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DNA-directed RNA polymerase III subunit RPC1 [Archocentrus centrarchus]
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: 1655.75
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 24 S A E QMRQQAHIQ V VSK NLY SQD T KH t PLPYGVLD H R M GTS E KD RP C L TCG K NLADC L GH Y GY LD LELP C FH V GYFKA T I G 103
Cdd:cd02583 2 S P E DIIRLSEVE V TNR NLY DIE T RK - PLPYGVLD P R L GTS D KD GI C E TCG L NLADC V GH F GY IK LELP V FH I GYFKA I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 104 ILQ M ICKTCSR IM L TK EEK LQ F MDY L K RPNL AY LQK RG LKKKI SD KC R K RTV C LN C S afngpvkkcgllkiihekykttk 183
Cdd:cd02583 81 ILQ C ICKTCSR VL L PE EEK RK F LKR L R RPNL DN LQK KA LKKKI LE KC K K VRK C PH C G ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 184 kvvdafvsdflqsfdtaiehnklvep LL TR AQE N LNPL VA LNLFK R IP QD D IP LLLMNP E AG K P AD LI I TR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL KV LNLFK N IP PE D VE LLLMNP L AG R P EN LI L TR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RMT 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 1735312367 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILTYPERV NKA N L E LM RKLV R NGPDVHPGANF IQN 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILTYPERV TRY N I E KL RKLV L NGPDVHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 424 R HTQM K R FLKYGNR E KIA Q EL RF GD V VERHL I DGD V VLFNRQPSLH K LSIMAH I A R V K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R KIA R EL KI GD I VERHL E DGD I VLFNRQPSLH R LSIMAH R A K V M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDR SKA CQ IVASI L V G KDE rvr I S L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDR AQF CQ LCSYM L D G EIK --- I D L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 584 P R PAI M KP IA LWTGKQIFSL I L K P S K EC PV RA NL RT K G K Q Y CG K GE D L C H ND SF VVI H NSEL M CG SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 P P PAI L KP VE LWTGKQIFSL L L R P N K KS PV LV NL EA K E K S Y TK K SP D M C P ND GY VVI R NSEL L CG RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 664 FY I LLRD W G QLE AA N AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K QD L L D D GY Q KCDEYI EALQT 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 EE L V D N GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 744 AE E TLEA L I LK ELS V IR DR AG S ACL R EL D KSNSPLIMALCGSKGS 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 KSNSPLIMALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1735312367 824 H SK L PAAKGFVA D SFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVA N SFYSGLTPTEFFFHTM 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; ...
1021-1360
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: 568.00
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITA H L DVED D ADF AR L 1100
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITA K L ENDR D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1101 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysicmsklrvkpgdiavhgeavvcvspren 1180
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 1735312367 1181 SKS SM Y YV LQSLK ED LP K VVV Q GIPEV A RAVI HI D EQ sg K N KYKLLVEG DN LRAVM A T H GV N G S RTTSN NTY EVEK T LGI 1260
Cdd:cd02736 123 SKS NL Y FL LQSLK RK LP D VVV S GIPEV K RAVI NK D KK -- K G KYKLLVEG YG LRAVM N T P GV I G T RTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1261 EAARSTIINEIQYTM VN HGMSID R RH V MLLADLM SY KGE I LGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1340
Cdd:cd02736 201 EAARSTIINEIQYTM KS HGMSID P RH I MLLADLM TF KGE V LGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 1735312367 1341 C GVSECIIMG I PM N IGTGLF 1360
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: 1655.75
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 24 S A E QMRQQAHIQ V VSK NLY SQD T KH t PLPYGVLD H R M GTS E KD RP C L TCG K NLADC L GH Y GY LD LELP C FH V GYFKA T I G 103
Cdd:cd02583 2 S P E DIIRLSEVE V TNR NLY DIE T RK - PLPYGVLD P R L GTS D KD GI C E TCG L NLADC V GH F GY IK LELP V FH I GYFKA I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 104 ILQ M ICKTCSR IM L TK EEK LQ F MDY L K RPNL AY LQK RG LKKKI SD KC R K RTV C LN C S afngpvkkcgllkiihekykttk 183
Cdd:cd02583 81 ILQ C ICKTCSR VL L PE EEK RK F LKR L R RPNL DN LQK KA LKKKI LE KC K K VRK C PH C G ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 184 kvvdafvsdflqsfdtaiehnklvep LL TR AQE N LNPL VA LNLFK R IP QD D IP LLLMNP E AG K P AD LI I TR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL KV LNLFK N IP PE D VE LLLMNP L AG R P EN LI L TR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RMT 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 1735312367 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILTYPERV NKA N L E LM RKLV R NGPDVHPGANF IQN 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILTYPERV TRY N I E KL RKLV L NGPDVHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 424 R HTQM K R FLKYGNR E KIA Q EL RF GD V VERHL I DGD V VLFNRQPSLH K LSIMAH I A R V K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R KIA R EL KI GD I VERHL E DGD I VLFNRQPSLH R LSIMAH R A K V M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDR SKA CQ IVASI L V G KDE rvr I S L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDR AQF CQ LCSYM L D G EIK --- I D L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 584 P R PAI M KP IA LWTGKQIFSL I L K P S K EC PV RA NL RT K G K Q Y CG K GE D L C H ND SF VVI H NSEL M CG SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 P P PAI L KP VE LWTGKQIFSL L L R P N K KS PV LV NL EA K E K S Y TK K SP D M C P ND GY VVI R NSEL L CG RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 664 FY I LLRD W G QLE AA N AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K QD L L D D GY Q KCDEYI EALQT 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 EE L V D N GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 744 AE E TLEA L I LK ELS V IR DR AG S ACL R EL D KSNSPLIMALCGSKGS 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 KSNSPLIMALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1735312367 824 H SK L PAAKGFVA D SFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVA N SFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
7-932
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 933.50
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 7 RETDVA K K I SH I C FG MK S A E QM R QQAHIQVVSKNL Y SQ D T kh T P LPY G VL D H R M G TSEKDRP C L TCG KNLAD C L GH Y G YL 86
Cdd:PRK08566 1 SMMMIP K R I GS I K FG LL S P E EI 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 HI 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 87 D L EL P CF HVG YF K ATIGI L QMI C KT C S R IM LT K EE KLQFMDY L K R PNLAYLQKRG L K K KISDKCR KR T VC LN C SA fngpv 166
Cdd:PRK08566 79 E L AR P VI HVG FA K LIYKL L RAT C RE C G R LK LT E EE IEEYLEK L E R LKEWGSLADD L I K EVKKEAA KR M VC PH C GE ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 167 K K cgl L KI IH EK YK T tkkvvdafvsd F LQ sfdtaiehnklvep LLTRAQEN L N P LVALNLFKR IP QD D IP LL LM NPE AGK 246
Cdd:PRK08566 154 K Q --- Y KI KF EK PT T ----------- F YE -------------- ERKEGLVK L T P SDIRERLEK IP DE D LE LL GI NPE VAR 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 247 P ADLII T R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRMT GA K t Q M I M ED - W DF LQ LQCAL Y INS E 324
Cdd:PRK08566 206 P EWMVL T 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 1735312367 325 LS GIP lnma P ----- KKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT Y PERV 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 PERV TEW 358
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 400 N L E LM R KL V R NGP DV HPGAN FI qn RHTQMK R F - L KYG N R E KI A QE L RF G DV VERHLIDGD V VLFNRQPSLH KL SIMAH IA 478
Cdd:PRK08566 359 N I E EL R EY V L NGP EK HPGAN YV -- IRPDGR R I k L TDK N K E EL A EK L EP G WI VERHLIDGD I VLFNRQPSLH RM SIMAH RV 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 479 RV 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 RV 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 1735312367 559 F DRSK A CQIVASILVGKDE rvris L P R PAI MKPIAL WTGKQIFSL I L kpskec P VRA NL -- RT K GKQY C GKGED - L C HN D 635
Cdd:PRK08566 517 F TKEE A LDLLRAAGIDELP ----- E P E PAI ENGKPY WTGKQIFSL F L ------ P KDL NL ef KA K ICSG C DECKK e D C EH D 585
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 636 SF VVI H N SE L MC G SM DK GTL G SG s KNN I FYILLRDW G QLE A ANAMSRLA RLA PVYLSN RGF SI GI G D VTPGQGLLKAKQD 715
Cdd:PRK08566 586 AY VVI 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 EDIPEEAKEEIDE 664
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 716 LLDDGYQKCD E Y IEA LQT G K L QQQ PG C T A EETLE AL I LKE L SVI RD R AG SACLRE L DKS N SPL IMA LC G SK GS FI N IS QM 795
Cdd:PRK08566 665 IIEEAEKRVE 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 PAV IMA RT G AR GS ML N LT QM 744
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 796 I ACVGQQ AIS G S R VPD G FEN R S LPHF EKHSKLPA A K GFV AD S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GYMQRRL 875
Cdd:PRK08566 745 A 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 824
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*..
gi 1735312367 876 VKS 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 VLDNIRAVY 932
Cdd:PRK08566 825 INA L Q DL KVE YD G TVR DTR G N I V QF K YG E DG V DP MKSDH - GK P VDVD R IIERVLGKE 880
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: 868.26
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 13 KKI SH I C FG MK S A E QM R QQAHIQ VV SKNL Y SQ D T kh T P LPY G VL D H R M G TS E KDRP C L TCG KNLAD C L GH Y G YLD L EL P C 92
Cdd:TIGR02390 2 KKI GS I K FG LL S P E EI R KMSVVE VV TADT Y DD D G -- Y P IEG G LM D P R L G VI E PGLR C K TCG GKVGE C P GH F G HIE L AR P V 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 93 F HVG YF K ATIG IL QMI C KT C S RI M LT K EE KL Q FMD - YL K RPNLAYLQKRG L KK KI SDKCR KR TV C LN C SA fngpvkkc GL 171
Cdd:TIGR02390 80 V HVG FA K EIYK IL RAT C RK C G RI T LT E EE IE Q YLE k IN K LKEEGGDLAST L IE KI VKEAA KR MK C PH C GE -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 172 L KI IH EK ---- Y KTT K K vvdafvsdflqsfdtaiehnklveplltr AQEN L N P LVALNLFKR IP QD D IP LL LM NP EAGK P 247
Cdd:TIGR02390 152 K KI KF EK ptyf Y EEG K E ----------------------------- GDVK L T P SEIRERLEK IP DE D AE LL GI NP KVAR P 202
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 248 ADLII T R L L VPP LCI RPS VV sd L KS G T - N EDDLT M KL TE II FL N DVI K KHRMT GA KTQM I MED W DF LQ LQC A L Y INS EL S 326
Cdd:TIGR02390 203 EWMVL T 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 280
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 327 GIP - LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT Y PERV NKA N LELM R 405
Cdd:TIGR02390 281 GIP p ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PERV TPW N IDEL R 360
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 406 KL V R NGPD VH PGAN FIQN rh TQMK R F - LKYG N R E KI A QE L RF G D VVERHLIDGD V VLFNRQPSLH KL S I M A H IAR V K P HR 484
Cdd:TIGR02390 361 EY V L NGPD SW PGAN YVIR -- PDGR R I k IRDE N K E EL A ER L EP G W VVERHLIDGD I VLFNRQPSLH RM S M M G H KVK V L P GK 438
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 485 TFR F 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 DRSKA 564
Cdd:TIGR02390 439 TFR L 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 TKEEV 518
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 565 CQ I VASI lvgkde RVRISL P R PAI M KP IAL WTGKQIFS LI L KPSKECPV RA NL r TK G KQY C G K G E dl C HN D SF VVI H N SE 644
Cdd:TIGR02390 519 QT I LGVA ------ GYFGDP P E PAI E KP KEY WTGKQIFS AF L PEDLNFEG RA KI - CS G SDA C K K E E -- C PH D AY VVI K N GK 589
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 645 L MC G SM DK GTL G S g S K NN I FYILL R DW G QLE A ANAMSRLA RL APVYLSN RGF SI GI G D VTPGQGLLKAKQD L LDDGYQKC 724
Cdd:TIGR02390 590 L LK G VI DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT RL FIRFITL RGF TT GI D D IDIPKEAKEEIEE L IEKAEKRV 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 725 D EY IE ALQT G K L QQQ PG C T A EETLE AL I LKE L SVI RD R AG SACLRE LD KS N SPL IMA LC G SK GS FI NI S QM I A C VGQQ AI 804
Cdd:TIGR02390 669 D NL IE RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG EVAEKY LD PE N HAV IMA RT G AR GS LL NI T QM A A M VGQQ SV 748
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 805 S G S R VPD G FE NR S LPHF E K HSKLPA A K GFV AD SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GYMQRRL VKS L E DL CS 884
Cdd:TIGR02390 749 R G G R 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 YV 828
890 900 910 920
....*....|....*....|....*....|....*....|..
gi 1735312367 885 Q YD L TVR SST G DI IQF I YG G DG L DP AAME - GK de P LEF K RVL 925
Cdd:TIGR02390 829 E YD G 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; ...
1021-1360
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: 568.00
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITA H L DVED D ADF AR L 1100
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITA K L ENDR D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1101 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysicmsklrvkpgdiavhgeavvcvspren 1180
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 1735312367 1181 SKS SM Y YV LQSLK ED LP K VVV Q GIPEV A RAVI HI D EQ sg K N KYKLLVEG DN LRAVM A T H GV N G S RTTSN NTY EVEK T LGI 1260
Cdd:cd02736 123 SKS NL Y FL LQSLK RK LP D VVV S GIPEV K RAVI NK D KK -- K G KYKLLVEG YG LRAVM N T P GV I G T RTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1261 EAARSTIINEIQYTM VN HGMSID R RH V MLLADLM SY KGE I LGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1340
Cdd:cd02736 201 EAARSTIINEIQYTM KS HGMSID P RH I MLLADLM TF KGE V LGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 1735312367 1341 C GVSECIIMG I PM N IGTGLF 1360
Cdd:cd02736 281 E GVSECIIMG K PM P IGTGLF 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
249-550
8.44e-149
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 452.74
E-value: 8.44e-149
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 249 DL I I T R L L VPP L C I RPSV VS D L k SGTN EDDLT MK L TE II FL N DVI K KHRMT GA KTQM I MEDWDF LQ LQCALY I NS E l SGI 328
Cdd:smart00663 2 WM I L T 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 - GLP 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 329 PL N MAPKKWTRGFV QRLKGK Q GRFR G NL S GKRVDFS G R T VI S PDPNL RID EV A VP VHV A KI LT Y PE R V NKA N LELM RKLV 408
Cdd:smart00663 80 RA N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLN EV G VP KEI A LE LT F PE I V TPL N IDKL RKLV 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 409 RNGP dvh P GA NF I QN rht QM K RF LK YGNRE KIA QE L RF GD V VERH L IDGDVVLFNRQP S LH KL SI M AH IA RV KPHR T F R F 488
Cdd:smart00663 160 RNGP --- N GA KY I IR --- GK K TN LK LAKKS KIA NH L KI GD I VERH V IDGDVVLFNRQP T LH RM SI Q AH RV RV LEGK T I R L 233
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1735312367 489 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 234 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
2.55e-120
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: 377.79
E-value: 2.55e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 12 A KKI SH I C FG MK S A E QM R QQAHIQ V VSKNL Y S q DTKHT P LPY G V LD H RMGT SE KD RP C L TCGK NLA DC L GH Y G YLD L EL P 91
Cdd:pfam04997 1 L KKI KE I Q FG IA S P E EI R KWSVGE V TKPET Y N - YGSLK P EEG G L LD E RMGT ID KD YE C E TCGK KKK DC P GH F G HIE L AK P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 92 C FH V G Y FK A T IG IL QMI CK T CS RIM L TKEEKLQ F MDYL KR PN L AY L QKR gl K K K I SDK C R K RTV C LN C SAF NG pvkkcgl 171
Cdd:pfam04997 80 V FH I G F FK K T LK IL ECV CK Y CS KLL L DPGKPKL F NKDK KR LG L EN L KMG -- A K A I LEL C K K KDL C EH C GGK NG ------- 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 172 lkiihekykt TKKVVDAFVSDFLQSFDT AI EHN K LV E plltr AQ E N LNP LVA L NL FKRI PQD D IPL L LM NP EAGK P ADL I 251
Cdd:pfam04997 151 ---------- VCGSQQPVSRKEGLKLKA AI KKS K EE E ----- EK E I LNP EKV L KI FKRI SDE D VEI L GF NP SGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 252 I T R L L VPP L CIRPSV VS D LK s GTN EDDLT M KL TE II FL N DVI KK HRMT GA KTQM I M E D W DF LQ LQC A LYINS E LS G I P L - 330
Cdd:pfam04997 216 L T 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 1735312367 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 ...
841-1316
3.57e-119
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 382.47
E-value: 3.57e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 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 - EPL 919
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 r FTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 920 EF KRVLDNIRAVYTCP D EPA L SQNELVLTADA I MK R ADF L C -- CRDSFLE E IK T FIKSISERI ---- K KT R DKYGI N DN g 993
Cdd:pfam04998 81 EF SDLKLEDKFKNDLL D DLL L LSEFSLSYKKE I LV R DSK L G rd RLSKEAQ E RA T LLFELLLKS gles K RV R SELTC N SK - 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 994 tsepkvlyqldrvtpt QLEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL K TFHFAGVAS M N I TLGVPR I KEI 1073
Cdd:pfam04998 160 ---------------- AFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL N TFHFAGVAS K N V TLGVPR L KEI 223
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1074 IN A SKNI ST P II T AH L -- D V EDDADF A RL V K G R IEK TL LG EIS E YI E ------------------------------ EVF 1121
Cdd:pfam04998 224 IN V SKNI KS P SL T VY L fd E V GRELEK A KK V Y G A IEK VT LG SVV E SG E ilydpdpfntpiisdvkgvvkffdiidevt NEE 303
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1122 LP D DCFI L VK L SLERIRL L RLEVNAETVRYS I CM S -- KLRVKPG DIA V ----------------- H G EAVVCVSPRENSK 1182
Cdd:pfam04998 304 EI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I PR S ir NKVDEGR DIA I geitafiikiskkirqd T G GLRRVDELFMEED 383
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1183 SSMYYVLQ SL ked L PKVVVQ GIP EVA R AVIHI D E q S GK NK -- YK L LV EG D NL RA V MATH G - V NGS R TT SN NTY E VEKT LG 1259
Cdd:pfam04998 384 PKLAILVA SL --- L GNITLR GIP GIK R ILVNE D D - K GK VE pd WV L ET EG V NL LR V LLVP G f V DAG R IL SN DIH E ILEI LG 459
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 1735312367 1260 IEAAR STII NEI QYTMVNH G MS I DR RH VM L L AD L M SY KG E I LG I T R F G LA K MKE S V L 1316
Cdd:pfam04998 460 IEAAR NALL NEI RNVYRFQ G IY I ND RH LE L I AD Q M TR KG Y I MA I G R H G IN K AEL S A L 516
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1006-1363
1.92e-97
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 317.94
E-value: 1.92e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1006 V T PTQL 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 NI STP II 1085
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 1735312367 1086 T AH L DV E -- D D ADF 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 1161
Cdd:PRK04309 115 T IY L KD E 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 1735312367 1162 P G DIAVH G EAVV c V SP R E N S kssm Y YV L QS L K E DLPKVVVQ GI PEVA R AV I HIDE qsgk NK Y KLLV EG D NL RA V MATH GV 1241
Cdd:PRK04309 185 G G EVEIE G NTLI - I SP 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 1735312367 1242 NGS RTT S NN TY E V E KT LGIEAAR ST II N EI QY T MVNH G MSI D R RH V ML L AD L M SYK GE ILG I T R F G LAKM K E SVL ML A S F 1321
Cdd:PRK04309 256 DAT RTT T NN IH E I E EV LGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML V AD M M TWD GE VRQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 1735312367 1322 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 1363
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 ...
1010-1365
5.70e-84
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 279.63
E-value: 5.70e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1010 Q L EKFLETCRDK 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 NI STP II T AH L 1089
Cdd:TIGR02389 24 E L DEIIKRVEEE 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 1735312367 1090 DV E D -- D ADF A RL V KGR IE K T L L GEISEY I e EVF L P D DC f ILVK L SL E RIRLLRLE V na ET V RYS I CMS KL RVK pg DIAV 1167
Cdd:TIGR02389 104 ED E Y ek D REK A EE V AKK IE A T K L EDVAKD I - SID L A D MT - VIIE L DE E QLKERGIT V -- DD V EKA I KKA KL GKV -- IEID 177
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1168 HGEAVVCVS P REN S kssm YYV L QS LKE DLPKVVVQ GI PEVA R A VI hide QSGKNK Y KLLV EG D NL RA V MATH GV NGS RTT 1247
Cdd:TIGR02389 178 MDNNTITIK P GNP S ---- LKE L RK LKE KIKNLHIK GI KGIK R V VI ---- RKEGDE Y VIYT EG S NL KE V LKLE GV DKT RTT 249
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1248 S N NTY E VEKT LGIEAAR ST II N EI QY T MVNH G MSI D R RH V ML L ADLM SYK GE ILG I T R F G LAKM K E SVL ML A S FE K T AD H 1327
Cdd:TIGR02389 250 T N DIH E IAEV LGIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML V ADLM TWD GE VRQ I G R H G ISGE K A SVL AR A A FE V T VK H 329
330 340 350
....*....|....*....|....*....|....*...
gi 1735312367 1328 L F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L LHK 1365
Cdd:TIGR02389 330 L 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 ...
345-1120
9.39e-52
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: 200.00
E-value: 9.39e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TY P E rvnkanle LM RKL VRN G pdvhpganfiq NR 424
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 -------- IY RKL EER G ----------- LA 381
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 425 H T qmkrf L K YGNREKIAQ E LRFG D VV E R h L I DGDV VL F NR Q P S LH K L S I M A HIARVKPHRTFRFNEC VCT PY NADFDGD E 504
Cdd:COG0086 382 T T ----- I K SAKKMVERE E PEVW D IL E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD Q 455
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 505 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 RSKACQIVASIL V GKD 576
Cdd:COG0086 456 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 DLH 535
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 577 E R -- VRI SLPRPAIM K PIALWT G KQIFSL IL kp SK E C P vranlrtkgkqycgkgedlchnds F V vih N SE lmcgs MD K GT 654
Cdd:COG0086 536 A R ik VRI TEDGEQVG K IVETTV G RYLVNE IL -- PQ E V P ------------------------ F Y --- N QV ----- IN K KH 581
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 655 LG sgskn N I FYILL R DW G QL E AANAMS RL AR L APV Y LSNR G F SIG IG D - V T P gqgll K A KQ DLLDDGYQKCD E YIEALQT 733
Cdd:COG0086 582 IE ----- 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 KQ EIFEEANKEVK E IEKQYAE 651
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 734 G KL qqqpgc T AE E TLEAL I L k ELSVIRDRAG S ACLRELDKS N SPLI MA LC G SK GS FINIS Q MIACV G QQ A isgsr V P D G - 812
Cdd:COG0086 652 G LI ------ T EP E RYNKV I D - GWTKASLETE S FLMAAFSSQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A ----- K P S G n 719
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 813 - F E NR slphfekhsklpaakgf VADS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV KSLE D L csqydltvr 891
Cdd:COG0086 720 i 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 1735312367 892 sstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E --- FK RV - LDNIRAVY T cpdepalsq N E LVLT A DAIM kradflccr 962
Cdd:COG0086 774 ----- I VTEEDC G td R G IT v T A IK EG GE vi EPL K eri LG RV a AEDVVDPG T --------- G E VLVP A GTLI --------- 830
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 963 dsf L EE IKTF I KSISERIK K T R dkygindngtsepkvlyqldrv TPTQL E KFLET C RDK Y M R -- A QMEP --- G S AVG ALC 1037
Cdd:COG0086 831 --- D EE VAEI I EEAGIDSV K V R ---------------------- SVLTC E TRGGV C AKC Y G R dl A RGHL vni G E AVG VIA 885
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1038 AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS K NISTPIITAHLD V EDDADFARL V KGRI E KTLLGEISEYI 1117
Cdd:COG0086 886 AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA K AGGIVRLNNLKV V VNEEGKGVV V SRNS E LVIVDDGGRRE 958
...
gi 1735312367 1118 EE V 1120
Cdd:COG0086 959 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: 1655.75
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 24 S A E QMRQQAHIQ V VSK NLY SQD T KH t PLPYGVLD H R M GTS E KD RP C L TCG K NLADC L GH Y GY LD LELP C FH V GYFKA T I G 103
Cdd:cd02583 2 S P E DIIRLSEVE V TNR NLY DIE T RK - PLPYGVLD P R L GTS D KD GI C E TCG L NLADC V GH F GY IK LELP V FH I GYFKA I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 104 ILQ M ICKTCSR IM L TK EEK LQ F MDY L K RPNL AY LQK RG LKKKI SD KC R K RTV C LN C S afngpvkkcgllkiihekykttk 183
Cdd:cd02583 81 ILQ C ICKTCSR VL L PE EEK RK F LKR L R RPNL DN LQK KA LKKKI LE KC K K VRK C PH C G ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 184 kvvdafvsdflqsfdtaiehnklvep LL TR AQE N LNPL VA LNLFK R IP QD D IP LLLMNP E AG K P AD LI I TR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL KV LNLFK N IP PE D VE LLLMNP L AG R P EN LI L TR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RMT 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 1735312367 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILTYPERV NKA N L E LM RKLV R NGPDVHPGANF IQN 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILTYPERV TRY N I E KL RKLV L NGPDVHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 424 R HTQM K R FLKYGNR E KIA Q EL RF GD V VERHL I DGD V VLFNRQPSLH K LSIMAH I A R V K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R KIA R EL KI GD I VERHL E DGD I VLFNRQPSLH R LSIMAH R A K V M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDR SKA CQ IVASI L V G KDE rvr I S L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDR AQF CQ LCSYM L D G EIK --- I D L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 584 P R PAI M KP IA LWTGKQIFSL I L K P S K EC PV RA NL RT K G K Q Y CG K GE D L C H ND SF VVI H NSEL M CG SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 P P PAI L KP VE LWTGKQIFSL L L R P N K KS PV LV NL EA K E K S Y TK K SP D M C P ND GY VVI R NSEL L CG RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 664 FY I LLRD W G QLE AA N AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K QD L L D D GY Q KCDEYI EALQT 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 EE L V D N GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 744 AE E TLEA L I LK ELS V IR DR AG S ACL R EL D KSNSPLIMALCGSKGS 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 KSNSPLIMALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1735312367 824 H SK L PAAKGFVA D SFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVA N SFYSGLTPTEFFFHTM 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: 955.54
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 12 A K K I SH I C FG MK S A E QM R QQAHIQVVSKNL Y SQ D T kh T P LPY G VL D H R M G TS E KDRP C L TCG KNLAD C L GH Y G YLD L EL P 91
Cdd:cd02582 1 P K R I KG I K FG LL S P E EI 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 HIE L AR P 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 92 CF HVG YF K ATIGI L QMI C KT C S RI M L TK EE KLQFMDYLK R -- PNLAY L Q KR g LKK K ISD K CR KR T VC LN C S A fngpvkkc 169
Cdd:cd02582 79 VI HVG FA K HIYDL L RAT C RS C G RI L L PE EE IEKYLERIR R lk EKWPE L V KR - VIE K VKK K AK KR K VC PH C G A -------- 149
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 170 GLL KI IH EK ykttkkvvdaf VSD F LQSFD ta IEHN KL veplltraqenl N P LVALNLFKR IP QD D IP LL LMN P EAGK P AD 249
Cdd:cd02582 150 PQY KI KL EK ----------- PTT F YEEKE -- EGEV KL ------------ T P SEIRERLEK IP DE D LE LL GID P KTAR P EW 204
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 250 LII T R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRMT GA KTQM I MED WD F LQ LQCAL Y INS E LS GI 328
Cdd:cd02582 205 MVL T 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 GI 282
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 329 P ln M A PKKWT R --- GFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT Y PERV NKA N L E L MR 405
Cdd:cd02582 283 P -- P A RHRSG R plk TLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EDI AK E LT V PERV TEW N I E K MR 360
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 406 KLV R NGPD VH PGAN FIQ n R HTQMKRF L K Y G NRE KI A QE L RF G DV VERHLIDGD V VLFNRQPSLH KL SIMAH IA RV K P HR T 485
Cdd:cd02582 361 KLV L NGPD KW PGAN YVI - R PDGRRIR L R Y V NRE EL A ER L EP G WI VERHLIDGD I VLFNRQPSLH RM SIMAH RV RV L P GK T 439
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 486 FR 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 DRSK A C 565
Cdd:cd02582 440 FR 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 519
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 566 Q IVASI lvgkde RVRIS LP R PAI MK P IA LWTGKQ I FSL I L kpskec P VRA N LRT K G K QYC G KG E --- DL C H ND SF VVI H N 642
Cdd:cd02582 520 Q LLSAA ------ GYDGL LP E PAI LE P KP LWTGKQ L FSL F L ------ P KDL N FEG K A K VCS G CS E ckd ED C P ND GY VVI K N 587
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 643 SE L MC G SM DK GTL G SGSKNNIFYILLRDW G QLE A ANAMSRLA RLA PVYLSN RGF S IGI G D VTPGQGLL K AKQDLLDDGYQ 722
Cdd:cd02582 588 GK L LE G VI DK KAI G AEQPGSLLHRIAKEY G NEV A RRFLDSVT RLA IRFIEL RGF T IGI D D EDIPEEAR K EIEEIIKEAEK 667
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 723 K CD E Y IE ALQT G K L QQQ PG C T A EETLE AL I LKE L SVI RD R AG SACLRE LD KS N SPL IMA LC G SK GS FI N IS QM I AC V GQQ 802
Cdd:cd02582 668 K VY 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 NAV IMA RT G AR GS ML N LT QM A AC L GQQ 747
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 803 AIS G S R VPD G FE NR S LPHF EKHSKL P A A K GFV AD SF YS GL T PTEFFFH T M A GREGLVDTAV K T AET GYMQRRL VKS L E DL 882
Cdd:cd02582 748 SVR 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 827
890 900
....*....|....*....|....*...
gi 1735312367 883 CSQ YD L TVR S S T G D IIQF I YG G DG L DPA 910
Cdd:cd02582 828 YVE 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
7-932
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 933.50
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 7 RETDVA K K I SH I C FG MK S A E QM R QQAHIQVVSKNL Y SQ D T kh T P LPY G VL D H R M G TSEKDRP C L TCG KNLAD C L GH Y G YL 86
Cdd:PRK08566 1 SMMMIP K R I GS I K FG LL S P E EI 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 HI 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 87 D L EL P CF HVG YF K ATIGI L QMI C KT C S R IM LT K EE KLQFMDY L K R PNLAYLQKRG L K K KISDKCR KR T VC LN C SA fngpv 166
Cdd:PRK08566 79 E L AR P VI HVG FA K LIYKL L RAT C RE C G R LK LT E EE IEEYLEK L E R LKEWGSLADD L I K EVKKEAA KR M VC PH C GE ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 167 K K cgl L KI IH EK YK T tkkvvdafvsd F LQ sfdtaiehnklvep LLTRAQEN L N P LVALNLFKR IP QD D IP LL LM NPE AGK 246
Cdd:PRK08566 154 K Q --- Y KI KF EK PT T ----------- F YE -------------- ERKEGLVK L T P SDIRERLEK IP DE D LE LL GI NPE VAR 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 247 P ADLII T R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRMT GA K t Q M I M ED - W DF LQ LQCAL Y INS E 324
Cdd:PRK08566 206 P EWMVL T 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 1735312367 325 LS GIP lnma P ----- KKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT Y PERV 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 PERV TEW 358
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 400 N L E LM R KL V R NGP DV HPGAN FI qn RHTQMK R F - L KYG N R E KI A QE L RF G DV VERHLIDGD V VLFNRQPSLH KL SIMAH IA 478
Cdd:PRK08566 359 N I E EL R EY V L NGP EK HPGAN YV -- IRPDGR R I k L TDK N K E EL A EK L EP G WI VERHLIDGD I VLFNRQPSLH RM SIMAH RV 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 479 RV 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 RV 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 1735312367 559 F DRSK A CQIVASILVGKDE rvris L P R PAI MKPIAL WTGKQIFSL I L kpskec P VRA NL -- RT K GKQY C GKGED - L C HN D 635
Cdd:PRK08566 517 F TKEE A LDLLRAAGIDELP ----- E P E PAI ENGKPY WTGKQIFSL F L ------ P KDL NL ef KA K ICSG C DECKK e D C EH D 585
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 636 SF VVI H N SE L MC G SM DK GTL G SG s KNN I FYILLRDW G QLE A ANAMSRLA RLA PVYLSN RGF SI GI G D VTPGQGLLKAKQD 715
Cdd:PRK08566 586 AY VVI 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 EDIPEEAKEEIDE 664
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 716 LLDDGYQKCD E Y IEA LQT G K L QQQ PG C T A EETLE AL I LKE L SVI RD R AG SACLRE L DKS N SPL IMA LC G SK GS FI N IS QM 795
Cdd:PRK08566 665 IIEEAEKRVE 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 PAV IMA RT G AR GS ML N LT QM 744
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 796 I ACVGQQ AIS G S R VPD G FEN R S LPHF EKHSKLPA A K GFV AD S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GYMQRRL 875
Cdd:PRK08566 745 A 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 824
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*..
gi 1735312367 876 VKS 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 VLDNIRAVY 932
Cdd:PRK08566 825 INA L Q DL KVE YD G TVR DTR G N I V QF K YG E DG V DP MKSDH - GK P VDVD R IIERVLGKE 880
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
13-1363
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 882.83
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 13 K K I SH I C FG MK S AEQM R QQAHIQVVSKNL Y SQ D T kh T P LPY G V LD H R M GT S E KDRP CLTCG KNL A D C L GH Y G YLD L EL P C 92
Cdd:PRK14977 7 K A I DG I I FG LI S PADA R KIGFAEITAPEA Y DE D G -- L P VQG G L LD G R L GT I E PGQK CLTCG NLA A N C P GH F G HIE L AE P V 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 93 F H VGYFKATIGI L QMI C KT C SRIM L t KE E K L QFMDYLKRPNL A Y lqk R GLKK K IS D KCRKRT V CLNCSAFNGPV K K C GLL 172
Cdd:PRK14977 85 I H IAFIDNIKDL L NST C HK C AKLK L - PQ E D L NVFKLIEEAHA A A --- R DIPE K RI D DEIIEE V RDQVKVYAKKA K E C PHC 160
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 173 K iiheky KTTKKVVDAFVSD F LQS fd T A IE HNK L V eplltraqenln P LVALNL F KR I PQ DD IP L LLMN P EAGK P ADLII 252
Cdd:PRK14977 161 G ------ APQHELEFEEPTI F IEK -- T E IE EHR L L ------------ P IEIRDI F EK I ID DD LE L IGFD P KKAR P EWAVL 220
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 253 TRL LVPPL CI RPS VV sd L KS G T - N EDDLT MK L TE II FL N DVI K KHRMT GA KTQMIMEDW D F LQ LQCALYINSELS GIP LN 331
Cdd:PRK14977 221 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 YHTSTFFDNATA GIP QA 298
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 332 M -- APKKWTRGFV QRLKGK Q GRFRGNL S GKRVDFS G RTVISPDP NLR IDEV A VP VHV A KI LT Y PE R VN KA N L E L M RK LV R 409
Cdd:PRK14977 299 H hk GSGRPLKSLF QRLKGK E GRFRGNL I GKRVDFS A RTVISPDP MID IDEV G VP EAI A MK LT I PE I VN EN N I E K M KE LV I 378
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 410 NGPD VH PGAN F I Q n RHTQM K RF L KYGNRE ------ KI A QE L RF GD V VERHL I DGD V V L FNRQPSLHKLSI M AH IAR V K P H 483
Cdd:PRK14977 379 NGPD EF PGAN A I R - KGDGT K IR L DFLEDK gkdalr EA A EQ L EI GD I VERHL A DGD I V I FNRQPSLHKLSI L AH RVK V L P G 457
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 484 R 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 LK D TF FD RSK 563
Cdd:PRK14977 458 A 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 KD D AL FD KNE 537
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 564 A CQ I VA si L V G KDE rvri S LP R PAI - M K PIAL WTGKQ I FSL I L kpskec P VRA N LRTKG K QYC GK G ---- EDL C HN D SF V 638
Cdd:PRK14977 538 A SN I AM -- L A G ITD ---- P LP E PAI k T K DGPA WTGKQ L FSL F L ------ P KDF N FEGIA K WSA GK A geak DPS C LG D GY V 605
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 639 V I HNS EL MC G SM D KGTL G SGSKN -- NIFYILLR D W G QLE A ANAMSRLARL A PVYLSNR GFS I G I GD VTPGQ gll K AKQ DL 716
Cdd:PRK14977 606 L I KEG EL IS G VI D DNII G ALVEE pe SLIDRIAK D Y G EAV A IEFLNKILII A KKEILHY GFS N G P GD LIIPD --- E AKQ EI 682
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 717 L DD g Y Q KCDEYIEA L ------------ QT GK LQQQP G CTA EE T LEA L I LK EL SVI RD R AGS ACLREL D KS N SPL IMA LC G 784
Cdd:PRK14977 683 E DD - I Q GMKDEVSD L idqrkitrkiti YK GK EELLR G MKE EE A LEA D I VN EL DKA RD K AGS SANDCI D AD N AGK IMA KT G 761
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 785 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 ADSFYS GL TPT EFFFH T M A GRE 856
Cdd:PRK14977 762 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 KNNYRE GL NAA EFFFH A M G GRE 841
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 857 GL 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 VLDNIR avytcpd 936
Cdd:PRK14977 842 GL 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 IIEKQK ------- 913
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 937 epalsqnelvltada I MK R A dflcc RDSFLE EI KTFI K SISERIKKTRD K YGINDNGTS E P K vlyqldrvt PTQ LE KFLE 1016
Cdd:PRK14977 914 --------------- I ED R G ----- KGASKD EI EELA K EYTKTFNANLP K LLADAIHGA E L K --------- EDE LE AICA 964
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1017 TCRDKYMR A QM EPG S A V G ALC AQSI G EPGTQMTL K TFH F AG VAS M NI T L G VP R IK E IIN A SKNI STP IITAH LD V E DDA D 1096
Cdd:PRK14977 965 EGKEGFEK A KV EPG Q A I G IIS AQSI A EPGTQMTL R TFH A AG IKA M DV T H G LE R FI E LVD A RAKP STP TMDIY LD D E CKE D 1044
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1097 FARLVK gr I EKT L LG - EISEY I EEVFLPDDCF I LVKLSLE R IR --- LLRL E VN AE TVR ysicm SKLRV K PGDIAVHGEAV 1172
Cdd:PRK14977 1045 IEKAIE -- I ARN L KE l KVRAL I ADSAIDNANE I KLIKPDK R AL eng CIPM E RF AE IEA ----- ALAKG K KFEMELEDDLI 1117
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1173 VCVSPRENSKSSMYYV L QSLKEDLPKVV V Q G I P EVA RA VIHID E QS G KNKYKLLVE G D NL R AV MATHGVNGSR T TS N NTY 1252
Cdd:PRK14977 1118 ILDLVEAADRDKPLAT L IAIRNKILDKP V K G V P DIE RA WVELV E KD G RDEWIIQTS G S NL A AV LEMKCIDIAN T IT N DCF 1197
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1253 E VEK TLGIEAAR ST I I NE IQYTMVNH G MSI D R R HV ML L AD L M SYK G E I LG I ------ T R F G L A KM K E S V L ML A S FE K T AD 1326
Cdd:PRK14977 1198 E IAG TLGIEAAR NA I F NE LASILEDQ G LEV D N R YI ML V AD I M CSR G T I EA I glqaag V R H G F A GE K D S P L AK A A FE I T TH 1277
1370 1380 1390
....*....|....*....|....*....|....*..
gi 1735312367 1327 HLFD AA YF G QKDSVC G VSECI IMG IPMN IG T G LFK LL 1363
Cdd:PRK14977 1278 TIAH AA LG G EIEKIK G ILDAL IMG QNIP IG S G KVD LL 1314
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: 868.26
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 13 KKI SH I C FG MK S A E QM R QQAHIQ VV SKNL Y SQ D T kh T P LPY G VL D H R M G TS E KDRP C L TCG KNLAD C L GH Y G YLD L EL P C 92
Cdd:TIGR02390 2 KKI GS I K FG LL S P E EI R KMSVVE VV TADT Y DD D G -- Y P IEG G LM D P R L G VI E PGLR C K TCG GKVGE C P GH F G HIE L AR P V 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 93 F HVG YF K ATIG IL QMI C KT C S RI M LT K EE KL Q FMD - YL K RPNLAYLQKRG L KK KI SDKCR KR TV C LN C SA fngpvkkc GL 171
Cdd:TIGR02390 80 V HVG FA K EIYK IL RAT C RK C G RI T LT E EE IE Q YLE k IN K LKEEGGDLAST L IE KI VKEAA KR MK C PH C GE -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 172 L KI IH EK ---- Y KTT K K vvdafvsdflqsfdtaiehnklveplltr AQEN L N P LVALNLFKR IP QD D IP LL LM NP EAGK P 247
Cdd:TIGR02390 152 K KI KF EK ptyf Y EEG K E ----------------------------- GDVK L T P SEIRERLEK IP DE D AE LL GI NP KVAR P 202
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 248 ADLII T R L L VPP LCI RPS VV sd L KS G T - N EDDLT M KL TE II FL N DVI K KHRMT GA KTQM I MED W DF LQ LQC A L Y INS EL S 326
Cdd:TIGR02390 203 EWMVL T 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 280
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 327 GIP - LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT Y PERV NKA N LELM R 405
Cdd:TIGR02390 281 GIP p ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PERV TPW N IDEL R 360
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 406 KL V R NGPD VH PGAN FIQN rh TQMK R F - LKYG N R E KI A QE L RF G D VVERHLIDGD V VLFNRQPSLH KL S I M A H IAR V K P HR 484
Cdd:TIGR02390 361 EY V L NGPD SW PGAN YVIR -- PDGR R I k IRDE N K E EL A ER L EP G W VVERHLIDGD I VLFNRQPSLH RM S M M G H KVK V L P GK 438
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 485 TFR F 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 DRSKA 564
Cdd:TIGR02390 439 TFR L 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 TKEEV 518
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 565 CQ I VASI lvgkde RVRISL P R PAI M KP IAL WTGKQIFS LI L KPSKECPV RA NL r TK G KQY C G K G E dl C HN D SF VVI H N SE 644
Cdd:TIGR02390 519 QT I LGVA ------ GYFGDP P E PAI E KP KEY WTGKQIFS AF L PEDLNFEG RA KI - CS G SDA C K K E E -- C PH D AY VVI K N GK 589
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 645 L MC G SM DK GTL G S g S K NN I FYILL R DW G QLE A ANAMSRLA RL APVYLSN RGF SI GI G D VTPGQGLLKAKQD L LDDGYQKC 724
Cdd:TIGR02390 590 L LK G VI DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT RL FIRFITL RGF TT GI D D IDIPKEAKEEIEE L IEKAEKRV 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 725 D EY IE ALQT G K L QQQ PG C T A EETLE AL I LKE L SVI RD R AG SACLRE LD KS N SPL IMA LC G SK GS FI NI S QM I A C VGQQ AI 804
Cdd:TIGR02390 669 D NL IE RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG EVAEKY LD PE N HAV IMA RT G AR GS LL NI T QM A A M VGQQ SV 748
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 805 S G S R VPD G FE NR S LPHF E K HSKLPA A K GFV AD SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GYMQRRL VKS L E DL CS 884
Cdd:TIGR02390 749 R G G R 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 YV 828
890 900 910 920
....*....|....*....|....*....|....*....|..
gi 1735312367 885 Q YD L TVR SST G DI IQF I YG G DG L DP AAME - GK de P LEF K RVL 925
Cdd:TIGR02390 829 E YD G TVR DTR G NL IQF K YG E DG V DP MKSD h GK -- P VDV K KIF 868
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: 834.11
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 20 FG MK S AEQM R QQAHIQVVSK nl YSQDTKHT P LPY G VL D H RMGT SEKDRP C L TCG KNLAD C L GH Y G YLD L EL P C FH V G YFK 99
Cdd:cd02733 5 FG IL S PDEI R AMSVAEIEHP -- ETYENGGG P KLG G LN D P RMGT IDRNSR C Q TCG GDMKE C P GH F G HIE L AK P V FH I G FLT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 100 ATIG IL QMI CK tcsr IM L TK E E klqfmdylkrpnlaylqkrglkkkisdkcrkrtvclncsafngpvkkcgllkiiheky 179
Cdd:cd02733 83 KILK IL RCV CK ---- RE L SA E R ---------------------------------------------------------- 100
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 180 kttkkvvdafvsdflqsfdtaiehnklveplltraqenlnplv A L NL FKRI PQD D IPL L LMN P EAGK P ADL I I T R L L VPP 259
Cdd:cd02733 101 ------------------------------------------- V L EI FKRI SDE D CRI L GFD P KFSR P DWM I L T V L P VPP 137
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 260 LCI RPSVV S D L k S GTN EDDLT M KL TE II FL N DVI K KHRMT 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 1735312367 340 --- GFV QRLKGK Q GR F RGNL S GKRVDFS G RTVI S PDPNL RI D E V A VP VHV A KI LT Y PE R V NKA N LELMRK LVRNGP DVH 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 LT F PE I V TPF N IDRLQE LVRNGP NEY P 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 417 GA NF I Q n R HTQMKRF L K Y GNR e KIAQE L RF G DV VERHL I DGDVVLFNRQPSLHK L S I M A H IAR V 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 QY G YI VERHL Q DGDVVLFNRQPSLHK M S M M G H RVK V L P YS TFR L N LS V T TPY 372
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 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 FDRSKACQIVASI 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 1735312367 577 ERVRISL P R PAI M KP IA LWTGKQIFSLI L kpskec P VRA NL RTKGKQYC G KGEDLCHN D SF V V I H N S EL MC G SMD K G T L G 656
Cdd:cd02733 448 PDWDGKI P Q PAI L KP KP LWTGKQIFSLI I ------ P KIN NL IRSSSHHD G DKKWISPG D TK V I I E N G EL LS G ILC K K T V G 521
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 657 SG S k NNIFYILLRDW G QLE A ANAMSRLA R LAPVY L SNR GFSIGIGD VTPGQGLL K AK Q DLLDDGYQKCDEY IE AL Q T G K L 736
Cdd:cd02733 522 AS S - GGLIHVIWLEY G PEA A RDFIGNIQ R VVNNW L LHN GFSIGIGD TIADKETM K KI Q ETIKKAKRDVIKL IE KA Q N G E L 600
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 737 QQ QPG C T AE E TL E ALILKE L SVI RD R AG SACLRE L DKS N SPLI 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 1735312367 817 S LPHF E K HSKL P AAK GFV AD S 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 EN S 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: 684.93
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 23 K S A E QM R QQAHIQ V VSKNLYSQD T KHTPLP y G VL D H R M G TSEKDRP C L TCG KN L A DC L GH Y G YLD L EL P C FHVG YF K ATI 102
Cdd:cd00399 1 M S P E EI R KWSVAK V IKPETIDNR T LKAERG - G KY D P R L G SIDRCEK C G TCG TG L N DC P GH F G HIE L AK P V FHVG FI K KVP 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 103 GI L Q micktcsrimltkeeklqfmdylkrpnlaylqkrglkkkisdkcrkrtvclncsafngpvkkcgllkiihekyktt 182
Cdd:cd00399 80 SF L G ---------------------------------------------------------------------------- 83
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 183 kkvvdafvsdflqsfdtaiehnklveplltraqenlnplvalnlfkripqddiplllmnpeagk P ADL I I T R L L VPP L C I 262
Cdd:cd00399 84 ---------------------------------------------------------------- P EWM I L T C L P VPP P C L 99
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 263 RPSV vsdlksgtneddltmklteiiflndvikkhrmtgaktq 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 1735312367 343 QRLKGK Q GRFRGNL S GKRVDFSGR T VISPDPNLR I D E V A VP VHV A KI L typervnkanlelmrklvrngpdvhpganfiq 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 1735312367 423 nrhtqmkrflkygnrekiaqelrfgdvverhli DGD V VLFNRQPSLHKLSIMAH IA RV K P HR TFR F N EC VC T PYNADFDG 502
Cdd:cd00399 190 --------------------------------- DGD P VLFNRQPSLHKLSIMAH RV RV L P GS TFR L N PL VC S PYNADFDG 236
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 503 DEMNLH L PQ T EEA K AEA LV LM GTKA N LVT P R NGEPLI AAI QD F L T GAYLLTL kdtffdrskacqivasilvgkdervris 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 1735312367 583 lprpaimkpialwt GKQI F S LI L K pskecpvranlrtkgkqycgkgedlchndsfvvihnselmcgsmdkgtlgsgsk NN 662
Cdd:cd00399 289 -------------- GKQI V S AA L P ------------------------------------------------------ GG 300
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 663 IFYILL R DW G QLE AA NAM S R L A R LAP V Y L SNR GFS I GIGDV TPGQGLLKA K QD L LDDGYQ K C DE YI EA L Q T 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 TE L IEEAKK K V DE VE EA F Q A G L L TA Q E G M 380
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 743 T A EE T LE AL IL KE L SVI RD R AGSA CLRE LD --- K S NS PLI 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 1735312367 820 HF E K HSKL P A AKGF VAD SF 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 IRN SF 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: 570.67
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 20 F GMK SAE QM R QQAHIQVVSKNLY sq D TKHT P L P Y G VL D HRM G TSE KD RP C L TCG K N LAD C L GH Y G YLD L E LP CFHVGY F K 99
Cdd:cd01435 2 F SFY SAE EI R KLSVKEITNPVTF -- D SLGH P V P G G LY D PAL G PLD KD DI C S TCG L N YLN C P GH F G HIE L P LP VYNPLF F D 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 100 ATIGI L QMI C KT C S R IMLT K E E KLQ F mdylkrpnlaylqkrglkkkisdkcrkrtvclncsafngp V K K CG LL kiiheky 179
Cdd:cd01435 80 LLYKL L RGS C FY C H R FRIS K W E VKL F ---------------------------------------- V A K LK LL ------- 112
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 180 kttkkvvdafvsdflqsfdtai EHNK LVE plltr A Q E NLNPL val NL F kripqddiplllmnpeagkpadl IITR LLVPP 259
Cdd:cd01435 113 ---------------------- DKGL LVE ----- A A E LDFGY --- DM F ----------------------- FLDV LLVPP 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 260 LCI RP sv V S D L KSGTN E DDLTMK L TE I IFL N DV I KKHR -- M TG A KT Q MIMEDWD ----------- 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 RDLL as M RQ A ES Q SKLDLIS gktnseklina W LQLQ S A vn ELFD S T 217
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 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 LT Y PE R V NKA N L E LM 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 LT F PE P V TPF N V E EL 293
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 405 R KL V R NGPDV H PGAN F I QNRHTQMKRFLKYGNREKI A QELRF ------------ GDV V E RHL I DGDVVL F NRQP S LHK L S 472
Cdd:cd01435 294 R QA V I NGPDV Y PGAN A I EDEDGRLILLSALSEERRK A LAKLL lllssaklllng PKK V Y RHL L DGDVVL L NRQP T LHK P S 373
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 473 IMAH IA RV - 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 KV RV 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 1735312367 552 LT LK DTFF D R SKAC Q I V ASI L VGK --- D ERV RI S L PR PAI M KP IA LWTGKQ IF S L ILK --- P SK e C P VRANLRT K GKQYC 625
Cdd:cd01435 454 LT SR DTFF T R EEYQ Q L V YAA L RPL fts D KDG RI K L LP PAI L KP KP LWTGKQ VI S T ILK nli P GN - A P LLNLSGK K KTKKK 532
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 626 GK G EDLCH -- ND S F V V I H N S EL MC G SM DK GTL G S g S KNNI --- F Y I L lrd W G QLE A ANAM S R L A RL APV YL SN RGF SI GI 700
Cdd:cd01435 533 VG G GKWGG gs EE 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 608
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 701 G D V tpgqg LL KA K Q D L lddgy QKCDEYIE A LQT G K lqqqpg CT A E E T L EALIL K EL S V I RD rags ACL RE -- L DK -- S N S 776
Cdd:cd01435 609 E D L ----- LL TP K A D E ----- KRRKILRK 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 N 668
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 777 PLI 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 VA D S F YS G LT P T E F FFH T MAGRE 856
Cdd:cd01435 669 LQL 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 IT D R F LT G IR P Q E Y FFH C MAGRE 748
890 900 910
....*....|....*....|....*....|.
gi 1735312367 857 GL V DTAVKT AET GY M QR R L V K S LE D L CSQ YD 887
Cdd:cd01435 749 GL 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; ...
1021-1360
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: 568.00
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITA H L DVED D ADF AR L 1100
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITA K L ENDR D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1101 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysicmsklrvkpgdiavhgeavvcvspren 1180
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 1735312367 1181 SKS SM Y YV LQSLK ED LP K VVV Q GIPEV A RAVI HI D EQ sg K N KYKLLVEG DN LRAVM A T H GV N G S RTTSN NTY EVEK T LGI 1260
Cdd:cd02736 123 SKS NL Y FL LQSLK RK LP D VVV S GIPEV K RAVI NK D KK -- K G KYKLLVEG YG LRAVM N T P GV I G T RTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1261 EAARSTIINEIQYTM VN HGMSID R RH V MLLADLM SY KGE I LGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1340
Cdd:cd02736 201 EAARSTIINEIQYTM KS HGMSID P RH I MLLADLM TF KGE V LGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 1735312367 1341 C GVSECIIMG I PM N IGTGLF 1360
Cdd:cd02736 281 E GVSECIIMG K PM P IGTGLF 300
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
249-550
8.44e-149
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 452.74
E-value: 8.44e-149
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 249 DL I I T R L L VPP L C I RPSV VS D L k SGTN EDDLT MK L TE II FL N DVI K KHRMT GA KTQM I MEDWDF LQ LQCALY I NS E l SGI 328
Cdd:smart00663 2 WM I L T 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 - GLP 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 329 PL N MAPKKWTRGFV QRLKGK Q GRFR G NL S GKRVDFS G R T VI S PDPNL RID EV A VP VHV A KI LT Y PE R V NKA N LELM RKLV 408
Cdd:smart00663 80 RA N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLN EV G VP KEI A LE LT F PE I V TPL N IDKL RKLV 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 409 RNGP dvh P GA NF I QN rht QM K RF LK YGNRE KIA QE L RF GD V VERH L IDGDVVLFNRQP S LH KL SI M AH IA RV KPHR T F R F 488
Cdd:smart00663 160 RNGP --- N GA KY I IR --- GK K TN LK LAKKS KIA NH L KI GD I VERH V IDGDVVLFNRQP T LH RM SI Q AH RV RV LEGK T I R L 233
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1735312367 489 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 234 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
2.55e-120
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: 377.79
E-value: 2.55e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 12 A KKI SH I C FG MK S A E QM R QQAHIQ V VSKNL Y S q DTKHT P LPY G V LD H RMGT SE KD RP C L TCGK NLA DC L GH Y G YLD L EL P 91
Cdd:pfam04997 1 L KKI KE I Q FG IA S P E EI R KWSVGE V TKPET Y N - YGSLK P EEG G L LD E RMGT ID KD YE C E TCGK KKK DC P GH F G HIE L AK P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 92 C FH V G Y FK A T IG IL QMI CK T CS RIM L TKEEKLQ F MDYL KR PN L AY L QKR gl K K K I SDK C R K RTV C LN C SAF NG pvkkcgl 171
Cdd:pfam04997 80 V FH I G F FK K T LK IL ECV CK Y CS KLL L DPGKPKL F NKDK KR LG L EN L KMG -- A K A I LEL C K K KDL C EH C GGK NG ------- 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 172 lkiihekykt TKKVVDAFVSDFLQSFDT AI EHN K LV E plltr AQ E N LNP LVA L NL FKRI PQD D IPL L LM NP EAGK P ADL I 251
Cdd:pfam04997 151 ---------- VCGSQQPVSRKEGLKLKA AI KKS K EE E ----- EK E I LNP EKV L KI FKRI SDE D VEI L GF NP SGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 252 I T R L L VPP L CIRPSV VS D LK s GTN EDDLT M KL TE II FL N DVI KK HRMT GA KTQM I M E D W DF LQ LQC A LYINS E LS G I P L - 330
Cdd:pfam04997 216 L T 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 1735312367 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 ...
841-1316
3.57e-119
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain]
Cd Length: 516
Bit Score: 382.47
E-value: 3.57e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 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 - EPL 919
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 r FTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 920 EF KRVLDNIRAVYTCP D EPA L SQNELVLTADA I MK R ADF L C -- CRDSFLE E IK T FIKSISERI ---- K KT R DKYGI N DN g 993
Cdd:pfam04998 81 EF SDLKLEDKFKNDLL D DLL L LSEFSLSYKKE I LV R DSK L G rd RLSKEAQ E RA T LLFELLLKS gles K RV R SELTC N SK - 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 994 tsepkvlyqldrvtpt QLEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL K TFHFAGVAS M N I TLGVPR I KEI 1073
Cdd:pfam04998 160 ---------------- AFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL N TFHFAGVAS K N V TLGVPR L KEI 223
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1074 IN A SKNI ST P II T AH L -- D V EDDADF A RL V K G R IEK TL LG EIS E YI E ------------------------------ EVF 1121
Cdd:pfam04998 224 IN V SKNI KS P SL T VY L fd E V GRELEK A KK V Y G A IEK VT LG SVV E SG E ilydpdpfntpiisdvkgvvkffdiidevt NEE 303
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1122 LP D DCFI L VK L SLERIRL L RLEVNAETVRYS I CM S -- KLRVKPG DIA V ----------------- H G EAVVCVSPRENSK 1182
Cdd:pfam04998 304 EI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I PR S ir NKVDEGR DIA I geitafiikiskkirqd T G GLRRVDELFMEED 383
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1183 SSMYYVLQ SL ked L PKVVVQ GIP EVA R AVIHI D E q S GK NK -- YK L LV EG D NL RA V MATH G - V NGS R TT SN NTY E VEKT LG 1259
Cdd:pfam04998 384 PKLAILVA SL --- L GNITLR GIP GIK R ILVNE D D - K GK VE pd WV L ET EG V NL LR V LLVP G f V DAG R IL SN DIH E ILEI LG 459
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 1735312367 1260 IEAAR STII NEI QYTMVNH G MS I DR RH VM L L AD L M SY KG E I LG I T R F G LA K MKE S V L 1316
Cdd:pfam04998 460 IEAAR NALL NEI RNVYRFQ G IY I ND RH LE L I AD Q M TR KG Y I MA I G R H G IN K AEL S A L 516
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
978-1363
5.22e-98
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: 318.81
E-value: 5.22e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 978 E RIKKTRDKY G indngtsepkvlyqldr V T PTQL E KFLETCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMTL K TFH F AG 1057
Cdd:cd06528 5 E KLEEVLKEH G ----------------- L T LSEA E EIIKEVLRE Y L R SLI EPG E AVG IVA AQSIGEPGTQMTL R TFH Y AG 67
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1058 VA SM N I TLG V PR IK EI IN A S K NI STP II T AH L DV E -- D D ADF A RL V KGR IE K T L L GEIS E Y I E ev FLPDDCF I LVK L SL E 1135
Cdd:cd06528 68 VA EI N V TLG L PR LI EI VD A R K EP STP TM T IY L EE E yk Y D REK A EE V ARK IE E T T L ENLA E D I S -- IDLFNMR I TIE L DE E 145
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1136 RI -- R LLRLEVNAETVR ysicmskl RV K P G DIAVH G EAVVC V SPR E NSK ssm YYV L QS L K E DLPKVVVQ GI PEVA R AVIH 1213
Cdd:cd06528 146 ML ed R GITVDDVLKAIE -------- KL K K G KVGEE G DVTLI V LKA E EPS --- IKE L RK L A E KILNTKIK GI KGIK R VIVR 214
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1214 ID E qsgk NK Y KLLV EG D NL R AV MATH GV NGS RTT S NN TY E V E KT LGIEAAR ST IINEI QY T MVNH G MSI D R RH V ML L AD L 1293
Cdd:cd06528 215 KE E ---- DE Y VIYT EG S NL K AV LKVE GV DPT RTT T NN IH E I E EV LGIEAAR NA IINEI KR T LEEQ G LDV D I RH I ML V AD I 290
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1294 M S Y K GE ILG 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 C II M G I P MNI GTG LFK L L 1363
Cdd:cd06528 291 M T Y D GE VRQ I G R H G I A GE K P SVL 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
1006-1363
1.92e-97
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 317.94
E-value: 1.92e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1006 V T PTQL 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 NI STP II 1085
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 1735312367 1086 T AH L DV E -- D D ADF 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 1161
Cdd:PRK04309 115 T IY L KD E 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 1735312367 1162 P G DIAVH G EAVV c V SP R E N S kssm Y YV L QS L K E DLPKVVVQ GI PEVA R AV I HIDE qsgk NK Y KLLV EG D NL RA V MATH GV 1241
Cdd:PRK04309 185 G G EVEIE G NTLI - I SP 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 1735312367 1242 NGS RTT S NN TY E V E KT LGIEAAR ST II N EI QY T MVNH G MSI D R RH V ML L AD L M SYK GE ILG I T R F G LAKM K E SVL ML A S F 1321
Cdd:PRK04309 256 DAT RTT T NN IH E I E EV LGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML V AD M M TWD GE VRQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 1735312367 1322 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 1363
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_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
358-525
1.26e-96
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: 306.92
E-value: 1.26e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 358 GKRVDFS G RTVISPDPNL RI DEV A VP VHV AK I LT Y PE R V NKA N LELM R K LV R NGP D V H PGAN F I Q n R HTQMK R F L K Y GN R 437
Cdd:pfam00623 1 GKRVDFS A RTVISPDPNL KL DEV G VP ISF AK T LT F PE I V TPY N IKRL R 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 1735312367 438 e KIAQ EL RF GD V VERH L IDGDVVLFNRQPSLH K LSIM A H IA RV K P HR TFR F N EC V C TPYNADFDGDEMNLH L PQ T EEA K A 517
Cdd:pfam00623 80 - RLDK EL EI GD I VERH V IDGDVVLFNRQPSLH R LSIM G H RV RV L P GK TFR L N LS V T TPYNADFDGDEMNLH V PQ S EEA R A 158
....*...
gi 1735312367 518 EA LV LM GT 525
Cdd:pfam00623 159 EA EE LM LV 166
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
953-1365
2.37e-86
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 291.33
E-value: 2.37e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 953 M KR AD flccr DSF L E E IKT F ik S IS E RIKKT - RDK Y GI N D N GTSE -------------- P K V LYQLDR ------ VTPTQL 1011
Cdd:PRK14897 91 F KR LF ----- GRI L D E NMS F -- S TG E LLTAE e KEY Y EE N S N EDVL kviddvkklgfrlp P S V IEEIAK amkkke LSDDEY 163
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1012 E KF L ETC R DK Y M RA QME P GS AVG ALC AQSIGEPGTQMT LK TFH F AGVA S MN I TLG V PR IK EI IN A S K NI STP II T AH L -- 1089
Cdd:PRK14897 164 E EI L RRI R EE Y E RA RVD P YE AVG IVA AQSIGEPGTQMT MR TFH Y AGVA E MN V TLG L PR LI EI VD A R K KP STP TM T IY L kk 243
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1090 D VED D ADFA R L V KGR IE K T L L GEISEY I EEV flp DDCFIL V K L SL E RI rllrlev NAETVR Y SICMSKLRVKPGDIAVHG 1169
Cdd:PRK14897 244 D YRE D EEKV R E V AKK IE N T T L IDVADI I TDI --- AEMSVV V E L DE E KM ------- KERLIE Y DDILAAISKLTFKTVEID 313
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1170 EAVVCVS P REN S kssm YYV L QS L K E DLPKVVVQ GI PEVA RA VIHIDEQ sg KNKYKLLVE G D NL RA V MATHG V NGS RT TS N 1249
Cdd:PRK14897 314 DGIIRLK P QQP S ---- FKK L YL L A E KVKSLTIK GI KGIK RA IARKEND -- ERRWVIYTQ G S NL KD V LEIDE V DPT RT YT N 387
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1250 NTY E VEKT LGIEAAR ST II N E IQY T MVNH G MSI D R RH V ML L AD L M SYK G EILG I T R F G LAKM K E SVL ML A S FE K T AD HL F 1329
Cdd:PRK14897 388 DII E IATV LGIEAAR NA II H E AKR T LQEQ G LNV D I RH I ML V AD M M TFD G SVKA I G R H G ISGE K S SVL AR A A FE I T GK HL L 467
410 420 430
....*....|....*....|....*....|....*.
gi 1735312367 1330 D A AYF G QK D SVC GV S E C II M G I P MNI GTG LFK L LH K 1365
Cdd:PRK14897 468 R A GIL G EV D KLA GV A E N II V G Q P ITL GTG AVS L VY K 503
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1010-1365
5.70e-84
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 279.63
E-value: 5.70e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1010 Q L EKFLETCRDK 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 NI STP II T AH L 1089
Cdd:TIGR02389 24 E L DEIIKRVEEE 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 1735312367 1090 DV E D -- D ADF A RL V KGR IE K T L L GEISEY I e EVF L P D DC f ILVK L SL E RIRLLRLE V na ET V RYS I CMS KL RVK pg DIAV 1167
Cdd:TIGR02389 104 ED E Y ek D REK A EE V AKK IE A T K L EDVAKD I - SID L A D MT - VIIE L DE E QLKERGIT V -- DD V EKA I KKA KL GKV -- IEID 177
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1168 HGEAVVCVS P REN S kssm YYV L QS LKE DLPKVVVQ GI PEVA R A VI hide QSGKNK Y KLLV EG D NL RA V MATH GV NGS RTT 1247
Cdd:TIGR02389 178 MDNNTITIK P GNP S ---- LKE L RK LKE KIKNLHIK GI KGIK R V VI ---- RKEGDE Y VIYT EG S NL KE V LKLE GV DKT RTT 249
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1248 S N NTY E VEKT LGIEAAR ST II N EI QY T MVNH G MSI D R RH V ML L ADLM SYK GE ILG I T R F G LAKM K E SVL ML A S FE K T AD H 1327
Cdd:TIGR02389 250 T N DIH E IAEV LGIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML V ADLM TWD GE VRQ I G R H G ISGE K A SVL AR A A FE V T VK H 329
330 340 350
....*....|....*....|....*....|....*...
gi 1735312367 1328 L F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L LHK 1365
Cdd:TIGR02389 330 L L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L VMD 367
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1005-1363
3.11e-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: 273.31
E-value: 3.11e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1005 R VTPTQLEKF L ETCRDKYM R AQME PG SA VG ALC AQSIGEP G TQMTL K TFHFAGV ASM N I TLGVPR I KEIIN AS KNI S TP I 1084
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 KNI K TP S 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1085 I T AH L -- DVED D ADF A RLVKG R I E K T L L GEISEYI E EVFL PD DCFILVK ---------------- LSLE R IR -- LLR L E V 1144
Cdd:cd02584 82 L T VY L ep GFAK 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 1735312367 1145 N - AETVRYSIC M SKLRV K ----- PG D IA V HGE --------- AVVCVSPR E NSKSSM --- YYVLQSLKED L PKVVVQ GI PE 1206
Cdd:cd02584 162 D r KKMTDKKLS M EQIAK K ikeef KD D LN V IFS ddnaeklvi RIRIINDD E EKEEDS edd VFLKKIESNM L SDMTLK GI EG 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1207 VARAV I HID ------- E QSGKN K YK --- L LVE G D NLR A V MATH GV NGS RTTSN NTY E VEKT LGIEAAR STIIN E IQYTMV 1276
Cdd:cd02584 242 IRKVF I REE nkkkvdi E TGEFK K RE ewv L ETD G V NLR E V LSHP GV DPT RTTSN DIV E IFEV LGIEAAR KALLK E LRNVIS 321
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1277 NH G MSIDR RH VM LL A D L M SYK G EILG 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 IG 1356
Cdd:cd02584 322 FD G SYVNY RH LA LL C D V M TQR 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 IG 401
....*..
gi 1735312367 1357 TG L F K LL 1363
Cdd:cd02584 402 TG C F D LL 408
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
55-891
4.87e-81
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: 283.14
E-value: 4.87e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 55 V LDH R M G TSEKDRP C L TCG - K NLAD C L GH Y G YLD L ELPCF H VGYFKATIG IL QM IC KT C srimltkeeklqfmdylkrpn 133
Cdd:cd10506 20 V TNP R L G LPNESGQ C T TCG a K DNKK C E GH F G VIK L PVTIY H PYFISEVAQ IL NK IC PG C --------------------- 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 134 laylqkrglkkkisdkcrkrtvclncsafngpvkkcgl LK I IHE K Y K TTKKVVDAFVS DF LQ sf DTAIEHNKL V EPL L tr 213
Cdd:cd10506 79 -------------------------------------- KS I KQK K K K PPRETLPPDYW DF IP -- KDGQQEESC V TKN L -- 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 214 aqenln P LVA L NLF K R I PQDDI P L L LMN pea G K P A -- D L IITR 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 LKEID P K L IAK --- G L P R qe G L FLKC L P VPP N C H R --- V TEFTH G FST --- GSR L IFDERTRA 181
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 292 VI K K hrmtgaktqmimedwdflqlqc 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 1735312367 372 DP N L RID E VAV P VHV A KI LT YP ERV NKA N L E LMRKLV rngp D VHPGANFIQNRHT qmkrflk Y G N -- REKIAQE L RF GDV 449
Cdd:cd10506 226 DP Y L ELN E IGI P CEI A ER LT VS ERV SSW N R E RLQEYC ---- D LTLLLKGVIGVRR ------- N G R lv GVRSHNT L QI GDV 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 450 VE R H L I DGDVVL F NR Q PS L H KL S IM A HIAR V 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 LSVK V 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 1735312367 529 L VTPRN G EP L IAAI QD F L TG A Y L L T LKDT F F D RSKAC Q I va SI L VGK dervri S LP R PAI M K ---- PIA LWTGKQ I F SLI 604
Cdd:cd10506 375 L ISSQS G QN L LSLT QD S L LA A H L M T ERGV F L D KAQMQ Q L -- QM L CPS ------ Q LP P PAI I K spps NGP LWTGKQ L F QML 446
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 605 L KP skecpvranlrtk GKQ Y CG kgedlchn D S FV V IHNSELMCG S MDKGTLGSG S KN N I F Y IL LRD w G QLE A ANAMSRLA 684
Cdd:cd10506 447 L PT ------------- DLD Y SF -------- P S NL V FISDGELIS S SGGSSWLRD S EG N L F S IL VKH - G PGK A LDFLDSAQ 504
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 685 R L APVY LS N RGFS IGIG D VTP g QGLLKAK Q DLLDD --- G YQKCDE ------------------- YI E ALQTGKLQQQPGC 742
Cdd:cd10506 505 G L LCEW LS M RGFS VSLS D LYL - SSDSYSR Q KMIEE isl G LREAEI acnikqllvdsrkdflsgs GE E NDVSSDVERVIYE 583
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 743 T -- AEETLE A LILKELS V I RD RA g SACLRELD K S NS P L I M ALC GSKGS FINIS Q MIA C V G Q Q -------- A I SGSRVPDG 812
Cdd:cd10506 584 R qk SAALSQ A SVSAFKQ V F RD IQ - NLVYKYAS K D NS L L A M IKA GSKGS LLKLV Q QSG C L G L Q lslvklsy R I PRQLSCAA 662
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 813 FENRSL P HFEKHSK ----- LPAAK G F V AD 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 Y 886
Cdd:cd10506 663 WNSQKS 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 Y 739
....*
gi 1735312367 887 D L TVR 891
Cdd:cd10506 740 D G TVR 744
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
246-1359
4.31e-79
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: 285.02
E-value: 4.31e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 246 K P ADLIITRLL V P P LCI RP S V -------- V SDL ksgtne D DL TMK lte I I FL N DVI K KHRMT GA ------- KTQ M IM E DW 310
Cdd:TIGR02386 215 R P EWMVLDVIP 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 1735312367 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 kil 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 --- 355
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 391 typervnkan LEL ----- MRK L VR ngpdv HPG A NF I Q nrht QM K RFLKYGNR E kiaqelr FG DV V E R h L I DGDV VL F NR Q 465
Cdd:TIGR02386 356 ---------- LEL fkpfi IKR L ID ----- REL A AN I K ---- SA K KMIEQEDP E ------- VW DV L E D - V I KEHP VL L NR A 408
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 466 P S LH K L S I M A HIARVKPHRTF 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 F 545
Cdd:TIGR02386 409 P T LH 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 M 488
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 546 LT G A Y L LT L -------- KDT F FDRSK A CQIVASIL V GKDERVRISL p RPA I MKPIA lwt G KQ IF SL IL K pskecpvranl 617
Cdd:TIGR02386 489 VL G L Y Y LT T ekpgakge GKI F SNVDE A IRAYDNGK V HLHALIGVRT - SGE I LETTV --- G RV IF NE IL P ----------- 553
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 618 rtkgkqycgkgedlchn DS F VV I HNS E lmcg SMD K GTLG S gsknn IFYI L LRDW G QL E A A NAMSRLAR L APV Y LSNR G FS 697
Cdd:TIGR02386 554 ----------------- EG F PY I NDN E ---- PLS K KEIS S ----- LIDL L YEVH G IE E T A EMLDKIKA L GFK Y ATKS G TT 607
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 698 I GIG D V - T P GQ gllka K QDL L DDGYQKCDEYIEALQT G KL qqqpgc T A EE TLEALI l KEL S VIR D RAGS A CLRE L D K S -- 774
Cdd:TIGR02386 608 I SAS D I v V P DE ----- K YEI L KEADKEVAKIQKFYNK G LI ------ T D EE RYRKVV - SIW S ETK D KVTD A MMKL L K K D ty 675
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 775 -- N SPLI MA LC G SK G SFINIS Q MIACV G QQ A isgsr V P D G f ENRS LP hfekhsklpaakgf VAD SF YS GLT PT E F F FH T M 852
Cdd:TIGR02386 676 kf N PIFM 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 H 735
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 853 AG R E 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 RVL D N 927
Cdd:TIGR02386 736 GA R K 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 -- SLK D R 797
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 928 I RAV Y TCP D EPALSQNE L VLT A DAI mkradflccrdsfleeiktfiks I S E R I KKTRDKY GI ndngt SEP KV LYQ L drvt 1007
Cdd:TIGR02386 798 I VGR Y SAE D VYDPDTGK L IAE A NTL ----------------------- I T E E I AEKIENS GI ----- EKV KV RSV L ---- 845
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1008 ptqlekfle TC RDKYMRA Q ------------ M E P G S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA S -- MN IT L G V PR I KE I 1073
Cdd:TIGR02386 846 --------- TC ESEHGVC Q kcygrdlatgkl V E I G E AVG VIA AQSIGEPGTQ L T MR TFH TG GVA G as GD IT Q G L PR V KE L 916
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1074 IN A skni S TP iitahldv E D D A DF A R l V K G RI E ktllgeiseyieev FLP D D cfil VK lsl ERIRLLRLEV N A E TVR Y S I 1153
Cdd:TIGR02386 917 FE A ---- R TP -------- K D K A VI A E - V D G TV E -------------- IIE D I ---- VK --- NKRVVVIKDE N D E EKK Y T I 962
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1154 CMSK - LRVK P GD IAVH G EAVV -- CVS P RE nskssmyy V L QSLK - EDLPKVV V QGIPE V A R AV - IH I D eqsgk N K YKLLVE 1228
Cdd:TIGR02386 963 PFGA q LRVK D GD SVSA G DKLT eg SID P HD -------- L L RIKG i QAVQEYL V KEVQK V Y R LQ g VE I N ----- D K HIEVIV 1029
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1229 GDN LR A V MA T - H G ---- VN G SRTTSNNTY E VEKT L g I E AARSTII neiqytmvnhgmsidrrhvmlladlms YKGEI LGI 1303
Cdd:TIGR02386 1030 RQM LR K V RI T d S G dsnl LP G ELIDIHEFN E ENRK L - L E QGKKPAS --------------------------- AIPQL LGI 1081
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*...
gi 1735312367 1304 T 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 1359
Cdd:TIGR02386 1082 T 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
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1046-1369
8.76e-68
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 246.73
E-value: 8.76e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1046 T QM T LK TFH F AGVA SM N I TLG V PR IK EI IN A S K NI STPI I T A HL DV E -- D D ADF A RL V KGR IE KTL LG EISEY I EEVFLP 1123
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 V HL KG E ya T D REK A EE V AKK IE SLT LG DVATS I AIDLWT 620
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1124 DD cf I L V K L SL E RI -- R L L RL E VNA E TVR ysicm S KL R VK pgd I AVH G e A V VCVS P REN S kssm Y YV L QSLKEDLPKV V V 1201
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 --- I DRK G - T V LYLK P KTP S ---- Y KA L RKRIPKIKNI V L 685
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1202 Q GIP EVA R AVIHID E QSGKNK Y K L LVE G D NLR A V MATH GV NG SRTT S NN TY E VEKT LGIEAAR ST IINE IQY T MVNH G MS 1281
Cdd:PRK14898 686 K GIP GIE R VLVKKE E HENDEE Y V L YTQ G S NLR E V FKIE GV DT SRTT T NN II E IQEV LGIEAAR NA IINE MMN T LEQQ G LE 765
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1282 I D R RH V ML L AD L M SYK GE ILG 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 1361
Cdd:PRK14898 766 V D I RH L ML V AD I M TAD GE VKP 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 1735312367 1362 L LHKADRD 1369
Cdd:PRK14898 846 L RIDREYE 853
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1021-1363
3.38e-66
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: 226.69
E-value: 3.38e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1021 KYMR AQM EPG S AVG A L C AQSIGEP G TQMTL K TFHFAG VAS MN I TLG V PR IK EI I - N ASKNI S TP II T AH L DVEDD A DF A R 1099
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 ASKNI K TP SM T LP L KNGKS A ER A E 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1100 LV K G R IEKTL L GEIS E YI E -- E VF lpd DCFIL V - K LS L ER irll RL EV NAET vrysicmsklrvkpgdiavhgeavvcvs 1176
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 TIKL ---------------------------- 125
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1177 prens KS S MYYV L QS -- LKEDLP K V V VQG IP EVA R AVIHIDEQS GK N KY KLLV EG D NL R A VMATHG - VNGS R TTS N NTYE 1253
Cdd:cd02735 126 ----- PL S SPKL L LL si VEKLAR K A V IRE IP GIT R CFVVEEDKG GK T KY LVIT EG V NL A A LWKFSD i LDVN R IYT N DIHA 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1254 VEK T L GIEAAR ST I IN EI QYTMVNH G MSI D R RH VM L L AD L M SYK G EILGIT R F G LAK m KE S V L MLA SFE K T ADH L FD A AY 1333
Cdd:cd02735 201 MLN T Y GIEAAR RA I VK EI SNVFKVY G IAV D P RH LS L I AD Y M TFE G GYRPFN R I G MES - ST S P L QKM SFE T T LAF L KK A TL 279
330 340 350
....*....|....*....|....*....|
gi 1735312367 1334 F G QK D SVCGV S ECIIM G I P M N I GTGLF K LL 1363
Cdd:cd02735 280 N G DI D NLSSP S SRLVV G K P V N G GTGLF D LL 309
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
246-1359
1.05e-61
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 232.84
E-value: 1.05e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 246 K PAD L I ITRLL V P P LCI RP S V vs D L KS G T - NED DL TMKLTEI I FL N DVI K KHRMT GA KTQMIMEDWDF LQ LQC - A L YI N S 323
Cdd:PRK14906 311 D PAD M I LDVIP 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 1735312367 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 kiltypervnkan LEL 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 ------------- LEL 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 404 MRKL V rngpdvhpganfiqnrhtq MKR FLKYGNREK I AQEL R -------- FG DV V E R h L I DGDV VL F NR Q P S LH K L S I M A 475
Cdd:PRK14906 455 FKPF V ------------------- MKR LVELEYAAN I KAAK R avdrgasy VW DV L E E - V I QDHP VL L NR A P T LH R L G I Q A 514
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 476 HIARVKPHRTFRFNEC 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 - L 554
Cdd:PRK14906 515 FEPVLVEGKAIKLHPL 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 E 594
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 555 K D T F FDRSKACQIVASI L VGK D E R VRIS L PRPAIMKPIALW T GKQIF slil KPSK E CPVRANLR T K gkqy C G K gedlchn 634
Cdd:PRK14906 595 R D G F EGEGRTFADFDDA L NAY D A R ADLD L QAKIVVRLSRDM T VRGSY ---- GDLE E TKAGERIE T T ---- V G R ------- 659
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 635 dsfv V I H N SE L ------ MCGS M D K GTL G sgsknnify I L LR D ---- WGQL E AANAMSRLARLAPV Y LSNR G FSIGIG D V T 704
Cdd:PRK14906 660 ---- I I F N QV L pedypy LNYK 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 1735312367 705 pgqg LLKA K QDL L DDGYQ K CDEYI E ALQT G K L qqqpgct A E ETLEALILKELSVIRDRA G S A C L REL D KS N SPLI MA LC G 784
Cdd:PRK14906 727 ---- IPDD K PEI 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 1735312367 785 SK G SFIN I S Q MIACV G QQ A ISGSRVP D gfenrs LP hfekhsklpaakgf VADS 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 1735312367 865 TA ET GY MQ RRLV KSLE dlcsqy D LT VR S stgdiiqfiyggdg L D PAAM EG KDE PL EFKRVLDNIRAVYT C PD E PALSQ 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 1735312367 945 L VL TA daimk RA D FLCCR D SFLEEIKTFIKSISE R IKK T - RDK YG INDN gtsepkv L Y QL D RV T ptqlekfletcrdkym 1023
Cdd:PRK14906 916 E VL LS ----- AG D YIESM D DLKRLVEAGVTKVQI R TLM T c HAE YG VCQK ------- C Y GW D LA T ---------------- 967
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1024 R AQMEP G S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA SMN IT L G V PR IK E IIN A S K NISTPIITA hldveddadfarl VK G 1103
Cdd:PRK14906 968 R RPVNI G T AVG IIA AQSIGEPGTQ L T MR TFH SG GVA GDD IT Q G L PR VA E LFE A R K PKGEAVLAE ------------- IS G 1034
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1104 RIEK T ll G EIS E YIEEVFLP D DCFILVKL S l E R IRLLRLEVNAET VR YSICMSKLR V K P G D IA vhgeavvcvs PRENSKS 1183
Cdd:PRK14906 1035 TLQI T -- G DKT E KTLTIHDQ D GNSREYVV S - A R VQFMPGVEDGVE VR VGQQITRGS V N P H D LL ---------- RLTDPNT 1101
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1184 SMY Y VLQSLKE dlp KV V V QG I p EVARAV I HIDEQSGKN K YKLLVE GD NL ---- R A V mathgvngsrttsn N T YE V E K T lg 1259
Cdd:PRK14906 1102 TLR Y IVSQVQD --- VY V S QG V - DINDKH I EVIARQMLR K VAVTNP GD SD ylpg R Q V -------------- N R YE F E D T -- 1161
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1260 ieaarsti I N EI qytmvnhgmsidrrhvm L L ADLMSYK G E -- I LGIT RFG LA km KE S V L ML ASF EK T ADH L F DAA YF G QK 1337
Cdd:PRK14906 1162 -------- A N NL ----------------- I L EGKQPPV G Q pl L LGIT KAS LA -- TD S W L SA ASF QE T TKV L T DAA IE G KV 1214
1130 1140
....*....|....*....|..
gi 1735312367 1338 D SVC G VS E CI I M G I P MNI GTGL 1359
Cdd:PRK14906 1215 D HLA G LK E NV I I G K P IPA GTGL 1236
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1030-1359
5.24e-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: 205.73
E-value: 5.24e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1030 G S AVG A L C AQSIGEPGTQMTL K TFHFAGVASMN I TLG V PR I KEI I NA S knistpiitahldveddadfarlvkgriektl 1109
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 1735312367 1110 lgeiseyieevflpddcfilvklslerirllrlevnaetvrysicmsklrvkpgdiavhgeavvcvsprenskssmyyvl 1189
Cdd:cd00630 --------------------------------------------------------------------------------
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1190 qslkedlpkvvvqgipevaravihideqsgknkykllvegdnlravmathgvngsrttsn NTY E VEKT LGIEAAR S TII N 1269
Cdd:cd00630 49 ------------------------------------------------------------ SIH E MLEA LGIEAAR E TII R 68
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1270 EIQ YTMVNH G M S I DRRH VM L L AD L M S Y K G EIL 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 1349
Cdd:cd00630 69 EIQ KVLASQ G V S V DRRH IE L I AD V M T Y 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 1735312367 1350 G I P MNI GTG L 1359
Cdd:cd00630 149 G R P APL GTG S 158
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
345-1359
2.53e-60
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 227.26
E-value: 2.53e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A kiltypervnkan LEL ----- M R KLV RN G pdvhpgan 419
Cdd:PRK00566 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A ------------- LEL fkpfi M K KLV ER G -------- 379
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 420 FIQNR h TQM K RFL kygnr E K ia QELRFG DV V E r HL I DGDV VL F NR Q P S LH K L S I M A ------------- H iarvk P hrtf 486
Cdd:PRK00566 380 LATTI - KSA K KMV ----- E R -- EDPEVW DV L E - EV I KEHP VL L NR A P T LH R L G I Q A fepvliegkaiql H ----- P ---- 441
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 487 rfne C 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 558
Cdd:PRK00566 442 ---- L 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 517
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 559 FDRSK A CQIVASIL V GKDE R VRISLPRPAIMK pialw T -- G KQ IF SL IL k P skecpvranlrtkgkqycgkg E D L chnd S 636
Cdd:PRK00566 518 SSPEE A LRAYENGE V DLHA R IKVRITSKKLVE ----- T tv G RV IF NE IL - P --------------------- E G L ---- P 566
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 637 F VVIH nselmc GSMD K GTLG sgskn N I FYILL R DW G QL E AANAMSRLAR L APV Y LSNR G F SIGI G D VT pgqg LLKA K QDL 716
Cdd:PRK00566 567 F INVN ------ KPLK K KEIS ----- K I INEVY R RY G LK E TVIFLDKIKD L GFK Y ATRS G I SIGI D D IV ---- IPPE K KEI 631
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 717 LDDGYQKCD E YIEALQT G KL qqqpgc T AE E TLEAL I l KEL S VIR D RAGS A CLRE L D K SNSPL ---- I MA LC G SK GS FIN I 792
Cdd:PRK00566 632 IEEAEKEVA 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 704
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 793 S Q miacvgqqa IS G S R vpdgfenrslphfekhsklpaak G FV A D ------------ S F YS GLT PT E F F FH T MAG R E GL V D 860
Cdd:PRK00566 705 R Q --------- LA G M R ----------------------- G LM A K psgeiietpiks N F RE GLT VL E Y F IS T HGA R K GL A D 752
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 861 TA V KTA 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 IRA 930
Cdd:PRK00566 753 TA L KTA 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 814
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 931 V Y t C P DE palsq N E LVLT A DAI mkradflccrdsfleeiktfiks I S E R I KKT rdkyg I NDN G TS E P K V lyqld R v TPT q 1010
Cdd:PRK00566 815 V V - D P ET ----- G E VIVP A GTL ----------------------- I D E E I ADK ----- I EEA G IE E V K I ----- R - SVL - 853
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1011 lekfle TC RDKY ----------- MRAQM - EP G S AVG ALC AQSIGEPGTQ M T LK TFH FA GV asm N IT L G V PR IK E IIN A S K 1078
Cdd:PRK00566 854 ------ TC ETRH gvcakcygrdl ATGKL v NI G E AVG VIA AQSIGEPGTQ L T MR TFH TG GV --- D IT G G L PR VA E LFE A R K 924
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1079 nist P iitahldv EDD A DF A R l VK G RIEK tll G EISEYIEEVFLPD D cfilvklslerirllrlev NA E TVR Y S I CMS K - 1157
Cdd:PRK00566 925 ---- P -------- KGP A II A E - ID G TVSF --- G KETKGKRRIVITP D ------------------- DG E ERE Y L I PKG K h 969
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1158 L R V KP GD IAVH G EA vvcvsprenskssmyyvlqslkedlpkvvvqgipevaravihideqsgknkykl L VE G dnlravma 1237
Cdd:PRK00566 970 L L V QE GD HVEA G DK ------------------------------------------------------ L TD G -------- 987
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1238 thgvngsrtt S NNTYEVEKT LG I EA ARSTII NE I Q -- Y TM vn H G MS I DRR H V ------ ML ----------------- L A D 1292
Cdd:PRK00566 988 ---------- S IDPHDILRV LG V EA VQNYLV NE V Q kv Y RL -- Q G VK I NDK H I evivrq ML rkvritdpgdtdflpge L V D 1055
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1293 LMSYKG E ----------------- I LGIT RFG LA km K ES V L ML ASF EK T ADH L FD AA YF G QK D SVC G VS E CI I M G -- IP M 1353
Cdd:PRK00566 1056 RSEFEE E nrkliaegkepatgrpv L LGIT KAS LA -- T ES F L SA ASF QE T TRV L TE AA IK G KV D PLR G LK E NV I I G rl IP A 1133
....*.
gi 1735312367 1354 ni GTGL 1359
Cdd:PRK00566 1134 -- GTGL 1137
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
345-876
5.98e-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: 201.21
E-value: 5.98e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A kiltypervnkan LEL ----- M R K L VRN G pdvhpgan 419
Cdd:cd01609 236 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KEM A ------------- LEL fkpfv I R E L IER G -------- 294
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 420 FIQ N rhtqmkrf L K YGNREKIAQELRFG D VV E r HL I D G DV VL F NR Q P S LH K L S I M A HIARVKPHRTFRFNEC VCT PY NAD 499
Cdd:cd01609 295 LAP N -------- I K SAKKMIERKDPEVW D IL E - EV I K G HP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NAD 365
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 500 FDGD 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 ffdrskacqivasil VG K D E RV 579
Cdd:cd01609 366 FDGD 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 GI 430
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 580 RISLP rpaimkpialwt G KQ IF SL IL KP skecpvra N L RT kgkqycgkgedlc H N D sfvvihnselmcg SMD K GT L G sgs 659
Cdd:cd01609 431 IETTV ------------ G RV IF NE IL PE -------- G L PF ------------- I N K ------------- TLK K KV L K --- 461
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 660 kn NIFYILLRDW G QL E A A NAMSRLAR L APV Y LSNR G F SI G I G D - V T P gqgll KA K QDLLDDGYQ K CD E YIEALQT G K L qq 738
Cdd:cd01609 462 -- KLINECYDRY G LE E T A ELLDDIKE L GFK Y ATRS G I SI S I D D i V V P ----- PE K KEIIKEAEE K VK E IEKQYEK G L L -- 532
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 739 qpgc T A EE TLEAL I LKELS V i RDRAGS A CLRE LDK S -- N SPLI MA LC G SK GS FIN I S Q MIACV G QQ A - I SG SRVP dgfen 815
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 ----- 602
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1735312367 816 rs LP hfekhsklpaakgf VADS F YS GLT PT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV 876
Cdd:cd01609 603 -- LP -------------- IKSN F RE GLT VL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV 647
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
345-1120
9.39e-52
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: 200.00
E-value: 9.39e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TY P E rvnkanle LM RKL VRN G pdvhpganfiq NR 424
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 -------- IY RKL EER G ----------- LA 381
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 425 H T qmkrf L K YGNREKIAQ E LRFG D VV E R h L I DGDV VL F NR Q P S LH K L S I M A HIARVKPHRTFRFNEC VCT PY NADFDGD E 504
Cdd:COG0086 382 T T ----- I K SAKKMVERE E PEVW D IL E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD Q 455
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 505 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 RSKACQIVASIL V GKD 576
Cdd:COG0086 456 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 DLH 535
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 577 E R -- VRI SLPRPAIM K PIALWT G KQIFSL IL kp SK E C P vranlrtkgkqycgkgedlchnds F V vih N SE lmcgs MD K GT 654
Cdd:COG0086 536 A R ik VRI TEDGEQVG K IVETTV G RYLVNE IL -- PQ E V P ------------------------ F Y --- N QV ----- IN K KH 581
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 655 LG sgskn N I FYILL R DW G QL E AANAMS RL AR L APV Y LSNR G F SIG IG D - V T P gqgll K A KQ DLLDDGYQKCD E YIEALQT 733
Cdd:COG0086 582 IE ----- 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 KQ EIFEEANKEVK E IEKQYAE 651
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 734 G KL qqqpgc T AE E TLEAL I L k ELSVIRDRAG S ACLRELDKS N SPLI MA LC G SK GS FINIS Q MIACV G QQ A isgsr V P D G - 812
Cdd:COG0086 652 G LI ------ T EP E RYNKV I D - GWTKASLETE S FLMAAFSSQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A ----- K P S G n 719
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 813 - F E NR slphfekhsklpaakgf VADS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV KSLE D L csqydltvr 891
Cdd:COG0086 720 i 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 1735312367 892 sstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E --- FK RV - LDNIRAVY T cpdepalsq N E LVLT A DAIM kradflccr 962
Cdd:COG0086 774 ----- I VTEEDC G td R G IT v T A IK EG GE vi EPL K eri LG RV a AEDVVDPG T --------- G E VLVP A GTLI --------- 830
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 963 dsf L EE IKTF I KSISERIK K T R dkygindngtsepkvlyqldrv TPTQL E KFLET C RDK Y M R -- A QMEP --- G S AVG ALC 1037
Cdd:COG0086 831 --- D EE VAEI I EEAGIDSV K V R ---------------------- SVLTC E TRGGV C AKC Y G R dl A RGHL vni G E AVG VIA 885
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1038 AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS K NISTPIITAHLD V EDDADFARL V KGRI E KTLLGEISEYI 1117
Cdd:COG0086 886 AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA K AGGIVRLNNLKV V VNEEGKGVV V SRNS E LVIVDDGGRRE 958
...
gi 1735312367 1118 EE V 1120
Cdd:COG0086 959 EE Y 961
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
246-1060
4.89e-51
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 198.99
E-value: 4.89e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 246 K P ADLII T R L L V P P LCI RP S V -------- VSD L ksgtne DD L TMK lte I I FL N DVI K KHRMT GA KTQMIMEDWDF LQ LQC 317
Cdd:PRK09603 1622 R P EWMML T 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 1735312367 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 TY P E rvn 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 H --- 1769
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 398 kanle L MR KL VRN G pdvhpganfiqn RH T QM K RFLKYGNREK iaqelrf GD V V E -- RHLID G DV VL F NR Q P S LHK L SI M A 475
Cdd:PRK09603 1770 ----- L LS KL EER G ------------ YA T TL K QAKRMIEQKS ------- NE V W 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 1735312367 476 HIARVKPHRTFRFNEC 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 FHPKLIDGKAIQLHPL 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 1735312367 555 K DTFFDRS K ACQI V AS I LVGK D ------- ERV R ISLPR paim KP IA LWT G KQ I FSL IL kp SKEC P VRANL R TKG K QYC G K 627
Cdd:PRK09603 1906 K SGVKGEH K LFSS V NE I ITAI D tkeldih AKI R VLDQG ---- NI IA TSA G RM I IKS IL -- PDFI P TDLWN R PMK K KDI G V 1979
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 628 GE D LC H ND sfvvihnselmcgsmdk G TL G S gsknnifyillrdwgqle A A NAMSR L AR L APV Y LSNR G F SI GIG D V - TP g 706
Cdd:PRK09603 1980 LV D YV H KV ----------------- G GI G I ------------------ T 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 1735312367 707 qgll K A KQ DLLDDGYQKCDEYIEALQT G K L qqqpgc T AE E TLEAL I l KELSVIR D RAGSACLR -- EL DK S -- NS PLI MA L 782
Cdd:PRK09603 2024 ---- K D KQ KMVEKAKVEVKKIQQQYDQ G L L ------ T DQ E RYNKI I - DTWTEVN D KMSKEMMT ai AK DK E gf NS IYM MA D 2092
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 783 C G SK GS FIN I S Q MI A CV G QQA isgsr V PDG fenrslphfekhskl PAAKGFVADS F YS GL TPT E F F FH T MAG R E GL V DTA 862
Cdd:PRK09603 2093 S G AR 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 2152
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 863 V KTA 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 -- 925
Cdd:PRK09603 2153 L KTA 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 2211
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 926 D N I RAV ytcpdepals Q NE LV L T AD AIMK radflccr DSFLEEIKTF - IKSI SE R IKK T RDK -------- YG I N dng TS E 996
Cdd:PRK09603 2212 D V I DPI ---------- T NE IL L Y AD TLID -------- EEGAKKVVEA g IKSI TI R TPV T CKA pkgvcakc YG L N --- LG E 2270
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1735312367 997 P K VL Y qldrvtptqlekfletcrdkymraqme PG S AVG ALC AQSIGEPGTQ M TL K TFH FA G V AS 1060
Cdd:PRK09603 2271 G K MS Y --------------------------- PG E AVG VVA AQSIGEPGTQ L TL R TFH VG G T AS 2307
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
528-703
1.36e-50
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: 175.89
E-value: 1.36e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 528 N LVT P R NG E P L I AAI QD FLT GAYLLT LK DTFFDR SKAC Q IVASIL V gkdervris LP R PAI M KPI - A LWTGKQ I FS LI L K 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 PAI L KPI k P LWTGKQ T FS RL L P 71
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 607 P skecpv RA N LRT K G K QYC gkg EDLC H NDS F V V I H N S EL MC G SM DK G T L G s G S KNNIFY I LLRDW G QL E A A NAMS RL AR L 686
Cdd:pfam04983 72 N ------ EI N PKG K P K TNE --- EDLC E NDS Y V L I N N G EL IS G VI DK K T V G - K S LGSLIH I IYKEY G PE E T A KFLD RL QK L 141
170
....*....|....*..
gi 1735312367 687 APV YL SNR GFSIGI G D V 703
Cdd:pfam04983 142 GFR YL TKS GFSIGI D D I 158
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
246-1359
3.36e-48
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 189.83
E-value: 3.36e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 246 K P ADL I I T RLLVP P LCI RP S V vs D L K SG TNE - D DL TMKLTE II FL N DVIK K HRMTGAKTQ MI MEDWDF LQ LQC - A L YI NS 323
Cdd:PRK14844 1665 R P EWM I L T 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 1735312367 324 ELSGIPLNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A kiltypervnkan LEL 403
Cdd:PRK14844 1743 RRNALVNKAGAVGYKKSISDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P T L KLNQCGL P KRM A ------------- LEL 1809
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 404 MRKL V RNGPDVH pganfiqnrht Q M KRFL K YGNREKI A QELRFG D VV E R h L I DGDV VL F NR Q P S LH K L S I M A HIARVKPH 483
Cdd:PRK14844 1810 FKPF V YSKLKMY ----------- G 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 1735312367 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 1735312367 562 -- SKA C QIVA S I lvg K D ERVR I SLPRPAI M KP I alwtgkqifslil KP S K E CPVRANLR T K G K ---- Q YCG K G E D L chnd 635
Cdd:PRK14844 1958 sf GAF C EVEH S L --- S D GTLH I HSSIKYR M EY I ------------- NS S G E THYKTICT T P G R lilw Q IFP K H E N L ---- 2017
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 636 S F VV I HN selmcgsmdkg T L GSGSKNN I FYILL R DW GQ LEAANAMSR L AR L APV Y LSNR G F S IGIG D VT pgqg LLKA K QD 715
Cdd:PRK14844 2018 G F DL I NQ ----------- V L TVKEITS I VDLVY R NC GQ SATVAFSDK L MV L GFE Y ATFS G V S FSRC D MV ---- IPET K AT 2082
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 716 LL D DGYQKCDEY iealqtg KL Q Q Q P G CTAEETLEALILK E L S VIR D RAGSAC L REL ------ D K S NS PLI M ALC G SK GS f 789
Cdd:PRK14844 2083 HV D HARGEIKKF ------- 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 - 2154
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 790 in I SQM IACV G QQAISGS rv P D G f E NRSL P hfekhsklpaakgf VADS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET G 869
Cdd:PRK14844 2155 -- T SQM 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 G 2215
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 870 Y MQ RRLV KSLED - LCSQY D lt VRSST G DIIQ fiyggdgldp A AM EG kdeplefkrvl DN I R A vytcpdepal S QNEL VL T 948
Cdd:PRK14844 2216 Y LT RRLV DVSQN c IVTKH D -- CKTKN G LVVR ---------- A TV EG ----------- ST I V A ---------- S LESV VL G 2262
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 949 AD A imkradflc CR D SFLEEI K TFIKSIS E R I KKTRD K Y g IN DN G TSEP K VLYQ L D - RVT P TQLE kf L ETC RD KYMRAQM 1027
Cdd:PRK14844 2263 RT A --------- AN D IYNPVT K ELLVKAG E L I DEDKV K Q - IN IA G LDVV K IRSP L T c EIS P GVCS -- L CYG RD LATGKIV 2330
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1028 EP G S AVG ALC AQS I GEPGTQ M T LK TFH FA GV ----------- AS M N I ------------------------------ T LG 1066
Cdd:PRK14844 2331 SI G E AVG VIA AQS V GEPGTQ L T MR TFH IG GV mtrgvessnii AS I N A kiklnnsniiidkngnkivisrscevvlid S LG 2410
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1067 VPRI K E -------- IINASKNI ------------ ST PIIT ------ AHL D VE D DADFARL ------ VKGRIE K -- T L LGE 1112
Cdd:PRK14844 2411 SEKL K H svpygakl YVDEGGSV kigdkvaewdpy TL PIIT ektgtv SYQ D LK D GISITEV mdestg ISSKVV K dw K L YSG 2490
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1113 ISEYIEEVF L P DD cfilvklsle RIRLLR L EVNA E TVRYSICMSK L R V KP G D i A VH GEA V VCVS PRE NS K S smyyvl QSL 1192
Cdd:PRK14844 2491 GANLRPRIV L L DD ---------- NGKVMT L ASGV E ACYFIPIGAV L N V QD G Q - K VH AGD V ITRT PRE SV K T ------ RDI 2553
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1193 KED LP K V V --- VQGI P EVARA V IH ID ------ E QSGKN K YKL L VEGDNLRAVMATHG V NG S RTTSN N T ------------ 1251
Cdd:PRK14844 2554 TGG LP R V I elf EARR P KEHAI V SE ID gyvafs E KDRRG K RSI L IKPVDEQISPVEYL V SR S KHVIV N E gdfvrkgdllmd 2633
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1252 ----- YEVEKT LG I EA ARSTI I N EIQ YTMVNH G MS ID RR H VMLLADL M SY K G EI L ------------------------- 1301
Cdd:PRK14844 2634 gdpdl HDILRV LG L EA LAHYM I S EIQ QVYRLQ G VR ID NK H LEVILKQ M LQ K V EI T dpgdtmylvgesidklevdrendam 2713
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1735312367 1302 --------------- GITR FG L A km KE S VLML ASF EK T ADH L FD AA YF G QK D SVC G VS E CI I M G IPMNI GTGL 1359
Cdd:PRK14844 2714 snsgkrpahylpilq GITR AS L E -- TS S FISA ASF QE T TKV L TE AA FC G KS D PLS G 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 ...
734-834
1.80e-40
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: 144.81
E-value: 1.80e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 734 GKL QQQP G C T A EE TL EALI LKE L SVI RD R AG SACLRE LD KS NS PLI MA LC G S KGS F INISQ MIA C V GQQ AIS G S R V P D GF 813
Cdd:pfam05000 8 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 I P F GF 87
90 100
....*....|....*....|.
gi 1735312367 814 EN R S LPHF E K HSKL P AAK GFV 834
Cdd:pfam05000 88 SG R T LPHF K K DDEG P ESR GFV 108
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
345-553
1.11e-33
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 139.11
E-value: 1.11e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 345 LK GKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TY P ERVNK anlelmrk L V R N G pdvhpganf I Q N 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 401
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 425 HTQM K RFLKYGNR E kiaqelr FGD V V E R h L I D G DV VL F NR Q P S LH K L S I M A HIARVKPH R TFRFNEC VC TPY NADFDGD E 504
Cdd:PRK02625 402 IKAA K KLIQRADP E ------- VWQ V L 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 1735312367 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
rpoC1
CHL00018 RNA polymerase beta' subunit
315-554
1.50e-33
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 139.27
E-value: 1.50e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 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 TY 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 1735312367 393 P E rvnkanle LM R K L V R NGPDVHPG A -- NF I QNRHTQMKRF L K ygnrekiaqelrfgdvver HLID G DV VL F NR Q P S LH K 470
Cdd:CHL00018 408 P F -------- VI R G L I R QHLASNIR A ak SK I REKEPIVWEI L Q ------------------- EVMQ G HP VL L NR A P T LH R 460
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 471 L S I M A hiar VK P ---- H 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 546
Cdd:CHL00018 461 L G I Q A ---- FQ P ilve G 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 536
....*...
gi 1735312367 547 T G A Y L LT L 554
Cdd:CHL00018 537 L G L Y V LT I 544
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
650-1058
2.75e-19
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: 94.92
E-value: 2.75e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 650 M DK GT L gsgsk N N IFYILLRDW G QLEA A NAMSR L AR L APV Y LSNR G F SI GIG D VT pgqg LLK AKQDLL DDGYQKCDEYI 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 AKQDLL EAAEKEIRATE E 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 730 ALQT G KLQ ----- Q QPGC T AEE T L E A L ILK els V IRD ragsac L R EL D KS NS PLI 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 1735312367 805 SGS rv P D G f E NRS LP hfekhsklpaakgf VADS 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 1735312367 883 ---- C - SQYDLT VR SS T - GD ii QF I YG GD G L dpaamegkdeple FK R VLDN iravytcpdepalsqnelvlta D AIMKRA 956
Cdd:TIGR02388 209 reed C g TERSIV VR AM T e GD -- KK I SL GD R L ------------- LG R LVAE ---------------------- D VLHPEG 251
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 957 DFLCCRDS fleeiktfik S I SERIK KT rdkyg I NDN G T SE PK V L yqldrv T P TQL E KFLET CR DK Y MRA ----- QMEP G S 1031
Cdd:TIGR02388 252 EVIVPKNT ---------- A I DPDLA KT ----- I ETA G I SE VV V R ------ S P LTC E AARSV CR KC Y GWS lahah LVDL G E 310
410 420
....*....|....*....|....*..
gi 1735312367 1032 AVG ALC AQSIGEPGTQ M T LK TFH FA GV 1058
Cdd:TIGR02388 311 AVG IIA AQSIGEPGTQ L T MR TFH TG GV 337
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
769-1058
1.08e-15
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 83.12
E-value: 1.08e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 769 R EL D KS NS PLI MA LC G SK G sfi N I SQ MIAC VG QQAISGS rv P D G f E NRS LP hfekhsklpaakgf VADS 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 1735312367 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 1735312367 924 VL DNI ravytcpdepals QNE L V -- LT A DAIMKRAD - FLCC R DSFLEE iktfik SISER I K K T rdkygindn G TS E PK V l 1000
Cdd:PRK02597 231 VL IPL ------------- GDR L L gr VL A EDVVDPEG e VIAE R NTAIDP ------ DLAKK I E K A --------- G VE E VM V - 281
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1735312367 1001 yqld R v T P TQL E KFLET CR DK Y ---- MRAQM - EP G S AVG ALC AQSIGEPGTQ M T LK TFH FA GV 1058
Cdd:PRK02597 282 ---- R - S P LTC E AARSV CR KC Y gwsl AHNHL v DL G E AVG IIA AQSIGEPGTQ L T MR TFH TG GV 339
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1028-1079
4.87e-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: 75.26
E-value: 4.87e-15
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 1735312367 1028 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 N 1079
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 I 54
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1229-1363
2.26e-10
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain]
Cd Length: 381
Bit Score: 64.36
E-value: 2.26e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 1229 G DNLRA VM AT ----- HGVNGS R TTSNNTYEVEKT LGI E AA RSTIINEIQYTMVNH G M S ID R R H VM L L AD L M S Y K GE IL G I 1303
Cdd:cd02737 235 G NAWNV VM DA cipvm DLIDWE R SMPYSIQQIKSV LGI D AA FEQFVQRLESAVSMT G K S VL R E H LL L V AD S M T Y S GE FV G L 314
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1735312367 1304 TRF G LAKMKE S V ----- LML A S F EKTADHLFD AA YF G QK DS VC GV SECIIM G IPMNI GTG - L F KL L 1363
Cdd:cd02737 315 NAK 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
769-1058
4.27e-10
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 64.58
E-value: 4.27e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 769 R EL D KS N SPLI M ALC G SK G sfi N I SQ miac V G Q qaisgsrvpdgfenrslphfekhsk L PAAK G FVA D ------------ 836
Cdd:CHL00117 120 R MT D PL N PVYM M SFS G AR G --- N A SQ ---- V H Q ------------------------- L VGMR G LMS D pqgqiidlpiqs 167
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 837 S F YS GL TP TE FFFHTMAG R E G L VDTAV K TA ET GY MQ RRLV KSLEDL ------ C sqyd L T V R SST gdiiqfiyggdg LD P A 910
Cdd:CHL00117 168 N F RE GL SL TE YIISCYGA R K G V VDTAV R TA DA GY LT RRLV EVVQHI vvretd C ---- G T T R GIS ------------ VS P R 231
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 911 AMEGKDEP L EFK --- RVL - D N I R avytcpdepal SQNELVL T AD - A I mkradflcc RDSFLEEIK TF - IKS IS E R ikktr 984
Cdd:CHL00117 232 NGMMIERI L IQT lig RVL a D D I Y ----------- IGSRCIA T RN q D I --------- GIGLANRFI TF r AQP IS I R ----- 286
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735312367 985 dkygindngtsepkvlyqldrv T P T qlekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL 1050
Cdd:CHL00117 287 ---------------------- S P L ------- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL 335
....*...
gi 1735312367 1051 K TFH FA GV 1058
Cdd:CHL00117 336 R TFH TG GV 343
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1004-1050
9.41e-07
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 53.74
E-value: 9.41e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1735312367 1004 D R VT PTQL E KFLETCRDK Y MR A QM EP GS AVG ALC AQSIGEPGTQM T L 1050
Cdd:PRK14898 31 D G VT 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
