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DNA-directed RNA polymerase III subunit RPC1 [Homo sapiens]
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: 1668.46
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 24 SPE EMRQQAHIQ V VSK NLY SQDNQH a PL L YGVLD H R M GTS E KD RP CETCG K NLADC L GH Y GYI D LELP C FH V GYF R A V I G 103
Cdd:cd02583 2 SPE DIIRLSEVE V TNR NLY DIETRK - PL P YGVLD P R L GTS D KD GI CETCG L NLADC V GH F GYI K LELP V FH I GYF K A I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 104 ILQ M ICKTC CHIM L SQ EEK KQ FL DY L K RP G L TY LQK RG LKKKI SD KC R K KNI C H HCG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C P HCG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 184 kvvdpivsnflqsfetaiehnkevep LL GR AQE N LNPL V VLNLFK R IP A EDV P LLLMNP E AG K P SD LILTR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL K VLNLFK N IP P EDV E LLLMNP L AG R P EN LILTR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RIS GAKTQ M IMEDWDFLQLQCALYINSEL S G I PL N M A PKK WT RGF V Q 343
Cdd:cd02583 192 PSVV M D E KSGTNEDDLT V KL S EIIFLNDVIKKH LEK GAKTQ K IMEDWDFLQLQCALYINSEL P G L PL S M Q PKK PI RGF C Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV Q NGP E VHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGP D VHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 R HTQM K R FLKYGNR E K M A Q ELK Y GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L A R V K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R A K V M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDRA KA CQ IIASI L vgk D EK IK VR L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDRA QF CQ LCSYM L --- D GE IK ID L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C A ND S YV T I Q NSEL MS G SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 PPP A ILKPV E LWTGKQIFS LL LRP NKKS PV LV NL EA K E K S Y TK K SP D M C P ND G YV V I R NSEL LC G RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 664 FY I LLRD W G QNE AA D AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K Y EL LNA GY K KCDEYI EALNT GKL QQ QPGCT 743
Cdd:cd02583 589 FY V LLRD Y G PEA AA A AM N RLA K L SSRW LSNRGFSIGI D DVTP SKE LLK K K E EL VDN GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 744 AE E TLEA L I LK ELS V IR DH AG S ACL R EL D KSNSPL T MALCGSKGS F INISQMIACVGQQ A ISG S R V P D GFE N R S LPHF EK 823
Cdd:cd02583 669 AE Q TLEA K I SG ELS K IR ED AG K ACL K EL H KSNSPL I MALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 39725938 824 H SK L PAAKGFVANSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
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: 565.31
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DK D D D ADY AR L 1100
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK N ISTPIITA K L EN D R D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1101 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysictsklrvkpgdvavhgeavvcvtpren 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 39725938 1181 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek YKLLVEG DN LRAVM A T H GV K GTRTTSN NTY EVEK T LGI 1260
Cdd:cd02736 123 SKS NL Y FL LQ S LK RK LP D VVV S GIPEV K RAVI NK D KKK GK -- YKLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1261 EAAR T TIINEIQYTM VN HGMSID R RH V MLL S DLMT Y KGEVLGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1340
Cdd:cd02736 201 EAAR S TIINEIQYTM KS HGMSID P RH I MLL A DLMT F KGEVLGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 39725938 1341 C GVSECIIMG I PM N IGTGLF 1360
Cdd:cd02736 281 E GVSECIIMG K PM P IGTGLF 300
rpoC2 super family
cl33332 RNA polymerase beta'' subunit; Reviewed
841-1058
1.63e-08
RNA polymerase beta'' subunit; Reviewed
CHL00117 :Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 59.57
E-value: 1.63e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 841 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 AAMEG 914
Cdd:CHL00117 172 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 RNGMM 235
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 915 KDEP L EFK --- RVL - D N I K avfpcpsepal SKNEL I L T TE simkkseflcc QD SFLQEIKK FI K gvsekikktrdkygin 990
Cdd:CHL00117 236 IERI L IQT lig RVL a D D I Y ----------- IGSRC I A T RN ----------- QD IGIGLANR FI T ---------------- 277
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 991 dngtteprvl YQLDR I --- T P T qvekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL K TF 1053
Cdd:CHL00117 278 ---------- FRAQP I sir S P L ------- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL R TF 338
....*
gi 39725938 1054 H FA GV 1058
Cdd:CHL00117 339 H TG GV 343
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: 1668.46
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 24 SPE EMRQQAHIQ V VSK NLY SQDNQH a PL L YGVLD H R M GTS E KD RP CETCG K NLADC L GH Y GYI D LELP C FH V GYF R A V I G 103
Cdd:cd02583 2 SPE DIIRLSEVE V TNR NLY DIETRK - PL P YGVLD P R L GTS D KD GI CETCG L NLADC V GH F GYI K LELP V FH I GYF K A I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 104 ILQ M ICKTC CHIM L SQ EEK KQ FL DY L K RP G L TY LQK RG LKKKI SD KC R K KNI C H HCG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C P HCG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 184 kvvdpivsnflqsfetaiehnkevep LL GR AQE N LNPL V VLNLFK R IP A EDV P LLLMNP E AG K P SD LILTR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL K VLNLFK N IP P EDV E LLLMNP L AG R P EN LILTR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RIS GAKTQ M IMEDWDFLQLQCALYINSEL S G I PL N M A PKK WT RGF V Q 343
Cdd:cd02583 192 PSVV M D E KSGTNEDDLT V KL S EIIFLNDVIKKH LEK GAKTQ K IMEDWDFLQLQCALYINSEL P G L PL S M Q PKK PI RGF C Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV Q NGP E VHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGP D VHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 R HTQM K R FLKYGNR E K M A Q ELK Y GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L A R V K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R A K V M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDRA KA CQ IIASI L vgk D EK IK VR L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDRA QF CQ LCSYM L --- D GE IK ID L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C A ND S YV T I Q NSEL MS G SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 PPP A ILKPV E LWTGKQIFS LL LRP NKKS PV LV NL EA K E K S Y TK K SP D M C P ND G YV V I R NSEL LC G RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 664 FY I LLRD W G QNE AA D AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K Y EL LNA GY K KCDEYI EALNT GKL QQ QPGCT 743
Cdd:cd02583 589 FY V LLRD Y G PEA AA A AM N RLA K L SSRW LSNRGFSIGI D DVTP SKE LLK K K E EL VDN GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 744 AE E TLEA L I LK ELS V IR DH AG S ACL R EL D KSNSPL T MALCGSKGS F INISQMIACVGQQ A ISG S R V P D GFE N R S LPHF EK 823
Cdd:cd02583 669 AE Q TLEA K I SG ELS K IR ED AG K ACL K EL H KSNSPL I MALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 39725938 824 H SK L PAAKGFVANSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
7-930
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 955.84
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 7 RETDVA K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D N qh A P LLY G VL D H R M G TSEKDRP C E TCG KNLAD C L GH Y G Y I 86
Cdd:PRK08566 1 SMMMIP K R I GS I K FG LL SPEE I R KMSVTKIITADT Y DD D G -- Y P IDG G LM D P R L G VIDPGLR C K TCG GRAGE C P GH F G H I 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 87 D L EL P CF HVG YFRAVIGI L QMI C KT C CHIM L SQ EE KKQF L DY L K R PGLTYLQKRG L K K KISDKCR K KNI C H HCG A fngtv 166
Cdd:PRK08566 79 E L AR P VI HVG FAKLIYKL L RAT C RE C GRLK L TE EE IEEY L EK L E R LKEWGSLADD L I K EVKKEAA K RMV C P HCG E ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 167 K K cgl L KI IH EK yktnkkvvd P I vsnflqsfe T AI E HN KE VE pllgraq EN L N P LVVLNLFKR IP A ED VP LL LM NPE AGK 246
Cdd:PRK08566 154 K Q --- Y KI KF EK --------- P T --------- T FY E ER KE GL ------- VK L T P SDIRERLEK IP D ED LE LL GI NPE VAR 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 247 P SDLI LT R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRIS GA K t Q M I M ED - W DF LQ LQCAL Y INS E 324
Cdd:PRK08566 206 P EWMV LT V L P VPP VTV RPS IT -- L ET G q RS EDDLT H KL VD II RI N QRL K ENIEA GA P - Q L I I ED l W EL LQ YHVTT Y FDN E 282
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 325 LS GIP lnma P ----- KKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT F PE K V NKA 399
Cdd:PRK08566 283 IP GIP ---- P arhrs GRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EAI AK E LT V PE R V TEW 358
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 400 NI NF LR KL V Q NGPE V HPGAN FI qq RHTQMK R F - L KYG N R E KM A QE L KY G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA 478
Cdd:PRK08566 359 NI EE LR EY V L NGPE K HPGAN YV -- IRPDGR R I k L TDK N K E EL A EK L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RV 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 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 39725938 559 F DRAK A CQIIASILVGKDE kikvr L P P P T I LKPVTL WTGKQIFS VI L r P S D D N PVR anl RT K GKQY C GKGED - L C AN D S Y 637
Cdd:PRK08566 517 F TKEE A LDLLRAAGIDELP ----- E P E P A I ENGKPY WTGKQIFS LF L - P K D L N LEF --- KA K ICSG C DECKK e D C EH D A Y 587
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 638 V T I Q N SE L MS G SM DK GTL G SG s KNN I FYILLRDW G QNE A ADAMSRLA RLA PVYLSN RGF SI GI G D VT - P GQGLLKAK y E L 716
Cdd:PRK08566 588 V V I K N GK L LE G VI DK KAI G AE - QGS I LDRIVKEY G PER A RRFLDSVT RLA IRFIML RGF TT GI D D ED i P EEAKEEID - E I 665
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 717 LNAGY K KCD E Y IEA LNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE L DKS N SPLT MA LC G SK GS FI N IS QM I 796
Cdd:PRK08566 666 IEEAE K RVE E L IEA YEN G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG EIAEKY L GLD N PAVI MA RT G AR GS ML N LT QM A 745
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 797 ACVGQQ AIS G S R VPD G FEN R S LPHF EKHSKLPA A K GFV AN S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GYMQRRL V 876
Cdd:PRK08566 746 ACVGQQ SVR G E R IRR G YRD R T LPHF KPGDLGAE A R GFV RS S YK SGLTPTEFFFH A M G GREGLVDTAV R T SQS GYMQRRL I 825
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 39725938 877 KS L E DL CSQ YD L TVR SST G D I I QF I YG G DG L DP AAMEG k DE P LEFK R VLDNIKA 930
Cdd:PRK08566 826 NA L Q DL KVE YD G TVR DTR G N I V QF K YG E DG V DP MKSDH - GK P VDVD R IIERVLG 878
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-925
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 884.44
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 13 KKI SH I C FG MK SPEE M R QQAHIQ VV SKNL Y SQ D N qh A P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P C 92
Cdd:TIGR02390 2 KKI GS I K FG LL SPEE I 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 H I E L AR P V 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 93 F HVG YFRAVIG IL QMI C KT C CH I M L SQ EE KK Q F L D - YL K RPGLTYLQKRG L KK KI SDKCR K KNI C H HCG A fngtvkkc GL 171
Cdd:TIGR02390 80 V HVG FAKEIYK IL RAT C RK C GR I T L TE EE IE Q Y L E k IN K LKEEGGDLAST L IE KI VKEAA K RMK C P HCG E -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 172 L KI IH EK yktnkkvvd P iv SN F LQ sfetaiehnkevep LLGRAQEN L N P LVVLNLFKR IP A ED VP LL LM NP EAGK P SDLI 251
Cdd:TIGR02390 152 K KI KF EK --------- P -- TY F YE -------------- EGKEGDVK L T P SEIRERLEK IP D ED AE LL GI NP KVAR P EWMV 206
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 252 LT R L L VPP LCI RPS VV sd L KS G T - N EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I MED W DF LQ LQC A L Y INS EL S GIP - 329
Cdd:TIGR02390 207 LT V L P VPP VTV RPS IT -- L ET G E r S EDDLT H KL VD II RI N QRL K ENIEA GA PQLI I EDL W EL LQ YHV A T Y FDN EL P GIP p 284
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 330 LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT F PE K V NKA NI NF LR KL V Q 409
Cdd:TIGR02390 285 ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PE R V TPW NI DE LR EY V L 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 410 NGP EVH PGAN FIQQ rh TQMK R F - LKYG N R E KM A QE L KY G DI VERHLIDGD V VLFNRQPSLH KL S I M A H LAR V K P HR TFR F 488
Cdd:TIGR02390 365 NGP DSW PGAN YVIR -- PDGR R I k IRDE N K E EL A ER L EP G WV VERHLIDGD I VLFNRQPSLH RM S M M G H KVK V L P GK TFR L 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 489 N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLV TPR N G E P L I AA I Q D FLT GAYLLT L K D T F F DRAKACQ I I 568
Cdd:TIGR02390 443 N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RE LM LVEEHIL TPR Y G G P I I GG I H D YIS GAYLLT H K S T L F TKEEVQT I L 522
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 569 ASI lvgkde KIKVRL P P P T I L KP VTL WTGKQIFS VI L r P S D D N PVRANLRTK G KQY C G K G E dl C AN D S YV T I Q N SE L MS G 648
Cdd:TIGR02390 523 GVA ------ GYFGDP P E P A I E KP KEY WTGKQIFS AF L - P E D L N FEGRAKICS G SDA C K K E E -- C PH D A YV V I K N GK L LK G 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 649 SM DK GTL G S g S K NN I FYILL R DW G QNE A ADAMSRLA RL APVYLSN RGF SI GI G D VTPGQGLLKAKY EL LNAGY K KC D EY I 728
Cdd:TIGR02390 594 VI DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT RL FIRFITL RGF TT GI D D IDIPKEAKEEIE EL IEKAE K RV D NL I 672
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 729 E ALNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE LD KS N SPLT MA LC G SK GS FI NI S QM I A C VGQQ AIS G S R 808
Cdd:TIGR02390 673 E RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG EVAEKY LD PE N HAVI MA RT G AR GS LL NI T QM A A M VGQQ SVR G G R 752
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 809 VPD G FE NR S LPHF E K HSKLPA A K GFV AN SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GYMQRRL VKS L E DL CSQ YD L 888
Cdd:TIGR02390 753 IRR G YR NR T LPHF K K GDIGAK A R GFV RS SF KK GL D PTE Y FFH AAG GREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE YD G 832
890 900 910
....*....|....*....|....*....|....*...
gi 39725938 889 TVR SST G DI IQF I YG G DG L DP AAME - GK de P LEF K RVL 925
Cdd:TIGR02390 833 TVR DTR G NL IQF K YG E DG V DP MKSD h GK -- P VDV K KIF 868
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
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: 565.31
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DK D D D ADY AR L 1100
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK N ISTPIITA K L EN D R D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1101 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysictsklrvkpgdvavhgeavvcvtpren 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 39725938 1181 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek YKLLVEG DN LRAVM A T H GV K GTRTTSN NTY EVEK T LGI 1260
Cdd:cd02736 123 SKS NL Y FL LQ S LK RK LP D VVV S GIPEV K RAVI NK D KKK GK -- YKLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1261 EAAR T TIINEIQYTM VN HGMSID R RH V MLL S DLMT Y KGEVLGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1340
Cdd:cd02736 201 EAAR S TIINEIQYTM KS HGMSID P RH I MLL A DLMT F KGEVLGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 39725938 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;
248-550
8.40e-150
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 455.44
E-value: 8.40e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 248 SDL ILT R L L VPP L C I RPSV VS D L k SGTN EDDLT MK L TE II FL N DVI K KHRIS GA KTQM I MEDWDF LQ LQCALY I NS E l SG 327
Cdd:smart00663 1 EWM ILT V L P VPP P C L RPSV QL D G - GRFA EDDLT HL L RD II KR N NRL K RLLEL GA PSII I RNEKRL LQ EAVDTL I DN E - GL 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 328 IPL N MAPKKWTRGFV QRLKGK Q GRFR G NL S GKRVDFS G R T VI S PDPNL RID EV A VP VHV A KI LTFPE K V NKA NI NF LRKL 407
Cdd:smart00663 79 PRA N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLN EV G VP KEI A LE LTFPE I V TPL NI DK LRKL 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 408 V Q NGP evh P GA NF I QQ rht QM K RF LK YGNRE K M A QE LK Y GDIVERH L IDGDVVLFNRQP S LH KL SI M AH LA RV KPHR T F R 487
Cdd:smart00663 159 V R NGP --- N GA KY I IR --- GK K TN LK LAKKS K I A NH LK I GDIVERH V IDGDVVLFNRQP T LH RM SI Q AH RV RV LEGK T I R 232
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 39725938 488 F N EC VC T PYNADFDGDEMNLH L PQ TE EA K AEA LV LM GTKA N LVT P R NG E P L I AA IQD F L T G A Y 550
Cdd:smart00663 233 L N PL VC S PYNADFDGDEMNLH V PQ SL EA R AEA RE LM LVPN N ILS P K NG K P I I GP IQD M L L G L Y 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
12-356
4.12e-132
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: 409.76
E-value: 4.12e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 12 A KKI SH I C FG MK SPEE M R QQAHIQ V VSKNL Y S q DNQHA P LLY G V LD H RMGT SE KD RP CETCGK NLA DC L GH Y G Y I D L EL P 91
Cdd:pfam04997 1 L KKI KE I Q FG IA SPEE I R KWSVGE V TKPET Y N - YGSLK P EEG G L LD E RMGT ID KD YE CETCGK KKK DC P GH F G H I E L AK P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 92 C FH V G Y F RAVIG IL QMI CK T C CHIM L SQEEK K Q F LDYL KR P GL TY L QKR gl K K K I SDK C R KK NI C H HCG AF NG TVKK cgl 171
Cdd:pfam04997 80 V FH I G F F KKTLK IL ECV CK Y C SKLL L DPGKP K L F NKDK KR L GL EN L KMG -- A K A I LEL C K KK DL C E HCG GK NG VCGS --- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 172 lkiihekyktnkkv VD P IVSNFLQSFET AI EHN KE V E pllgr AQ E N LNP LV VL NL FKRI PA EDV PL L LM NP EAGK P SDL I 251
Cdd:pfam04997 155 -------------- QQ P VSRKEGLKLKA AI KKS KE E E ----- EK E I LNP EK VL KI FKRI SD EDV EI L GF NP SGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 252 LT R L L VPP L CIRPSV VS D LK s GTN EDDLT M KL TE II FL N DVI KK HRIS GA KTQM I M E D W DF LQ LQC A LYINS E LS G I P L - 330
Cdd:pfam04997 216 LT V L P VPP P CIRPSV QL D GG - RRA EDDLT H KL RD II KR N NRL KK LLEL GA PSHI I R E E W RL LQ EHV A TLFDN E IP G L P P a 294
330 340
....*....|....*....|....*.
gi 39725938 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
2.78e-117
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: 377.46
E-value: 2.78e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 841 GLTP T EFFFHTM A GREGL V DTAVKTAE T GY M QRRLVK S LEDL CSQ YD L TVR S S T G D I I QF I YG G DGLDP AAM E GKD e PLE 920
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G E I V QF L YG E DGLDP LKI E KQG - RFT 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 921 FKRVLDNIKAV F PCP - SEPA L SKN E LI L TTESIMKKSEFLCCQ D SFLQ E IKKFIKGVS E KI ------- K KT R DKYGI N DN 992
Cdd:pfam04998 80 IEFSDLKLEDK F KND l LDDL L LLS E FS L SYKKEILVRDSKLGR D RLSK E AQERATLLF E LL lksgles K RV R SELTC N SK 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 993 gtteprvlyqldritpt QVEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL K TFHFAGVAS M N I TLGVPR I KE 1072
Cdd:pfam04998 160 ----------------- AFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL N TFHFAGVAS K N V TLGVPR L KE 222
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1073 IIN A SK A I ST P II T AQ L -- DKDDDADY A RL V K G R IEK TL LG EIS E YI E ------------------------------ EV 1120
Cdd:pfam04998 223 IIN V SK N I KS P SL T VY L fd EVGRELEK A KK V Y G A IEK VT LG SVV E SG E ilydpdpfntpiisdvkgvvkffdiidevt NE 302
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1121 FLP D DCFI L VK L SLERIRL L RLEVNAETVRYS I c TSKL R V K pg DVAVHGE A VVCV T PRENSK S SMYY ------- VLQF L K 1193
Cdd:pfam04998 303 EEI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I - PRSI R N K -- VDEGRDI A IGEI T AFIIKI S KKIR qdtgglr RVDE L F 379
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1194 ED ------------ L PKVVVQ GIP EVS R AVIHI D E q S GK EK -- YK L LV EG D NL RA V MATH G - V KGT R TT SN NTY E VEKT L 1258
Cdd:pfam04998 380 ME edpklailvasl 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 L 458
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 39725938 1259 GIEAAR TTII NEI QYTMVNH G MS I DR RH VM L LS D L MT Y KG EVLG I T R F G LA K MKE S V L 1316
Cdd:pfam04998 459 GIEAAR NALL NEI RNVYRFQ G IY I ND RH LE L IA D Q MT R KG YIMA I G R H G IN K AEL S A L 516
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1006-1363
1.03e-96
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 316.02
E-value: 1.03e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1006 I T PTQ VE KFL E TCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II 1085
Cdd:PRK04309 35 L T EEE VE 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 39725938 1086 T AQ L DKD -- D D ADY A RL V KGR IE K T L L GEISEY I E ev FLPDDCF I LVK L SL E RI -- R L L RLEVNA E TVR ysictskl RV K 1161
Cdd:PRK04309 115 T IY L KDE ya Y D REK A EE V ARK IE A T T L ENLAKD I S -- VDLANMT I IIE L DE E ML ed R G L TVDDVK E AIE -------- KK K 184
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1162 P G D V AVH G EAVV c VT P R E N S kssm Y YV L QF L K E DLPKVVVQ GI PEVS R AV I HIDE qsgk EK Y KLLV EG D NL RA V MATH GV 1241
Cdd:PRK04309 185 G G E V EIE G NTLI - IS P K E P S ---- Y RE L RK L A E KIRNIKIK GI KGIK R VI I RKEG ---- DE Y VIYT EG S NL KE V LKVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1242 KG TRTT S NN TY E V E KT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS D L MT YK GEV LG I T R F G LAKM K E SVL ML A S F 1321
Cdd:PRK04309 256 DA TRTT T NN IH E I E EV LGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML VA D M MT WD GEV RQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 39725938 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
1.49e-85
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 283.87
E-value: 1.49e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1010 QVEKFLETCRDK Y M R AQME PG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L 1089
Cdd:TIGR02389 24 ELDEIIKRVEEE Y L R SLID PG E AVG IVA AQSIGEPGTQMT MR TFH Y AGVA EL N V TLG L PR LI EI VD A R K TP STP SM T IY L 103
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1090 DKDD -- D ADY A RL V KGR IE K T L L GEISEY I E evflpddcfil VK L SLERI rll RL E VNA E TVRYSIC T SKL ------ RV K 1161
Cdd:TIGR02389 104 EDEY ek D REK A EE V AKK IE A T K L EDVAKD I S ----------- ID L ADMTV --- II E LDE E QLKERGI T VDD vekaik KA K 169
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1162 P G D V AV -- HGEAVVCVT P REN S kssm YYV L QF LKE DLPKVVVQ GI PEVS R A VI hide QSGKEK Y KLLV EG D NL RA V MATH 1239
Cdd:TIGR02389 170 L G K V IE id MDNNTITIK P GNP S ---- LKE L RK LKE KIKNLHIK GI KGIK R V VI ---- RKEGDE Y VIYT EG S NL KE V LKLE 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1240 GV KG TRTT S N NTY E VEKT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS DLMT YK GEV LG I T R F G LAKM K E SVL ML A 1319
Cdd:TIGR02389 242 GV DK TRTT T N DIH E IAEV LGIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML VA DLMT WD GEV RQ I G R H G ISGE K A SVL AR A 321
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 39725938 1320 S FE K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L LHK 1365
Cdd:TIGR02389 322 A FE V T VK HL L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L VMD 367
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
345-1120
5.43e-53
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: 203.85
E-value: 5.43e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - RKL VQN G pevhp G A NF I QQ 423
Cdd:COG0086 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A LE L FK P --------- F I y RKL EER G ----- L A TT I KS 386
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 rhtq M K RFL kygnr E KMAQ E LK yg DI V E R h L I DGDV VL F NR Q P S LH K L S I M A HLARVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:COG0086 387 ---- A K KMV ----- E REEP E VW -- DI L E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 504 E M NL H L P QTE EA KA EA LV LM GTKA N LVT P R NG E P L I AAI QD FLT G A Y L LT LKD -------- T F F D RAKACQIIASIL V GK 575
Cdd:COG0086 455 Q M AV H V P LSL EA QL EA RL LM LSTN N ILS P A NG K P I I VPS QD MVL G L Y Y LT RER egakgegm I F A D PEEVLRAYENGA V DL 534
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 576 DEK IKVR LPPPTILKPVTLW T -- G KQIFSV IL r P SD dnpvranlrtkgkqycgkgedlcandsy V TIQ N SE lmsgs MD K G 653
Cdd:COG0086 535 HAR IKVR ITEDGEQVGKIVE T tv G RYLVNE IL - P QE ---------------------------- V PFY N QV ----- IN K K 580
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 654 TLG sgskn N I FYILL R DW G QN E AADAMS RL AR L APV Y LSNR G F SIG IG D - V T P gqgll K A K Y E LLNAGY K KCD E YIEALN 732
Cdd:COG0086 581 HIE ----- V I IRQMY R RC G LK E TVIFLD RL KK L GFK Y ATRA G I SIG LD D m V V P ----- K E K Q E IFEEAN K EVK E IEKQYA 650
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 733 T G KL qqqpgc T AE E TLEAL I L kelsv IRDH A G ---- S ACLRELDKS N SPLT MA LC G SK GS FINIS Q MIACV G QQ A isgsr 808
Cdd:COG0086 651 E G LI ------ T EP E RYNKV I D ----- GWTK A S lete S FLMAAFSSQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A ----- 714
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 809 V P D G -- F E NR slphfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV KSLE D L csqy 886
Cdd:COG0086 715 K P S G ni I E TP ----------------- IGSN F RE GL GVL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV DVAQ D V ---- 773
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 887 dltvrsstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E f K R V L DNIK A --- V F P CPS E PALSKNE LI LT tesimkksef 958
Cdd:COG0086 774 ---------- I VTEEDC G td R G IT v T A IK EG GE vi EPL K - E R I L GRVA A edv V D P GTG E VLVPAGT LI DE ---------- 832
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 959 lccqdsflq E IKKF I KGVSEKIK K T R dkygindngtteprvlyqldri TPTQV E KFLET C RDK Y M R -- A QMEP --- G S AV 1033
Cdd:COG0086 833 --------- E VAEI I EEAGIDSV K V R ---------------------- SVLTC E TRGGV C AKC Y G R dl A RGHL vni G E AV 881
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1034 G ALC AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS KA ISTPIITAQLDKDDDADYARL V KGRI E KTLLGEI 1113
Cdd:COG0086 882 G VIA AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA KA GGIVRLNNLKVVVNEEGKGVV V SRNS E LVIVDDG 954
....*..
gi 39725938 1114 SEYI EE V 1120
Cdd:COG0086 955 GRRE EE Y 961
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
841-1058
1.63e-08
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 59.57
E-value: 1.63e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 841 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 AAMEG 914
Cdd:CHL00117 172 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 RNGMM 235
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 915 KDEP L EFK --- RVL - D N I K avfpcpsepal SKNEL I L T TE simkkseflcc QD SFLQEIKK FI K gvsekikktrdkygin 990
Cdd:CHL00117 236 IERI L IQT lig RVL a D D I Y ----------- IGSRC I A T RN ----------- QD IGIGLANR FI T ---------------- 277
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 991 dngtteprvl YQLDR I --- T P T qvekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL K TF 1053
Cdd:CHL00117 278 ---------- FRAQP I sir S P L ------- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL R TF 338
....*
gi 39725938 1054 H FA GV 1058
Cdd:CHL00117 339 H TG GV 343
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: 1668.46
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 24 SPE EMRQQAHIQ V VSK NLY SQDNQH a PL L YGVLD H R M GTS E KD RP CETCG K NLADC L GH Y GYI D LELP C FH V GYF R A V I G 103
Cdd:cd02583 2 SPE DIIRLSEVE V TNR NLY DIETRK - PL P YGVLD P R L GTS D KD GI CETCG L NLADC V GH F GYI K LELP V FH I GYF K A I I N 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 104 ILQ M ICKTC CHIM L SQ EEK KQ FL DY L K RP G L TY LQK RG LKKKI SD KC R K KNI C H HCG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C P HCG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 184 kvvdpivsnflqsfetaiehnkevep LL GR AQE N LNPL V VLNLFK R IP A EDV P LLLMNP E AG K P SD LILTR LL VPPLCIR 263
Cdd:cd02583 138 -------------------------- LL KK AQE D LNPL K VLNLFK N IP P EDV E LLLMNP L AG R P EN LILTR IP VPPLCIR 191
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 264 PSVV S D L KSGTNEDDLT M KL T EIIFLNDVIKKH RIS GAKTQ M IMEDWDFLQLQCALYINSEL S G I PL N M A PKK WT RGF V Q 343
Cdd:cd02583 192 PSVV M D E KSGTNEDDLT V KL S EIIFLNDVIKKH LEK GAKTQ K IMEDWDFLQLQCALYINSEL P G L PL S M Q PKK PI RGF C Q 271
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV Q NGP E VHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGP D VHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 R HTQM K R FLKYGNR E K M A Q ELK Y GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L A R V K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R A K V M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 504 EMNLH L PQTEEA K AEAL V LMG T K A NLVTPRNGEPLIAA I QDFLT GA YLLT L KD T FFDRA KA CQ IIASI L vgk D EK IK VR L 583
Cdd:cd02583 432 EMNLH V PQTEEA R AEAL E LMG V K N NLVTPRNGEPLIAA T QDFLT AS YLLT S KD V FFDRA QF CQ LCSYM L --- D GE IK ID L 508
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C A ND S YV T I Q NSEL MS G SM DK G TLGSGSKN NI 663
Cdd:cd02583 509 PPP A ILKPV E LWTGKQIFS LL LRP NKKS PV LV NL EA K E K S Y TK K SP D M C P ND G YV V I R NSEL LC G RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 664 FY I LLRD W G QNE AA D AM S RLA R L APVY LSNRGFSIGI G DVTP GQG LLK A K Y EL LNA GY K KCDEYI EALNT GKL QQ QPGCT 743
Cdd:cd02583 589 FY V LLRD Y G PEA AA A AM N RLA K L SSRW LSNRGFSIGI D DVTP SKE LLK K K E EL VDN GY A KCDEYI KQYKK GKL EL QPGCT 668
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 744 AE E TLEA L I LK ELS V IR DH AG S ACL R EL D KSNSPL T MALCGSKGS F INISQMIACVGQQ A ISG S R V P D GFE N R S LPHF EK 823
Cdd:cd02583 669 AE Q TLEA K I SG ELS K IR ED AG K ACL K EL H KSNSPL I MALCGSKGS N INISQMIACVGQQ I ISG K R I P N GFE D R T LPHF PR 748
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 39725938 824 H SK L PAAKGFVANSFYSGLTPTEFFFHTM A GREGLVDTAVKTAETGYMQRRL V K S LEDL CS QYD L TVR 891
Cdd:cd02583 749 N SK T PAAKGFVANSFYSGLTPTEFFFHTM S GREGLVDTAVKTAETGYMQRRL M K A LEDL SV QYD G TVR 816
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
12-910
0e+00
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain]
Cd Length: 861
Bit Score: 969.79
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 12 A K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D N qh A P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P 91
Cdd:cd02582 1 P K R I KG I K FG LL SPEE I R KMSVVEIITPDT Y DE D G -- Y P IEG G LM D P R L G VI E PGLR C K TCG NTAGE C P GH F G H I E L AR P 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 92 CF HVG YFRAVIGI L QMI C KT C CH I M L SQ EE KKQF L DYLK R - PGLTYLQKRGLKK K ISD K CR K KNI C H HCGA fngtvkkc G 170
Cdd:cd02582 79 VI HVG FAKHIYDL L RAT C RS C GR I L L PE EE IEKY L ERIR R l KEKWPELVKRVIE K VKK K AK K RKV C P HCGA -------- P 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 171 LL KI IH EK yktnkkvvdpi VSN F LQSF E ta IEHN K evepllgraqen L N P LVVLNLFKR IP A ED VP LL LMN P EAGK P SDL 250
Cdd:cd02582 151 QY KI KL EK ----------- PTT F YEEK E -- EGEV K ------------ L T P SEIRERLEK IP D ED LE LL GID P KTAR P EWM 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 251 I LT R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I MED WD F LQ LQCAL Y INS E LS GIP 329
Cdd:cd02582 206 V LT V L P VPP VTV RPS IT -- L ET G e RS EDDLT H KL VD II RI N QRL K ENIEA GA PQLI I EDL WD L LQ YHVTT Y FDN E IP GIP 283
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 330 ln M A PKKWT R --- GFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT F PE K V NKA NI NFL RK 406
Cdd:cd02582 284 -- P A RHRSG R plk TLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EDI AK E LT V PE R V TEW NI EKM RK 361
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 407 LV Q NGP EVH PGAN FIQQRHTQMK R f L K Y G NRE KM A QE L KY G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA RV K P HR TF 486
Cdd:cd02582 362 LV L NGP DKW PGAN YVIRPDGRRI R - L R Y V NRE EL A ER L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RV RV L P GK TF 440
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 487 R F N EC VC T PYNADFDGDEMNLH L PQ T EEA K AEA LV LM GTKANLVT PR N G E P L I AA IQD FLT GAYLLT L K D T F F DRAK A C Q 566
Cdd:cd02582 441 R L N LA VC P PYNADFDGDEMNLH V PQ S EEA R AEA RE LM LVQEHILS PR Y G G P I I GG IQD YIS GAYLLT R K T T L F TKEE A L Q 520
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 567 IIASI lvgkde KIKVR LP P P T IL K P VT LWTGKQ I FS VI L r P S D D N PVR anl RT K GKQY C GKGE D - L C A ND S YV T I Q N SE L 645
Cdd:cd02582 521 LLSAA ------ GYDGL LP E P A IL E P KP LWTGKQ L FS LF L - P K D L N FEG --- KA K VCSG C SECK D e D C P ND G YV V I K N GK L 590
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 646 MS G SM DK GTL G SGSKNNIFYILLRDW G QNE A ADAMSRLA RLA PVYLSN RGF S IGI G D VTPGQGLL K AKY E LLNAGY KK CD 725
Cdd:cd02582 591 LE G VI DK KAI G AEQPGSLLHRIAKEY G NEV A RRFLDSVT RLA IRFIEL RGF T IGI D D EDIPEEAR K EIE E IIKEAE KK VY 670
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 726 E Y IE ALNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE LD KS N SPLT MA LC G SK GS FI N IS QM I AC V GQQ AIS 805
Cdd:cd02582 671 E L IE QYKN G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG KVASKY LD PF N NAVI MA RT G AR GS ML N LT QM A AC L GQQ SVR 750
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 806 G S R VPD G FE NR S LPHF EKHSKL P A A K GFV AN SF YS GL T PTEFFFH T M A GREGLVDTAV K T AET GYMQRRL VKS L E DL CSQ 885
Cdd:cd02582 751 G E R INR G YR NR T LPHF KPGDLG P E A R GFV RS SF RD GL S PTEFFFH A M G GREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE 830
890 900
....*....|....*....|....*
gi 39725938 886 YD L TVR S S T G D IIQF I YG G DG L DPA 910
Cdd:cd02582 831 YD G TVR D S R G N IIQF K YG E DG V DPA 855
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
7-930
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 955.84
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 7 RETDVA K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D N qh A P LLY G VL D H R M G TSEKDRP C E TCG KNLAD C L GH Y G Y I 86
Cdd:PRK08566 1 SMMMIP K R I GS I K FG LL SPEE I R KMSVTKIITADT Y DD D G -- Y P IDG G LM D P R L G VIDPGLR C K TCG GRAGE C P GH F G H I 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 87 D L EL P CF HVG YFRAVIGI L QMI C KT C CHIM L SQ EE KKQF L DY L K R PGLTYLQKRG L K K KISDKCR K KNI C H HCG A fngtv 166
Cdd:PRK08566 79 E L AR P VI HVG FAKLIYKL L RAT C RE C GRLK L TE EE IEEY L EK L E R LKEWGSLADD L I K EVKKEAA K RMV C P HCG E ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 167 K K cgl L KI IH EK yktnkkvvd P I vsnflqsfe T AI E HN KE VE pllgraq EN L N P LVVLNLFKR IP A ED VP LL LM NPE AGK 246
Cdd:PRK08566 154 K Q --- Y KI KF EK --------- P T --------- T FY E ER KE GL ------- VK L T P SDIRERLEK IP D ED LE LL GI NPE VAR 205
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 247 P SDLI LT R L L VPP LCI RPS VV sd L KS G - TN EDDLT M KL TE II FL N DVI K KHRIS GA K t Q M I M ED - W DF LQ LQCAL Y INS E 324
Cdd:PRK08566 206 P EWMV LT V L P VPP VTV RPS IT -- L ET G q RS EDDLT H KL VD II RI N QRL K ENIEA GA P - Q L I I ED l W EL LQ YHVTT Y FDN E 282
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 325 LS GIP lnma P ----- KKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPNL R I D EV A VP VHV AK I LT F PE K V NKA 399
Cdd:PRK08566 283 IP GIP ---- P arhrs GRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPNL S I N EV G VP EAI AK E LT V PE R V TEW 358
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 400 NI NF LR KL V Q NGPE V HPGAN FI qq RHTQMK R F - L KYG N R E KM A QE L KY G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA 478
Cdd:PRK08566 359 NI EE LR EY V L NGPE K HPGAN YV -- IRPDGR R I k L TDK N K E EL A EK L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RV 436
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 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 39725938 559 F DRAK A CQIIASILVGKDE kikvr L P P P T I LKPVTL WTGKQIFS VI L r P S D D N PVR anl RT K GKQY C GKGED - L C AN D S Y 637
Cdd:PRK08566 517 F TKEE A LDLLRAAGIDELP ----- E P E P A I ENGKPY WTGKQIFS LF L - P K D L N LEF --- KA K ICSG C DECKK e D C EH D A Y 587
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 638 V T I Q N SE L MS G SM DK GTL G SG s KNN I FYILLRDW G QNE A ADAMSRLA RLA PVYLSN RGF SI GI G D VT - P GQGLLKAK y E L 716
Cdd:PRK08566 588 V V I K N GK L LE G VI DK KAI G AE - QGS I LDRIVKEY G PER A RRFLDSVT RLA IRFIML RGF TT GI D D ED i P EEAKEEID - E I 665
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 717 LNAGY K KCD E Y IEA LNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE L DKS N SPLT MA LC G SK GS FI N IS QM I 796
Cdd:PRK08566 666 IEEAE K RVE E L IEA YEN G E L EPL PG R T L EETLE MK I MQV L GKA RD E AG EIAEKY L GLD N PAVI MA RT G AR GS ML N LT QM A 745
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 797 ACVGQQ AIS G S R VPD G FEN R S LPHF EKHSKLPA A K GFV AN S FY SGLTPTEFFFH T M A GREGLVDTAV K T AET GYMQRRL V 876
Cdd:PRK08566 746 ACVGQQ SVR G E R IRR G YRD R T LPHF KPGDLGAE A R GFV RS S YK SGLTPTEFFFH A M G GREGLVDTAV R T SQS GYMQRRL I 825
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....
gi 39725938 877 KS L E DL CSQ YD L TVR SST G D I I QF I YG G DG L DP AAMEG k DE P LEFK R VLDNIKA 930
Cdd:PRK08566 826 NA L Q DL KVE YD G TVR DTR G N I V QF K YG E DG V DP MKSDH - GK P VDVD R IIERVLG 878
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-925
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 884.44
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 13 KKI SH I C FG MK SPEE M R QQAHIQ VV SKNL Y SQ D N qh A P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P C 92
Cdd:TIGR02390 2 KKI GS I K FG LL SPEE I 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 H I E L AR P V 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 93 F HVG YFRAVIG IL QMI C KT C CH I M L SQ EE KK Q F L D - YL K RPGLTYLQKRG L KK KI SDKCR K KNI C H HCG A fngtvkkc GL 171
Cdd:TIGR02390 80 V HVG FAKEIYK IL RAT C RK C GR I T L TE EE IE Q Y L E k IN K LKEEGGDLAST L IE KI VKEAA K RMK C P HCG E -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 172 L KI IH EK yktnkkvvd P iv SN F LQ sfetaiehnkevep LLGRAQEN L N P LVVLNLFKR IP A ED VP LL LM NP EAGK P SDLI 251
Cdd:TIGR02390 152 K KI KF EK --------- P -- TY F YE -------------- EGKEGDVK L T P SEIRERLEK IP D ED AE LL GI NP KVAR P EWMV 206
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 252 LT R L L VPP LCI RPS VV sd L KS G T - N EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I MED W DF LQ LQC A L Y INS EL S GIP - 329
Cdd:TIGR02390 207 LT V L P VPP VTV RPS IT -- L ET G E r S EDDLT H KL VD II RI N QRL K ENIEA GA PQLI I EDL W EL LQ YHV A T Y FDN EL P GIP p 284
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 330 LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT F PE K V NKA NI NF LR KL V Q 409
Cdd:TIGR02390 285 ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PE R V TPW NI DE LR EY V L 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 410 NGP EVH PGAN FIQQ rh TQMK R F - LKYG N R E KM A QE L KY G DI VERHLIDGD V VLFNRQPSLH KL S I M A H LAR V K P HR TFR F 488
Cdd:TIGR02390 365 NGP DSW PGAN YVIR -- PDGR R I k IRDE N K E EL A ER L EP G WV VERHLIDGD I VLFNRQPSLH RM S M M G H KVK V L P GK TFR L 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 489 N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLV TPR N G E P L I AA I Q D FLT GAYLLT L K D T F F DRAKACQ I I 568
Cdd:TIGR02390 443 N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RE LM LVEEHIL TPR Y G G P I I GG I H D YIS GAYLLT H K S T L F TKEEVQT I L 522
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 569 ASI lvgkde KIKVRL P P P T I L KP VTL WTGKQIFS VI L r P S D D N PVRANLRTK G KQY C G K G E dl C AN D S YV T I Q N SE L MS G 648
Cdd:TIGR02390 523 GVA ------ GYFGDP P E P A I E KP KEY WTGKQIFS AF L - P E D L N FEGRAKICS G SDA C K K E E -- C PH D A YV V I K N GK L LK G 593
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 649 SM DK GTL G S g S K NN I FYILL R DW G QNE A ADAMSRLA RL APVYLSN RGF SI GI G D VTPGQGLLKAKY EL LNAGY K KC D EY I 728
Cdd:TIGR02390 594 VI DK KAI G A - E K GK I LHRIV R EY G PEA A RRFLDSVT RL FIRFITL RGF TT GI D D IDIPKEAKEEIE EL IEKAE K RV D NL I 672
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 729 E ALNT G K L QQQ PG C T A EETLE AL I LKE L SVI RD H AG SACLRE LD KS N SPLT MA LC G SK GS FI NI S QM I A C VGQQ AIS G S R 808
Cdd:TIGR02390 673 E RYRN G E L EPL PG R T V EETLE MK I MEV L GKA RD E AG EVAEKY LD PE N HAVI MA RT G AR GS LL NI T QM A A M VGQQ SVR G G R 752
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 809 VPD G FE NR S LPHF E K HSKLPA A K GFV AN SF YS GL T PTE F FFH TMA GREGLVDTAV K T AET GYMQRRL VKS L E DL CSQ YD L 888
Cdd:TIGR02390 753 IRR G YR NR T LPHF K K GDIGAK A R GFV RS SF KK GL D PTE Y FFH AAG GREGLVDTAV R T SQS GYMQRRL INA L Q DL YVE YD G 832
890 900 910
....*....|....*....|....*....|....*...
gi 39725938 889 TVR SST G DI IQF I YG G DG L DP AAME - GK de P LEF K RVL 925
Cdd:TIGR02390 833 TVR DTR G NL IQF K YG E DG V DP MKSD h GK -- P VDV K KIF 868
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
13-1363
0e+00
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 880.51
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 13 K K I SH I C FG MK SP EEM R QQAHIQVVSKNL Y SQ D NQ ha P LLY G V LD H R M GT S E KDRP C E TCG KNL A D C L GH Y G Y I D L EL P C 92
Cdd:PRK14977 7 K A I DG I I FG LI SP ADA R KIGFAEITAPEA Y DE D GL -- P VQG G L LD G R L GT I E PGQK C L TCG NLA A N C P GH F G H I E L AE P V 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 93 F H VGYFRAVIGI L QMI C KT C CHIM L S QE EKKQ F l DYLKRPGLTYL --- Q KR --- GLKKKIS D KC ---- R K KNI C H HCGA F 162
Cdd:PRK14977 85 I H IAFIDNIKDL L NST C HK C AKLK L P QE DLNV F - KLIEEAHAAAR dip E KR idd EIIEEVR D QV kvya K K AKE C P HCGA P 163
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 163 NGTV kkcgllk IIH E KYKTNK K V vdpivsnflqsfetaiehnk E V E P llgraq EN L N P LVVLNL F KR I PAE D VP L LLMN P 242
Cdd:PRK14977 164 QHEL ------- EFE E PTIFIE K T -------------------- E I E E ------ HR L L P IEIRDI F EK I IDD D LE L IGFD P 210
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 243 EAGK P SDLI L TRL LVPPL CI RPS VV sd L KS G T - N EDDLT MK L TE II FL N DVI K KHRIS GA KTQMIMEDW D F LQ LQCALYI 321
Cdd:PRK14977 211 KKAR P EWAV L QAF LVPPL TA RPS II -- L ET G E r S EDDLT HI L VD II KA N QKL K ESKDA GA PPLIVEDEV D H LQ YHTSTFF 288
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 322 NSELS GIP LNM -- APKKWTRGFV QRLKGK Q GRFRGNL S GKRVDFS G RTVISPDP NLR IDEV A VP VHV A KI LT F PE K VN KA 399
Cdd:PRK14977 289 DNATA GIP QAH hk GSGRPLKSLF QRLKGK E GRFRGNL I GKRVDFS A RTVISPDP MID IDEV G VP EAI A MK LT I PE I VN EN 368
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 400 NI NFLRK LV Q NGP EVH PGAN F I QQ ------ R HTQMKRFL K YGN RE k M A QE L KY GDIVERHL I DGD V V L FNRQPSLHKLSI 473
Cdd:PRK14977 369 NI EKMKE LV I NGP DEF PGAN A I RK gdgtki R LDFLEDKG K DAL RE - A A EQ L EI GDIVERHL A DGD I V I FNRQPSLHKLSI 447
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 474 M AH LAR V K P HR TFR FNEC VC T PYNADFDGDEMNLH L PQ T E E A K AEA LV LMG T K A NL VT PR N G E P L I A A I QDF L T G AYL L T 553
Cdd:PRK14977 448 L AH RVK V L P GA TFR LHPA VC P PYNADFDGDEMNLH V PQ I E D A R AEA IE LMG V K D NL IS PR T G G P I I G A L QDF I T A AYL I T 527
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 554 LK D TF FD RAK A CQ I IA si L V G kdek I KVR LP P P T I - L K PVTL WTGKQ I FS VI L r P S D D N PVRANLRTK GK Q yc G KGE D - L 631
Cdd:PRK14977 528 KD D AL FD KNE A SN I AM -- L A G ---- I TDP LP E P A I k T K DGPA WTGKQ L FS LF L - P K D F N FEGIAKWSA GK A -- G EAK D p S 598
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 632 C AN D S YV T I QNS EL M SG SM D KGTL G SGSKN -- NIFYILLR D W G QNE A ADAMSRLARL A PVYLSNR GFS I G I GD VTPGQ gl 709
Cdd:PRK14977 599 C LG D G YV L I KEG EL I SG VI D DNII G ALVEE pe SLIDRIAK D Y G EAV A IEFLNKILII A KKEILHY GFS N G P GD LIIPD -- 676
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 710 l K AK Y E LLNAGYKKC DE YIEALNT ----------- GK LQQQP G CTA EE T LEA L I LK EL SVI RD H AGS ACLREL D KS N SPL 778
Cdd:PRK14977 677 - E AK Q E IEDDIQGMK DE VSDLIDQ rkitrkitiyk GK EELLR G MKE EE A LEA D I VN EL DKA RD K AGS SANDCI D AD N AGK 755
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 779 T MA LC G SK GS FI N IS Q MIACV GQQ AI -------- S G S R VPD G FEN R S L P HF EKHSKL P A A K GFV A N SFYS GL TPT EFFFH 850
Cdd:PRK14977 756 I MA KT G AR GS MA N LA Q IAGAL GQQ KR ktrigfvl T G G R LHE G YKD R A L S HF QEGDDN P D A H GFV K N NYRE GL NAA EFFFH 835
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 851 T M A GREGL V D T A VK T AET GY M QRRL VKS LED LCSQ YD L TVR SST G D IIQF IY G G DG L DP AAME g KD E PLEFK R VLDNI K A 930
Cdd:PRK14977 836 A M G GREGL I D K A RR T EDS GY F QRRL ANA LED IRLE YD E TVR DPH G H IIQF KF G E DG I DP QKLD - HG E AFNLE R IIEKQ K I 914
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 931 V fpc PSEPAL SK N E L iltt E SIM K KSE flccqdsf LQEIKKFI K GVSEK I KKTRD K ygindngtteprvlyqldrit PTQ 1010
Cdd:PRK14977 915 E --- DRGKGA SK D E I ---- E ELA K EYT -------- KTFNANLP K LLADA I HGAEL K --------------------- EDE 958
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1011 V E KFLETCRDKYMR 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 SKAI STP IITAQ LD 1090
Cdd:PRK14977 959 L E AICAEGKEGFEK 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 1038
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1091 KDDDA D YARLVK gr I EKT L LG - EISEY I EEVFLPDDCF I LVKLSLE R IR --- LLRL E VN AE TVR ysi CTS K lr V K PGDVA 1166
Cdd:PRK14977 1039 DECKE D IEKAIE -- I ARN L KE l KVRAL I ADSAIDNANE I KLIKPDK R AL eng CIPM E RF AE IEA --- ALA K -- G K KFEME 1111
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1167 VHGEAVVCVTPRENSKSSMYYV L QFLKEDLPKVV V Q G I P EVS RA VIHID E QS G KEKYKLLVE G D NL R AV MATHGVKGTR T 1246
Cdd:PRK14977 1112 LEDDLIILDLVEAADRDKPLAT L IAIRNKILDKP V K G V P DIE RA WVELV E KD G RDEWIIQTS G S NL A AV LEMKCIDIAN T 1191
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1247 TS N NTY E VEK TLGIEAAR TT I I NE IQYTMVNH G MSI D R R HV ML LS D L M TYK G EVLG I ------ T R F G L A KM K E S V L ML A S 1320
Cdd:PRK14977 1192 IT N DCF E IAG TLGIEAAR NA I F NE LASILEDQ G LEV D N R YI ML VA D I M CSR G TIEA I glqaag V R H G F A GE K D S P L AK A A 1271
1370 1380 1390 1400
....*....|....*....|....*....|....*....|...
gi 39725938 1321 FE K T ADHLFD AA YF G QKDSVC G VSECI IMG IPMN IG T G LFK LL 1363
Cdd:PRK14977 1272 FE I T THTIAH AA LG G EIEKIK G ILDAL IMG QNIP IG S G KVD LL 1314
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
20-887
0e+00
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain]
Cd Length: 751
Bit Score: 852.60
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 20 FG MK SP E E M R QQAHIQVVSK nl YSQD N QHA P L L Y G VL D H RMGT SEKDRP C E TCG KNLAD C L GH Y G Y I D L EL P C FH V G YFR 99
Cdd:cd02733 5 FG IL SP D E I R AMSVAEIEHP -- ETYE N GGG P K L G G LN D P RMGT IDRNSR C Q TCG GDMKE C P GH F G H I E L AK P V FH I G FLT 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 100 AVIG IL QMI CK tcch IM LS Q E E kkqfldylkrpgltylqkrglkkkisdkcrkknichhcgafngtvkkcgllkiiheky 179
Cdd:cd02733 83 KILK IL RCV CK ---- RE LS A E R ---------------------------------------------------------- 100
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 180 ktnkkvvdpivsnflqsfetaiehnkevepllgraqenlnplv VL NL FKRI PA ED VPL L LMN P EAGK P SDL ILT R L L VPP 259
Cdd:cd02733 101 ------------------------------------------- VL EI FKRI SD ED CRI L GFD P KFSR P DWM ILT V L P VPP 137
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 260 LCI RPSVV S D L k S GTN EDDLT M KL TE II FL N DVI K KHRIS GA KTQM I M ED WDF LQ LQC A L Y INS E LS G I P ln M A PK K WT R 339
Cdd:cd02733 138 PAV RPSVV M D G - S ARS EDDLT H KL AD II KA N NQL K RQEQN GA PAHI I E ED EQL LQ FHV A T Y MDN E IP G L P -- Q A TQ K SG R 214
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 340 --- GFV QRLKGK Q GR F RGNL S GKRVDFS G RTVI S PDPNL RI D E V A VP VHV A KI LTFPE K V NKA NI NF L RK LV Q NGP EVH P 416
Cdd:cd02733 215 plk SIR QRLKGK E GR I RGNL M GKRVDFS A RTVI T PDPNL EL D Q V G VP RSI A MN LTFPE I V TPF NI DR L QE LV R NGP NEY P 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 417 GA NF I Q q R HTQMKRF L K Y GNR e KMAQE L K YG D IVERHL I DGDVVLFNRQPSLHK L S I M A H LAR 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 Q YG Y IVERHL 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 39725938 497 NADFDGDEMNLH L PQ TE E AK AE ALV LM GTKANL V T P RNGE P LIAAI QD F L T G AYL LT LK DTF FDRAKACQIIASI lvgkd 576
Cdd:cd02733 373 NADFDGDEMNLH V PQ SL E TR AE LKE LM MVPRQI V S P QSNK P VMGIV QD T L L G VRK LT KR DTF LEKDQVMNLLMWL ----- 447
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 577 EKIKVRL P P P T ILKP VT LWTGKQIFS V I L r P SDD N PV R ANLRTK G KQY cgkge DLCAN D SY V T I Q N S EL M SG SMD K G T L G 656
Cdd:cd02733 448 PDWDGKI P Q P A ILKP KP LWTGKQIFS L I I - P KIN N LI R SSSHHD G DKK ----- WISPG D TK V I I E N G EL L SG ILC K K T V G 521
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 657 SG S k NNIFYILLRDW G QNE A A D AMSRLA R LAPVY L SNR GFSIGIGD VTPGQGLL K AKY E LLNAGYKKCDEY IE ALNT G K L 736
Cdd:cd02733 522 AS S - GGLIHVIWLEY G PEA A R D FIGNIQ R VVNNW L LHN GFSIGIGD TIADKETM K KIQ E TIKKAKRDVIKL IE KAQN G E L 600
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 737 QQ QPG C T AE E TL E ALILKE L SVI RD H AG SACLRE L DKS N SPLT M ALC GSKGSFINISQ M IACVGQQ AIS G S R V P D GF EN R 816
Cdd:cd02733 601 EP QPG K T LR E SF E NKVNRI L NKA RD K AG KSAQKS L SED N NFKA M VTA GSKGSFINISQ I IACVGQQ NVE G K R I P F GF RR R 680
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 39725938 817 S LPHF E K HSKL P AAK GFV A NS FYS GLTP T EFFFH T M A GREGL V DTAVKTAETGY M QRRLVK SL ED LCSQ YD 887
Cdd:cd02733 681 T LPHF I K DDYG P ESR GFV E NS YLR GLTP Q EFFFH A M G GREGL I DTAVKTAETGY I QRRLVK AM ED VMVK YD 751
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
23-887
0e+00
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain]
Cd Length: 528
Bit Score: 709.59
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 23 K SPEE M R QQAHIQ V VSKNLYSQDNQH A PL l Y G VL D H R M G TSEKDRP C E TCG KN L A DC L GH Y G Y I D L EL P C FHVG YFRA V I 102
Cdd:cd00399 1 M SPEE I R KWSVAK V IKPETIDNRTLK A ER - G G KY D P R L G SIDRCEK C G TCG TG L N DC P GH F G H I E L AK P V FHVG FIKK V P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 103 GI L Q micktcchimlsqeekkqfldylkrpgltylqkrglkkkisdkcrkknichhcgafngtvkkcgllkiihekyktn 182
Cdd:cd00399 80 SF L G ---------------------------------------------------------------------------- 83
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 183 kkvvdpivsnflqsfetaiehnkevepllgraqenlnplvvlnlfkripaedvplllmnpeagk P SDL ILT R L L VPP L C I 262
Cdd:cd00399 84 ---------------------------------------------------------------- P EWM ILT C L P VPP P C L 99
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 263 RPSV vsdlksgtneddltmklteiiflndvikkhrisgaktq M I M E D W DF LQ LQCAL Y INSELS G I P LNMAPKKWT R GFV 342
Cdd:cd00399 100 RPSV -------------------------------------- I I E E R W RL LQ EHVDT Y LDNGIA G Q P QTQKSGRPL R SLA 141
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 343 QRLKGK Q GRFRGNL S GKRVDFSGR T VISPDPNLR I D E V A VP VHV A KI L tfpekvnkaninflrklvqngpevhpganfiq 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 39725938 423 qrhtqmkrflkygnrekmaqelkygdiverhli DGD V VLFNRQPSLHKLSIMAH LA 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 39725938 503 DEMNLH L PQ T EEA K AEA LV LM GTKA N LVT P R NGEPLI AAI QD F L T GAYLLTL kdtffdrakacqiiasilvgkdekikvr 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 39725938 583 lppptilkpvtlwt GKQI F S VI L rpsddnpvranlrtkgkqycgkgedlcandsyvtiqnselmsgsmdkgtlgsgs KNN 662
Cdd:cd00399 289 -------------- GKQI V S AA L ------------------------------------------------------ PGG 300
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 663 IFYILL R DW G QNE AA DAM S R L A R LAP V Y L SNR GFS I GIGDV TPGQGLLKA K Y EL LNAGY KK C DE YI EA LNT G K L QQ Q P G C 742
Cdd:cd00399 301 LLHTVT R EL G PEK AA KLL S N L Q R VGF V F L TTS GFS V GIGDV IDDGVIPEE K T EL IEEAK KK V DE VE EA FQA G L L TA Q E G M 380
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 743 T A EE T LE AL IL KE L SVI RD H AGSA CLRE LD --- K S NS PLT MA LC G S KGSFINI S QM I ACVGQQ AIS G S R V P D GF EN R S LP 819
Cdd:cd00399 381 T L EE S LE DN IL DF L NEA RD K AGSA ASVN LD lvs K F NS IYV MA MS G A KGSFINI R QM S ACVGQQ SVE G K R I P R GF SD R T LP 460
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 39725938 820 HF E K HSKL P A AKGF VA NSF YS GLTP T E F FFH T M A GREGLVDTAVKTAE T GY M QRRLVK S LEDL CSQ YD 887
Cdd:cd00399 461 HF S K DDYS P E AKGF IR NSF LE GLTP L E Y FFH A M G GREGLVDTAVKTAE S GY L QRRLVK A LEDL VVH YD 528
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
20-887
0e+00
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain]
Cd Length: 779
Bit Score: 574.13
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 20 F GMK S P EE M R QQAHIQVVSKNLY sq D NQHA P LLY G VL D HRM G TSE KD RP C E TCG K N LAD C L GH Y G Y I D L E LP CFHVGY F R 99
Cdd:cd01435 2 F SFY S A EE I R KLSVKEITNPVTF -- D SLGH P VPG G LY D PAL G PLD KD DI C S TCG L N YLN C P GH F G H I E L P LP VYNPLF F D 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 100 AVIGI L QMI C KT C CHIML S QE E K K Q F ldylkrpgltylqkrglkkkisdkcrkknichhcgafngt V K K CG LL kiiheky 179
Cdd:cd01435 80 LLYKL L RGS C FY C HRFRI S KW E V K L F ---------------------------------------- V A K LK LL ------- 112
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 180 ktnkkvvdpivsnflqsfetai EHNKE VE pllgr A Q E NLNPL vvl NL F kripaedvplllmnpeagkpsdl I L TR LLVPP 259
Cdd:cd01435 113 ---------------------- DKGLL VE ----- A A E LDFGY --- DM F ----------------------- F L DV LLVPP 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 260 LCI RP sv V S D L KSGTN E DDLTMK L TE I IFL N DV I KKHRI S GAKTQMIMEDWD ------------- F LQLQ C A -- LYIN S E 324
Cdd:cd01435 140 NRF RP -- P S F L GDKVF E NPQNVL L SK I LKD N QQ I RDLLA S MRQAESQSKLDL isgktnseklina W LQLQ S A vn ELFD S T 217
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 325 LSGIPLNMA P K kwtr G FV Q R L KG K Q G R FR G N LS GKRV DFSG R T VISPDP NLRID E VAV P VHV AK I LTFPE K V NKA N INF L 404
Cdd:cd01435 218 KAPKSGKKS P P ---- G IK Q L L EK K E G L FR M N MM GKRV NYAA R S VISPDP FIETN E IGI P LVF AK K LTFPE P V TPF N VEE L 293
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 405 R KL V Q NGP E V H PGAN F I QQR ----------- HTQM K RFL K YGNREKM A QE L KY G - DI V E RHL I DGDVVL F NRQP S LHK L S 472
Cdd:cd01435 294 R QA V I NGP D V Y PGAN A I EDE dgrlillsals EERR K ALA K LLLLLSS A KL L LN G p KK V Y RHL L DGDVVL L NRQP T LHK P S 373
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 473 IMAH LA 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 39725938 552 LT LK DTFF D R AKAC Q IIASI L VGK --- D EKIKVR L P PP T ILKP VT LWTGKQ IF S V IL RPSDDNPVRANLRTKG K QYCG K G 628
Cdd:cd01435 454 LT SR DTFF T R EEYQ Q LVYAA L RPL fts D KDGRIK L L PP A ILKP KP LWTGKQ VI S T IL KNLIPGNAPLLNLSGK K KTKK K V 533
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 629 EDLC ---- AND S Y V T I Q N S EL MS G SM DK GTL G S g S KNNI --- F Y I L lrd W G QNE A ADAM S R L A RL APV YL SN RGF SI GI G 701
Cdd:cd01435 534 GGGK wggg SEE S Q V I I R N G EL LT G VL DK SQF G A - S AYGL vha V Y E L --- Y G GET A GKLL S A L G RL FTA YL QM RGF TC GI E 609
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 702 D V tpgqg LL KA K YEL lnagy K KCDEYIE A LNT G K lqqqpg CT A E E T L EALIL K EL S V I RD hags ACL RE -- L DK -- S N SP 777
Cdd:cd01435 610 D L ----- LL TP K ADE ----- K RRKILRK A KKL G L ------ EA A A E F L GLKLN K VT S S I IK ---- ACL PK gl L KP fp E N NL 669
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 778 LT M ALC G S KGS FI N I SQ MIACV GQQ AIS G S RVP DGFENRS LP H F EKHSKL P A A K GF VANS F YS G LT P T E F FFH T MAGREG 857
Cdd:cd01435 670 QL M VQS G A KGS MV N A SQ ISCLL GQQ ELE G R RVP LMVSGKT LP S F PPYDTS P R A G GF ITDR F LT G IR P Q E Y FFH C MAGREG 749
890 900 910
....*....|....*....|....*....|
gi 39725938 858 L V DTAVKT AET GY M QR R L V K S LE D L CSQ YD 887
Cdd:cd01435 750 L I DTAVKT SRS GY L QR C L I K H LE G L KVN YD 779
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
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: 565.31
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DK D D D ADY AR L 1100
Cdd:cd02736 1 KYMRA KV EPG T AVGA IA AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK N ISTPIITA K L EN D R D EKS AR I 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1101 VKGRIEKT L LGE ISE YIEEV FL PDDC F IL V KL SLER I RL L R L evnaetvrysictsklrvkpgdvavhgeavvcvtpren 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 39725938 1181 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek YKLLVEG DN LRAVM A T H GV K GTRTTSN NTY EVEK T LGI 1260
Cdd:cd02736 123 SKS NL Y FL LQ S LK RK LP D VVV S GIPEV K RAVI NK D KKK GK -- YKLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1261 EAAR T TIINEIQYTM VN HGMSID R RH V MLL S DLMT Y KGEVLGITRFG L AKMKESVLMLASFEKT A DHLF D AA YF G Q KDS V 1340
Cdd:cd02736 201 EAAR S TIINEIQYTM KS HGMSID P RH I MLL A DLMT F KGEVLGITRFG I AKMKESVLMLASFEKT T DHLF N AA LH G R KDS I 280
330 340
....*....|....*....|
gi 39725938 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;
248-550
8.40e-150
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 455.44
E-value: 8.40e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 248 SDL ILT R L L VPP L C I RPSV VS D L k SGTN EDDLT MK L TE II FL N DVI K KHRIS GA KTQM I MEDWDF LQ LQCALY I NS E l SG 327
Cdd:smart00663 1 EWM ILT V L P VPP P C L RPSV QL D G - GRFA EDDLT HL L RD II KR N NRL K RLLEL GA PSII I RNEKRL LQ EAVDTL I DN E - GL 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 328 IPL N MAPKKWTRGFV QRLKGK Q GRFR G NL S GKRVDFS G R T VI S PDPNL RID EV A VP VHV A KI LTFPE K V NKA NI NF LRKL 407
Cdd:smart00663 79 PRA N QKSGRPLKSLS QRLKGK E GRFR Q NL L GKRVDFS A R S VI T PDPNL KLN EV G VP KEI A LE LTFPE I V TPL NI DK LRKL 158
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 408 V Q NGP evh P GA NF I QQ rht QM K RF LK YGNRE K M A QE LK Y GDIVERH L IDGDVVLFNRQP S LH KL SI M AH LA RV KPHR T F R 487
Cdd:smart00663 159 V R NGP --- N GA KY I IR --- GK K TN LK LAKKS K I A NH LK I GDIVERH V IDGDVVLFNRQP T LH RM SI Q AH RV RV LEGK T I R 232
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 39725938 488 F N EC VC T PYNADFDGDEMNLH L PQ TE EA K AEA LV LM GTKA N LVT P R NG E P L I AA IQD F L T G A Y 550
Cdd:smart00663 233 L N PL VC S PYNADFDGDEMNLH V PQ SL EA R AEA RE LM LVPN N ILS P K NG K P I I GP IQD M L L G L Y 295
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
12-356
4.12e-132
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: 409.76
E-value: 4.12e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 12 A KKI SH I C FG MK SPEE M R QQAHIQ V VSKNL Y S q DNQHA P LLY G V LD H RMGT SE KD RP CETCGK NLA DC L GH Y G Y I D L EL P 91
Cdd:pfam04997 1 L KKI KE I Q FG IA SPEE I R KWSVGE V TKPET Y N - YGSLK P EEG G L LD E RMGT ID KD YE CETCGK KKK DC P GH F G H I E L AK P 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 92 C FH V G Y F RAVIG IL QMI CK T C CHIM L SQEEK K Q F LDYL KR P GL TY L QKR gl K K K I SDK C R KK NI C H HCG AF NG TVKK cgl 171
Cdd:pfam04997 80 V FH I G F F KKTLK IL ECV CK Y C SKLL L DPGKP K L F NKDK KR L GL EN L KMG -- A K A I LEL C K KK DL C E HCG GK NG VCGS --- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 172 lkiihekyktnkkv VD P IVSNFLQSFET AI EHN KE V E pllgr AQ E N LNP LV VL NL FKRI PA EDV PL L LM NP EAGK P SDL I 251
Cdd:pfam04997 155 -------------- QQ P VSRKEGLKLKA AI KKS KE E E ----- EK E I LNP EK VL KI FKRI SD EDV EI L GF NP SGSR P EWM I 215
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 252 LT R L L VPP L CIRPSV VS D LK s GTN EDDLT M KL TE II FL N DVI KK HRIS GA KTQM I M E D W DF LQ LQC A LYINS E LS G I P L - 330
Cdd:pfam04997 216 LT V L P VPP P CIRPSV QL D GG - RRA EDDLT H KL RD II KR N NRL KK LLEL GA PSHI I R E E W RL LQ EHV A TLFDN E IP G L P P a 294
330 340
....*....|....*....|....*.
gi 39725938 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
2.78e-117
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: 377.46
E-value: 2.78e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 841 GLTP T EFFFHTM A GREGL V DTAVKTAE T GY M QRRLVK S LEDL CSQ YD L TVR S S T G D I I QF I YG G DGLDP AAM E GKD e PLE 920
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G E I V QF L YG E DGLDP LKI E KQG - RFT 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 921 FKRVLDNIKAV F PCP - SEPA L SKN E LI L TTESIMKKSEFLCCQ D SFLQ E IKKFIKGVS E KI ------- K KT R DKYGI N DN 992
Cdd:pfam04998 80 IEFSDLKLEDK F KND l LDDL L LLS E FS L SYKKEILVRDSKLGR D RLSK E AQERATLLF E LL lksgles K RV R SELTC N SK 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 993 gtteprvlyqldritpt QVEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL K TFHFAGVAS M N I TLGVPR I KE 1072
Cdd:pfam04998 160 ----------------- AFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL N TFHFAGVAS K N V TLGVPR L KE 222
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1073 IIN A SK A I ST P II T AQ L -- DKDDDADY A RL V K G R IEK TL LG EIS E YI E ------------------------------ EV 1120
Cdd:pfam04998 223 IIN V SK N I KS P SL T VY L fd EVGRELEK A KK V Y G A IEK VT LG SVV E SG E ilydpdpfntpiisdvkgvvkffdiidevt NE 302
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1121 FLP D DCFI L VK L SLERIRL L RLEVNAETVRYS I c TSKL R V K pg DVAVHGE A VVCV T PRENSK S SMYY ------- VLQF L K 1193
Cdd:pfam04998 303 EEI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I - PRSI R N K -- VDEGRDI A IGEI T AFIIKI S KKIR qdtgglr RVDE L F 379
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1194 ED ------------ L PKVVVQ GIP EVS R AVIHI D E q S GK EK -- YK L LV EG D NL RA V MATH G - V KGT R TT SN NTY E VEKT L 1258
Cdd:pfam04998 380 ME edpklailvasl 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 L 458
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 39725938 1259 GIEAAR TTII NEI QYTMVNH G MS I DR RH VM L LS D L MT Y KG EVLG I T R F G LA K MKE S V L 1316
Cdd:pfam04998 459 GIEAAR NALL NEI RNVYRFQ G IY I ND RH LE L IA D Q MT R KG YIMA I G R H G IN K AEL S A L 516
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
358-525
5.33e-100
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498
Cd Length: 166
Bit Score: 316.17
E-value: 5.33e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 358 GKRVDFS G RTVISPDPNL RI DEV A VP VHV AK I LTFPE K V NKA NI NF LR K LV Q NGP E V H PGAN F I Q q R HTQMK R F L K Y GN R 437
Cdd:pfam00623 1 GKRVDFS A RTVISPDPNL KL DEV G VP ISF AK T LTFPE I V TPY NI KR LR Q LV E NGP N V Y PGAN Y I I - R INGAR R D L R Y QK R 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 438 e KMAQ EL KY GDIVERH L IDGDVVLFNRQPSLH K LSIM A H LA RV K P HR TFR F N EC V C TPYNADFDGDEMNLH L PQ T EEA K A 517
Cdd:pfam00623 80 - RLDK EL EI GDIVERH V IDGDVVLFNRQPSLH R LSIM G H RV RV L P GK TFR L N LS V T TPYNADFDGDEMNLH V PQ S EEA R A 158
....*...
gi 39725938 518 EA LV LM GT 525
Cdd:pfam00623 159 EA EE LM LV 166
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
978-1363
4.27e-99
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain]
Cd Length: 363
Bit Score: 321.51
E-value: 4.27e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 978 EK IKKTRDKY G I ndngtteprvlyqldri T PTQV E KFLETCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMTL K TFH F AG 1057
Cdd:cd06528 5 EK LEEVLKEH 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 39725938 1058 VA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L DKD -- D D ADY A RL V KGR IE K T L L GEIS E Y I E ev FLPDDCF I LVK L SL E 1135
Cdd:cd06528 68 VA EI N V TLG L PR LI EI VD A R K EP STP TM T IY L EEE yk Y D REK A EE V ARK IE E T T L ENLA E D I S -- IDLFNMR I TIE L DE E 145
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1136 RI -- R LLRLEVNAETVR ysictskl RV K P G D V AVH G EAVVC V TPR E NSK ssm YYV L QF L K E DLPKVVVQ GI PEVS R AVI h 1213
Cdd:cd06528 146 ML ed R GITVDDVLKAIE -------- KL K K G K V GEE G DVTLI V LKA E EPS --- IKE L RK L A E KILNTKIK GI KGIK R VIV - 213
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1214 id EQSGK E k Y KLLV EG D NL R AV MATH GV KG TRTT S NN TY E V E KT LGIEAAR TT IINEI QY T MVNH G MSI D R RH V ML LS D L 1293
Cdd:cd06528 214 -- RKEED E - Y VIYT EG S NL K AV LKVE GV DP TRTT T NN IH E I E EV LGIEAAR NA IINEI KR T LEEQ G LDV D I RH I ML VA D I 290
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1294 MTY K GEV LG I T R F G L A KM K E SVL ML A S FE K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L L 1363
Cdd:cd06528 291 MTY D GEV RQ 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
1.03e-96
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 316.02
E-value: 1.03e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1006 I T PTQ VE KFL E TCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II 1085
Cdd:PRK04309 35 L T EEE VE 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 39725938 1086 T AQ L DKD -- D D ADY A RL V KGR IE K T L L GEISEY I E ev FLPDDCF I LVK L SL E RI -- R L L RLEVNA E TVR ysictskl RV K 1161
Cdd:PRK04309 115 T IY L KDE ya Y D REK A EE V ARK IE A T T L ENLAKD I S -- VDLANMT I IIE L DE E ML ed R G L TVDDVK E AIE -------- KK K 184
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1162 P G D V AVH G EAVV c VT P R E N S kssm Y YV L QF L K E DLPKVVVQ GI PEVS R AV I HIDE qsgk EK Y KLLV EG D NL RA V MATH GV 1241
Cdd:PRK04309 185 G G E V EIE G NTLI - IS P K E P S ---- Y RE L RK L A E KIRNIKIK GI KGIK R VI I RKEG ---- DE Y VIYT EG S NL KE V LKVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1242 KG TRTT S NN TY E V E KT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS D L MT YK GEV LG I T R F G LAKM K E SVL ML A S F 1321
Cdd:PRK04309 256 DA TRTT T NN IH E I E EV LGIEAAR NA II E EI KN T LEEQ G LDV D I RH I ML VA D M MT WD GEV RQ I G R H G VSGE K A SVL AR A A F 335
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 39725938 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
1.49e-85
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 283.87
E-value: 1.49e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1010 QVEKFLETCRDK Y M R AQME PG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L 1089
Cdd:TIGR02389 24 ELDEIIKRVEEE Y L R SLID PG E AVG IVA AQSIGEPGTQMT MR TFH Y AGVA EL N V TLG L PR LI EI VD A R K TP STP SM T IY L 103
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1090 DKDD -- D ADY A RL V KGR IE K T L L GEISEY I E evflpddcfil VK L SLERI rll RL E VNA E TVRYSIC T SKL ------ RV K 1161
Cdd:TIGR02389 104 EDEY ek D REK A EE V AKK IE A T K L EDVAKD I S ----------- ID L ADMTV --- II E LDE E QLKERGI T VDD vekaik KA K 169
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1162 P G D V AV -- HGEAVVCVT P REN S kssm YYV L QF LKE DLPKVVVQ GI PEVS R A VI hide QSGKEK Y KLLV EG D NL RA V MATH 1239
Cdd:TIGR02389 170 L G K V IE id MDNNTITIK P GNP S ---- LKE L RK LKE KIKNLHIK GI KGIK R V VI ---- RKEGDE Y VIYT EG S NL KE V LKLE 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1240 GV KG TRTT S N NTY E VEKT LGIEAAR TT II N EI QY T MVNH G MSI D R RH V ML LS DLMT YK GEV LG I T R F G LAKM K E SVL ML A 1319
Cdd:TIGR02389 242 GV DK TRTT T N DIH E IAEV LGIEAAR NA II E EI KR T LEEQ G LDV D I RH L ML VA DLMT WD GEV RQ I G R H G ISGE K A SVL AR A 321
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 39725938 1320 S FE K T AD HL F DAA YF G QK D SVC GV S E C II M G I P MNI GTG LFK L LHK 1365
Cdd:TIGR02389 322 A FE V T VK HL L DAA IR G EV D ELK GV I E N II V G Q P IPL GTG DVD L VMD 367
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
935-1365
4.72e-85
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 287.86
E-value: 4.72e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 935 PSE P ALSK N EL I LTTESIM K K --------------- S EF LCCQDSF L Q E IKK F IK G VSEK i KKTRDK Y GI N D N GTTEPRV 999
Cdd:PRK14897 53 KIA P YSNS N GI I KKKKPVL K T vleieseekieaidl M EF KRLFGRI L D E NMS F ST G ELLT - AEEKEY Y EE N S N EDVLKVI 131
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1000 LYQLD --- R IT P TQV E KFLETCRD K ----------------- Y M RA QME P GS AVG ALC AQSIGEPGTQMT LK TFH F AGVA 1059
Cdd:PRK14897 132 DDVKK lgf R LP P SVI E EIAKAMKK K elsddeyeeilrriree Y E RA RVD P YE AVG IVA AQSIGEPGTQMT MR TFH Y AGVA 211
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1060 S MN I TLG V PR IK EI IN A S K AI STP II T AQ L D KD -- D D ADYA R L V KGR IE K T L L GEISEY I EEV flp DDCFIL V K L SL E RI 1137
Cdd:PRK14897 212 E MN V TLG L PR LI EI VD A R K KP STP TM T IY L K KD yr E D EEKV R E V AKK IE N T T L IDVADI I TDI --- AEMSVV V E L DE E KM 288
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1138 rllrlev NAETVR Y SICTSKLRVKPGDVAVHGEAVVCVT P REN S kssm YYV L QF L K E DLPKVVVQ GI PEVS RA VIHID eq 1217
Cdd:PRK14897 289 ------- KERLIE Y DDILAAISKLTFKTVEIDDGIIRLK P QQP S ---- FKK L YL L A E KVKSLTIK GI KGIK RA IARKE -- 355
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1218 s GK E K - YKLLVE G D NL RA V MATHG V KG TRT TS N NTY E VEKT LGIEAAR TT II N E IQY T MVNH G MSI D R RH V ML LS D L MT Y 1296
Cdd:PRK14897 356 - ND E R r WVIYTQ G S NL KD V LEIDE V DP TRT YT N DII E IATV LGIEAAR NA II H E AKR T LQEQ G LNV D I RH I ML VA D M MT F 434
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 39725938 1297 K G E V LG I T R F G LAKM K E SVL ML A S FE K T AD HL FD A AYF G QK D SVC GV S E C II M G I P MNI GTG LFK L LH K 1365
Cdd:PRK14897 435 D G S V KA I G R H G ISGE K S SVL AR A A FE I T GK HL LR A GIL G EV D KLA GV A E N II V G Q P ITL GTG AVS L VY K 503
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
55-891
4.38e-84
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain]
Cd Length: 744
Bit Score: 292.00
E-value: 4.38e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 55 V LDH R M G TSEKDRP C E TCG - K NLAD C L GH Y G Y I D L ELPCF H VGYFRA V IG IL QM IC KT C chimlsqeekkqfldylkrpg 133
Cdd:cd10506 20 V TNP R L G LPNESGQ C T TCG a K DNKK C E GH F G V I K L PVTIY H PYFISE V AQ IL NK IC PG C --------------------- 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 134 ltylqkrglkkkisdkcrkknichhcgafngtvkkcgl LK I IHE K Y K TNKKVVD P IVSN F LQSFET ai EHNKE V EPL L gr 213
Cdd:cd10506 79 -------------------------------------- KS I KQK K K K PPRETLP P DYWD F IPKDGQ -- QEESC V TKN L -- 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 214 aqenln P LVV L NLF K R I PA E DV P L L LMN -- P eag KPSD L I L TR L L VPP L C I R psv V SDLKS G TNE ddl TMK L TEIIFLND 291
Cdd:cd10506 117 ------ P ILS L AQV K K I LK E ID P K L IAK gl P --- RQEG L F L KC L P VPP N C H R --- V TEFTH G FST --- GSR L IFDERTRA 181
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 292 VI K K hrisgaktqmimedwdflqlqc ALY I NSELSGIPLNMAPK KW trgfvqrlkgkqgr FRGN L S GKR VDF S G R T V ISP 371
Cdd:cd10506 182 YK K L ---------------------- VDF I GTANESAASKKSGL KW -------------- MKDL L L GKR SGH S F R S V VVG 225
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 372 DP N L RID E VAV P VHV A KI LT FP E K V NKA N INF L RKLVQNGP evhpganfi QQRHTQMK R fl KY G N -- REKMAQE L KY GD I 449
Cdd:cd10506 226 DP Y L ELN E IGI P CEI A ER LT VS E R V SSW N RER L QEYCDLTL --------- LLKGVIGV R -- RN G R lv GVRSHNT L QI GD V 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 450 VE R H L I DGDVVL F NR Q PS L H KL S IM A HLAR 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 39725938 529 L VTPRN G EP L IAAI QD F L TG A Y L L T LKDT F F D R A KAC Q I ia SI L VGK dekikv R LPPP T I L K PVT ---- LWTGKQ I F SVI 604
Cdd:cd10506 375 L ISSQS G QN L LSLT QD S L LA A H L M T ERGV F L D K A QMQ Q L -- QM L CPS ------ Q LPPP A I I K SPP sngp LWTGKQ L F QML 446
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 605 L r P S D DN pvranlrtkgkqycgkgedl CAND S Y - V T I QNS EL M S G S m DKGTLGSG S KN N I F Y IL LRD w G QNE A A D AMSRL 683
Cdd:cd10506 447 L - P T D LD -------------------- YSFP S N l V F I SDG EL I S S S - GGSSWLRD S EG N L F S IL VKH - G PGK A L D FLDSA 503
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 684 AR L APVY LS N RGFS IGIG D VTPGQGLLKAK -- Y E LLNA G Y -- KKCDEY I EA L NTGKLQQQPGCTA EE TLEALILKELSVI 759
Cdd:cd10506 504 QG L LCEW LS M RGFS VSLS D LYLSSDSYSRQ km I E EISL G L re AEIACN I KQ L LVDSRKDFLSGSG EE NDVSSDVERVIYE 583
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 760 R DHAGSAC ------------------ LRELD K S NS P L T M ALC GSKGS FINIS Q MIA C V G Q Q -------- A I SGSRVPDGF 813
Cdd:cd10506 584 R QKSAALS qasvsafkqvfrdiqnlv YKYAS K D NS L L A M IKA GSKGS LLKLV Q QSG C L G L Q lslvklsy R I PRQLSCAAW 663
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 814 ENRSL P HFEKHSK ----- LPAAK G F V AN SF YS GL T P T E F F F H TMAG R EGLVD tav KT A ET - G YMQ R R L VKSLE D LCSQ YD 887
Cdd:cd10506 664 NSQKS P RVIEKDG secte SYIPY G V V ES SF LD GL N P L E C F V H SITS R DSSFS --- SN A DL p G TLF R K L MFFMR D IYVA YD 740
....
gi 39725938 888 L TVR 891
Cdd:cd10506 741 G TVR 744
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1005-1363
5.11e-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: 272.93
E-value: 5.11e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1005 R ITPTQVEKF L ETCRDKYM R AQME PG SA VG ALC AQSIGEP G TQMTL K TFHFAGV ASM N I TLGVPR I KEIIN AS K A I S TP I 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 K N I K TP S 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1085 I T AQ L DKDD -- D ADY A RLVKG R I E K T L L GEISEYI E EVFL PD DCFILVK ---------------- LSLE R IR -- LLR L E V 1144
Cdd:cd02584 82 L T VY L EPGF ak D EEK A KKIQS R L E H T T L KDVTAAT E IYYD PD PQNTVIE edkefvesyfefpded VEQD R LS pw LLR I E L 161
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1145 NAETV rysic T S K l RVKPGDV A ----- VHGEAVVCVTPRE N S --------------- K SSMYYVLQ FLK ED ---- L PKVV 1200
Cdd:cd02584 162 DRKKM ----- T D K - KLSMEQI A kkike EFKDDLNVIFSDD N A eklviririinddee K EEDSEDDV FLK KI esnm L SDMT 235
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1201 VQ GI PEVSRAV I H ------ I D EQS G KE K ---- YK L LVE G D NLR A V MATH GV KG TRTTSN NTY E VEKT LGIEAAR TTIIN E 1270
Cdd:cd02584 236 LK GI EGIRKVF I R eenkkk V D IET G EF K kree WV L ETD G V NLR E V LSHP GV DP TRTTSN DIV E IFEV LGIEAAR KALLK E 315
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1271 IQYTMVNH G MSIDR RH VM LL S D L MT YK G EVLG ITR F G LAKMKESV LM LA SFE K T A D H L FD AA Y FG QK D SVC GVSE C I IM G 1350
Cdd:cd02584 316 LRNVISFD G SYVNY RH LA LL C D V MT QR G HLMA ITR H G INRQDTGP LM RC SFE E T V D I L LE AA A FG ET D DLK GVSE N I ML G 395
410
....*....|...
gi 39725938 1351 IPMN IGTG L F K LL 1363
Cdd:cd02584 396 QLAP IGTG C F D LL 408
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
246-1359
5.03e-80
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain]
Cd Length: 1140
Bit Score: 288.10
E-value: 5.03e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 246 K P SDLI L TRLL V P P LCI RP S V -------- V SDL ksgtne D DL TMK lte I I FL N DVI K KHRIS GA ------- KTQ M IM E DW 310
Cdd:TIGR02386 215 R P EWMV L DVIP V I P PEL RP M V qldggrfa T SDL ------ N DL YRR --- V I NR N NRL K RLLEL GA peiivrn EKR M LQ E AV 285
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 311 D flqlqc AL YI N SE l S G I P LNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L 390
Cdd:TIGR02386 286 D ------ AL FD N GR - R G K P VVGKNNRPLKSLSDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KMYQCGL P KKM A LE L 358
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 391 TF P EKVNK ------- ANI NFLR K LVQNG - PEV H pganfiqqrhtqmkrflkygnrekmaqelkyg D IV E R h L I DGDV VL F 462
Cdd:TIGR02386 359 FK P FIIKR lidrela ANI KSAK K MIEQE d PEV W -------------------------------- D VL E D - V I KEHP VL L 405
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 463 NR Q P S LH K L S I M A HLARVKPHRTF 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 542
Cdd:TIGR02386 406 NR A 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 485
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 543 QD FLT G A Y L LT L -------- KDT F FDRAK A CQIIASIL V GKDEK I K VR LPPPTILKP V tlwt G KQ IF SV IL rpsddn P V r 614
Cdd:TIGR02386 486 QD MVL G L Y Y LT T ekpgakge GKI F SNVDE A IRAYDNGK V HLHAL I G VR TSGEILETT V ---- G RV IF NE IL ------ P E - 554
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 615 anlrtkgkqycgkgedlca NDS Y VTIQN selmsg SMD K GTLG S gsknn IFYI L LRDW G QN E A A DAMSRLAR L APV Y LSNR 694
Cdd:TIGR02386 555 ------------------- GFP Y INDNE ------ PLS K KEIS S ----- LIDL L YEVH G IE E T A EMLDKIKA L GFK Y ATKS 604
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 695 G FS I GIG D V - T P GQ gllka KYE L L NAGY K KCDEYIEAL N T G KL qqqpgc T A EE TLEALI l KEL S VIR D HAGS A CLRE L D K 773
Cdd:TIGR02386 605 G TT I SAS D I v V P DE ----- KYE I L KEAD K EVAKIQKFY N K G LI ------ T D EE RYRKVV - SIW S ETK D KVTD A MMKL L K K 672
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 774 S ---- N SPLT MA LC G SK G SFINIS Q MIACV G QQ A isgsr V P D G f ENRS LP hfekhsklpaakgf VAN SF YS GLT PT E F F F 849
Cdd:TIGR02386 673 D tykf 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 I 732
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 850 H T MAG 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 922
Cdd:TIGR02386 733 S T HGA 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 sl KD 796
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 923 R VLDNIK A --- VF P CPSEPALSK N E LI lt TE S I MK K S E FL ccqdsflqeikkfik G VSE - K IKKT --- RDKY G IN dngtt 995
Cdd:TIGR02386 797 R IVGRYS A edv YD P DTGKLIAEA N T LI -- TE E I AE K I E NS --------------- G IEK v K VRSV ltc ESEH G VC ----- 854
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 996 ep RVL Y QL D RI T PTQ VE K fletcrdkymraqmep G S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA S -- MN IT L G V PR I KE I 1073
Cdd:TIGR02386 855 -- QKC Y GR D LA T GKL VE 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 39725938 1074 IN A skai S TP iitaqldk D D D A DY A R l V K G RI E ktllgeiseyieev FLP D D cfil VK lsl 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 39725938 1154 - CTSK LRVK P GD VAVH G EAVV -- CVT P RE nskssmyy V L QFLK - EDLPKVV V QGIPE V S R AV - IH I D eqsgk E K YKLLVE 1228
Cdd:TIGR02386 963 p FGAQ 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 39725938 1229 GDN LR A V MA T - H G ---- VK G TRTTSNNTY E VEKT L g I E AARTTII neiqytmvnhgmsidrrhvmllsdlmt YKGEV 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 39725938 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
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1021-1363
2.47e-68
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain]
Cd Length: 309
Bit Score: 232.85
E-value: 2.47e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1021 KYMR AQM EPG S AVG A L C AQSIGEP G TQMTL K TFHFAG VAS MN I TLG V PR IK EI I - N ASK A I S TP II T AQ L DKDDD A DY A R 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 ASK N I K TP SM T LP L KNGKS A ER A E 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1100 LV K G R IEKTL L GEIS E YI E -- E VF lpd DCFIL V - K LS L ER irll RL EV nae T VRYSICTS KL rvkpgdvavhgeavvcvt 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 --- T IKLPLSSP KL ------------------ 132
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1177 prenskssmy YV L QFLKEDLP K V V VQG IP EVS R AVIHIDEQS GK E KY KLLV EG D NL R A VMATHG - VKGT R TTS N NTYEVE 1255
Cdd:cd02735 133 ---------- LL L SIVEKLAR K A V IRE IP GIT R CFVVEEDKG GK T KY LVIT EG V NL A A LWKFSD i LDVN R IYT N DIHAML 202
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1256 K T L GIEAAR TT I IN EI QYTMVNH G MSI D R RH VM L LS D L MT YK G EVLGIT R F G LAK m KE S V L MLA SFE K T ADH L FD A AYF G 1335
Cdd:cd02735 203 N T Y GIEAAR RA I VK EI SNVFKVY G IAV D P RH LS L IA D Y MT FE G GYRPFN R I G MES - ST S P L QKM SFE T T LAF L KK A TLN G 281
330 340
....*....|....*....|....*...
gi 39725938 1336 QK D SVCGV S ECIIM G I P M N I GTGLF K LL 1363
Cdd:cd02735 282 DI D NLSSP S SRLVV G K P V N G GTGLF D LL 309
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1046-1369
1.63e-66
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 242.88
E-value: 1.63e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1046 T QM T LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STPI I T AQ L DKD -- D D ADY A RL V KGR IE KTL LG EISEY I EEVFLP 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 VH L KGE ya T D REK A EE V AKK IE SLT LG DVATS I AIDLWT 620
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1124 DD cf I L V K L SL E RI -- R L L RL E VNA E TVR ysict S KL R VK pgd VAVH G e A V VCVT P REN S kssm Y YV L QFLKEDLPKV 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 --- IDRK G - T V LYLK P KTP S ---- Y KA L RKRIPKIKNI V L 685
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1202 Q GIP EVS R AVIHID E QSGK E K Y K L LVE G D NLR A V MATH GV KGT RTT S NN TY E VEKT LGIEAAR TT IINE IQY T MVNH G MS 1281
Cdd:PRK14898 686 K GIP GIE R VLVKKE E HEND E E Y V L YTQ G S NLR E V FKIE GV DTS RTT T NN II E IQEV LGIEAAR NA IINE MMN T LEQQ G LE 765
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1282 I D R RH V ML LS D L MT YK GEV LG I T R F G L A KM K E SVL ML A S FE K T AD HL F DAA YF G QK D SVC GV S E CI I M G I P MNI GTG LFK 1361
Cdd:PRK14898 766 V D I RH L ML VA D I MT AD GEV KP I G R H G V A GE K G SVL AR A A FE E T VK HL Y DAA EH G EV D KLK GV I E NV I V G K P IKL GTG CVD 845
....*...
gi 39725938 1362 L LHKADRD 1369
Cdd:PRK14898 846 L RIDREYE 853
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
345-1359
4.72e-63
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 235.73
E-value: 4.72e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F - LR KLV QN G pevhpganf IQQ 423
Cdd:PRK00566 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A LE L FK P --------- F i MK KLV ER G --------- LAT 382
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 RHTQM K RFL kygnr E KMAQ E L ky G D IV E r HL I DGDV VL F NR Q P S LH K L S I M A ------------- H - L arvkphrtfrfn 489
Cdd:PRK00566 383 TIKSA K KMV ----- E REDP E V -- W D VL E - EV I KEHP VL L NR A P T LH R L G I Q A fepvliegkaiql H p L ------------ 442
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 490 ec VCT PY NADFDGD E M NL H L P QTE EA K AEA L VLM GTKA N LVT P R NG E P L I AAI QD FLT G A Y L LT LKD -------- T F FDR 561
Cdd:PRK00566 443 -- VCT AF NADFDGD Q M AV H V P LSL EA Q AEA R VLM LSSN N ILS P A NG K P I I VPS QD MVL G L Y Y LT RER egakgegm V F SSP 520
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 562 AK A CQIIASIL V GKDEK IKVR LPPPTILK p V T L wt G KQ IF SV IL r P SD --- D N PVRA nlrtkgkqycgkgedlcandsyv 638
Cdd:PRK00566 521 EE A LRAYENGE V DLHAR IKVR ITSKKLVE - T T V -- G RV IF NE IL - P EG lpf I N VNKP ----------------------- 573
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 639 tiqnselmsgs MD K GTLG sgskn N I FYILL R DW G QN E AADAMSRLAR L APV Y LSNR G F SIGI G D VT pgqg LLKA K Y E LLN 718
Cdd:PRK00566 574 ----------- LK K KEIS ----- K I INEVY R RY G LK E TVIFLDKIKD L GFK Y ATRS G I SIGI D D IV ---- IPPE K K E IIE 633
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 719 AGY K KCD E YIEALNT G KL qqqpgc T AE E TLEAL I l KEL S VIR D HAGS A CLRE L D K SNSPL ---- T MA LC G SK GS FIN I S Q 794
Cdd:PRK00566 634 EAE K EVA E IEKQYRR G LI ------ T DG E RYNKV I - DIW S KAT D EVAK A MMKN L S K DQESF npiy M MA DS G AR GS ASQ I R Q 706
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 795 miacvgqqa IS G S R vpdgfenrslphfekhsklpaak G FV A N ------------ S F YS GLT PT E F F FH T MAG R E GL V DTA 862
Cdd:PRK00566 707 --------- LA G M R ----------------------- G LM A K psgeiietpiks N F RE GLT VL E Y F IS T HGA R K GL A DTA 754
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 863 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 IKA V F 932
Cdd:PRK00566 755 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 V V 816
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 933 - P CPS E PALSKNE LI lt T E S I MK K S E flccq DSFLQ E I K kf I --------- K GV SE K I kktrdk YG IN dngtteprvlyq 1002
Cdd:PRK00566 817 d P ETG E VIVPAGT LI -- D E E I AD K I E ----- EAGIE E V K -- I rsvltcetr H GV CA K C ------ YG RD ------------ 869
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1003 L DRITPTQV ekfletcrdkymraqmep 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 870 L ATGKLVNI ------------------ G E AVG VIA AQSIGEPGTQ L T MR TFH TG GV --- D IT G G L PR VA E LFE A R K pkgp 928
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1079 AI STP I itaqldkdddadyarlv K G RIEK tll G EISEYIEEVFLPD D cfilvklslerirllrlev NA E TVR Y S I CTS K - 1157
Cdd:PRK00566 929 AI IAE I ----------------- D G TVSF --- G KETKGKRRIVITP D ------------------- DG E ERE Y L I PKG K h 969
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1158 L R V KP GD VAVH G EA vvcvtprenskssmyyvlqflkedlpkvvvqgipevsravihideqsgkekykl 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 39725938 1238 thgvkgtrtt S NNTYEVEKT LG I EA ARTTII NE I Q -- Y TM vn H G MS I DRR H V ------ ML L --------- S D LM ------ 1294
Cdd:PRK00566 988 ---------- S IDPHDILRV LG V EA VQNYLV NE V Q kv Y RL -- Q G VK I NDK H I evivrq ML R kvritdpgd T D FL pgelvd 1055
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1295 ------------------- T YKGEV 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 rsefeeenrkliaegkepa T GRPVL 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 39725938 1354 ni GTGL 1359
Cdd:PRK00566 1134 -- GTGL 1137
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1030-1359
3.49e-61
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain]
Cd Length: 158
Bit Score: 206.11
E-value: 3.49e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1030 G S AVG A L C AQSIGEPGTQMTL K TFHFAGVASMN I TLG V PR I KEI I NA S kaistpiitaqldkdddadyarlvkgriektl 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 39725938 1110 lgeiseyieevflpddcfilvklslerirllrlevnaetvrysictsklrvkpgdvavhgeavvcvtprenskssmyyvl 1189
Cdd:cd00630 --------------------------------------------------------------------------------
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1190 qflkedlpkvvvqgipevsravihideqsgkekykllvegdnlravmathgvkgtrttsn NTY E VEKT LGIEAAR T TII N 1269
Cdd:cd00630 49 ------------------------------------------------------------ SIH E MLEA LGIEAAR E TII R 68
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1270 EIQ YTMVNH G M S I DRRH VM L LS D L MTY K G EVL G I TR F G LAKM K E S V LM L ASFEKT AD HL F DAA YF G Q KD SVC GVSE C II M 1349
Cdd:cd00630 69 EIQ KVLASQ G V S V DRRH IE L IA D V MTY S G GLR G V TR S G FRAS K T S P LM R ASFEKT TK HL L DAA AA G E KD ELE GVSE N II L 148
330
....*....|
gi 39725938 1350 G I P MNI GTG L 1359
Cdd:cd00630 149 G R P APL GTG S 158
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
246-1359
1.50e-58
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 222.82
E-value: 1.50e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 246 K P S D L IL TRLL V P P LCI RP S V vs D L KS G T - NED DL TMKLTEI I FL N DVI K KHRIS GA KTQMIMEDWDF LQ LQC - A L YI N S 323
Cdd:PRK14906 311 D P A D M IL DVIP V I P PDL RP M V -- Q L DG G R f ATS DL NDLYRRV I NR N NRL K RLLDL GA PEIIVNNEKRM LQ EAV d S L FD N G 388
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 324 E l S G I P LNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkani NF 403
Cdd:PRK14906 389 R - R G R P VTGPGNRPLKSLADM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P H L KLHQCGL P SAM A LE L FK P -------- FV 459
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 404 LRK LV qngp E VHPG AN f I QQRHTQMK R FLK Y gnrekmaqelk YG D IV E R h L I DGDV VL F NR Q P S LH K L S I M A HLARVKPH 483
Cdd:PRK14906 460 MKR LV ---- E LEYA AN - I KAAKRAVD R GAS Y ----------- VW D VL E E - V I QDHP VL L NR A P T LH R L G I Q A FEPVLVEG 522
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 484 RTFRFNEC VCT PY NADFDGD E M NL H L P QTEE A K AEA L VLM GTKA N LVT P RN G E PL IAAI QD FLT G A Y L LT - LK D T F ---- 558
Cdd:PRK14906 523 KAIKLHPL VCT AF NADFDGD Q M AV H V P LSTQ A Q AEA R VLM LSSN N IKS P AH G R PL TVPT QD MII G V Y Y LT t ER D G F egeg 602
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 559 ----- FD R A KAC q II A SILVGKDE KI K VRL PPPTIL ------------- KPVTLWT G KQ IF SVI L rp SD D N P V r A N LRTK 620
Cdd:PRK14906 603 rtfad FD D A LNA - YD A RADLDLQA KI V VRL SRDMTV rgsygdleetkag ERIETTV G RI IF NQV L -- PE D Y P Y - L N YKMV 678
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 621 G K QYCGKGE D L C an DS Y V T IQ nsel MSGSM D kgtlgs G S K NNI F Y illrdwgqneaadamsrlarlapv Y LSNR G FSIGI 700
Cdd:PRK14906 679 K K DIGRLVN D C C -- NR Y S T AE ---- VEPIL D ------ G I K KTG F H ------------------------ Y ATRA G LTVSV 722
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 701 G D V T pgqg LLKA K Y E L L NAGYK K CDEYI E ALNT G K L qqqpgct A E ETLEALILKELSVIRDHA G S A C L REL D KS N SPLT M 780
Cdd:PRK14906 723 Y D A T ---- IPDD K P E I L AEADE K VAAID E DYED G F L ------- S E RERHKQVVDIWTEATEEV G E A M L AGF D ED N PIYM M 791
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 781 A LC G SK G SFIN I S Q MIACV G QQ A ISGSRVP D gfenrs LP hfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GLVD 860
Cdd:PRK14906 792 A DS G 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 GLVD 851
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 861 TA VK TA ET GY MQ RRLV KSLE dlcsqy D LT VR S stgdiiqfiyggdg L D PAAM EG KDE PL EFKRVLDNIKAVFP C PS E PAL 940
Cdd:PRK14906 852 TA LR TA DS GY LT RRLV DVAQ ------ D VI VR E -------------- E D CGTD EG VTY PL VKPKGDVDTNLIGR C LL E DVC 911
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 941 SK N elilt T E SIMKKSEFLCCQ D SFLQEIKKFIKG V SEKIKK T - RDK YG INDN gtteprv L Y QL D RI T ptqvekfletcr 1019
Cdd:PRK14906 912 DP N ----- G E VLLSAGDYIESM D DLKRLVEAGVTK V QIRTLM T c HAE YG VCQK ------- C Y GW D LA T ------------ 967
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1020 dkym 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 AISTPII taqldkddd A DYA r 1099
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 PKGEAVL --------- A EIS - 1033
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1100 lvk G RIEK T ll G EIS E YIEEVFLP D D cfilvklsle RI R LLR le V N A ETVRYSICTSKLR V KP G DVAVH G E avvc V T P RE 1179
Cdd:PRK14906 1034 --- G TLQI T -- G DKT E KTLTIHDQ D G ---------- NS R EYV -- V S A RVQFMPGVEDGVE V RV G QQITR G S ---- V N P HD 1092
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1180 ----- NSKSSMY Y VLQFLKE dlp KV V V QG I p EVSRAV I HIDEQSGKE K YKLLVE GD NL ---- R A V mathgvkgtrttsn N 1250
Cdd:PRK14906 1093 llrlt DPNTTLR Y IVSQVQD --- VY V S QG V - DINDKH I EVIARQMLR K VAVTNP GD SD ylpg R Q V -------------- N 1154
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1251 T YE V E K T lgieaartti I N EI qytmvnhgmsidrrhvm L L SDLMTYK G E -- V LGIT RFG LA km KE S V L ML ASF EK T ADH L 1328
Cdd:PRK14906 1155 R YE F E D T ---------- A N NL ----------------- I L EGKQPPV G Q pl L LGIT KAS LA -- TD S W L SA ASF QE T TKV L 1205
1130 1140 1150
....*....|....*....|....*....|.
gi 39725938 1329 F DAA YF G QK D SVC G VS E CI I M G I P MNI GTGL 1359
Cdd:PRK14906 1206 T DAA IE G KV D HLA G LK E NV I I G K P IPA GTGL 1236
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
345-876
3.83e-53
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: 198.90
E-value: 3.83e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - R K L VQN G pevhp G A NF I QQ 423
Cdd:cd01609 236 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KEM A LE L FK P --------- F V i R E L IER G ----- L A PN I KS 301
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 rhtq M K RFL kygnr E KMAQ E L ky G DI V E r HL I D G DV VL F NR Q P S LH K L S I M A HLARVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:cd01609 302 ---- A K KMI ----- E RKDP E V -- W DI L E - EV I K G HP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 369
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 504 E M NL H L P QTE EA K AEA L VLM GTKA N LVT P RN G E P LIAAI QD FLT G A Y L LT LKDT ffdrakacqiiasil VG K D E K I KVRL 583
Cdd:cd01609 370 Q M AV H V P LSL EA Q AEA R VLM LSSN N ILS P AS G K P IVTPS QD MVL G L Y Y LT KERK --------------- GD K G E G I IETT 434
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 584 P pptilkpvtlwt G KQ IF SV IL RP sddnpvra N L R tkgkqycgkgedlcands YVTI qnselmsg SMD K GT L G sgskn NI 663
Cdd:cd01609 435 V ------------ G RV IF NE IL PE -------- G L P ------------------ FINK -------- TLK K KV L K ----- KL 463
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 664 FYILLRDW G QN E A A DAMSRLAR L APV Y LSNR G F SI G I G D - V T P gqgll KA K Y E LLNAGYK K CD E YIEALNT G K L qqqpgc 742
Cdd:cd01609 464 INECYDRY G LE E T A ELLDDIKE L GFK Y ATRS G I SI S I D D i V V P ----- PE K K E IIKEAEE K VK E IEKQYEK G L L ------ 532
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 743 T A EE TLEAL I LKELS V i RDHAGS A CLRE LDK S -- N SPLT MA LC G SK GS FIN I S Q MIACV G QQ A - I SG SRVP dgfenrs LP 819
Cdd:cd01609 533 T E EE RYNKV I EIWTE V - TEKVAD A MMKN LDK D pf N PIYM MA DS G AR GS KSQ I R Q LAGMR G LM A k P SG KIIE ------- LP 604
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 39725938 820 hfekhsklpaakgf VANS F YS GLT PT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV 876
Cdd:cd01609 605 -------------- IKSN F RE GLT VL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV 647
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
345-1120
5.43e-53
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: 203.85
E-value: 5.43e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - RKL VQN G pevhp G A NF I QQ 423
Cdd:COG0086 321 LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P E L KLHQCGL P KKM A LE L FK P --------- F I y RKL EER G ----- L A TT I KS 386
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 424 rhtq M K RFL kygnr E KMAQ E LK yg DI V E R h L I DGDV VL F NR Q P S LH K L S I M A HLARVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:COG0086 387 ---- A K KMV ----- E REEP E VW -- DI L E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 504 E M NL H L P QTE EA KA EA LV LM GTKA N LVT P R NG E P L I AAI QD FLT G A Y L LT LKD -------- T F F D RAKACQIIASIL V GK 575
Cdd:COG0086 455 Q M AV H V P LSL EA QL EA RL LM LSTN N ILS P A NG K P I I VPS QD MVL G L Y Y LT RER egakgegm I F A D PEEVLRAYENGA V DL 534
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 576 DEK IKVR LPPPTILKPVTLW T -- G KQIFSV IL r P SD dnpvranlrtkgkqycgkgedlcandsy V TIQ N SE lmsgs MD K G 653
Cdd:COG0086 535 HAR IKVR ITEDGEQVGKIVE T tv G RYLVNE IL - P QE ---------------------------- V PFY N QV ----- IN K K 580
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 654 TLG sgskn N I FYILL R DW G QN E AADAMS RL AR L APV Y LSNR G F SIG IG D - V T P gqgll K A K Y E LLNAGY K KCD E YIEALN 732
Cdd:COG0086 581 HIE ----- V I IRQMY R RC G LK E TVIFLD RL KK L GFK Y ATRA G I SIG LD D m V V P ----- K E K Q E IFEEAN K EVK E IEKQYA 650
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 733 T G KL qqqpgc T AE E TLEAL I L kelsv IRDH A G ---- S ACLRELDKS N SPLT MA LC G SK GS FINIS Q MIACV G QQ A isgsr 808
Cdd:COG0086 651 E G LI ------ T EP E RYNKV I D ----- GWTK A S lete S FLMAAFSSQ N TTYM MA DS G AR GS ADQLR Q LAGMR G LM A ----- 714
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 809 V P D G -- F E NR slphfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA ET GY MQ RRLV KSLE D L csqy 886
Cdd:COG0086 715 K P S G ni I E TP ----------------- IGSN F RE GL GVL E Y F IS T HGA R K GL A DTA L KTA DS GY LT RRLV DVAQ D V ---- 773
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 887 dltvrsstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E f K R V L DNIK A --- V F P CPS E PALSKNE LI LT tesimkksef 958
Cdd:COG0086 774 ---------- I VTEEDC G td R G IT v T A IK EG GE vi EPL K - E R I L GRVA A edv V D P GTG E VLVPAGT LI DE ---------- 832
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 959 lccqdsflq E IKKF I KGVSEKIK K T R dkygindngtteprvlyqldri TPTQV E KFLET C RDK Y M R -- A QMEP --- G S AV 1033
Cdd:COG0086 833 --------- E VAEI I EEAGIDSV K V R ---------------------- SVLTC E TRGGV C AKC Y G R dl A RGHL vni G E AV 881
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1034 G ALC AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS KA ISTPIITAQLDKDDDADYARL V KGRI E KTLLGEI 1113
Cdd:COG0086 882 G VIA AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA KA GGIVRLNNLKVVVNEEGKGVV V SRNS E LVIVDDG 954
....*..
gi 39725938 1114 SEYI EE V 1120
Cdd:COG0086 955 GRRE EE Y 961
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
246-1060
5.79e-52
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 202.08
E-value: 5.79e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 246 K P SDLI LT R L L V P P LCI RP S V -------- VSD L ksgtne DD L TMK lte I I FL N DVI K KHRIS GA KTQMIMEDWDF LQ LQC 317
Cdd:PRK09603 1622 R P EWMM LT V L P V L P PDL RP L V aldggkfa VSD V ------ NE L YRR --- V I NR N QRL K RLMEL GA PEIIVRNEKRM LQ EAV 1692
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 318 ALYINSEL S GIPLNM A P K KWTRGFVQRL KGKQGRFR G NL S GKRVDFSGR T VI SPD PNL RI DE VAV P VHV A KI L TF P ekvn 397
Cdd:PRK09603 1693 DVLFDNGR S TNAVKG A N K RPLKSLSEII KGKQGRFR Q NL L GKRVDFSGR S VI VVG PNL KM DE CGL P KNM A LE L FK P ---- 1768
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 398 kani NF L R KL VQN G pevhpganfiqq RH T QM K R flkygn REK M AQE l K YGDIV E -- RHLID G DV VL F NR Q P S LHK L SI M A 475
Cdd:PRK09603 1769 ---- HL L S KL EER G ------------ YA T TL K Q ------ AKR M IEQ - K SNEVW E cl QEITE G YP VL L NR A P T LHK Q SI Q A 1825
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 476 HLARVKPHRTFRFNEC 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 39725938 555 K DTFFDRA K ACQIIAS I LVGK D E K --- I KVRLPPPTILKPVTLWT G KQ I FSV IL rp S D DN P VRANL R TKG K Q ycgkgedl 631
Cdd:PRK09603 1906 K SGVKGEH K LFSSVNE I ITAI D T K eld I HAKIRVLDQGNIIATSA G RM I IKS IL -- P D FI P TDLWN R PMK K K -------- 1975
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 632 candsyvtiqnselmsgsm D K G T L gsgsknn IF Y I l LRDW G QNEA A DAMSR L AR L APV Y LSNR G F SI GIG D V - TP gqgll 710
Cdd:PRK09603 1976 ------------------- D I G V L ------- VD Y V - HKVG G IGIT A TFLDN L KT L GFR Y ATKA G I SI SME D I i TP ----- 2023
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 711 K A K YELLNAGYKKCDEYIEALNT G K L qqqpgc T AE E TLEAL I l KELSVIR D HAGSACLR -- EL DK S -- NS PLT MA LC G SK 786
Cdd:PRK09603 2024 K D K QKMVEKAKVEVKKIQQQYDQ G L L ------ T DQ E RYNKI I - DTWTEVN D KMSKEMMT ai AK DK E gf NS IYM MA DS G AR 2096
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 787 GS FIN I S Q MI A CV G QQA isgsr V PDG fenrslphfekhskl PAAKGFVANS F YS GL TPT E F F FH T MAG R E GL V DTA V KTA 866
Cdd:PRK09603 2097 GS AAQ I R Q LS A MR G LMT ----- K PDG --------------- SIIETPIISN F KE GL NVL E Y F NS T HGA R K GL A DTA L KTA 2156
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 867 ET GY MQ R R L ------ VK SLE D L C SQY ------ D LT V R S stg DI I qfiyggdgldpaamegkd EPLE --- F K RVL DN i KAV 931
Cdd:PRK09603 2157 NA GY LT R K L idvsqn VK VVS D D C GTH egieit D IA V G S --- EL I ------------------ EPLE eri F G RVL LE - DVI 2214
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 932 F P CPS E PA L SKNE LI LTT ---------- E SI MKKSEFL C cqdsflqeik K FI KGV SE K I kktrdk YG I N dng TT E PRVL Y 1001
Cdd:PRK09603 2215 D P ITN E IL L YADT LI DEE gakkvveagi K SI TIRTPVT C ---------- K AP KGV CA K C ------ YG L N --- LG E GKMS Y 2275
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*....
gi 39725938 1002 qldritptqvekfletcrdkymraqme PG S AVG ALC AQSIGEPGTQ M TL K TFH FA G V AS 1060
Cdd:PRK09603 2276 --------------------------- 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
4.02e-51
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507
Cd Length: 158
Bit Score: 177.44
E-value: 4.02e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 528 N LVT P R NG E P L I AAI QD FLT GAYLLT LK DTFFDR AKAC Q IIASIL V gkdekikvr LP P P T ILKP VT - LWTGKQ I FS VI L R 606
Cdd:pfam04983 1 N ILS P Q NG K P I I GPS QD MVL GAYLLT RE DTFFDR EEVM Q LLMYGI V --------- LP H P A ILKP IK p LWTGKQ T FS RL L P 71
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 607 P sddnpv RA N LRT K G K QYC gkg EDLC A NDSYV T I Q N S EL M SG SM DK G T L G s G S KNNIFY I LLRDW G QN E A A DAMS RL AR L 686
Cdd:pfam04983 72 N ------ EI N PKG K P K TNE --- EDLC E NDSYV L I N N G EL I SG VI DK K T V G - K S LGSLIH I IYKEY G PE E T A KFLD RL QK L 141
170
....*....|....*..
gi 39725938 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
1.88e-49
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 194.07
E-value: 1.88e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 246 K P SDL ILT RLLVP P LCI RP S V vs D L K SG TNE - D DL TMKLTE II FL N DVIK K HRISGAKTQ MI MEDWDF LQ LQC - A L YI NS 323
Cdd:PRK14844 1665 R P EWM ILT TIPIL P PDL RP L V -- S L E SG RPA v S DL NHHYRT II NR N NRLR K LLSLNPPEI MI RNEKRM LQ EAV d S L FD NS 1742
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 324 ELSGIPLNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P EKVN K A ninf 403
Cdd:PRK14844 1743 RRNALVNKAGAVGYKKSISDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P T L KLNQCGL P KRM A LE L FK P FVYS K L ---- 1818
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 404 lr K LVQNG P EV hpganfiqqrhtqmkrfl K YGNREKM A QELKYG D IV E r HL I DGDV VL F NR Q P S LH K L S I M A HLARVKPH 483
Cdd:PRK14844 1819 -- K MYGMA P TI ------------------ K FASKLIR A EKPEVW D ML E - EV 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 39725938 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 39725938 562 -- AKA C QIIA S ILV G K --- DEK IK V R L ----- PPP T IL K PVTLWT G KQ I FSV I L rpsddn P VRA NL rtkgkqycgk G E DL 631
Cdd:PRK14844 1958 sf GAF C EVEH S LSD G T lhi HSS IK Y R M eyins SGE T HY K TICTTP G RL I LWQ I F ------ P KHE NL ---------- G F DL 2021
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 632 C an DSYV T IQ ns E LM S gsmdkgtlgsgsknn I FYILL R DW GQ NEAADAMSR L AR L APV Y LSNR G F S IGIG D VT pgqg LLK 711
Cdd:PRK14844 2022 I -- NQVL T VK -- E IT S --------------- I VDLVY R NC GQ SATVAFSDK L MV L GFE Y ATFS G V S FSRC D MV ---- IPE 2078
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 712 A K YELLNAGYKKCDEY iealntg KL Q Q Q P G CTAEETLEALILK E L S VIR D HAGSAC L REL ------ D K S NS PLT M ALC G S 785
Cdd:PRK14844 2079 T K ATHVDHARGEIKKF ------- SM Q Y Q D G LITRSERYNKVID E W S KCT D MIANDM L KAI siydgn S K Y NS VYM M VNS G A 2151
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 786 K GS fin I SQM IACV G QQAISGS rv P D G f E NRSL P hfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GL V DTA V KT 865
Cdd:PRK14844 2152 R GS --- 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 KT 2211
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 866 A ET GY MQ RRLV KSLED - LCSQY D lt VRSST G DIIQFIYG G DGL d P A AM E GK deplefkr VL DNIK A vfpcpsepalsk N E 944
Cdd:PRK14844 2212 A NS GY LT RRLV DVSQN c IVTKH D -- CKTKN G LVVRATVE G STI - V A SL E SV -------- VL GRTA A ------------ N D 2268
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 945 LI -- L T T E SIM K KS E FL ccqdsflqeikkfikg VSE K I K K trdkyg IN DN G TTEPRVLYQ L D - R I T P TQVE kf L ETC RD K 1021
Cdd:PRK14844 2269 IY np V T K E LLV K AG E LI ---------------- DED K V K Q ------ IN IA G LDVVKIRSP L T c E I S P GVCS -- L CYG RD L 2324
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1022 YMRAQMEP G S AVG ALC AQS I GEPGTQ M T LK TFH FA GV ----------- AS M N I --------------------------- 1063
Cdd:PRK14844 2325 ATGKIVSI G E AVG VIA AQS V GEPGTQ L T MR TFH IG GV mtrgvessnii AS I N A kiklnnsniiidkngnkivisrscevv 2404
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1064 --- T LG VPRI K E -------- IINASKAI ------------ ST PIIT aql D K DDDAD Y AR L VK G r I EK T LLGEI S EY I EEV 1120
Cdd:PRK14844 2405 lid S LG SEKL K H svpygakl YVDEGGSV kigdkvaewdpy TL PIIT --- E K TGTVS Y QD L KD G - I SI T EVMDE S TG I SSK 2480
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1121 FLP D -------- DCFILVK L SLERIRLLR L EVNA E TVRYSICTSK L R V KP G D v A VH GEA V VCV TPRE NS K S ----- SMYY 1187
Cdd:PRK14844 2481 VVK D wklysgga NLRPRIV L LDDNGKVMT L ASGV E ACYFIPIGAV L N V QD G Q - K VH AGD V ITR TPRE SV K T rditg GLPR 2559
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1188 V LQFLKEDL PK -- VV V QG I P ------------ EV S RAVIHI DEQ S ------- GKE K YKLLV EGD NL R avmathgv KG TRT 1246
Cdd:PRK14844 2560 V IELFEARR PK eh AI V SE I D gyvafsekdrrg KR S ILIKPV DEQ I spveylv SRS K HVIVN EGD FV R -------- KG DLL 2631
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1247 TSNNT -- YEVEKT LG I EA ARTTI I N EIQ YTMVNH G MS ID RR H VMLLSDL M TY K G E VL ----------------------- 1301
Cdd:PRK14844 2632 MDGDP dl HDILRV LG L EA LAHYM I S EIQ QVYRLQ G VR ID NK H LEVILKQ M LQ K V E IT dpgdtmylvgesidklevdrend 2711
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 39725938 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 2712 amsnsgkrpahylpilq 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 ...
729-834
1.31e-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: 145.20
E-value: 1.31e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 729 E A LNT GKL QQQP G C T A EE TL EALI LKE L SVI RD H AG SACLRE LD KS NS PLT MA LC G S KGS F INISQ MIA C V GQQ AIS G S R 808
Cdd:pfam05000 3 D A ERY GKL EDIW G M T L EE SF EALI NNI L NKA RD P AG NIASKS LD PN NS IYM MA DS G A KGS I INISQ IAG C R GQQ NVE G K R 82
90 100
....*....|....*....|....*.
gi 39725938 809 V P D GF EN R S LPHF E K HSKL P AAK GFV 834
Cdd:pfam05000 83 I P F GF SG R T LPHF K K DDEG P ESR GFV 108
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
345-553
6.26e-33
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 136.80
E-value: 6.26e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 345 LK GKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P EKVNK ------- A NI NFLR KL V Q NG - PEV H p 416
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 lirqgiv N NI KAAK KL I Q RA d PEV W - 417
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 417 ganfiqqrhtqmkrflkygnrekmaqelkyg DIV E R h L I D G DV VL F NR Q P S LH K L S I M A HLARVKPH R TFRFNEC VC TPY 496
Cdd:PRK02625 418 ------------------------------- QVL E E - V I E G HP VL L NR A P T LH R L G I Q A FEPILVEG R AIQLHPL VC PAF 465
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 39725938 497 NADFDGD E 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 466 NADFDGD Q 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
2.13e-32
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 135.42
E-value: 2.13e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 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 k I LT F 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 - I EL F 406
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 393 PEK V NKAN I N fl RK L VQ N gpe VHPGANF I QQRHTQMKRF L K ygnrekmaqelkygdiver HLID G DV VL F NR Q P S LH K L S 472
Cdd:CHL00018 407 QPF V IRGL I R -- QH L AS N --- IRAAKSK I REKEPIVWEI L Q ------------------- EVMQ G HP VL L NR A P T LH R L G 462
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 473 I M A hlar 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 T G 548
Cdd:CHL00018 463 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 L G 538
....*.
gi 39725938 549 A Y L LT L 554
Cdd:CHL00018 539 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
1.09e-17
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain]
Cd Length: 1227
Bit Score: 89.52
E-value: 1.09e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 650 M DK GT L gsgsk N N IFYILLRDW G QNEA A DAMSR L AR L APV Y LSNR G F SI GIG D VT pgqg LLK AK YE LL N A GY K KCDEYI E 729
Cdd:TIGR02388 7 V DK KA L ----- K N LISWAYKTY G TART A AMADK L KD L GFR Y ATRA G V SI SVD D LK ---- VPP AK QD LL E A AE K EIRATE E 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 730 ALNT G KLQ ----- Q QPGC T AEE T L E A L ILK els V IRD hagsac L R EL D KS NS PLT MA LC G SK G sfi N I SQ MIAC VG QQAI 804
Cdd:TIGR02388 78 RYRR G EIT everf Q KVID T WNG T N E E L KDE --- V VNN ------ F R QT D PL NS VYM MA FS G AR G --- N M SQ VRQL VG MRGL 145
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 805 SGS rv P D G f E NRS LP hfekhsklpaakgf VANS F YS GLT P TE FFFHTMAG R E GLVDTA VK TA ET GY MQ RRLV KSLE D L -- 882
Cdd:TIGR02388 146 MAN -- P Q G - E IID LP -------------- IKTN F RE GLT V TE YVISSYGA R K GLVDTA LR TA DS GY LT RRLV DVSQ D V iv 208
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 883 ---- C - SQYDLT VR SS T - GD ii QF I YG GD G L dpaamegkdeple FK R VL dn IKA V FPCPS E PALS KN EL I lttesimkks 956
Cdd:TIGR02388 209 reed C g TERSIV VR AM T e GD -- KK I SL GD R L ------------- LG R LV -- AED V LHPEG E VIVP KN TA I ---------- 261
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 957 eflccqdsflqeikkfikgv SEKIK KT rdkyg I NDN G TT E PR V L yqldri T P TQV E KFLET CR DK Y MRA ----- QMEP G S 1031
Cdd:TIGR02388 262 -------------------- DPDLA KT ----- I ETA G IS E VV V R ------ S P LTC E AARSV CR KC Y GWS lahah LVDL G E 310
410 420
....*....|....*....|....*..
gi 39725938 1032 AVG ALC AQSIGEPGTQ M T LK TFH FA GV 1058
Cdd:TIGR02388 311 AVG IIA AQSIGEPGTQ L T MR TFH TG GV 337
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1028-1078
1.14e-14
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain]
Cd Length: 204
Bit Score: 74.10
E-value: 1.14e-14
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 39725938 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 1078
Cdd:cd02655 4 E L G E AVG IIA AQSIGEPGTQ L T MR TFH TG GVA T - D IT Q G L PR VE E LFE A R K 53
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
769-1058
1.74e-14
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 78.88
E-value: 1.74e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 769 R EL D KS NS PLT MA LC G SK G sfi N I SQ MIAC VG QQAISGS rv P D G f E NRS LP hfekhsklpaakgf VANS F YS GLT P TE FF 848
Cdd:PRK02597 114 R QN D PL NS VYM MA FS G AR G --- N M SQ VRQL VG MRGLMAN -- P Q G - E IID LP -------------- IKTN F RE GLT V TE YV 173
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 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 39725938 924 VL DNIK avfpcpsepalsk NE L I -- LTT E SIM - KKS E FLCCQD sfl QE I KK fik GVSE KI K K T rdkygindn G TT E PR V l 1000
Cdd:PRK02597 231 VL IPLG ------------- DR L L gr VLA E DVV d PEG E VIAERN --- TA I DP --- DLAK KI E K A --------- G VE E VM V - 281
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 39725938 1001 yqld R i T P TQV 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_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1030-1363
7.96e-11
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain]
Cd Length: 381
Bit Score: 65.52
E-value: 7.96e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1030 G SA VG A L C A QS I G EP GTQMT L KT fhfagv ASMNITLGVPRI KE IINASKAISTP ------ I ITAQ L D K D D --- DADY A R L 1100
Cdd:cd02737 1 G EP VG S L A A TA I S EP AYKAL L DP ------ PQSLESSPLELL KE VLECRSKSKSK endrrv I LSLH L C K C D hgf EYER A A L 74
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1101 - VK GRI E KTL L GEISEYIEEVFL P DDCFIL V KLSLERIRLLRLEVNAE tv RY S ICTSKLRVK P GDVAV H ------- GEAV 1172
Cdd:cd02737 75 e VK NHL E RVT L EDLATTSMIKYS P QATEAI V GEIGDQLNTKKKGKKKA -- IF S TSLKITKFS P WVCHF H ldkecqk LSDG 152
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1173 V C V T --- PR E N SKSS MY y V L QF L KE ---- D L PKV V VQ G IPEV ----------- S RAVIHIDEQ S GKEKYK L L V ------- 1227
Cdd:cd02737 153 P C L T fsv SK E V SKSS EE - L L DV L RD riip F L LET V IK G DERI ksvnilwedsp S TSWVKSVGK S SRGELV L E V tveesck 231
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 1228 -- E G DNLRA VM AT ----- HGVKGT R TTSNNTYEVEKT LGI E AA RTTIINEIQYTMVNH G M S ID R R H VM L LS D L MTY K GE V 1300
Cdd:cd02737 232 kt R G NAWNV VM DA cipvm DLIDWE R SMPYSIQQIKSV LGI D AA FEQFVQRLESAVSMT G K S VL R E H LL L VA D S MTY S GE F 311
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 39725938 1301 L G ITRF G LAKMKE S V ----- LML A S F EKTADHLFD AA YF G QK DS VC GV SECIIM G IPMNI GTG - L F KL L 1363
Cdd:cd02737 312 V G LNAK G YKAQRR S L kisap FTE A C F SSPIKCFLK AA KK G AS DS LS GV LDACAW G KEAPV GTG s K F EI L 380
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
841-1058
1.63e-08
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 59.57
E-value: 1.63e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 841 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 AAMEG 914
Cdd:CHL00117 172 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 RNGMM 235
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 915 KDEP L EFK --- RVL - D N I K avfpcpsepal SKNEL I L T TE simkkseflcc QD SFLQEIKK FI K gvsekikktrdkygin 990
Cdd:CHL00117 236 IERI L IQT lig RVL a D D I Y ----------- IGSRC I A T RN ----------- QD IGIGLANR FI T ---------------- 277
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39725938 991 dngtteprvl YQLDR I --- T P T qvekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL K TF 1053
Cdd:CHL00117 278 ---------- FRAQP I sir S P L ------- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL R TF 338
....*
gi 39725938 1054 H FA GV 1058
Cdd:CHL00117 339 H TG GV 343
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1004-1050
3.40e-07
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 54.90
E-value: 3.40e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 39725938 1004 D RI T PTQ VE KFLETCRDK Y MR A QM EP GS AVG ALC AQSIGEPGTQM T L 1050
Cdd:PRK14898 31 D GV T EEM VE 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
