
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 797 ACVGQQ AIS G S R VPD G FEN R S LPHF EKHSKLPA A K GFV AN S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GYMQRRL V 876
Cdd:PRK08566 746 ACVGQQ SVR G E R IRR G YRD R T LPHF KPGDLGAE A R GFV RS S YK SGLTPTEFFFH A M G GREGLVDTAV R T SQS GYMQRRL I 825
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 1570460116 877 KS L E DL CSQ YD L TVR SST G D I I QF I YG G DG L DP AAMEG k DE P LEFK R VLDNIKA 930
Cdd:PRK08566 826 NA L Q DL KVE YD G TVR DTR G N I V QF K YG E DG V DP MKSDH - GK P VDVD R IIERVLG 878
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-925
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 885.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 13 KKI SH I C FG MK SPEE M R QQAHIQ VV SKNL Y SQ D NH ha P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P C 92
Cdd:TIGR02390 2 KKI GS I K FG LL SPEE I R KMSVVE VV TADT Y DD D GY -- P IEG G LM D P R L G VI E PGLR C K TCG GKVGE C P GH F G H I E L AR P V 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 93 F HVG YFRAVIG IL QMI C KT C CH I M L SQ EE KK Q F L D - YL K RPGLTYLQKRG L KK KI SDKCR K KNI C HY CG A fngtvkkc GL 171
Cdd:TIGR02390 80 V HVG FAKEIYK IL RAT C RK C GR I T L TE EE IE Q Y L E k IN K LKEEGGDLAST L IE KI VKEAA K RMK C PH CG E -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 172 L KI IH EK yktnkkvvd P vv SN F LQ sfetaiehnkevep LLGRAQEN L N P LVVLNLFKR IP A ED VP LL LM NP EAGK P SDLI 251
Cdd:TIGR02390 152 K KI KF EK --------- P -- TY F YE -------------- EGKEGDVK L T P SEIRERLEK IP D ED AE LL GI NP KVAR P EWMV 206
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 252 LT R L L VPP LCI RPS VV sd L KS G T - N EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I MED W DF LQ LQC A L Y INS EL S GIP - 329
Cdd:TIGR02390 207 LT V L P VPP VTV RPS IT -- L ET G E r S EDDLT H KL VD II RI N QRL K ENIEA GA PQLI I EDL W EL LQ YHV A T Y FDN EL P GIP p 284
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 330 LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT F PE K V NKA NI NF LR KL V R 409
Cdd:TIGR02390 285 ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PE R V TPW NI DE LR EY V L 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 410 NGP EVH PGAN FIQQ rh TQMK R F - LKYG N R E KM A QE L KY G DI VERHLIDGD V VLFNRQPSLH KL S I M A H LA KV K P HR TFR F 488
Cdd:TIGR02390 365 NGP DSW PGAN YVIR -- PDGR R I k IRDE N K E EL A ER L EP G WV VERHLIDGD I VLFNRQPSLH RM S M M G H KV KV L P GK TFR L 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 489 N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLV TPR N G E P L I AA I Q D FLT GAYLLT L K D T F F DRAKACQ I I 568
Cdd:TIGR02390 443 N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RE LM LVEEHIL TPR Y G G P I I GG I H D YIS GAYLLT H K S T L F TKEEVQT I L 522
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 569 ASI lvgkde KIKVHL P P P T I L KP VTL WTGKQIFS VI L r P S D D N PVRANLRTK G KQY C G K G E dl C VN D S YV T I Q N SE L MS G 648
Cdd:TIGR02390 523 GVA ------ GYFGDP P E P A I E KP KEY WTGKQIFS AF L - P E D L N FEGRAKICS G SDA C K K E E -- C PH D A YV V I K N GK L LK G 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 649 SM DK GTL G S g S K NN I FYILL R DW G QNE A ADAMSRLA RL APVYLSN RGF SI GI G D VTPGQGLLKAKY EL LNAGY K KC D EY I 728
Cdd:TIGR02390 594 VI DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT RL FIRFITL RGF TT GI D D IDIPKEAKEEIE EL IEKAE K RV D NL I 672
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 729 E ALNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE LD KS N SPLT MA LC G SK GS FI NI S QM I A C VGQQ AIS G S R 808
Cdd:TIGR02390 673 E RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG EVAEKY LD PE N HAVI MA RT G AR GS LL NI T QM A A M VGQQ SVR G G R 752
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 809 VPD G FE NR S LPHF E K HSKLPA A K GFV AN SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GYMQRRL VKS L E DL CSQ YD L 888
Cdd:TIGR02390 753 IRR G YR NR T LPHF K K GDIGAK A R GFV RS SF KK GL D PTE Y FFH AAG GREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE YD G 832
890 900 910
....*....|....*....|....*....|....*...
gi 1570460116 889 TVR SST G DI IQF I YG G DG L DP AAME - GK de P LEF K RVL 925
Cdd:TIGR02390 833 TVR DTR G NL IQF K YG E DG V DP MKSD h GK -- P VDV K KIF 868
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
13-1393
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 871.27
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 13 K K I SH I C FG MK SP EEM R QQAHIQVVSKNL Y SQ D N hh A P LLY G V LD H R M GT S E KDRP C E TCG KNL A D C L GH Y G Y I D L EL P C 92
Cdd:PRK14977 7 K A I DG I I FG LI SP ADA R KIGFAEITAPEA Y DE D G -- L P VQG G L LD G R L GT I E PGQK C L TCG NLA A N C P GH F G H I E L AE P V 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 93 F H VGYFRAVIGI L QMI C KT C CHIM L S QE EKKQ F l DYLKRPGLTYL --- Q KR --- GLKKKIS D KC ---- R K KNI C HY CG af 162
Cdd:PRK14977 85 I H IAFIDNIKDL L NST C HK C AKLK L P QE DLNV F - KLIEEAHAAAR dip E KR idd EIIEEVR D QV kvya K K AKE C PH CG -- 161
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 163 ngtvkkcgllkiiheky KTNKKVVDPVVSN F LQ sfetaieh NK E V E P llgraq EN L N P LVVLNL F KR I PAE D VP L LLMN P 242
Cdd:PRK14977 162 ----------------- APQHELEFEEPTI F IE -------- KT E I E E ------ HR L L P IEIRDI F EK I IDD D LE L IGFD P 210
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 243 EAGK P SDLI L TRL LVPPL CI RPS VV sd L KS G T - N EDDLT MK L TE II FL N DVI K KHRIS GA KTQMIMEDW D F LQ LQCALYI 321
Cdd:PRK14977 211 KKAR P EWAV L QAF LVPPL TA RPS II -- L ET G E r S EDDLT HI L VD II KA N QKL K ESKDA GA PPLIVEDEV D H LQ YHTSTFF 288
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 322 NSELS GIP LNM -- APKKWTRGFV QRLKGK Q GRFRGNL S GKRVDFS G RTVISPDP NLR IDEV A VP VHV A KI LT F PE K VN KA 399
Cdd:PRK14977 289 DNATA GIP QAH hk GSGRPLKSLF QRLKGK E GRFRGNL I GKRVDFS A RTVISPDP MID IDEV G VP EAI A MK LT I PE I VN EN 368
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 400 NI NFLRK LV R NGP EVH PGAN F I QQ ------ R HTQMKRFL K YGN RE k M A QE L KY GDIVERHL I DGD V V L FNRQPSLHKLSI 473
Cdd:PRK14977 369 NI EKMKE LV I NGP DEF PGAN A I RK gdgtki R LDFLEDKG K DAL RE - A A EQ L EI GDIVERHL A DGD I V I FNRQPSLHKLSI 447
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 474 M AH LA KV K P HR TFR FNEC VC T PYNADFDGDEMNLH L PQ T E E A K AEA LV LMG T K A NL VT PR N G E P L I A A I QDF L T G AYL L T 553
Cdd:PRK14977 448 L AH RV KV L P GA TFR LHPA VC P PYNADFDGDEMNLH V PQ I E D A R AEA IE LMG V K D NL IS PR T G G P I I G A L QDF I T A AYL I T 527
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 554 LK D TF FD RAK A CQ I IA si L V G kdek I KVH LP P P T I - L K PVTL WTGKQ I FS VI L r P S D D N PVRANLRTK GK Q yc G KGE D - L 631
Cdd:PRK14977 528 KD D AL FD KNE A SN I AM -- L A G ---- I TDP LP E P A I k T K DGPA WTGKQ L FS LF L - P K D F N FEGIAKWSA GK A -- G EAK D p S 598
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 632 C VN D S YV T I QNS EL M SG SM D KGTL G SGSKN -- NIFYILLR D W G QNE A ADAMSRLARL A PVYLSNR GFS I G I GD VTPGQ gl 709
Cdd:PRK14977 599 C LG D G YV L I KEG EL I SG VI D DNII G ALVEE pe SLIDRIAK D Y G EAV A IEFLNKILII A KKEILHY GFS N G P GD LIIPD -- 676
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 710 l K AK Y E LLNAGYKKC DE YIEALNT ----------- GK LQQQP G CTA EE T LEA L I LK EL SVI RD H AGS ACLREL D KS N SPL 778
Cdd:PRK14977 677 - E AK Q E IEDDIQGMK DE VSDLIDQ rkitrkitiyk GK EELLR G MKE EE A LEA D I VN EL DKA RD K AGS SANDCI D AD N AGK 755
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 779 T MA LC G SK GS FI N IS Q MIACV GQQ AI -------- S G S R VPD G FEN R S L P HF EKHSKL P A A K GFV A N SFYS GL TPT EFFFH 850
Cdd:PRK14977 756 I MA KT G AR GS MA N LA Q IAGAL GQQ KR ktrigfvl T G G R LHE G YKD R A L S HF QEGDDN P D A H GFV K N NYRE GL NAA EFFFH 835
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 851 T M A GREGL V D T A VK T AET GY M QRRL VKS LED LCSQ YD L TVR SST G D IIQF IY G G DG L DP AAME g KD E PLEFK R VLDN ika 930
Cdd:PRK14977 836 A M G GREGL I D K A RR T EDS GY F QRRL ANA LED IRLE YD E TVR DPH G H IIQF KF G E DG I DP QKLD - HG E AFNLE R IIEK --- 911
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 931 vfpcqsepalsknelvlttesimkkteflccqdsfl Q E I KNFV KG V S - EK I KKTRDK Y GIND N gt TEVALSFP D GL gcpq 1009
Cdd:PRK14977 912 ------------------------------------ Q K I EDRG KG A S k DE I EELAKE Y TKTF N -- ANLPKLLA D AI ---- 949
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1010 rarvpqpdphtwflflqprvly QLDRITPTQI E KFLETCRDKYMR A QM EPG S A V G ALC AQSI G EPGTQMTL K TFH F AG VA 1089
Cdd:PRK14977 950 ---------------------- HGAELKEDEL E AICAEGKEGFEK A KV EPG Q A I G IIS AQSI A EPGTQMTL R TFH A AG IK 1007
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1090 S M NI T L G VP R IK E IIN A SKAI STP IITAQ LD KDDDA D YARLVK gr I EKT L LG - EISEY I EEVFLPDDCF I LVKLSLE R IR 1168
Cdd:PRK14977 1008 A M DV T H G LE R FI E LVD A RAKP STP TMDIY LD DECKE D IEKAIE -- I ARN L KE l KVRAL I ADSAIDNANE I KLIKPDK R AL 1085
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1169 --- LLRL E VN AE TVR ysicm SKLRV K PGDVAVHGEAVVCVTPRENSKSSMYYV L QFLKEDLPKVV V Q G I P EVS RA VIHID 1245
Cdd:PRK14977 1086 eng CIPM E RF AE IEA ----- ALAKG K KFEMELEDDLIILDLVEAADRDKPLAT L IAIRNKILDKP V K G V P DIE RA WVELV 1160
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1246 E QS G KEKYKLLVE G D NL R AV MATHGVKGTR T TS N NTY E VEK TLGIEAAR TT I I NE IQYTMVNH G MSI D R R HV ML LS D L M T 1325
Cdd:PRK14977 1161 E KD G RDEWIIQTS G S NL A AV LEMKCIDIAN T IT N DCF E IAG TLGIEAAR NA I F NE LASILEDQ G LEV D N R YI ML VA D I M C 1240
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1570460116 1326 YK G EVLG I ------ T R F G L A KM K E S V L ML A S FE K T ADHLFD AA YF G QKDSVC G VSECI IMG IPMN IG T G LFK LL 1393
Cdd:PRK14977 1241 SR G TIEA I glqaag V R H G F A GE K D S P L AK A A FE I T THTIAH AA LG G EIEKIK G ILDAL IMG QNIP IG S G KVD LL 1314
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
20-887
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: 852.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 20 FG MK SP E E M R QQAHIQVVSK nl YSQD N HHA P L L Y G VL D H RMGT SEKDRP C E TCG KNLAD C L GH Y G Y I D L EL P C FH V G YFR 99
Cdd:cd02733 5 FG IL SP D E I R AMSVAEIEHP -- ETYE N GGG P K L G G LN D P RMGT IDRNSR C Q TCG GDMKE C P GH F G H I E L AK P V FH I G FLT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 100 AVIG IL QMI CK tcch IM LS Q E E kkqfldylkrpgltylqkrglkkkisdkcrkknichycgafngtvkkcgllkiiheky 179
Cdd:cd02733 83 KILK IL RCV CK ---- RE LS A E R ---------------------------------------------------------- 100
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 180 ktnkkvvdpvvsnflqsfetaiehnkevepllgraqenlnplv VL NL FKRI PA ED VPL L LMN P EAGK P SDL ILT R L L VPP 259
Cdd:cd02733 101 ------------------------------------------- VL EI FKRI SD ED CRI L GFD P KFSR P DWM ILT V L P VPP 137
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 260 LCI RPSVV S D L k S GTN EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I M ED WDF LQ LQC A L Y INS E LS G I P ln M A PK K WT R 339
Cdd:cd02733 138 PAV RPSVV M D G - S ARS EDDLT H KL AD II KA N NQL K RQEQN GA PAHI I E ED EQL LQ FHV A T Y MDN E IP G L P -- Q A TQ K SG R 214
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 340 --- GFV QRLKGK Q GR F RGNL S GKRVDFS G RTVI S PDPNL RI D E V A VP VHV A KI LTFPE K V NKA NI NF L RK LVRNGP EVH P 416
Cdd:cd02733 215 plk SIR QRLKGK E GR I RGNL M GKRVDFS A RTVI T PDPNL EL D Q V G VP RSI A MN LTFPE I V TPF NI DR L QE LVRNGP NEY P 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 417 GA NF I Q q R HTQMKRF L K Y GNR e KMAQE L K YG D IVERHL I DGDVVLFNRQPSLHK L S I M A H LA KV K P HR TFR F N EC V C TPY 496
Cdd:cd02733 295 GA KY I I - R DDGERID L R Y LKK - ASDLH L Q YG Y IVERHL Q DGDVVLFNRQPSLHK M S M M G H RV KV L P YS TFR L N LS V T TPY 372
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 497 NADFDGDEMNLH L PQ TE E AK AE ALV LM GTKANL V T P RNGE P LIAAI QD F L T G AYL LT LK DTF FDRAKACQIIASI lvgkd 576
Cdd:cd02733 373 NADFDGDEMNLH V PQ SL E TR AE LKE LM MVPRQI V S P QSNK P VMGIV QD T L L G VRK LT KR DTF LEKDQVMNLLMWL ----- 447
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 577 EKIKVHL P P P T ILKP VT LWTGKQIFS V I L r P SDD N PV R ANLRTK G KQY cgkge DLCVN D SY V T I Q N S EL M SG SMD K G T L G 656
Cdd:cd02733 448 PDWDGKI P Q P A ILKP KP LWTGKQIFS L I I - P KIN N LI R SSSHHD G DKK ----- WISPG D TK V I I E N G EL L SG ILC K K T V G 521
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 657 SG S k NNIFYILLRDW G QNE A A D AMSRLA R LAPVY L SNR GFSIGIGD VTPGQGLL K AKY E LLNAGYKKCDEY IE ALNT G K L 736
Cdd:cd02733 522 AS S - GGLIHVIWLEY G PEA A R D FIGNIQ R VVNNW L LHN GFSIGIGD TIADKETM K KIQ E TIKKAKRDVIKL IE KAQN G E L 600
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 737 QQ QPG C T AE E TL E ALILKE L SVI RD H AG SACLRE L DKS N SPLT M ALC GSKGSFINISQ M IACVGQQ AIS G S R V P D GF EN R 816
Cdd:cd02733 601 EP QPG K T LR E SF E NKVNRI L NKA RD K AG KSAQKS L SED N NFKA M VTA GSKGSFINISQ I IACVGQQ NVE G K R I P F GF RR R 680
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1570460116 817 S LPHF E K HSKL P AAK GFV A NS FYS GLTP T EFFFH T M A GREGL V DTAVKTAETGY M QRRLVK SL ED LCSQ YD 887
Cdd:cd02733 681 T LPHF I K DDYG P ESR GFV E NS YLR GLTP Q EFFFH A M G GREGL 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 ...
23-887
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: 711.51
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 23 K SPEE M R QQAHIQ V VSKNLYSQDNHH A PL l Y G VL D H R M G TSEKDRP C E TCG KN L A DC L GH Y G Y I D L EL P C FHVG YFRA V I 102
Cdd:cd00399 1 M SPEE I R KWSVAK V IKPETIDNRTLK A ER - G G KY D P R L G SIDRCEK C G TCG TG L N DC P GH F G H I E L AK P V FHVG FIKK V P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 103 GI L Q micktcchimlsqeekkqfldylkrpgltylqkrglkkkisdkcrkknichycgafngtvkkcgllkiihekyktn 182
Cdd:cd00399 80 SF L G ---------------------------------------------------------------------------- 83
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 183 kkvvdpvvsnflqsfetaiehnkevepllgraqenlnplvvlnlfkripaedvplllmnpeagk P SDL ILT R L L VPP L C I 262
Cdd:cd00399 84 ---------------------------------------------------------------- P EWM ILT C L P VPP P C L 99
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 263 RPSV vsdlksgtneddltmklteiiflndvikkhrisgaktq M I M E D W DF LQ LQCAL Y INSELS G I P LNMAPKKWT R GFV 342
Cdd:cd00399 100 RPSV -------------------------------------- I I E E R W RL LQ EHVDT Y LDNGIA G Q P QTQKSGRPL R SLA 141
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 343 QRLKGK Q GRFRGNL S GKRVDFSGR T VISPDPNLR I D E V A VP VHV A KI L tfpekvnkaninflrklvrngpevhpganfiq 422
Cdd:cd00399 142 QRLKGK E GRFRGNL M GKRVDFSGR S VISPDPNLR L D Q V G VP KSI A LT L -------------------------------- 189
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 423 qrhtqmkrflkygnrekmaqelkygdiverhli DGD V VLFNRQPSLHKLSIMAH LAK V K P HR TFR F N EC VC T PYNADFDG 502
Cdd:cd00399 190 --------------------------------- DGD P VLFNRQPSLHKLSIMAH RVR V L P GS TFR L N PL VC S PYNADFDG 236
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 503 DEMNLH L PQ T EEA K AEA LV LM GTKA N LVT P R NGEPLI AAI QD F L T GAYLLTL kdtffdrakacqiiasilvgkdekikvh 582
Cdd:cd00399 237 DEMNLH V PQ S EEA R AEA RE LM LVPN N ILS P Q NGEPLI GLS QD T L L GAYLLTL ---------------------------- 288
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 583 lppptilkpvtlwt GKQI F S VI L rpsddnpvranlrtkgkqycgkgedlcvndsyvtiqnselmsgsmdkgtlgsgs KNN 662
Cdd:cd00399 289 -------------- GKQI V S AA L ------------------------------------------------------ PGG 300
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 663 IFYILL R DW G QNE AA DAM S R L A R LAP V Y L SNR GFS I GIGDV TPGQGLLKA K Y EL LNAGY KK C DE YI EA LNT G K L QQ Q P G C 742
Cdd:cd00399 301 LLHTVT R EL G PEK AA KLL S N L Q R VGF V F L TTS GFS V GIGDV IDDGVIPEE K T EL IEEAK KK V DE VE EA FQA G L L TA Q E G M 380
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 743 T A EE T LE AL IL KE L SVI RD H AGSA CLRE LD --- K S NS PLT MA LC G S KGSFINI S QM I ACVGQQ AIS G S R V P D GF EN R S LP 819
Cdd:cd00399 381 T L EE S LE DN IL DF L NEA RD K AGSA ASVN LD lvs K F NS IYV MA MS G A KGSFINI R QM S ACVGQQ SVE G K R I P R GF SD R T LP 460
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1570460116 820 HF E K HSKL P A AKGF VA NSF YS GLTP T E F FFH T M A GREGLVDTAVKTAE T GY M QRRLVK S LEDL CSQ YD 887
Cdd:cd00399 461 HF S K DDYS P E AKGF IR NSF LE GLTP L E Y FFH A M G GREGLVDTAVKTAE 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 ...
20-887
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: 576.44
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 20 F GMK S P EE M R QQAHIQVVSKNLYSQDN H ha P LLY G VL D HRM G TSE KD RP C E TCG K N LAD C L GH Y G Y I D L E LP CFHVGY F R 99
Cdd:cd01435 2 F SFY S A EE I R KLSVKEITNPVTFDSLG H -- P VPG G LY D PAL G PLD KD DI C S TCG L N YLN C P GH F G H I E L P LP VYNPLF F D 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 100 AVIGI L QMI C KT C CHIML S QE E K K Q F ldylkrpgltylqkrglkkkisdkcrkknichycgafngt V K K CG LL kiiheky 179
Cdd:cd01435 80 LLYKL L RGS C FY C HRFRI S KW E V K L F ---------------------------------------- V A K LK LL ------- 112
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 180 ktnkkvvdpvvsnflqsfetai EHNKE VE pllgr A Q E NLNPL vvl NL F kripaedvplllmnpeagkpsdl I L TR LLVPP 259
Cdd:cd01435 113 ---------------------- DKGLL VE ----- A A E LDFGY --- DM F ----------------------- F L DV LLVPP 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 260 LCI RP sv V S D L KSGTN E DDLTMK L TE I IFL N DV I KKHRI S GAKTQMIMEDWD ------------- F LQLQ C A -- LYIN S E 324
Cdd:cd01435 140 NRF RP -- P S F L GDKVF E NPQNVL L SK I LKD N QQ I RDLLA S MRQAESQSKLDL isgktnseklina W LQLQ S A vn ELFD S T 217
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 325 LSGIPLNMA P K kwtr G FV Q R L KG K Q G R FR G N LS GKRV DFSG R T VISPDP NLRID E VAV P VHV AK I LTFPE K V NKA N INF L 404
Cdd:cd01435 218 KAPKSGKKS P P ---- G IK Q L L EK K E G L FR M N MM GKRV NYAA R S VISPDP FIETN E IGI P LVF AK K LTFPE P V TPF N VEE L 293
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 405 R KL V R NGP E V H PGAN F I QQR ----------- HTQM K RFL K YGNREKM A QE L KY G - DI V E RHL I DGDVVL F NRQP S LHK L S 472
Cdd:cd01435 294 R QA V I NGP D V Y PGAN A I EDE dgrlillsals EERR K ALA K LLLLLSS A KL L LN G p KK V Y RHL L DGDVVL L NRQP T LHK P S 373
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 473 IMAH LAK V - KPHR T F R FNECV C TP YNADFDGDEMNLH L PQ T E E A K AEA LVLMG T KANLVT P RN G E PL IAA IQD FLTGAY L 551
Cdd:cd01435 374 IMAH KVR V l PGEK T L R LHYAN C KS YNADFDGDEMNLH F PQ S E L A R AEA YYIAS T DNQYLV P TD G K PL RGL IQD HVVSGV L 453
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 552 LT LK DTFF D R AKAC Q IIASI L VGK --- D EKIKVH L P PP T ILKP VT LWTGKQ IF S V IL RPSDDNPVRANLRTKG K QYCG K G 628
Cdd:cd01435 454 LT SR DTFF T R EEYQ Q LVYAA L RPL fts D KDGRIK L L PP A ILKP KP LWTGKQ VI S T IL KNLIPGNAPLLNLSGK K KTKK K V 533
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 629 EDLC ---- VND S Y V T I Q N S EL MS G SM DK GTL G S g S KNNI --- F Y I L lrd W G QNE A ADAM S R L A RL APV YL SN RGF SI GI G 701
Cdd:cd01435 534 GGGK wggg SEE S Q V I I R N G EL LT G VL DK SQF G A - S AYGL vha V Y E L --- Y G GET A GKLL S A L G RL FTA YL QM RGF TC GI E 609
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 702 D V tpgqg LL KA K YEL lnagy K KCDEYIE A LNT G K lqqqpg CT A E E T L EALIL K EL S V I RD hags ACL RE -- L DK -- S N SP 777
Cdd:cd01435 610 D L ----- LL TP K ADE ----- K RRKILRK A KKL G L ------ EA A A E F L GLKLN K VT S S I IK ---- ACL PK gl L KP fp E N NL 669
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 778 LT M ALC G S KGS FI N I SQ MIACV GQQ AIS G S RVP DGFENRS LP H F EKHSKL P A A K GF VANS F YS G LT P T E F FFH T MAGREG 857
Cdd:cd01435 670 QL M VQS G A KGS MV N A SQ ISCLL GQQ ELE G R RVP LMVSGKT LP S F PPYDTS P R A G GF ITDR F LT G IR P Q E Y FFH C MAGREG 749
890 900 910
....*....|....*....|....*....|
gi 1570460116 858 L V DTAVKT AET GY M QR R L V K S LE D L CSQ YD 887
Cdd:cd01435 750 L 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; ...
1051-1390
0e+00
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: 567.62
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1051 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DK D D D ADY AR L 1130
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK N ISTPIITA K L EN D R D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1131 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysicmsklrvkpgdvavhgeavvcvtpren 1210
Cdd:cd02736 81 VKGRIEKT Y LGE VAS YIEEV YS PDDC Y IL I KL DKKI I EK L Q L -------------------------------------- 122
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1211 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek YKLLVEG DN LRAVM A T H GV K GTRTTSN NTY EVEK T LGI 1290
Cdd:cd02736 123 SKS NL Y FL LQ S LK RK LP D VVV S GIPEV K RAVI NK D KKK GK -- YKLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1291 EAAR T TIINEIQYTM VN HGMSID R RH V MLL S DLMT Y KGEVLGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1370
Cdd:cd02736 201 EAAR S TIINEIQYTM KS HGMSID P RH I MLL A DLMT F KGEVLGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 1570460116 1371 C GVSECIIMG I PM N IGTGLF 1390
Cdd:cd02736 281 E GVSECIIMG K PM P IGTGLF 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
248-550
5.81e-150
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 456.60
E-value: 5.81e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 248 SDL ILT R L L VPP L C I RPSV VS D L k SGTN EDDLT MK L TE II FL N DVI K KHRIS GA KTQM I MEDWDF LQ LQCALY I NS E l SG 327
Cdd:smart00663 1 EWM ILT V L P VPP P C L RPSV QL D G - GRFA EDDLT HL L RD II KR N NRL K RLLEL GA PSII I RNEKRL LQ EAVDTL I DN E - GL 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 328 IPL N MAPKKWTRGFV QRLKGK Q GRFR G NL S GKRVDFS G R T VI S PDPNL RID EV A VP VHV A KI LTFPE K V NKA NI NF LRKL 407
Cdd:smart00663 79 PRA N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLN EV G VP KEI A LE LTFPE I V TPL NI DK LRKL 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 408 VRNGP evh P GA NF I QQ rht QM K RF LK YGNRE K M A QE LK Y GDIVERH L IDGDVVLFNRQP S LH KL SI M AH LAK V KPHR T F R 487
Cdd:smart00663 159 VRNGP --- N GA KY I IR --- GK K TN LK LAKKS K I A NH LK I GDIVERH V IDGDVVLFNRQP T LH RM SI Q AH RVR V LEGK T I R 232
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1570460116 488 F N EC VC T PYNADFDGDEMNLH L PQ TE EA K AEA LV LM GTKA N LVT P R NG E P L I AA IQD F L T G A Y 550
Cdd:smart00663 233 L N PL VC S PYNADFDGDEMNLH V PQ SL EA R AEA RE LM LVPN N ILS P K NG K P I I GP IQD M L L G L Y 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
12-356
7.69e-131
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: 406.68
E-value: 7.69e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 12 A KKI SH I C FG MK SPEE M R QQAHIQ V VSKNL Y S q DNHHA P LLY G V LD H RMGT SE KD RP CETCGK NLA DC L GH Y G Y I D L EL P 91
Cdd:pfam04997 1 L KKI KE I Q FG IA SPEE I R KWSVGE V TKPET Y N - YGSLK P EEG G L LD E RMGT ID KD YE CETCGK KKK DC P GH F G H I E L AK P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 92 C FH V G Y F RAVIG IL QMI CK T C CHIM L SQEEK K Q F LDYL KR P GL TY L QKR gl K K K I SDK C R KK NI C HY CG AF NG TVKK cgl 171
Cdd:pfam04997 80 V FH I G F F KKTLK IL ECV CK Y C SKLL L DPGKP K L F NKDK KR L GL EN L KMG -- A K A I LEL C K KK DL C EH CG GK NG VCGS --- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 172 lkiihekyktnkkv VD PV VSNFLQSFET AI EHN KE V E pllgr AQ E N LNP LV VL NL FKRI PA EDV PL L LM NP EAGK P SDL I 251
Cdd:pfam04997 155 -------------- QQ PV SRKEGLKLKA AI KKS KE E E ----- EK E I LNP EK VL KI FKRI SD EDV EI L GF NP SGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 252 LT R L L VPP L CIRPSV VS D LK s GTN EDDLT M KL TE II FL N DVI KK HRIS GA KTQM I M E D W DF LQ LQC A LYINS E LS G I P L - 330
Cdd:pfam04997 216 LT V L P VPP P CIRPSV QL D GG - RRA EDDLT H KL RD II KR N NRL KK LLEL GA PSHI I R E E W RL LQ EHV A TLFDN E IP G L P P a 294
330 340
....*....|....*....|....*.
gi 1570460116 331 NMAP K KWTRGFV QRLKGK Q GRFRGNL 356
Cdd:pfam04997 295 LQKS K RPLKSIS QRLKGK E GRFRGNL 320
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
841-1346
1.55e-114
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: 370.15
E-value: 1.55e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 841 GLTP T EFFFHTM A GREGL V DTAVKTAE T GY M QRRLVK S LEDL CSQ YD L TVR S S T G D I I QF I YG G DGLDP AAM E GKD e PLE 920
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G E I V QF L YG E DGLDP LKI E KQG - RFT 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 921 FKRVLDNIKAV F PCQ sepa L SKNE L V L ttesimkkteflccq DS F LQEI K NFVKGVSE K IKKT R DKYGINDNG T TEVA L S 1000
Cdd:pfam04998 80 IEFSDLKLEDK F KND ---- L LDDL L L L --------------- SE F SLSY K KEILVRDS K LGRD R LSKEAQERA T LLFE L L 140
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1001 FPD G lgcpqrarvpqpdphtwflf L QPRVLYQLDRITPTQIEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL 1080
Cdd:pfam04998 141 LKS G -------------------- L ESKRVRSELTCNSKAFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1081 K TFHFAGVAS M N I TLGVPR I KEIIN A SK A I ST P II T AQ L -- DKDDDADY A RL V K G R IEK TL LG EIS E YI E ---------- 1148
Cdd:pfam04998 201 N TFHFAGVAS K N V TLGVPR L KEIIN V SK N I KS P SL T VY L fd EVGRELEK A KK V Y G A IEK VT LG SVV E SG E ilydpdpfnt 280
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1149 -------------------- EVFLP D DCFI L VK L SLERIRL L RLEVNAETVRYS I CM S k L R V K pg DVAVHGE A VVCV T PR 1208
Cdd:pfam04998 281 piisdvkgvvkffdiidevt NEEEI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I PR S - I R N K -- VDEGRDI A IGEI T AF 357
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1209 ENSK S SMYY ------- VLQF L KED ------------ L PKVVVQ GIP EVS R AVIHI D E q S GK EK -- YK L LV EG D NL RA V MA 1267
Cdd:pfam04998 358 IIKI S KKIR qdtgglr RVDE L FME edpklailvasl L GNITLR GIP GIK R ILVNE D D - K GK VE pd WV L ET EG V NL LR V LL 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1268 TH G - V KGT R TT SN NTY E VEKT LGIEAAR TTII NEI QYTMVNH G MS I DR RH VM L LS D L MT Y KG EVLG I T R F G LA K MKE S V L 1346
Cdd:pfam04998 437 VP G f V DAG R IL SN DIH E ILEI LGIEAAR NALL NEI RNVYRFQ G IY I ND RH LE L IA D Q MT R KG 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 ...
358-525
4.17e-100
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: 316.55
E-value: 4.17e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 358 GKRVDFS G RTVISPDPNL RI DEV A VP VHV AK I LTFPE K V NKA NI NF LR K LV R NGP E V H PGAN F I Q q R HTQMK R F L K Y GN R 437
Cdd:pfam00623 1 GKRVDFS A RTVISPDPNL KL DEV G VP ISF AK T LTFPE I V TPY NI KR LR Q LV E NGP N V Y PGAN Y I I - R INGAR R D L R Y QK R 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 438 e KMAQ EL KY GDIVERH L IDGDVVLFNRQPSLH K LSIM A H LAK V K P HR TFR F N EC V C TPYNADFDGDEMNLH L PQ T EEA K A 517
Cdd:pfam00623 80 - RLDK EL EI GDIVERH V IDGDVVLFNRQPSLH R LSIM G H RVR V L P GK TFR L N LS V T TPYNADFDGDEMNLH V PQ S EEA R A 158
....*...
gi 1570460116 518 EA LV LM GT 525
Cdd:pfam00623 159 EA EE LM LV 166
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1030-1393
6.89e-99
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: 321.51
E-value: 6.89e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1030 LYQLDRI T PTQI E KFLETCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMTL K TFH F AGVA SM N I TLG V PR IK EI IN A S K A 1109
Cdd:cd06528 10 VLKEHGL T LSEA E EIIKEVLRE Y L R SLI EPG E AVG IVA AQSIGEPGTQMTL R TFH Y AGVA EI N V TLG L PR LI EI VD A R K E 89
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1110 I STP II T AQ L DKD -- D D ADY A RL V KGR IE K T L L GEIS E Y I E ev FLPDDCF I LVK L SL E RI -- R LLRLEVNAETVR ysicm 1185
Cdd:cd06528 90 P STP TM T IY L EEE yk Y D REK A EE V ARK IE E T T L ENLA E D I S -- IDLFNMR I TIE L DE E ML ed R GITVDDVLKAIE ----- 162
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1186 skl RV K P G D V AVH G EAVVC V TPR E NSK ssm YYV L QF L K E DLPKVVVQ GI PEVS R AVI hid EQSGK E k Y KLLV EG D NL R AV 1265
Cdd:cd06528 163 --- KL K K G K V GEE G DVTLI V LKA E EPS --- IKE L RK L A E KILNTKIK GI KGIK R VIV --- RKEED E - Y VIYT EG S NL K AV 232
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1266 MATH GV KG TRTT S NN TY E V E KT LGIEAAR TT IINEI QY T MVNH G MSI D R RH V ML LS D L MTY K GEV LG I T R F G L A KM K E SV 1345
Cdd:cd06528 233 LKVE GV DP TRTT T NN IH E I E EV LGIEAAR NA IINEI KR T LEEQ G LDV D I RH I ML VA D I MTY D GEV RQ I G R H G I A GE K P SV 312
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 1570460116 1346 L ML A S FE K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L L 1393
Cdd:cd06528 313 L AR A A FE V T VK HL L DAA VR G EV D ELR GV I E N II V G Q P IPL GTG DVE L T 360
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1036-1393
5.80e-97
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 316.79
E-value: 5.80e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1036 I T PTQI E KFL E TCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II 1115
Cdd:PRK04309 35 L T EEEV E EII E EVVRE Y L R SLV EPG E AVG VVA AQSIGEPGTQMT MR TFH Y AGVA EI N V TLG L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1116 T AQ L DKD -- D D ADY A RL V KGR IE K T L L GEISEY I E ev FLPDDCF I LVK L SL E RI -- R L L RLEVNA E TVR ysicmskl RV K 1191
Cdd:PRK04309 115 T IY L KDE ya Y D REK A EE V ARK IE A T T L ENLAKD I S -- VDLANMT I IIE L DE E ML ed R G L TVDDVK E AIE -------- KK K 184
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1192 P G D V AVH G EAVV c VT P R E N S kssm Y YV L QF L K E DLPKVVVQ GI PEVS R AV I HIDE qsgk EK Y KLLV EG D NL RA V MATH GV 1271
Cdd:PRK04309 185 G G E V EIE G NTLI - IS P K E P S ---- Y RE L RK L A E KIRNIKIK GI KGIK R VI I RKEG ---- DE Y VIYT EG S NL KE V LKVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1272 KG TRTT S NN TY E V E KT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS D L MT YK GEV LG I T R F G LAKM K E SVL ML A S F 1351
Cdd:PRK04309 256 DA TRTT T NN IH E I E EV LGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML VA D M MT WD GEV RQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 1570460116 1352 E K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L L 1393
Cdd:PRK04309 336 E V T VK HL L DAA VR G EV D ELK GV T E N II V G Q P IPL GTG DVE L T 377
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
937-1395
4.02e-86
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 290.94
E-value: 4.02e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 937 E P ALSK N ELVLTTESIM K K --------------- T EF LCCQDSF L Q E IKN F VK G VSEK i KKTRDK Y GI N D N GTTEVALSF 1001
Cdd:PRK14897 55 A P YSNS N GIIKKKKPVL K T vleieseekieaidl M EF KRLFGRI L D E NMS F ST G ELLT - AEEKEY Y EE N S N EDVLKVIDD 133
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1002 PDG LG cpqr A R V P qpdphtwflflq P R V LYQLDR ------ ITPTQI E KF L ETC R DK Y M RA QME P GS AVG ALC AQSIGEPG 1075
Cdd:PRK14897 134 VKK LG ---- F R L P ------------ P S V IEEIAK amkkke LSDDEY E EI L RRI R EE Y E RA RVD P YE AVG IVA AQSIGEPG 197
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1076 TQMT LK TFH F AGVA S MN I TLG V PR IK EI IN A S K AI STP II T AQ L D KD -- D D ADYA R L V KGR IE K T L L GEISEY I EEV flp 1153
Cdd:PRK14897 198 TQMT MR TFH Y AGVA E MN V TLG L PR LI EI VD A R K KP STP TM T IY L K KD yr E D EEKV R E V AKK IE N T T L IDVADI I TDI --- 274
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1154 DDCFIL V K L SL E RI rllrlev NAETVR Y SICMSKLRVKPGDVAVHGEAVVCVT P REN S kssm YYV L QF L K E DLPKVVVQ G 1233
Cdd:PRK14897 275 AEMSVV V E L DE E KM ------- KERLIE Y DDILAAISKLTFKTVEIDDGIIRLK P QQP S ---- FKK L YL L A E KVKSLTIK G 343
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1234 I PEVS RA VIHID eqs GK E K - YKLLVE G D NL RA V MATHG V KG TRT TS N NTY E VEKT LGIEAAR TT II N E IQY T MVNH G MSI 1312
Cdd:PRK14897 344 I KGIK RA IARKE --- ND E R r WVIYTQ G S NL KD V LEIDE V DP TRT YT N DII E IATV LGIEAAR NA II H E AKR T LQEQ G LNV 420
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1313 D R RH V ML LS D L MT YK G E V LG I T R F G LAKM K E SVL ML A S FE K T AD HL FD A AYF G QK D SVC GV S E C II M G I P MNI GTG LFK L 1392
Cdd:PRK14897 421 D I RH I ML VA D 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 GIL G EV D KLA GV A E N II V G Q P ITL GTG AVS L 500
...
gi 1570460116 1393 LH K 1395
Cdd:PRK14897 501 VY K 503
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1040-1395
1.06e-85
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 284.64
E-value: 1.06e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1040 QIEKFLETCRDK Y M R AQME PG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L 1119
Cdd:TIGR02389 24 ELDEIIKRVEEE Y L R SLID PG E AVG IVA AQSIGEPGTQMT MR TFH Y AGVA EL N V TLG L PR LI EI VD A R K TP STP SM T IY L 103
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1120 DKDD -- D ADY A RL V KGR IE K T L L GEISEY I E evflpddcfil VK L SLERI rll RL E VNA E TVRYS - I CMSKL ----- RV K 1191
Cdd:TIGR02389 104 EDEY ek D REK A EE V AKK IE A T K L EDVAKD I S ----------- ID L ADMTV --- II E LDE E QLKER g I TVDDV ekaik KA K 169
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1192 P G D V AV -- HGEAVVCVT P REN S kssm YYV L QF LKE DLPKVVVQ GI PEVS R A VI hide QSGKEK Y KLLV EG D NL RA V MATH 1269
Cdd:TIGR02389 170 L G K V IE id MDNNTITIK P GNP S ---- LKE L RK LKE KIKNLHIK GI KGIK R V VI ---- RKEGDE Y VIYT EG S NL KE V LKLE 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1270 GV KG TRTT S N NTY E VEKT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS DLMT YK GEV LG I T R F G LAKM K E SVL ML A 1349
Cdd:TIGR02389 242 GV DK TRTT T N DIH E IAEV LGIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML VA DLMT WD GEV RQ I G R H G ISGE K A SVL AR A 321
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 1570460116 1350 S FE K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L LHK 1395
Cdd:TIGR02389 322 A FE V T VK HL L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L VMD 367
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
55-891
4.95e-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: 292.00
E-value: 4.95e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 55 V LDH R M G TSEKDRP C E TCG - K NLAD C L GH Y G Y I D L ELPCF H VGYFRA V IG IL QM IC KT C chimlsqeekkqfldylkrpg 133
Cdd:cd10506 20 V TNP R L G LPNESGQ C T TCG a K DNKK C E GH F G V I K L PVTIY H PYFISE V AQ IL NK IC PG C --------------------- 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 134 ltylqkrglkkkisdkcrkknichycgafngtvkkcgl LK I IHE K Y K TNKKVVD P VVSN F LQSFET ai EHNKE V EPL L gr 213
Cdd:cd10506 79 -------------------------------------- KS I KQK K K K PPRETLP P DYWD F IPKDGQ -- QEESC V TKN L -- 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 214 aqenln P LVV L NLF K R I PA E DV P L L LMN -- P eag KPSD L I L TR L L VPP L C I R psv V SDLKS G TNE ddl TMK L TEIIFLND 291
Cdd:cd10506 117 ------ P ILS L AQV K K I LK E ID P K L IAK gl P --- RQEG L F L KC L P VPP N C H R --- V TEFTH G FST --- GSR L IFDERTRA 181
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 292 VI K K hrisgaktqmimedwdflqlqc ALY I NSELSGIPLNMAPK KW trgfvqrlkgkqgr FRGN L S GKR VDF S G R T V ISP 371
Cdd:cd10506 182 YK K L ---------------------- VDF I GTANESAASKKSGL KW -------------- MKDL L L GKR SGH S F R S V VVG 225
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 372 DP N L RID E VAV P VHV A KI LT FP E K V NKA N INF L RKLVRNGP evhpganfi QQRHTQMK R fl KY G N -- REKMAQE L KY GD I 449
Cdd:cd10506 226 DP Y L ELN E IGI P CEI A ER LT VS E R V SSW N RER L QEYCDLTL --------- LLKGVIGV R -- RN G R lv GVRSHNT L QI GD V 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 450 VE R H L I DGDVVL F NR Q PS L H KL S IM A HLA KV K P HR - TFRF N ECV C T P YNA DFDGD EMNLHL PQ TEE A K AE ALV L MGTKAN 528
Cdd:cd10506 295 IH R P L V DGDVVL V NR P PS I H QH S LI A LSV KV L P TN s VVSI N PLC C S P FRG DFDGD CLHGYI PQ SLQ A R AE LEE L VALPKQ 374
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 529 L VTPRN G EP L IAAI QD F L TG A Y L L T LKDT F F D R A KAC Q I ia SI L VGK dekikv H LPPP T I L K PVT ---- LWTGKQ I F SVI 604
Cdd:cd10506 375 L ISSQS G QN L LSLT QD S L LA A H L M T ERGV F L D K A QMQ Q L -- QM L CPS ------ Q LPPP A I I K SPP sngp LWTGKQ L F QML 446
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 605 L r P S D DN pvranlrtkgkqycgkgedl CVND S Y - V T I QNS EL M S G S m DKGTLGSG S KN N I F Y IL LRD w G QNE A A D AMSRL 683
Cdd:cd10506 447 L - P T D LD -------------------- YSFP S N l V F I SDG EL I S S S - GGSSWLRD S EG N L F S IL VKH - G PGK A L D FLDSA 503
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 684 AR L APVY LS N RGFS IGIG D VTPGQGLLKAK -- Y E LLNA G Y -- KKCDEY I EA L NTGKLQQQPGCTA EE TLEALILKELSVI 759
Cdd:cd10506 504 QG L LCEW LS M RGFS VSLS D LYLSSDSYSRQ km I E EISL G L re AEIACN I KQ L LVDSRKDFLSGSG EE NDVSSDVERVIYE 583
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 760 R DHAGSAC ------------------ LRELD K S NS P L T M ALC GSKGS FINIS Q MIA C V G Q Q -------- A I SGSRVPDGF 813
Cdd:cd10506 584 R QKSAALS qasvsafkqvfrdiqnlv YKYAS K D NS L L A M IKA GSKGS LLKLV Q QSG C L G L Q lslvklsy R I PRQLSCAAW 663
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 814 ENRSL P HFEKHSK ----- LPAAK G F V AN SF YS GL T P T E F F F H TMAG R EGLVD tav KT A ET - G YMQ R R L VKSLE D LCSQ YD 887
Cdd:cd10506 664 NSQKS P RVIEKDG secte SYIPY 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 YD 740
....
gi 1570460116 888 L TVR 891
Cdd:cd10506 741 G TVR 744
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1035-1393
2.34e-81
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: 273.70
E-value: 2.34e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1035 R ITPTQIEKF L ETCRDKYM R AQME PG SA VG ALC AQSIGEP G TQMTL K TFHFAGV ASM N I TLGVPR I KEIIN AS K A I S TP I 1114
Cdd:cd02584 2 R LNKEAFDWI L GEIETRFN R SLVH PG EM VG TIA AQSIGEP A TQMTL N TFHFAGV SAK N V TLGVPR L KEIIN VA K N I K TP S 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1115 I T AQ L DKDD -- D ADY A RLVKG R I E K T L L GEISEYI E EVFL PD DCFILVK ---------------- LSLE R IR -- LLR L E V 1174
Cdd:cd02584 82 L T VY L EPGF ak D EEK A KKIQS R L E H T T L KDVTAAT E IYYD PD PQNTVIE edkefvesyfefpded VEQD R LS pw LLR I E L 161
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1175 N - AETVRYSIC M SKLRV K ----- PG D VA V HGE --------- AVVCVTPR E N s K SSMYYVLQ FLK ED ---- L PKVVVQ GI P 1235
Cdd:cd02584 162 D r KKMTDKKLS M EQIAK K ikeef KD D LN V IFS ddnaeklvi RIRIINDD E E - K EEDSEDDV FLK KI esnm L SDMTLK GI E 240
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1236 EVSRAV I H ------ I D EQS G KE K ---- YK L LVE G D NLR A V MATH GV KG TRTTSN NTY E VEKT LGIEAAR TTIIN E IQYTM 1305
Cdd:cd02584 241 GIRKVF I R eenkkk V D IET G EF K kree WV L ETD G V NLR E V LSHP GV DP TRTTSN DIV E IFEV LGIEAAR KALLK E LRNVI 320
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1306 VNH G MSIDR RH VM LL S D L MT YK G EVLG ITR F G LAKMKESV LM LA SFE K T A D H L FD AA Y FG QK D SVC GVSE C I IM G IPMN I 1385
Cdd:cd02584 321 SFD G SYVNY RH LA LL C D V MT QR G HLMA ITR H G INRQDTGP LM RC SFE E T V D I L LE AA A FG ET D DLK GVSE N I ML G QLAP I 400
....*...
gi 1570460116 1386 GTG L F K LL 1393
Cdd:cd02584 401 GTG C F D LL 408
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
246-1389
3.04e-77
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: 279.63
E-value: 3.04e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 246 K P SDLI L TRLL V P P LCI RP S V -------- V SDL ksgtne D DL TMK lte I I FL N DVI K KHRIS GA ------- KTQ M IM E DW 310
Cdd:TIGR02386 215 R P EWMV L DVIP V I P PEL RP M V qldggrfa T SDL ------ N DL YRR --- V I NR N NRL K RLLEL GA peiivrn EKR M LQ E AV 285
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 311 D flqlqc AL YI N SE l S G I P LNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L 390
Cdd:TIGR02386 286 D ------ AL FD N GR - R G K P VVGKNNRPLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KMYQCGL P KKM A LE L 358
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 391 TF P ekvnkanin F - LRK L VR ngpev HPG A NF I QQ rhtq M K RFLK ygnrekm AQELKYG D IV E R h L I DGDV VL F NR Q P S LH 469
Cdd:TIGR02386 359 FK P --------- F i IKR L ID ----- REL A AN I KS ---- A K KMIE ------- QEDPEVW D VL E D - V I KEHP VL L NR A P T LH 412
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 470 K L S I M A HLAKVKPHRTF R FNEC VCT PY NADFDGD E M NL H L P QTE EA K AEA LV LM GTKA N LVT P RN G E P LIAAI QD FLT G A 549
Cdd:TIGR02386 413 R L G I Q A FEPVLVEGKAI R LHPL VCT AF NADFDGD Q M AV H V P LSP EA Q AEA RA LM LASN N ILN P KD G K P IVTPS QD MVL G L 492
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 550 Y L LT L -------- KDT F FDRAK A CQIIASIL V GKDEK I K V HLPPPTILKP V tlwt G KQ IF SV IL rpsddnpvranlr TK G 621
Cdd:TIGR02386 493 Y Y LT T ekpgakge GKI F SNVDE A IRAYDNGK V HLHAL I G V RTSGEILETT V ---- G RV IF NE IL ------------- PE G 555
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 622 KQ Y cgkgedlc V ND SYV tiqnselmsgs MD K GTLG S gsknn IFYI L LRDW G QN E A A DAMSRLAR L APV Y LSNR G FS I GIG 701
Cdd:TIGR02386 556 FP Y -------- I ND NEP ----------- LS K KEIS S ----- LIDL L YEVH G IE E T A EMLDKIKA L GFK Y ATKS G TT I SAS 611
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 702 D V - T P GQ gllka KYE L L NAGY K KCDEYIEAL N T G KL qqqpgc T A EE TLEALI l KEL S VIR D HAGS A CLRE L D K S ---- N S 776
Cdd:TIGR02386 612 D I v V P DE ----- KYE I L KEAD K EVAKIQKFY N K G LI ------ T D EE RYRKVV - SIW S ETK D KVTD A MMKL L K K D tykf N P 679
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 777 PLT MA LC G SK G SFINIS Q MIACV G QQ A isgsr V P D G f ENRS LP hfekhsklpaakgf VAN SF YS GLT PT E F F FH T MAG R E 856
Cdd:TIGR02386 680 IFM MA DS G AR G NISQFR Q LAGMR G LM A ----- K P S G - DIIE LP -------------- IKS SF RE GLT VL E Y F IS T HGA R K 739
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 857 GL V DTA V KTA ET GY MQ RRLV KS ledlc S Q y D LT VR ----- SST G DII qfiyggdgld P A AM EGKDE PL E -- FK R VLDNIK 929
Cdd:TIGR02386 740 GL A DTA L KTA DS GY LT RRLV DV ----- A Q - D VV VR eedcg TEE G IEV ---------- E A IV EGKDE II E sl KD R IVGRYS 803
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 930 A --- VF P CQSEPALSK N E L V lt TE S I MK K teflccqdsflqeiknfvkgvsekikktrdkyg I NDN G TTE V ALSFP dg L G 1006
Cdd:TIGR02386 804 A edv YD P DTGKLIAEA N T L I -- TE E I AE K --------------------------------- I ENS G IEK V KVRSV -- L T 846
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1007 C PQRAR V P Q P dphtwflflqprv L Y QL D RI T PTQI E K fletcrdkymraqmep G S AVG ALC AQSIGEPGTQ M T LK TFH FA 1086
Cdd:TIGR02386 847 C ESEHG V C Q K ------------- C Y GR D LA T GKLV E I ---------------- G E AVG VIA AQSIGEPGTQ L T MR TFH TG 897
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1087 GVA S -- MN IT L G V PR I KE IIN A skai S TP iitaqldk D D D A DY A R l V K G RI E ktllgeiseyieev FLP D D cfil VK lsl 1164
Cdd:TIGR02386 898 GVA G as GD IT Q G L PR V KE LFE A ---- R TP -------- K D K A VI A E - V D G TV E -------------- IIE D I ---- VK --- 943
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1165 ERIRLLRLEV N A E TVR Y S I CMSK - LRVK P GD VAVH G EAVV -- CVT P RE nskssmyy V L QFLK - EDLPKVV V QGIPE V S R A 1240
Cdd:TIGR02386 944 NKRVVVIKDE N D E EKK Y T I PFGA q LRVK D GD SVSA G DKLT eg SID P HD -------- L L RIKG i QAVQEYL V KEVQK V Y R L 1015
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1241 V - IH I D eqsgk E K YKLLVEGDN LR A V MA T - H G ---- VK G TRTTSNNTY E VEKT L g I E AARTTII neiqytmvnhgmsidr 1314
Cdd:TIGR02386 1016 Q g VE I N ----- D K HIEVIVRQM LR K V RI T d S G dsnl LP G ELIDIHEFN E ENRK L - L E QGKKPAS ---------------- 1073
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1570460116 1315 rhvmllsdlmt YKGEV LGIT RFG L A km K ES V L ML ASF EK T ADH L F DAA YF G QK D SVC G VS E CI I M G -- IP M ni GTGL 1389
Cdd:TIGR02386 1074 ----------- AIPQL LGIT KAS L N -- T ES F L SA ASF QE T TKV L T DAA IK G KV D YLL G LK E NV I I G nl IP A -- GTGL 1135
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1051-1393
1.52e-68
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: 233.24
E-value: 1.52e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1051 KYMR AQM EPG S AVG A L C AQSIGEP G TQMTL K TFHFAG VAS MN I TLG V PR IK EI I - N ASK A I S TP II T AQ L DKDDD A DY A R 1129
Cdd:cd02735 1 KYMR SLV EPG E AVG L L A AQSIGEP S TQMTL N TFHFAG RGE MN V TLG I PR LR EI L m T ASK N I K TP SM T LP L KNGKS A ER A E 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1130 LV K G R IEKTL L GEIS E YI E -- E VF lpd DCFIL V - K LS L ER irll RL EV nae T VRYSICMS KL rvkpgdvavhgeavvcvt 1206
Cdd:cd02735 81 TL K K R LSRVT L SDVV E KV E vt E IL --- KTIER V f K KL L GK ---- WC EV --- T IKLPLSSP KL ------------------ 132
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1207 prenskssmy YV L QFLKEDLP K V V VQG IP EVS R AVIHIDEQS GK E KY KLLV EG D NL R A VMATHG - VKGT R TTS N NTYEVE 1285
Cdd:cd02735 133 ---------- LL L SIVEKLAR K A V IRE IP GIT R CFVVEEDKG GK T KY LVIT EG V NL A A LWKFSD i LDVN R IYT N DIHAML 202
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1286 K T L GIEAAR TT I IN EI QYTMVNH G MSI D R RH VM L LS D L MT YK G EVLGIT R F G LAK m KE S V L MLA SFE K T ADH L FD A AYF G 1365
Cdd:cd02735 203 N T Y GIEAAR RA I VK EI SNVFKVY G IAV D P RH LS L IA D Y MT FE G GYRPFN R I G MES - ST S P L QKM SFE T T LAF L KK A TLN G 281
330 340
....*....|....*....|....*...
gi 1570460116 1366 QK D SVCGV S ECIIM G I P M N I GTGLF K LL 1393
Cdd:cd02735 282 DI D NLSSP S SRLVV G K P V N G GTGLF D LL 309
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1076-1399
1.73e-66
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 242.88
E-value: 1.73e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1076 T QM T LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STPI I T AQ L DKD -- D D ADY A RL V KGR IE KTL LG EISEY I EEVFLP 1153
Cdd:PRK14898 541 T HN T MR TFH Y AGVA EI N V TLG L PR MI EI VD A R K EP STPI M T VH L KGE ya T D REK A EE V AKK IE SLT LG DVATS I AIDLWT 620
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1154 DD cf I L V K L SL E RI -- R L L RL E VNA E TVR ysicm S KL R VK pgd VAVH G e A V VCVT P REN S kssm Y YV L QFLKEDLPKV V V 1231
Cdd:PRK14898 621 QS -- I K V E L DE E TL ad R G L TI E SVE E AIE ----- K KL G VK --- IDRK G - T V LYLK P KTP S ---- Y KA L RKRIPKIKNI V L 685
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1232 Q GIP EVS R AVIHID E QSGK E K Y K L LVE G D NLR A V MATH GV KGT RTT S NN TY E VEKT LGIEAAR TT IINE IQY T MVNH G MS 1311
Cdd:PRK14898 686 K GIP GIE R VLVKKE E HEND E E Y V L YTQ G S NLR E V FKIE GV DTS RTT T NN II E IQEV LGIEAAR NA IINE MMN T LEQQ G LE 765
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1312 I D R RH V ML LS D L MT YK GEV LG I T R F G L A KM K E SVL ML A S FE K T AD HL F DAA YF G QK D SVC GV S E CI I M G I P MNI GTG LFK 1391
Cdd:PRK14898 766 V D I RH L ML VA D I MT AD GEV KP I G R H G V A GE K G SVL AR A A FE E T VK HL Y DAA EH G EV D KLK GV I E NV I V G K P IKL GTG CVD 845
....*...
gi 1570460116 1392 L LHKADRD 1399
Cdd:PRK14898 846 L RIDREYE 853
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1060-1389
3.57e-61
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: 206.11
E-value: 3.57e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1060 G S AVG A L C AQSIGEPGTQMTL K TFHFAGVASMN I TLG V PR I KEI I NA S kaistpiitaqldkdddadyarlvkgriektl 1139
Cdd:cd00630 1 G E AVG V L A AQSIGEPGTQMTL R TFHFAGVASMN V TLG L PR L KEI L NA A -------------------------------- 48
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1140 lgeiseyieevflpddcfilvklslerirllrlevnaetvrysicmsklrvkpgdvavhgeavvcvtprenskssmyyvl 1219
Cdd:cd00630 --------------------------------------------------------------------------------
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1220 qflkedlpkvvvqgipevsravihideqsgkekykllvegdnlravmathgvkgtrttsn NTY E VEKT LGIEAAR T TII N 1299
Cdd:cd00630 49 ------------------------------------------------------------ SIH E MLEA LGIEAAR E TII R 68
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1300 EIQ YTMVNH G M S I DRRH VM L LS D L MTY K G EVL G I TR F G LAKM K E S V LM L ASFEKT AD HL F DAA YF G Q KD SVC GVSE C II M 1379
Cdd:cd00630 69 EIQ KVLASQ G V S V DRRH IE L IA D V MTY S G GLR G V TR S G FRAS K T S P LM R ASFEKT TK HL L DAA AA G E KD ELE GVSE N II L 148
330
....*....|
gi 1570460116 1380 G I P MNI GTG L 1389
Cdd:cd00630 149 G R P APL GTG S 158
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
345-1389
8.50e-60
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 225.72
E-value: 8.50e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F - LR KLV RN G pevhpganf IQQ 423
Cdd:PRK00566 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A LE L FK P --------- F i MK KLV ER G --------- LAT 382
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 RHTQM K RFL kygnr E KMAQ E L ky G D IV E r HL I DGDV VL F NR Q P S LH K L S I M A ------------- H - L akvkphrtfrfn 489
Cdd:PRK00566 383 TIKSA K KMV ----- E REDP E V -- W D VL E - EV I KEHP VL L NR A P T LH R L G I Q A fepvliegkaiql H p L ------------ 442
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 490 ec VCT PY NADFDGD E M NL H L P QTE EA K AEA L VLM GTKA N LVT P R NG E P L I AAI QD FLT G A Y L LT LKD -------- T F FDR 561
Cdd:PRK00566 443 -- VCT AF NADFDGD Q M AV H V P LSL EA Q AEA R VLM LSSN N ILS P A NG K P I I VPS QD MVL G L Y Y LT RER egakgegm V F SSP 520
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 562 AK A CQIIASIL V GKDEK IKV HLPPPTILK p V T L wt G KQ IF SV IL r P sddnpvranlrt K G KQY cgkgedlc V N DSYV tiq 641
Cdd:PRK00566 521 EE A LRAYENGE V DLHAR IKV RITSKKLVE - T T V -- G RV IF NE IL - P ------------ E G LPF -------- I N VNKP --- 573
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 642 nselmsgs MD K GTLG sgskn N I FYILL R DW G QN E AADAMSRLAR L APV Y LSNR G F SIGI G D VT pgqg LLKA K Y E LLNAGY 721
Cdd:PRK00566 574 -------- LK K KEIS ----- K I INEVY R RY G LK E TVIFLDKIKD L GFK Y ATRS G I SIGI D D IV ---- IPPE K K E IIEEAE 636
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 722 K KCD E YIEALNT G KL qqqpgc T AE E TLEAL I l KEL S VIR D HAGS A CLRE L D K SNSPL ---- T MA LC G SK GS FIN I S Q mia 797
Cdd:PRK00566 637 K EVA E IEKQYRR G LI ------ T DG E RYNKV I - DIW S KAT D EVAK A MMKN L S K DQESF npiy M MA DS G AR GS ASQ I R Q --- 706
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 798 cvgqqa IS G S R vpdgfenrslphfekhsklpaak G FV A N ------------ S F YS GLT PT E F F FH T MAG R E GL V DTA V KT 865
Cdd:PRK00566 707 ------ LA G M R ----------------------- G LM A K psgeiietpiks N F RE GLT VL E Y F IS T HGA R K GL A DTA L KT 757
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 866 A ET GY MQ RRLV ksle D L c S Q y D LT VR ----- SST G DII qfiyggdgld P A AM EG KD -- EPLE --- FK RVL dn IKA V F - P C 934
Cdd:PRK00566 758 A DS GY LT RRLV ---- D V - A Q - D VI VR eddcg TDR G IEV ---------- T A II EG GE vi EPLE eri LG RVL -- AED V V d P E 819
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 935 QS E PALSKNE L V lt T E S I MK K teflccqdsflqeiknfvkgvsekikktrdkyg I NDN G TT EV alsfpdglgcpqra RV p 1014
Cdd:PRK00566 820 TG E VIVPAGT L I -- D E E I AD K --------------------------------- I EEA G IE EV -------------- KI - 849
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1015 qpdphtwflflqp R - VL yqldritptqiekfle TC RDKY ----------- MRAQM - EP G S AVG ALC AQSIGEPGTQ M T LK 1081
Cdd:PRK00566 850 ------------- R s VL ---------------- TC ETRH gvcakcygrdl ATGKL v NI G E AVG VIA AQSIGEPGTQ L T MR 900
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1082 TFH FA GV asm N IT L G V PR IK E IIN A S K ---- AI STP I itaqldkdddadyarlv K G RIEK tll G EISEYIEEVFLPD D cf 1157
Cdd:PRK00566 901 TFH TG GV --- D IT G G L PR VA E LFE A R K pkgp AI IAE I ----------------- D G TVSF --- G KETKGKRRIVITP D -- 955
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1158 ilvklslerirllrlev NA E TVR Y S I CMS K - L R V KP GD VAVH G EA vvcvtprenskssmyyvlqflkedlpkvvvqgipe 1236
Cdd:PRK00566 956 ----------------- DG E ERE Y L I PKG K h L L V QE GD HVEA G DK ----------------------------------- 983
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1237 vsravihideqsgkekykl L VE G dnlravmathgvkgtrtt S NNTYEVEKT LG I EA ARTTII NE I Q -- Y TM vn H G MS I DR 1314
Cdd:PRK00566 984 ------------------- L TD G ------------------ S IDPHDILRV LG V EA VQNYLV NE V Q kv Y RL -- Q G VK I ND 1024
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1315 R H V ------ ML L --------- S D LM ------------------------- T YKGEV LGIT RFG LA km K ES V L ML ASF EK T 1354
Cdd:PRK00566 1025 K H I evivrq ML R kvritdpgd T D FL pgelvdrsefeeenrkliaegkepa T GRPVL LGIT KAS LA -- T ES F L SA ASF QE T 1102
1130 1140 1150
....*....|....*....|....*....|....*..
gi 1570460116 1355 ADH L FD AA YF G QK D SVC G VS E CI I M G -- IP M ni GTGL 1389
Cdd:PRK00566 1103 TRV L TE AA IK G KV D PLR G LK E NV I I G rl IP A -- GTGL 1137
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
246-1389
1.44e-56
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 216.28
E-value: 1.44e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 246 K P S D L IL TRLL V P P LCI RP S V vs D L KS G T - NED DL TMKLTEI I FL N DVI K KHRIS GA KTQMIMEDWDF LQ LQC - A L YI N S 323
Cdd:PRK14906 311 D P A D M IL DVIP V I P PDL RP M V -- Q L DG G R f ATS DL NDLYRRV I NR N NRL K RLLDL GA PEIIVNNEKRM LQ EAV d S L FD N G 388
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 324 E l S G I P LNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkani NF 403
Cdd:PRK14906 389 R - R G R P VTGPGNRPLKSLADM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P H L KLHQCGL P SAM A LE L FK P -------- FV 459
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 404 LRK LV rngp E VHPG AN f I QQRHTQMK R FLK Y gnrekmaqelk YG D IV E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPH 483
Cdd:PRK14906 460 MKR LV ---- E LEYA AN - I KAAKRAVD R GAS Y ----------- VW D VL E E - V I QDHP VL L NR A P T LH R L G I Q A FEPVLVEG 522
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 484 RTFRFNEC VCT PY NADFDGD E M NL H L P QTEE A K AEA L VLM GTKA N LVT P RN G E PL IAAI QD FLT G A Y L LT - LK D T F FDRA 562
Cdd:PRK14906 523 KAIKLHPL VCT AF NADFDGD Q M AV H V P LSTQ A Q AEA R VLM LSSN N IKS P AH G R PL TVPT QD MII G V Y Y LT t ER D G F EGEG 602
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 563 KACQIIASI L VGK D EKIKVH L PP ptilkpvtlwtgkqif SVIL R P S D D NP VR anlrtkgkqyc G KGE DL CVNDSYVT I QN 642
Cdd:PRK14906 603 RTFADFDDA L NAY D ARADLD L QA ---------------- KIVV R L S R D MT VR ----------- G SYG DL EETKAGER I ET 655
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 643 S -------------- ELMSGS M D K GTL G sgsknnify I L LR D ---- WGQN E AADAMSRLARLAPV Y LSNR G FSIGIG D V T 704
Cdd:PRK14906 656 T vgriifnqvlpedy PYLNYK M V K KDI G --------- R L VN D ccnr YSTA E VEPILDGIKKTGFH Y ATRA G LTVSVY D A T 726
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 705 pgqg LLKA K Y E L L NAGYK K CDEYI E ALNT G K L qqqpgct A E ETLEALILKELSVIRDHA G S A C L REL D KS N SPLT MA LC G 784
Cdd:PRK14906 727 ---- IPDD K P E I L AEADE K VAAID E DYED G F L ------- S E RERHKQVVDIWTEATEEV G E A M L AGF D ED N PIYM MA DS G 795
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 785 SK G SFIN I S Q MIACV G QQ A ISGSRVP D gfenrs LP hfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GLVDTA VK 864
Cdd:PRK14906 796 AR G NIKQ I R Q LAGMR G LM A DMKGEII D ------ LP -------------- IKAN F RE GL SVL E Y F IS T HGA R K GLVDTA LR 855
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 865 TA ET GY MQ RRLV KSLE dlcsqy D LT VR S stgdiiqfiyggdg L D PAAM EG KDE PL EFKRVLDNIKAVFP C QS E PALSK N E 944
Cdd:PRK14906 856 TA DS GY LT RRLV DVAQ ------ D VI VR E -------------- E D CGTD EG VTY PL VKPKGDVDTNLIGR C LL E DVCDP N G 915
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 945 L VL ttesimkkteflccqdsflqeikn FVK G vs EK I KKTR D KYGINDN G T T E V ALS fp DGLG C PQRAR V P Q P dphtwflf 1024
Cdd:PRK14906 916 E VL ------------------------ LSA G -- DY I ESMD D LKRLVEA G V T K V QIR -- TLMT C HAEYG V C Q K -------- 959
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1025 lqprv L Y QL D RI T -- P TQ I ekfletcrdkymraqmep G S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA SMN IT L G V PR IK E 1102
Cdd:PRK14906 960 ----- C Y GW D LA T rr P VN I ------------------ G T AVG IIA AQSIGEPGTQ L T MR TFH SG GVA GDD IT Q G L PR VA E 1016
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1103 IIN A S K AISTPII taqldkddd A DYA rlvk G RIEK T ll G EIS E YIEEVFLP D DCFILVKL S l E R IRLLRLEVNAET VR YS 1182
Cdd:PRK14906 1017 LFE A R K PKGEAVL --------- A EIS ---- G TLQI T -- G DKT E KTLTIHDQ D GNSREYVV S - A R VQFMPGVEDGVE VR VG 1080
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1183 ICMSKLR V K P G D vavhgeavvc VTPRENSKSSMY Y VLQFLKE dlp KV V V QG I p EVSRAV I HIDEQSGKE K YKLLVE GD NL 1262
Cdd:PRK14906 1081 QQITRGS V N P H D ---------- LLRLTDPNTTLR Y IVSQVQD --- VY V S QG V - DINDKH I EVIARQMLR K VAVTNP GD SD 1146
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1263 ---- R A V mathgvkgtrttsn N T YE V E K T lgieaartti I N EI qytmvnhgmsidrrhvm L L SDLMTYK G E -- V LGIT RF 1336
Cdd:PRK14906 1147 ylpg R Q V -------------- N R YE F E D T ---------- A N NL ----------------- I L EGKQPPV G Q pl L LGIT KA 1185
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|...
gi 1570460116 1337 G LA km KE S V L ML ASF EK T ADH L F DAA YF G QK D SVC G VS E CI I M G I P MNI GTGL 1389
Cdd:PRK14906 1186 S LA -- TD S W L SA ASF QE T TKV L T DAA IE G KV D HLA G LK E NV I I G K P IPA GTGL 1236
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
345-876
3.37e-54
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain]
Cd Length: 659
Bit Score: 201.98
E-value: 3.37e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - R K L VRN G pevhp G A NF I QQ 423
Cdd:cd01609 236 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KEM A LE L FK P --------- F V i R E L IER G ----- L A PN I KS 301
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 rhtq M K RFL kygnr E KMAQ E L ky G DI V E r HL I D G DV VL F NR Q P S LH K L S I M A HLAKVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:cd01609 302 ---- A K KMI ----- E RKDP E V -- W DI L E - EV I K G HP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 369
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 504 E M NL H L P QTE EA K AEA L VLM GTKA N LVT P RN G E P LIAAI QD FLT G A Y L LT LKDT ffdrakacqiiasil VG K D E K I KVHL 583
Cdd:cd01609 370 Q M AV H V P LSL EA Q AEA R VLM LSSN N ILS P AS G K P IVTPS QD MVL G L Y Y LT KERK --------------- GD K G E G I IETT 434
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 584 P pptilkpvtlwt G KQ IF SV IL RP sddnpvra N L RT kgkqycgkgedlc V N D syvtiqnselmsg SMD K GT L G sgskn NI 663
Cdd:cd01609 435 V ------------ G RV IF NE IL PE -------- G L PF ------------- I N K ------------- TLK K KV L K ----- KL 463
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 664 FYILLRDW G QN E A A DAMSRLAR L APV Y LSNR G F SI G I G D - V T P gqgll KA K Y E LLNAGYK K CD E YIEALNT G K L qqqpgc 742
Cdd:cd01609 464 INECYDRY G LE E T A ELLDDIKE L GFK Y ATRS G I SI S I D D i V V P ----- PE K K E IIKEAEE K VK E IEKQYEK G L L ------ 532
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 743 T A EE TLEAL I LKELS V i RDHAGS A CLRE LDK S -- N SPLT MA LC G SK GS FIN I S Q MIACV G QQ A - I SG SRVP dgfenrs LP 819
Cdd:cd01609 533 T E EE RYNKV I EIWTE V - TEKVAD A MMKN LDK D pf N PIYM MA DS G AR GS KSQ I R Q LAGMR G LM A k P SG KIIE ------- LP 604
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 1570460116 820 hfekhsklpaakgf VANS F YS GLT PT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV 876
Cdd:cd01609 605 -------------- IKSN F RE GLT VL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV 647
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
528-703
2.56e-51
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: 177.82
E-value: 2.56e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 528 N LVT P R NG E P L I AAI QD FLT GAYLLT LK DTFFDR AKAC Q IIASIL V gkdekikvh LP P P T ILKP VT - LWTGKQ I FS VI L R 606
Cdd:pfam04983 1 N ILS P Q NG K P I I GPS QD MVL GAYLLT RE DTFFDR EEVM Q LLMYGI V --------- LP H P A ILKP IK p LWTGKQ T FS RL L P 71
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 607 P sddnpv RA N LRT K G K QYC gkg EDLC V NDSYV T I Q N S EL M SG SM DK G T L G s G S KNNIFY I LLRDW G QN E A A DAMS RL AR L 686
Cdd:pfam04983 72 N ------ EI N PKG K P K TNE --- EDLC E NDSYV L I N N G EL I SG VI DK K T V G - K S LGSLIH I IYKEY G PE E T A KFLD RL QK L 141
170
....*....|....*..
gi 1570460116 687 APV YL SNR GFSIGI G D V 703
Cdd:pfam04983 142 GFR YL TKS GFSIGI D D I 158
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
246-1090
9.38e-49
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 191.68
E-value: 9.38e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 246 K P SDLI LT R L L V P P LCI RP S V -------- VSD L ksgtne DD L TMK lte I I FL N DVI K KHRIS GA KTQMIMEDWDF LQ LQC 317
Cdd:PRK09603 1622 R P EWMM LT V L P V L P PDL RP L V aldggkfa VSD V ------ NE L YRR --- V I NR N QRL K RLMEL GA PEIIVRNEKRM LQ EAV 1692
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 318 ALYINSEL S GIPLNM A P K KWTRGFVQRL KGKQGRFR G NL S GKRVDFSGR T VI SPD PNL RI DE VAV P VHV A KI L TF P ekvn 397
Cdd:PRK09603 1693 DVLFDNGR S TNAVKG A N K RPLKSLSEII KGKQGRFR Q NL L GKRVDFSGR S VI VVG PNL KM DE CGL P KNM A LE L FK P ---- 1768
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 398 kani NF L R KL VRN G pevhpganfiqq RH T QM K R flkygn REK M AQE l K YGDIV E -- RHLID G DV VL F NR Q P S LHK L SI M A 475
Cdd:PRK09603 1769 ---- HL L S KL EER G ------------ YA T TL K Q ------ AKR M IEQ - K SNEVW E cl QEITE G YP VL L NR A P T LHK Q SI Q A 1825
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 476 HLA K VKPHRTFRFNEC VC TPY NADFDGD E M NL H L P QTE EA K AE AL VLM GTKA N LVT P RN G EPLIAAI QD FLT G A Y L L T L - 554
Cdd:PRK09603 1826 FHP K LIDGKAIQLHPL VC SAF NADFDGD Q M AV H V P LSQ EA I AE CK VLM LSSM N ILL P AS G KAVAIPS QD MVL G L Y Y L S L e 1905
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 555 K DTFFDRA K ACQIIAS I LVGK D E K - IKV H LPPPTILKPVTLW T -- G KQ I FSV IL rp S D DN P VRANL R TKG K Q ycgkgedl 631
Cdd:PRK09603 1906 K SGVKGEH K LFSSVNE I ITAI D T K e LDI H AKIRVLDQGNIIA T sa G RM I IKS IL -- P D FI P TDLWN R PMK K K -------- 1975
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 632 cvndsyvtiqnselmsgsm D K G T L gsgsknn IF Y I l LRDW G QNEA A DAMSR L AR L APV Y LSNR G F SI GIG D V - TP gqgll 710
Cdd:PRK09603 1976 ------------------- D I G V L ------- VD Y V - HKVG G IGIT A TFLDN L KT L GFR Y ATKA G I SI SME D I i TP ----- 2023
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 711 K A K YELLNAGYKKCDEYIEALNT G K L qqqpgc T AE E TLEAL I l KELSVIR D HAGSACLR -- EL DK S -- NS PLT MA LC G SK 786
Cdd:PRK09603 2024 K D K QKMVEKAKVEVKKIQQQYDQ G L L ------ T DQ E RYNKI I - DTWTEVN D KMSKEMMT ai AK DK E gf NS IYM MA DS G AR 2096
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 787 GS FIN I S Q MI A CV G QQA isgsr V PDG fenrslphfekhskl PAAKGFVANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA 866
Cdd:PRK09603 2097 GS AAQ I R Q LS A MR G LMT ----- K PDG --------------- SIIETPIISN F KE GL NVL E Y F NS T HGA R K GL A DTA L KTA 2156
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 867 ET GY MQ R R L ------ VK SLE D L C SQY ------ D LT V R S stg DI I qfiyggdgldpaamegkd EPLE --- F K RVL DN i KAV 931
Cdd:PRK09603 2157 NA GY LT R K L idvsqn VK VVS D D C GTH egieit D IA V G S --- EL I ------------------ EPLE eri F G RVL LE - DVI 2214
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 932 F P CQS E PA L SKNE L VLTT ---------- E SI MKK T EFL C CQD sflqeiknfv KGV SE K I kktrdk YG I N dngttevalsf 1001
Cdd:PRK09603 2215 D P ITN E IL L YADT L IDEE gakkvveagi K SI TIR T PVT C KAP ---------- KGV CA K C ------ YG L N ----------- 2267
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1002 pdg LG cpqrarvpqpdphtwflfl QPRVL Y qldritptqiekfletcrdkymraqme PG S AVG ALC AQSIGEPGTQ M TL K 1081
Cdd:PRK09603 2268 --- LG ------------------- EGKMS Y --------------------------- PG E AVG VVA AQSIGEPGTQ L TL R 2298
....*....
gi 1570460116 1082 TFH FA G V AS 1090
Cdd:PRK09603 2299 TFH VG G T AS 2307
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
345-1150
1.75e-48
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: 189.60
E-value: 1.75e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - RKL VRN G pevhp G A NF I QQ 423
Cdd:COG0086 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A LE L FK P --------- F I y RKL EER G ----- L A TT I KS 386
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 424 rhtq M K RFL kygnr E KMAQ E LK yg DI V E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:COG0086 387 ---- A K KMV ----- E REEP E VW -- DI L E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 504 E M NL H L P QTE EA KA EA LV LM GTKA N LVT P R NG E P L I AAI QD FLT G A Y L LT LKD -------- T F F D RAKACQIIASIL V GK 575
Cdd:COG0086 455 Q M AV H V P LSL EA QL EA RL LM LSTN N ILS P A NG K P I I VPS QD MVL G L Y Y LT RER egakgegm I F A D PEEVLRAYENGA V DL 534
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 576 DEK IKV HLPPPTILKPVTLW T -- G KQIFSV IL r P SD dnpvranlrtkgkqycgkgedlcvndsy V TIQ N SE lmsgs MD K G 653
Cdd:COG0086 535 HAR IKV RITEDGEQVGKIVE T tv G RYLVNE IL - P QE ---------------------------- V PFY N QV ----- IN K K 580
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 654 TLG sgskn N I FYILL R DW G QN E AADAMS RL AR L APV Y LSNR G F SIG IG D - V T P gqgll K A K Y E LLNAGY K KCD E YIEALN 732
Cdd:COG0086 581 HIE ----- V I IRQMY R RC G LK E TVIFLD RL KK L GFK Y ATRA G I SIG LD D m V V P ----- K E K Q E IFEEAN K EVK E IEKQYA 650
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 733 T G KL qqqpgc T AE E TLEAL I L kelsv IRDH A G ---- S ACLRELDKS N SPLT MA LC G SK GS FINIS Q MIACV G QQ A isgsr 808
Cdd:COG0086 651 E G LI ------ T EP E RYNKV I D ----- GWTK A S lete S FLMAAFSSQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A ----- 714
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 809 V P D G -- F E NR slphfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV KSLE D L csqy 886
Cdd:COG0086 715 K P S G ni I E TP ----------------- IGSN F RE GL GVL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV DVAQ D V ---- 773
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 887 dltvrsstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E f K R V L DNIK A --- V F P CQS E PALSKNE L V lt T E SIMKKT E f 958
Cdd:COG0086 774 ---------- I VTEEDC G td R G IT v T A IK EG GE vi EPL K - E R I L GRVA A edv V D P GTG E VLVPAGT L I -- D E EVAEII E - 839
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 959 lccqdsflqeiknfvk GVSEKIK K T R dkygindngttevalsfpdglgcpqrarvpqpdphtwflflqprvlyqldri TP 1038
Cdd:COG0086 840 ---------------- EAGIDSV K V R ---------------------------------------------------- SV 851
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1039 TQI E KFLET C RDK Y M R -- A QMEP --- G S AVG ALC AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS KA ISTP 1113
Cdd:COG0086 852 LTC E TRGGV C AKC Y G R dl A RGHL vni G E AVG VIA AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA KA GGIV 924
810 820 830
....*....|....*....|....*....|....*..
gi 1570460116 1114 IITAQLDKDDDADYARL V KGRI E KTLLGEISEYI EE V 1150
Cdd:COG0086 925 RLNNLKVVVNEEGKGVV V SRNS E LVIVDDGGRRE EE Y 961
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
246-1389
2.75e-47
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 187.14
E-value: 2.75e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 246 K P SDL ILT RLLVP P LCI RP S V vs D L K SG TNE - D DL TMKLTE II FL N DVIK K HRISGAKTQ MI MEDWDF LQ LQC - A L YI NS 323
Cdd:PRK14844 1665 R P EWM ILT TIPIL P PDL RP L V -- S L E SG RPA v S DL NHHYRT II NR N NRLR K LLSLNPPEI MI RNEKRM LQ EAV d S L FD NS 1742
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 324 ELSGIPLNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P EKVN K ANI nf 403
Cdd:PRK14844 1743 RRNALVNKAGAVGYKKSISDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P T L KLNQCGL P KRM A LE L FK P FVYS K LKM -- 1820
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 404 lrklvrngpevhpganfiqqrh TQ M KRFL K YGNREKM A QELKYG D IV E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPH 483
Cdd:PRK14844 1821 ---------------------- YG M APTI K FASKLIR A EKPEVW D ML E E - V I KEHP VL L NR A P T LH R L G I Q A FEPILIEG 1877
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 484 RTFRFNEC VCT PY NADFDGD E M NL H L P QTE EA KA EA L VLM GTKA N LVT P R NG E P L I AAIQ D FLT G A Y L LTL KDTFF D R -- 561
Cdd:PRK14844 1878 KAIQLHPL VCT AF NADFDGD Q M AV H V P ISL EA QL EA R VLM MSTN N VLS P S NG R P I I VPSK D IVL G I Y Y LTL QEPKE D D lp 1957
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 562 -- AKA C QIIA S I lvg K D EKIKV H lppptilkpvtlwtgkqi F S VIL R PSDD N pvr ANLR T KG K QY C GKGED L CV nds YVT 639
Cdd:PRK14844 1958 sf GAF C EVEH S L --- S D GTLHI H ------------------ S S IKY R MEYI N --- SSGE T HY K TI C TTPGR L IL --- WQI 2010
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 640 IQNS E LMSGSMDKGT L GSGSKNN I FYILL R DW GQ NEAADAMSR L AR L APV Y LSNR G F S IGIG D VT pgqg LLKA K YELLNA 719
Cdd:PRK14844 2011 FPKH E NLGFDLINQV L TVKEITS I VDLVY R NC GQ SATVAFSDK L MV L GFE Y ATFS G V S FSRC D MV ---- IPET K ATHVDH 2086
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 720 GYKKCDEY iealntg KL Q Q Q P G CTAEETLEALILK E L S VIR D HAGSAC L REL ------ D K S NS PLT M ALC G SK GS fin I S 793
Cdd:PRK14844 2087 ARGEIKKF ------- SM Q Y Q D G LITRSERYNKVID E W S KCT D MIANDM L KAI siydgn S K Y NS VYM M VNS G AR GS --- T S 2156
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 794 QM IACV G QQAISGS rv P D G f E NRSL P hfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ R 873
Cdd:PRK14844 2157 QM KQLA G MRGLMTK -- P S G - E IIET P -------------- IISN F RE GL NVF E Y F NS T HGA R K GL A DTA L KTA NS GY LT R 2219
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 874 RLV KSLED - LCSQY D lt VRSST G DIIQ fiyggdgldp A AM EG KD eplefkr VLDNIKA V FPCQS epal SK N ELV -- L T T E 950
Cdd:PRK14844 2220 RLV DVSQN c IVTKH D -- CKTKN G LVVR ---------- A TV EG ST ------- IVASLES V VLGRT ---- AA N DIY np V T K E 2276
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 951 SIM K KT E FL ccqdsflqeiknfvkg VSE K I K K trdkyg IN DN G TTE V ALSF P dg L G C pqrarvpqpdphtwflflqprvl 1030
Cdd:PRK14844 2277 LLV K AG E LI ---------------- DED K V K Q ------ IN IA G LDV V KIRS P -- L T C ----------------------- 2309
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1031 yqld R I T P TQIE kf L ETC RD KYMRAQMEP G S AVG ALC AQS I GEPGTQ M T LK TFH FA GV ----------- AS M N I ------ 1093
Cdd:PRK14844 2310 ---- E I S P GVCS -- L CYG RD LATGKIVSI G E AVG VIA AQS V GEPGTQ L T MR TFH IG GV mtrgvessnii AS I N A kiklnn 2383
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1094 ------------------------ T LG VPRI K E -------- IINASKAI ------------ ST PIIT aql D K DDDAD Y AR 1129
Cdd:PRK14844 2384 sniiidkngnkivisrscevvlid S LG SEKL K H svpygakl YVDEGGSV kigdkvaewdpy TL PIIT --- E K TGTVS Y QD 2460
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1130 L VK G r I EK T LLGEI S EY I EEVFLP D DCFILVKLS L e R I R LLR L EV N AETVRYS ---- I C M ----- SK L R V KP G D v A VH GE 1200
Cdd:PRK14844 2461 L KD G - I SI T EVMDE S TG I SSKVVK D WKLYSGGAN L - R P R IVL L DD N GKVMTLA sgve A C Y fipig AV L N V QD G Q - K VH AG 2537
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1201 A V VCV TPRE NS K S ----- SMYY V LQFLKEDL PK -- VV V QG I P ------------ EV S RAVIHI DEQ S ------- GKE K YK 1254
Cdd:PRK14844 2538 D V ITR TPRE SV K T rditg GLPR V IELFEARR PK eh AI V SE I D gyvafsekdrrg KR S ILIKPV DEQ I spveylv SRS K HV 2617
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1255 LLV EGD NL R avmathgv KG TRTTSNNT -- YEVEKT LG I EA ARTTI I N EIQ YTMVNH G MS ID RR H VMLLSDL M TY K G E VL - 1331
Cdd:PRK14844 2618 IVN EGD FV R -------- KG DLLMDGDP dl HDILRV LG L EA LAHYM I S EIQ QVYRLQ G VR ID NK H LEVILKQ M LQ K V E IT d 2689
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1332 --------------------------------------- GITR FG L A km KE S VLML ASF EK T ADH L FD AA YF G QK D SVC G 1372
Cdd:PRK14844 2690 pgdtmylvgesidklevdrendamsnsgkrpahylpilq GITR AS L E -- TS S FISA ASF QE T TKV L TE AA FC G KS D PLS G 2767
1290
....*....|....*..
gi 1570460116 1373 VS E CI I M G IPMNI GTGL 1389
Cdd:PRK14844 2768 LK E NV I V G RLIPA GTGL 2784
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
729-834
8.32e-41
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: 145.97
E-value: 8.32e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 729 E A LNT GKL QQQP G C T A EE TL EALI LKE L SVI RD H AG SACLRE LD KS NS PLT MA LC G S KGS F INISQ MIA C V GQQ AIS G S R 808
Cdd:pfam05000 3 D A ERY GKL EDIW G M T L EE SF EALI NNI L NKA RD P AG NIASKS LD PN NS IYM MA DS G A KGS I INISQ IAG C R GQQ NVE G K R 82
90 100
....*....|....*....|....*.
gi 1570460116 809 V P D GF EN R S LPHF E K HSKL P AAK GFV 834
Cdd:pfam05000 83 I P F GF SG R T LPHF K K DDEG P ESR GFV 108
rpoC1
CHL00018 RNA polymerase beta' subunit
315-554
1.34e-33
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 139.27
E-value: 1.34e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 315 LQ C A L -- YINSELS G I P LNMAPK K WTRG F VQRLK GK Q GRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF 392
Cdd:CHL00018 328 LQ E A V da LLDNGIR G Q P MRDGHN K PYKS F SDVIE GK E GRFR E NL L GKRVD Y SGR S VI VVG P S L SLHQCGL P REI A IE L FQ 407
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 393 P ekvnkanin F L - R K L V R NGPEVHPG A -- NF I QQRHTQMKRF L K ygnrekmaqelkygdiver HLID G DV VL F NR Q P S LH 469
Cdd:CHL00018 408 P --------- F V i R G L I R QHLASNIR A ak SK I REKEPIVWEI L Q ------------------- EVMQ G HP VL L NR A P T LH 459
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 470 K L S I M A HLAKVKPH R TFRFNEC VC TPY NADFDGD E M NL H L P QTE EA K AEA LV LM GTKA NL VT P RN G E P LIAAI QD F L T G A 549
Cdd:CHL00018 460 R L G I Q A FQPILVEG R AICLHPL VC 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 L L G L 539
....*
gi 1570460116 550 Y L LT L 554
Cdd:CHL00018 540 Y V LT I 544
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
345-553
1.72e-33
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 138.73
E-value: 1.72e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 345 LK GKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P EKVNK aninflrk L V R N G P evhpg A N F I QQ r 424
Cdd:PRK02625 339 IE GKQGRFR Q NL L GKRVD Y SGR S VI VVG P K L KMHQCGL P KEM A IE L FQ P FVIHR -------- L I R Q G I ----- V N N I KA - 404
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 425 htq M K RFLKYGNR E KM aqelkyg DIV E R h L I D G DV VL F NR Q P S LH K L S I M A HLAKVKPH R TFRFNEC VC TPY NADFDGD E 504
Cdd:PRK02625 405 --- A K KLIQRADP E VW ------- QVL E E - V I E G HP VL L NR A P T LH R L G I Q A FEPILVEG R AIQLHPL VC PAF NADFDGD Q 473
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 1570460116 505 M NL H L P QTE EA K AEA LV LM GTKA N LVT P RN GEP LIAAI QD FLT G A Y L LT 553
Cdd:PRK02625 474 M AV H V P LSL EA Q AEA RL LM LASN N ILS P AT GEP IVTPS QD MVL G C Y Y LT 522
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
650-1088
1.02e-15
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: 82.98
E-value: 1.02e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 650 M DK GT L gsgsk N N IFYILLRDW G QNEA A DAMSR L AR L APV Y LSNR G F SI GIG D VT pgqg LLK AK YE LL N A GY K KCDEYI E 729
Cdd:TIGR02388 7 V DK KA L ----- K N LISWAYKTY G TART A AMADK L KD L GFR Y ATRA G V SI SVD D LK ---- VPP AK QD LL E A AE K EIRATE E 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 730 ALNT G KLQ ----- Q QPGC T AEE T L E A L ILK els V IRD hagsac L R EL D KS NS PLT MA LC G SK G sfi N I SQ MIAC VG QQAI 804
Cdd:TIGR02388 78 RYRR G EIT everf Q KVID T WNG T N E E L KDE --- V VNN ------ F R QT D PL NS VYM MA FS G AR G --- N M SQ VRQL VG MRGL 145
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 805 SGS rv P D G f E NRS LP hfekhsklpaakgf VANS F YS GLT P TE FFFHTMAG R E GLVDTA VK TA ET GY MQ RRLV KSLE D L -- 882
Cdd:TIGR02388 146 MAN -- P Q G - E IID LP -------------- IKTN F RE GLT V TE YVISSYGA R K GLVDTA LR TA DS GY LT RRLV DVSQ D V iv 208
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 883 ---- C - SQYDLT VR SS T - GD ii QF I YG GD G L dpaamegkdeple FK R VL dn IKA V FPCQS E PALS KN E lvlttesimkkt 956
Cdd:TIGR02388 209 reed C g TERSIV VR AM T e GD -- KK I SL GD R L ------------- LG R LV -- AED V LHPEG E VIVP KN T ------------ 259
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 957 eflccqdsflqeiknfvk GVSEKIK KT rdkyg I NDN G TT EV ALSF P dg L G C PQRAR V PQ p DPHT W F L FLQPR V lyqldri 1036
Cdd:TIGR02388 260 ------------------ AIDPDLA KT ----- I ETA G IS EV VVRS P -- L T C EAARS V CR - KCYG W S L AHAHL V ------- 306
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|..
gi 1570460116 1037 tptqiekfletcrdkymraqm EP G S AVG ALC AQSIGEPGTQ M T LK TFH FA GV 1088
Cdd:TIGR02388 307 --------------------- DL G E AVG IIA AQSIGEPGTQ L T MR TFH TG GV 337
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1058-1108
9.72e-15
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: 74.49
E-value: 9.72e-15
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1570460116 1058 E P G S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA S m N IT L G V PR IK E IIN A S K 1108
Cdd:cd02655 4 E L G E AVG IIA AQSIGEPGTQ L T MR TFH TG GVA T - D IT Q G L PR VE E LFE A R K 53
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
769-1088
1.83e-12
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 72.34
E-value: 1.83e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 769 R EL D KS NS PLT MA LC G SK G sfi N I SQ MIAC VG QQAISGS rv P D G f E NRS LP hfekhsklpaakgf VANS F YS GLT P TE FF 848
Cdd:PRK02597 114 R QN D PL NS VYM MA FS G AR G --- N M SQ VRQL VG MRGLMAN -- P Q G - E IID LP -------------- IKTN F RE GLT V TE YV 173
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 849 FHTMAG R E GLVDTA VK TA ET GY MQ RRLV ksle D L c SQ y D LT VR SS tgdiiqfiygg D ----- G LDPA AM EGK D eplefk R 923
Cdd:PRK02597 174 ISSYGA R K GLVDTA LR TA DS GY LT RRLV ---- D V - SQ - D VI VR EE ----------- D cgttr G IVVE AM DDG D ------ R 230
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 924 VL DNIK avfpcqsepalsk NE L V -- LTT E SIM - KKT E FLCCQD sfl QE I K nfv KGVSE KI K K T rdkygindn G TT EV ALS 1000
Cdd:PRK02597 231 VL IPLG ------------- DR L L gr VLA E DVV d PEG E VIAERN --- TA I D --- PDLAK KI E K A --------- G VE EV MVR 282
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1001 F P dg L G C p QR AR vpqpdphtwflflqprvlyqldritptqiekfl ET CR DK Y ---- MRAQM - EP G S AVG ALC AQSIGEPG 1075
Cdd:PRK02597 283 S P -- L T C - EA AR --------------------------------- SV CR KC Y gwsl AHNHL v DL G E AVG IIA AQSIGEPG 326
330
....*....|...
gi 1570460116 1076 TQ M T LK TFH FA GV 1088
Cdd:PRK02597 327 TQ L T MR TFH TG GV 339
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1060-1393
9.57e-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: 9.57e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1060 G SA VG A L C A QS I G EP GTQMT L KT fhfagv ASMNITLGVPRI KE IINASKAISTP ------ I ITAQ L D K D D --- DADY A R L 1130
Cdd:cd02737 1 G EP VG S L A A TA I S EP AYKAL L DP ------ PQSLESSPLELL KE VLECRSKSKSK endrrv I LSLH L C K C D hgf EYER A A L 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1131 - VK GRI E KTL L GEISEYIEEVFL P DDCFIL V KLSLERIRLLRLEVNAETVRY S ICMS K L rv K P GDVAV H ------- GEAV 1202
Cdd:cd02737 75 e VK NHL E RVT L EDLATTSMIKYS P QATEAI V GEIGDQLNTKKKGKKKAIFST S LKIT K F -- S P WVCHF H ldkecqk LSDG 152
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1203 V C V T --- PR E N SKSS MY y V L QF L KE ---- D L PKV V VQ G IPEV ----------- S RAVIHIDEQ S GKEKYK L L V ------- 1257
Cdd:cd02737 153 P C L T fsv SK E V SKSS EE - L L DV L RD riip F L LET V IK G DERI ksvnilwedsp S TSWVKSVGK S SRGELV L E V tveesck 231
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570460116 1258 -- E G DNLRA VM AT ----- HGVKGT R TTSNNTYEVEKT LGI E AA RTTIINEIQYTMVNH G M S ID R R H VM L LS D L MTY K GE V 1330
Cdd:cd02737 232 kt R G NAWNV VM DA cipvm DLIDWE R SMPYSIQQIKSV LGI D AA FEQFVQRLESAVSMT G K S VL R E H LL L VA D S MTY S GE F 311
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1570460116 1331 L G ITRF G LAKMKE S V ----- LML A S F EKTADHLFD AA YF G QK DS VC GV SECIIM G IPMNI GTG - L F KL L 1393
Cdd:cd02737 312 V G LNAK G YKAQRR S L kisap FTE A C F SSPIKCFLK AA KK G AS DS LS GV LDACAW G KEAPV GTG s K F EI L 380
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1060-1088
4.48e-08
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 58.03
E-value: 4.48e-08
10 20
....*....|....*....|....*....
gi 1570460116 1060 G S AVG ALCA QSIGEPGTQ M TL K TFH FA GV 1088
Cdd:CHL00117 315 G E AVG IIAG QSIGEPGTQ L TL R TFH TG GV 343
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1034-1080
4.98e-07
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 54.51
E-value: 4.98e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1570460116 1034 D RI T PTQI E KFLETCRDK Y MR A QM EP GS AVG ALC AQSIGEPGTQM T L 1080
Cdd:PRK14898 31 D GV T EEMV E EIIDEVVSA Y LN A LV EP YE AVG IVA AQSIGEPGTQM S L 77
Blast search parameters
Data Source:
Precalculated data, version = cdd.v.3.21
Preset Options: Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
