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DNA-directed RNA polymerase III subunit RPC1 [Rattus norvegicus]
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: 1671.16
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 24 SPE EMRQQAHIQ V VSK NLY SQDNNH 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 2412574953 104 ILQ M ICKTC CHIM L SQ EEK QQ FL DF L K RP G L TY LQK RG LKKKI SD KC R K KST C HY CG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C PH CG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV R NGPDVHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGPDVHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 424 R HMQM K R FLKYGNR E K M A Q ELK F GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L AKV K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R AKV M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C T ND S YV T I Q NSEL M CG 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 L CG RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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: 563.77
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DM 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 2412574953 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 2412574953 1181 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek F KLLVEG 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 -- Y KLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
7.39e-10
RNA polymerase beta'' subunit; Reviewed
CHL00117 :Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 63.80
E-value: 7.39e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 915 KDEP L EFK --- RVL - D N I K avypcqseralsknelt LTTEA I MKK N eflcc QD --- SFLQEIK TF - IKGV S ekikktrdk 986
Cdd:CHL00117 236 IERI L IQT lig RVL a D D I Y ----------------- IGSRC I ATR N ----- QD igi GLANRFI TF r AQPI S --------- 284
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 987 ygindngtteprvlyqldri T R TQI ekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL K T 1052
Cdd:CHL00117 285 -------------------- I R SPL ----- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL R T 337
....*.
gi 2412574953 1053 FH FA GV 1058
Cdd:CHL00117 338 FH 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: 1671.16
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 24 SPE EMRQQAHIQ V VSK NLY SQDNNH 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 2412574953 104 ILQ M ICKTC CHIM L SQ EEK QQ FL DF L K RP G L TY LQK RG LKKKI SD KC R K KST C HY CG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C PH CG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV R NGPDVHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGPDVHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 424 R HMQM K R FLKYGNR E K M A Q ELK F GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L AKV K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R AKV M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C T ND S YV T I Q NSEL M CG 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 L CG RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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
7-932
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 955.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 7 RETDVA K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y sq D NNHA 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 -- D DDGY 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 2412574953 87 D L EL P CF HVG YFRAVIGI L QMI C KT C CHIM L SQ EE KQQF L DF L K R PGLTYLQKRG L K K KISDKCR K KST C HY CG A fngtv 166
Cdd:PRK08566 79 E L AR P VI HVG FAKLIYKL L RAT C RE C GRLK L TE EE IEEY L EK L E R LKEWGSLADD L I K EVKKEAA K RMV C PH CG E ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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 2412574953 400 NI NF LR KL V R NGP DV HPGAN FIQQR hm QMK R F - L KYG N R E KM A QE L KF G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA 478
Cdd:PRK08566 359 NI EE LR EY V L NGP EK HPGAN YVIRP -- DGR 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 2412574953 479 K V K P HR TFR F N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLVT PR N G E P L I AA IQD FLT GAYLLT L K D T F 558
Cdd:PRK08566 437 R V L P GK TFR L N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RI LM LVQEHILS PR Y G G P I I GG IQD HIS GAYLLT R K S T L 516
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 TN 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 2412574953 638 V T I Q N SE L MC 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 2412574953 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 2412574953 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 2412574953 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 VLDNIKAVY 932
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 IIERVLGKE 880
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-925
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 888.68
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 13 KKI SH I C FG MK SPEE M R QQAHIQ VV SKNL Y SQ D N nh 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 2412574953 93 F HVG YFRAVIG IL QMI C KT C CH I M L SQ EE KQ Q F L D - FL K RPGLTYLQKRG L KK KI SDKCR K KST C HY CG A fngtvkkc GL 171
Cdd:TIGR02390 80 V HVG FAKEIYK IL RAT C RK C GR I T L TE EE IE Q Y L E k IN K LKEEGGDLAST L IE KI VKEAA K RMK C PH CG E -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 330 LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT F PE K V NKA NI NF LR KL V R 409
Cdd:TIGR02390 285 ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PE R V TPW NI DE LR EY V L 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 410 NGPD VH PGAN FIQQR hm QMK R F - LKYG N R E KM A QE L KF G DI VERHLIDGD V VLFNRQPSLH KL S I M A H LA KV K P HR TFR F 488
Cdd:TIGR02390 365 NGPD SW PGAN YVIRP -- DGR R I k IRDE N K E EL A ER L EP G WV VERHLIDGD I VLFNRQPSLH RM S M M G H KV KV L P GK TFR L 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 TN D S YV T I Q N SE L MC 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 2412574953 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 2412574953 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 2412574953 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 2412574953 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: 563.77
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DM 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 2412574953 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 2412574953 1181 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek F KLLVEG 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 -- Y KLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
7.80e-150
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 455.44
E-value: 7.80e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 408 VRNGP dvh P GA NF I QQ rhm QM K RF LK YGNRE K M A QE LK F GDIVERH L IDGDVVLFNRQP S LH KL SI M AH LAK V KPHR T F R 487
Cdd:smart00663 159 VRNGP --- N GA KY I IR --- GK K TN LK LAKKS K I A NH LK I GDIVERH V IDGDVVLFNRQP T LH RM SI Q AH RVR V LEGK T I R 232
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2412574953 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
1.13e-130
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: 405.91
E-value: 1.13e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 12 A KKI SH I C FG MK SPEE M R QQAHIQ V VSKNL Y S q DNNHA 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 2412574953 92 C FH V G Y F RAVIG IL QMI CK T C CHIM L SQEEKQQ F LDFL KR P GL TY L QKR gl K K K I SDK C R KK ST C HY CG AF NG TVKK cgl 171
Cdd:pfam04997 80 V FH I G F F KKTLK IL ECV CK Y C SKLL L DPGKPKL F NKDK KR L GL EN L KMG -- A K A I LEL C K KK DL C EH CG GK NG VCGS --- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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
1.37e-116
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: 375.54
E-value: 1.37e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 841 GLTP T EFFFHTM A GREGL V DTAVKTAE T GY M QRRLVK S LEDL CSQ YD L TVR S S T G D I I QF I YG G DGLDP AAM E GKD - EPL 919
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G E I V QF L YG E DGLDP LKI E KQG r FTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 920 EF KRVLDNI K AVYPCQSERA L SKNELTLTTEA I MKKNEF L C -- CQDSFL QE IK T FIKGVSE K I ---- K KT R DKYGI N DN g 993
Cdd:pfam04998 81 EF SDLKLED K FKNDLLDDLL L LSEFSLSYKKE I LVRDSK L G rd RLSKEA QE RA T LLFELLL K S gles K RV R SELTC N SK - 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 994 tteprvlyqldritrt QIEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL K TFHFAGVAS M N I TLGVPR I KEI 1073
Cdd:pfam04998 160 ---------------- AFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL N TFHFAGVAS K N V TLGVPR L KEI 223
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1074 IN A SK A I ST P II T AQ L -- DMDDDADY A RL V K G R IEK TL LG EIS E YI E ------------------------------ EVF 1121
Cdd:pfam04998 224 IN 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 NEE 303
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1122 LP D DCFI L VK L SLERIRL L RLEVNAETVRYS I c TSKL R V K pg DVAVHGE A VVCV T PRENSK S SMYY ------- VLQF L KE 1194
Cdd:pfam04998 304 EI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I - PRSI R N K -- VDEGRDI A IGEI T AFIIKI S KKIR qdtgglr RVDE L FM 380
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1195 D ------------ L PKVVVQ GIP EVS R AVIHI D E q S GK EK -- FK L LV EG D NL RA V MATH G - V KGT R TT SN NTY E VEKT LG 1259
Cdd:pfam04998 381 E 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 LG 459
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 2412574953 1260 IEAAR 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 460 IEAAR 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
7.20e-96
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 313.32
E-value: 7.20e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1006 I T RTQI E KFL E TCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II 1085
Cdd:PRK04309 35 L T EEEV E EII E EVVRE Y L R SLV EPG E AVG VVA AQSIGEPGTQMT MR TFH Y AGVA EI N V TLG L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1086 T AQ L DMD -- 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 2412574953 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 EKFKLLV 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 ---- DEYVIYT EG S NL KE V LKVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
1.69e-84
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 281.17
E-value: 1.69e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1010 QIEKFLETCRDK Y M R AQME PG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L 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 2412574953 1090 DMDD -- 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 2412574953 1162 P G D V AV -- HGEAVVCVT P REN S kssm YYV L QF LKE DLPKVVVQ GI PEVS R A VI hide QSGKEKFKLLV 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 ---- RKEGDEYVIYT EG S NL KE V LKLE 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
4.38e-52
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain]
Cd Length: 1165
Bit Score: 201.16
E-value: 4.38e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - RKL VRN G pdvhp 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 2412574953 424 rhmq M K RFL kygnr E KMAQ E LK fg DI V E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:COG0086 387 ---- A K KMV ----- E REEP E VW -- DI L E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 576 DEK IKVR LPPPTILKPVTLW T -- G KQIFSV IL r P SD dnpvranlrtkgkqycgkgedlctndsy V TIQ N SE lmcgs 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 2412574953 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 2412574953 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 2412574953 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 2412574953 887 dltvrsstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E f K R V L DNIK A -- V YPCQSERA L SKNELTLTT E AIMK knefl 959
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 ed V VDPGTGEV L VPAGTLIDE E VAEI ----- 837
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 960 ccqdsflqeiktf I KGVSEKIK K T R dkygindngtteprvlyqldri TRTQI E KFLET C RDK Y M R -- A QMEP --- G S AVG 1034
Cdd:COG0086 838 ------------- I EEAGIDSV K V R ---------------------- SVLTC E TRGGV C AKC Y G R dl A RGHL vni G E AVG 882
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1035 ALC AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS KA ISTPIITAQLDMDDDADYARL V KGRI E KTLLGEIS 1114
Cdd:COG0086 883 VIA AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA KA GGIVRLNNLKVVVNEEGKGVV V SRNS E LVIVDDGG 955
....*.
gi 2412574953 1115 EYI EE V 1120
Cdd:COG0086 956 RRE EE Y 961
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
841-1058
7.39e-10
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 63.80
E-value: 7.39e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 915 KDEP L EFK --- RVL - D N I K avypcqseralsknelt LTTEA I MKK N eflcc QD --- SFLQEIK TF - IKGV S ekikktrdk 986
Cdd:CHL00117 236 IERI L IQT lig RVL a D D I Y ----------------- IGSRC I ATR N ----- QD igi GLANRFI TF r AQPI S --------- 284
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 987 ygindngtteprvlyqldri T R TQI ekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL K T 1052
Cdd:CHL00117 285 -------------------- I R SPL ----- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL R T 337
....*.
gi 2412574953 1053 FH FA GV 1058
Cdd:CHL00117 338 FH 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: 1671.16
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 24 SPE EMRQQAHIQ V VSK NLY SQDNNH 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 2412574953 104 ILQ M ICKTC CHIM L SQ EEK QQ FL DF L K RP G L TY LQK RG LKKKI SD KC R K KST C HY CG afngtvkkcgllkiihekyktnk 183
Cdd:cd02583 81 ILQ C ICKTC SRVL L PE EEK RK FL KR L R RP N L DN LQK KA LKKKI LE KC K K VRK C PH CG ----------------------- 137
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 344 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID E V A VP V HVAKILT F PE K V NKA NI NF LRKLV R NGPDVHPGANF IQQ 423
Cdd:cd02583 272 RLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRID Q V G VP E HVAKILT Y PE R V TRY NI EK LRKLV L NGPDVHPGANF VIK 351
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 424 R HMQM K R FLKYGNR E K M A Q ELK F GDIVERHL I DGD V VLFNRQPSLH K LSIMAH L AKV K P H RTFRFNECVCTPYNADFDGD 503
Cdd:cd02583 352 R DGGK K K FLKYGNR R K I A R ELK I GDIVERHL E DGD I VLFNRQPSLH R LSIMAH R AKV M P W RTFRFNECVCTPYNADFDGD 431
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 584 PPP T ILKPV T LWTGKQIFS VI LRP SDDN PV RA NL RT K G K Q Y CG K GE D L C T ND S YV T I Q NSEL M CG 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 L CG RL DK S TLGSGSKN SL 588
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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: 970.18
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 12 A K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y SQ D NN ha P LLY G VL D H R M G TS E KDRP C E TCG KNLAD C L GH Y G Y I D L EL P 91
Cdd:cd02582 1 P K R I KG I K FG LL SPEE I R KMSVVEIITPDT Y DE D GY -- 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 2412574953 92 CF HVG YFRAVIGI L QMI C KT C CH I M L SQ EE KQQF L DFLK R - PGLTYLQKRGLKK K ISD K CR K KST C HY CGA fngtvkkc G 170
Cdd:cd02582 79 VI HVG FAKHIYDL L RAT C RS C GR I L L PE EE IEKY L ERIR R l KEKWPELVKRVIE K VKK K AK K RKV C PH CGA -------- P 150
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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 2412574953 407 LV R NGPD VH PGAN FIQQRHMQMK R f L K Y G NRE KM A QE L KF G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LAK V K P HR TF 486
Cdd:cd02582 362 LV L NGPD KW PGAN YVIRPDGRRI R - L R Y V NRE EL A ER L EP G W IVERHLIDGD I VLFNRQPSLH RM SIMAH RVR V L P GK TF 440
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 T 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 2412574953 646 MC 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 2412574953 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 2412574953 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 2412574953 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
7-932
0e+00
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 955.07
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 7 RETDVA K K I SH I C FG MK SPEE M R QQAHIQVVSKNL Y sq D NNHA 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 -- D DDGY 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 2412574953 87 D L EL P CF HVG YFRAVIGI L QMI C KT C CHIM L SQ EE KQQF L DF L K R PGLTYLQKRG L K K KISDKCR K KST C HY CG A fngtv 166
Cdd:PRK08566 79 E L AR P VI HVG FAKLIYKL L RAT C RE C GRLK L TE EE IEEY L EK L E R LKEWGSLADD L I K EVKKEAA K RMV C PH CG E ----- 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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 2412574953 400 NI NF LR KL V R NGP DV HPGAN FIQQR hm QMK R F - L KYG N R E KM A QE L KF G D IVERHLIDGD V VLFNRQPSLH KL SIMAH LA 478
Cdd:PRK08566 359 NI EE LR EY V L NGP EK HPGAN YVIRP -- DGR 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 2412574953 479 K V K P HR TFR F N EC VC T PYNADFDGDEMNLH L PQTEEA K AEA LV LM GTKANLVT PR N G E P L I AA IQD FLT GAYLLT L K D T F 558
Cdd:PRK08566 437 R V L P GK TFR L N LA VC P PYNADFDGDEMNLH V PQTEEA R AEA RI LM LVQEHILS PR Y G G P I I GG IQD HIS GAYLLT R K S T L 516
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 TN 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 2412574953 638 V T I Q N SE L MC 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 2412574953 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 2412574953 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 2412574953 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 VLDNIKAVY 932
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 IIERVLGKE 880
RNA_pol_rpoA1
TIGR02390 DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
13-925
0e+00
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Pssm-ID: 274106 [Multi-domain]
Cd Length: 868
Bit Score: 888.68
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 13 KKI SH I C FG MK SPEE M R QQAHIQ VV SKNL Y SQ D N nh 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 2412574953 93 F HVG YFRAVIG IL QMI C KT C CH I M L SQ EE KQ Q F L D - FL K RPGLTYLQKRG L KK KI SDKCR K KST C HY CG A fngtvkkc GL 171
Cdd:TIGR02390 80 V HVG FAKEIYK IL RAT C RK C GR I T L TE EE IE Q Y L E k IN K LKEEGGDLAST L IE KI VKEAA K RMK C PH CG E -------- EQ 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 330 LNMAPKKWTRGFV QRLKGK Q GRFRGNLSGKRV D FS G RTVISPDPN LR I D EV A VP VHV AK I LT F PE K V NKA NI NF LR KL V R 409
Cdd:TIGR02390 285 ARHRSGRPLKTLA QRLKGK E GRFRGNLSGKRV N FS A RTVISPDPN IS I N EV G VP EQI AK E LT V PE R V TPW NI DE LR EY V L 364
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 410 NGPD VH PGAN FIQQR hm QMK R F - LKYG N R E KM A QE L KF G DI VERHLIDGD V VLFNRQPSLH KL S I M A H LA KV K P HR TFR F 488
Cdd:TIGR02390 365 NGPD SW PGAN YVIRP -- DGR R I k IRDE N K E EL A ER L EP G WV VERHLIDGD I VLFNRQPSLH RM S M M G H KV KV L P GK TFR L 442
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 TN D S YV T I Q N SE L MC 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 2412574953 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 2412574953 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 2412574953 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 2412574953 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: 878.59
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 13 K K I SH I C FG MK SP EEM R QQAHIQVVSKNL Y SQ D N nh A P LLY G V LD H R M GT S E KDRP C E TCG KNL A D C L GH Y G Y I D L EL P C 92
Cdd:PRK14977 7 K A I DG I I FG LI SP ADA R KIGFAEITAPEA Y DE D G -- L P VQG G L LD G R L GT I E PGQK C L TCG NLA A N C P GH F G H I E L AE P V 84
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 93 F H VGYFRAVIGI L QMI C KT C CHIM L S QE EKQQ F l DFLKRPGLTYL --- Q KR --- GLKKKIS D KC ---- R K KST C HY CGA 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 PH CGA P 163
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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 2412574953 400 NI NFLRK LV R NGPD VH PGAN F I QQ ------ R HMQMKRFL K YGN RE k M A QE L KF GDIVERHL I DGD V V L FNRQPSLHKLSI 473
Cdd:PRK14977 369 NI EKMKE LV I NGPD EF 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 2412574953 474 M AH LA KV K P HR TFR FNEC VC T PYNADFDGDEMNLH L PQ T E E A K AEA LV LMG T K A NL VT PR N G E P L I A A I QDF L T G AYL L T 553
Cdd:PRK14977 448 L AH RV KV L P GA TFR LHPA VC P PYNADFDGDEMNLH V PQ I E D A R AEA IE LMG V K D NL IS PR T G G P I I G A L QDF I T A AYL I T 527
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 632 C TN D S YV T I QNS EL MC G 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 IS G 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 2412574953 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 2412574953 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 2412574953 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 2412574953 931 V ypc QSERAL SK N E L tltt E AIM K KNE flccqdsflqei KTF ikgvsekikktrdkygi N D N GTTEPRVLYQLDRITRTQ 1010
Cdd:PRK14977 915 E --- DRGKGA SK D E I ---- E ELA K EYT ------------ KTF ----------------- N A N LPKLLADAIHGAELKEDE 958
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1011 I 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 2412574953 1091 MDDDA 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 2412574953 1167 VHGEAVVCVTPRENSKSSMYYV L QFLKEDLPKVV V Q G I P EVS RA VIHID E QS G KEKFKLLVE 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 2412574953 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 2412574953 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: 851.06
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 20 FG MK SP E E M R QQAHIQVVSK nl YSQD N NHA 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 2412574953 100 AVIG IL QMI CK tcch IM LS Q E E kqqfldflkrpgltylqkrglkkkisdkcrkkstchycgafngtvkkcgllkiiheky 179
Cdd:cd02733 83 KILK IL RCV CK ---- RE LS A E R ---------------------------------------------------------- 100
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 340 --- GFV QRLKGK Q GR F RGNL S GKRVDFS G RTVI S PDPNL RI D E V A VP VHV A KI LTFPE K V NKA NI NF L RK LVRNGP DVH P 416
Cdd:cd02733 215 plk SIR QRLKGK E GR I RGNL M GKRVDFS A RTVI T PDPNL EL D Q V G VP RSI A MN LTFPE I V TPF NI DR L QE LVRNGP NEY P 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 417 GA NF I Q q R HMQMKRF L K Y GNR e KMAQE L KF G D IVERHL I DGDVVLFNRQPSLHK L S I M A H LA KV K P HR TFR F N EC V C TPY 496
Cdd:cd02733 295 GA KY I I - R DDGERID L R Y LKK - ASDLH L QY G Y IVERHL Q DGDVVLFNRQPSLHK M S M M G H RV KV L P YS TFR L N LS V T TPY 372
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 577 EKIKVRL P P P T ILKP VT LWTGKQIFS V I L r P SDD N PV R ANLRTK G KQY cgkge DLCTN D SY V T I Q N S EL MC G 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 LS G ILC K K T V G 521
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 817 S LPHF E K HSKL P AAK GFV A NS FYS GLTP T EFFFH T M A GREGL V DTAVKTAETGY M QRRLVK SL ED LCSQ YD 887
Cdd:cd02733 681 T LPHF I K DDYG P ESR GFV E NS YLR GLTP Q EFFFH A M G GREGL I DTAVKTAETGY I QRRLVK AM ED VMVK YD 751
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
23-887
0e+00
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain]
Cd Length: 528
Bit Score: 711.13
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 23 K SPEE M R QQAHIQ V VSKNLYSQDNNH 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 2412574953 103 GI L Q micktcchimlsqeekqqfldflkrpgltylqkrglkkkisdkcrkkstchycgafngtvkkcgllkiihekyktn 182
Cdd:cd00399 80 SF L G ---------------------------------------------------------------------------- 83
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 343 QRLKGK Q GRFRGNL S GKRVDFSGR T VISPDPNLR I D E V A VP VHV A KI L tfpekvnkaninflrklvrngpdvhpganfiq 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 2412574953 423 qrhmqmkrflkygnrekmaqelkfgdiverhli DGD V VLFNRQPSLHKLSIMAH LAK V K P HR TFR F N EC VC T PYNADFDG 502
Cdd:cd00399 190 --------------------------------- DGD P VLFNRQPSLHKLSIMAH RVR V L P GS TFR L N PL VC S PYNADFDG 236
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 583 lppptilkpvtlwt GKQI F S VI L rpsddnpvranlrtkgkqycgkgedlctndsyvtiqnselmcgsmdkgtlgsgs KNN 662
Cdd:cd00399 289 -------------- GKQI V S AA L ------------------------------------------------------ PGG 300
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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: 578.37
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 20 F GMK S P EE M R QQAHIQVVSKNLYSQDNN ha P LLY G VL D HRM G TSE KD RP C E TCG K N LAD C L GH Y G Y I D L E LP CFHVGY F R 99
Cdd:cd01435 2 F SFY S A EE I R KLSVKEITNPVTFDSLGH -- 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 2412574953 100 AVIGI L QMI C KT C CHIML S QE E KQQ F LDF LK R pgltylqkrglkkkisdkcrkkstchycgafngtvkkcgllkiiheky 179
Cdd:cd01435 80 LLYKL L RGS C FY C HRFRI S KW E VKL F VAK LK L ------------------------------------------------ 111
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 180 ktnkkvvdpivsnflqsfeta IEHNKE VE pllgr A Q E NLNPL vvl NL F kripaedvplllmnpeagkpsdl I L TR LLVPP 259
Cdd:cd01435 112 --------------------- LDKGLL VE ----- A A E LDFGY --- DM F ----------------------- F L DV LLVPP 139
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 405 R KL V R NGPDV H PGAN F I QQR -- HMQMKRF L KYGN R EKM A ---------- QE L KFGDI V E RHL I DGDVVL F NRQP S LHK L S 472
Cdd:cd01435 294 R QA V I NGPDV Y PGAN A I EDE dg RLILLSA L SEER R KAL A klllllssak LL L NGPKK V Y RHL L DGDVVL L NRQP T LHK P S 373
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 473 IMAH LAK V - KPHR T F R FNECV C TP YNADFDGDEMNLH L PQ T E E A K AEA LVLMG T KANLVT P RN G E PL IAA IQD FLTGAY L 551
Cdd:cd01435 374 IMAH KVR V l PGEK T L R LHYAN C KS YNADFDGDEMNLH F PQ S E L A R AEA YYIAS T DNQYLV P TD G K PL RGL IQD HVVSGV L 453
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 629 EDLC ---- TND S Y V T I Q N S EL MC 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 2412574953 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 2412574953 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 2412574953 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: 563.77
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1021 KYMRA QM EPG S AVGA LC AQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASK A ISTPIITA Q L DM 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 2412574953 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 2412574953 1181 SKS SM Y YV LQ F LK ED LP K VVV Q GIPEV S RAVI HI D EQS GK ek F KLLVEG 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 -- Y KLLVEG YG LRAVM N T P GV I GTRTTSN HIM EVEK V LGI 200
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
7.80e-150
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 455.44
E-value: 7.80e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 408 VRNGP dvh P GA NF I QQ rhm QM K RF LK YGNRE K M A QE LK F GDIVERH L IDGDVVLFNRQP S LH KL SI M AH LAK V KPHR T F R 487
Cdd:smart00663 159 VRNGP --- N GA KY I IR --- GK K TN LK LAKKS K I A NH LK I GDIVERH V IDGDVVLFNRQP T LH RM SI Q AH RVR V LEGK T I R 232
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2412574953 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
1.13e-130
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: 405.91
E-value: 1.13e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 12 A KKI SH I C FG MK SPEE M R QQAHIQ V VSKNL Y S q DNNHA 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 2412574953 92 C FH V G Y F RAVIG IL QMI CK T C CHIM L SQEEKQQ F LDFL KR P GL TY L QKR gl K K K I SDK C R KK ST C HY CG AF NG TVKK cgl 171
Cdd:pfam04997 80 V FH I G F F KKTLK IL ECV CK Y C SKLL L DPGKPKL F NKDK KR L GL EN L KMG -- A K A I LEL C K KK DL C EH CG GK NG VCGS --- 154
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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
1.37e-116
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: 375.54
E-value: 1.37e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 841 GLTP T EFFFHTM A GREGL V DTAVKTAE T GY M QRRLVK S LEDL CSQ YD L TVR S S T G D I I QF I YG G DGLDP AAM E GKD - EPL 919
Cdd:pfam04998 1 GLTP Q EFFFHTM G GREGL I DTAVKTAE S GY L QRRLVK A LEDL VVT YD D TVR N S G G E I V QF L YG E DGLDP LKI E KQG r FTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 920 EF KRVLDNI K AVYPCQSERA L SKNELTLTTEA I MKKNEF L C -- CQDSFL QE IK T FIKGVSE K I ---- K KT R DKYGI N DN g 993
Cdd:pfam04998 81 EF SDLKLED K FKNDLLDDLL L LSEFSLSYKKE I LVRDSK L G rd RLSKEA QE RA T LLFELLL K S gles K RV R SELTC N SK - 159
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 994 tteprvlyqldritrt QIEKF L ETC R DK Y MRAQME PG S AVG ALC AQSIGEPGTQMTL K TFHFAGVAS M N I TLGVPR I KEI 1073
Cdd:pfam04998 160 ---------------- AFVCL L CYG R LL Y QQSLIN PG E AVG IIA AQSIGEPGTQMTL N TFHFAGVAS K N V TLGVPR L KEI 223
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1074 IN A SK A I ST P II T AQ L -- DMDDDADY A RL V K G R IEK TL LG EIS E YI E ------------------------------ EVF 1121
Cdd:pfam04998 224 IN 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 NEE 303
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1122 LP D DCFI L VK L SLERIRL L RLEVNAETVRYS I c TSKL R V K pg DVAVHGE A VVCV T PRENSK S SMYY ------- VLQF L KE 1194
Cdd:pfam04998 304 EI D PETG L LI L VIRLLKI L NKSIKKVVKSEV I - PRSI R N K -- VDEGRDI A IGEI T AFIIKI S KKIR qdtgglr RVDE L FM 380
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1195 D ------------ L PKVVVQ GIP EVS R AVIHI D E q S GK EK -- FK L LV EG D NL RA V MATH G - V KGT R TT SN NTY E VEKT LG 1259
Cdd:pfam04998 381 E 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 LG 459
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 2412574953 1260 IEAAR 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 460 IEAAR 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
7.40e-99
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: 313.08
E-value: 7.40e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 358 GKRVDFS G RTVISPDPNL RI DEV A VP VHV AK I LTFPE K V NKA NI NF LR K LV R NGP D V H PGAN F I Q q R HMQMK 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 2412574953 438 e KMAQ EL KF GDIVERH L IDGDVVLFNRQPSLH K LSIM A H LAK V K P HR TFR F N EC V C TPYNADFDGDEMNLH L PQ T EEA K A 517
Cdd:pfam00623 80 - RLDK EL EI GDIVERH V IDGDVVLFNRQPSLH R LSIM G H RVR V L P GK TFR L N LS V T TPYNADFDGDEMNLH V PQ S EEA R A 158
....*...
gi 2412574953 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
2.92e-97
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain]
Cd Length: 363
Bit Score: 316.50
E-value: 2.92e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 978 EK IKKTRDKY G IND ngtteprvlyqldritr TQI E KFLETCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMTL K TFH F AG 1057
Cdd:cd06528 5 EK LEEVLKEH G LTL ----------------- SEA 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 2412574953 1058 VA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L DMD -- 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 2412574953 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 2412574953 1214 id EQSGK E k FKLLV 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 - YVIYT 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 2412574953 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
7.20e-96
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 313.32
E-value: 7.20e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1006 I T RTQI E KFL E TCRDK Y M R AQM EPG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II 1085
Cdd:PRK04309 35 L T EEEV E EII E EVVRE Y L R SLV EPG E AVG VVA AQSIGEPGTQMT MR TFH Y AGVA EI N V TLG L PR LI EI VD A R K EP STP MM 114
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1086 T AQ L DMD -- 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 2412574953 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 EKFKLLV 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 ---- DEYVIYT EG S NL KE V LKVE GV 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
1.69e-84
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain]
Cd Length: 367
Bit Score: 281.17
E-value: 1.69e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1010 QIEKFLETCRDK Y M R AQME PG S AVG ALC AQSIGEPGTQMT LK TFH F AGVA SM N I TLG V PR IK EI IN A S K AI STP II T AQ L 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 2412574953 1090 DMDD -- 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 2412574953 1162 P G D V AV -- HGEAVVCVT P REN S kssm YYV L QF LKE DLPKVVVQ GI PEVS R A VI hide QSGKEKFKLLV 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 ---- RKEGDEYVIYT EG S NL KE V LKLE 241
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
55-891
8.75e-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: 291.23
E-value: 8.75e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 chimlsqeekqqfldflkrpg 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 2412574953 134 ltylqkrglkkkisdkcrkkstchycgafngtvkkcgl 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 2412574953 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 2412574953 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 2412574953 372 DP N L RID E VAV P VHV A KI LT FP E K V NKA N INF L RKLV rngp D VHPGAN fi QQRHMQ mkrfl KY G N -- REKMAQE L KF 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 QEYC ---- D LTLLLK -- GVIGVR ----- RN G R lv GVRSHNT L QI GD V 294
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 450 VE R H L I DGDVVL F NR Q PS L H KL S IM A HLA KV K P HR - TFRF N ECV C T P YNA DFDGD EMNLHL PQ TEE A K AE ALV L MGTKAN 528
Cdd:cd10506 295 IH R P L V DGDVVL V NR P PS I H QH S LI A LSV KV L P TN s VVSI N PLC C S P FRG DFDGD CLHGYI PQ SLQ A R AE LEE L VALPKQ 374
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 605 L r P S D DN pvranlrtkgkqycgkgedl CTND S YVTIQNSELMCG S MDKGTLGSG S KN N I F Y IL LRD w G QNE A A D AMSRLA 684
Cdd:cd10506 447 L - P T D LD -------------------- YSFP S NLVFISDGELIS S SGGSSWLRD S EG N L F S IL VKH - G PGK A L D FLDSAQ 504
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 685 R L APVY LS N RGFS IGIG D VTPGQGLLKAK -- Y E LLNA G Y -- KKCDEY I EA L NTGKLQQQPGCTA EE TLEALILKELSVI R 760
Cdd:cd10506 505 G L LCEW LS M RGFS VSLS D LYLSSDSYSRQ km I E EISL G L re AEIACN I KQ L LVDSRKDFLSGSG EE NDVSSDVERVIYE R 584
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 761 DHAGSAC ------------------ LRELD K S NS P L T M ALC GSKGS FINIS Q MIA C V G Q Q -------- A I SGSRVPDGFE 814
Cdd:cd10506 585 QKSAALS qasvsafkqvfrdiqnlv YKYAS K D NS L L A M IKA GSKGS LLKLV Q QSG C L G L Q lslvklsy R I PRQLSCAAWN 664
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 815 NRSL 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 L 888
Cdd:cd10506 665 SQKS 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 G 741
...
gi 2412574953 889 TVR 891
Cdd:cd10506 742 TVR 744
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
920-1365
2.84e-83
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 282.85
E-value: 2.84e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 920 EFKR VLDN I kavypcq SERAL S KNELT L T T EAIMKKN E FLCCQ D SFLQEIKTFIK G ------ V S E K I K K TRD K YGIN D N g 993
Cdd:PRK14897 90 EFKR LFGR I ------- LDENM S FSTGE L L T AEEKEYY E ENSNE D VLKVIDDVKKL G frlpps V I E E I A K AMK K KELS D D - 161
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 994 tteprvlyqldritrt QI E KF L ETC R DK Y M RA QME P GS AVG ALC AQSIGEPGTQMT LK TFH F AGVA S MN I TLG V PR IK EI 1073
Cdd:PRK14897 162 ---------------- EY E EI L RRI R EE Y E RA RVD P YE AVG IVA AQSIGEPGTQMT MR TFH Y AGVA E MN V TLG L PR LI EI 225
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1074 IN A S K AI STP II T AQ L DM D -- D D ADYA R L V KGR IE K T L L GEISEY I EEV flp DDCFIL V K L SL E RI rllrlev NAETVR Y 1151
Cdd:PRK14897 226 VD A R K KP STP TM T IY L KK D yr E D EEKV R E V AKK IE N T T L IDVADI I TDI --- AEMSVV V E L DE E KM ------- KERLIE Y 295
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1152 SICTSKLRVKPGDVAVHGEAVVCVT P REN S kssm YYV L QF L K E DLPKVVVQ GI PEVS RA VIHID eqs GK E K - FKLLVE G D 1230
Cdd:PRK14897 296 DDILAAISKLTFKTVEIDDGIIRLK P QQP S ---- FKK L YL L A E KVKSLTIK GI KGIK RA IARKE --- ND E R r WVIYTQ G S 368
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1231 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 YK G E V LG I T R F G LAK 1310
Cdd:PRK14897 369 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 FD G S V KA I G R H G ISG 448
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 2412574953 1311 M 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 449 E 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_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1005-1363
2.12e-80
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: 271.00
E-value: 2.12e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1005 R ITRTQIEKF 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 2412574953 1085 I T AQ L DMDD -- 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 2412574953 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 2412574953 1201 VQ GI PEVSRAV I H ------ I D EQS G KE K ---- FK 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 2412574953 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 2412574953 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
2.65e-79
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain]
Cd Length: 1140
Bit Score: 285.79
E-value: 2.65e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 391 TF P ekvnkanin F - LRK L VR ngpdv HPG A NF I QQ rhmq M K RFLK ygnrekm AQELKFG D IV E R h L I DGDV VL F NR Q P S LH 469
Cdd:TIGR02386 359 FK P --------- F i IKR L ID ----- REL A AN I KS ---- A K KMIE ------- QEDPEVW D VL E D - V I KEHP VL L NR A P T LH 412
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 470 K L S I M A HLAKVKPHRTF R FNEC VCT PY NADFDGD E M NL H L P QTE EA K AEA LV LM GTKA N LVT P RN G E P LIAAI QD FLT G A 549
Cdd:TIGR02386 413 R L G I Q A FEPVLVEGKAI R LHPL VCT AF NADFDGD Q M AV H V P LSP EA Q AEA RA LM LASN N ILN P KD G K P IVTPS QD MVL G L 492
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 550 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 ranlrtkg 621
Cdd:TIGR02386 493 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 2412574953 622 kqycgkgedlct NDS Y VTIQN selmcg SMD K GTLG S gsknn IFYI L LRDW G QN E A A DAMSRLAR L APV Y LSNR G FS I GIG 701
Cdd:TIGR02386 555 ------------ GFP Y INDNE ------ PLS K KEIS S ----- LIDL L YEVH G IE E T A EMLDKIKA L GFK Y ATKS G TT I SAS 611
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 702 D V - T P GQ gllka KYE L L NAGY K KCDEYIEAL N T G KL qqqpgc T A EE TLEALI l KEL S VIR D HAGS A CLRE L D K S ---- N S 776
Cdd:TIGR02386 612 D I v V P DE ----- KYE I L KEAD K EVAKIQKFY N K G LI ------ T D EE RYRKVV - SIW S ETK D KVTD A MMKL L K K D tykf N P 679
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 777 PLT MA LC G SK G SFINIS Q MIACV G QQ A isgsr V P D G f ENRS LP hfekhsklpaakgf VAN SF YS GLT PT E F F FH T MAG R E 856
Cdd:TIGR02386 680 IFM MA DS G AR G NISQFR Q LAGMR G LM A ----- K P S G - DIIE LP -------------- IKS SF RE GLT VL E Y F IS T HGA R K 739
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 857 GL V DTA V KTA ET GY MQ RRLV KS ledlc S Q y D LT VR ----- SST G DII qfiyggdgld P A AM EGKDE PL E -- FK R VLDNIK 929
Cdd:TIGR02386 740 GL A DTA L KTA DS GY LT RRLV DV ----- A Q - D VV VR eedcg TEE G IEV ---------- E A IV EGKDE II E sl KD R IVGRYS 803
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 930 A --- VY P CQSERALSK N el TL T TE A I MK K N E FL ccqdsflqeiktfik G VSE - K IKKT --- RDKY G IN dngttep RVL Y Q 1002
Cdd:TIGR02386 804 A edv YD P DTGKLIAEA N -- TL I TE E I AE K I E NS --------------- G IEK v K VRSV ltc ESEH G VC ------- QKC Y G 859
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1003 L D RI T RTQI E K fletcrdkymraqmep G S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA S -- MN IT L G V PR I KE IIN A skai 1080
Cdd:TIGR02386 860 R D LA T GKLV E I ---------------- G E AVG VIA AQSIGEPGTQ L T MR TFH TG GVA G as GD IT Q G L PR V KE LFE A ---- 919
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1081 S TP iitaqldm 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 CTSK - LR 1159
Cdd:TIGR02386 920 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 PFGA q LR 969
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1160 VK 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 FKLLVEGDN LR A V 1235
Cdd:TIGR02386 970 VK 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 HIEVIVRQM LR K V 1036
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1236 MA T - H G ---- VK G TRTTSNNTY E VEKT L g I E AARTTII neiqytmvnhgmsidrrhvmllsdlmt YKGEV LGIT RFG L A k 1310
Cdd:TIGR02386 1037 RI T d S G dsnl LP G ELIDIHEFN E ENRK L - L E QGKKPAS --------------------------- AIPQL LGIT KAS L N - 1087
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|.
gi 2412574953 1311 m 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 1088 - 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
7.15e-67
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: 228.62
E-value: 7.15e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 DMDDD 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 2412574953 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 2412574953 1177 prenskssmy YV L QFLKEDLP K V V VQG IP EVS R AVIHIDEQS GK E K FKLLV 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 K YLVIT EG V NL A A LWKFSD i LDVN R IYT N DIHAML 202
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
1.27e-65
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 240.18
E-value: 1.27e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 DMD -- 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 2412574953 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 2412574953 1202 Q GIP EVS R AVIHID E QSGK E KFK 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 EYV 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 2412574953 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 2412574953 1362 L LHKANRD 1369
Cdd:PRK14898 846 L RIDREYE 853
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
345-1359
6.60e-63
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 235.35
E-value: 6.60e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F - LR KLV RN G pdvhpganf 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 2412574953 424 RHMQM K RFL kygnr E KMAQ E L kf G D IV E r HL I DGDV VL F NR Q P S LH K L S I M A ------------- H - L akvkphrtfrfn 489
Cdd:PRK00566 383 TIKSA K KMV ----- E REDP E V -- W D VL E - EV I KEHP VL L NR A P T LH R L G I Q A fepvliegkaiql H p L ------------ 442
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 562 AK A CQIIASIL V GKDEK IKVR LPPPTILK p V T L wt G KQ IF SV IL r P SD --- D N PVRA nlrtkgkqycgkgedlctndsyv 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 2412574953 639 tiqnselmcgs 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 2412574953 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 2412574953 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 2412574953 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 Y 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 2412574953 933 - P CQS E RALSKN el TL TT E A I MK K neflccqdsflqeiktfikgvsekikktrdkyg I NDN G TT E PRV lyqldrit R TQI 1011
Cdd:PRK00566 817 d P ETG E VIVPAG -- TL ID E E I AD K --------------------------------- I EEA G IE E VKI -------- R SVL 853
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1012 ekfle TC RDKY ----------- MRAQM - EP G S AVG ALC AQSIGEPGTQ M T LK TFH FA GV asm N IT L G V PR IK E IIN A S K - 1078
Cdd:PRK00566 854 ----- TC ETRH gvcakcygrdl ATGKL v NI G E AVG VIA AQSIGEPGTQ L T MR TFH TG GV --- D IT G G L PR VA E LFE A R K p 925
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1079 --- AI STP I itaqldmdddadyarlv K G RIEK tll G EISEYIEEVFLPD D cfilvklslerirllrlev NA E TVR Y S I CT 1155
Cdd:PRK00566 926 kgp AI IAE I ----------------- D G TVSF --- G KETKGKRRIVITP D ------------------- DG E ERE Y L I PK 966
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1156 S K - L R V KP GD VAVH G EA vvcvtprenskssmyyvlqflkedlpkvvvqgipevsravihideqsgkekfkl L VE G dnlra 1234
Cdd:PRK00566 967 G K h L L V QE GD HVEA G DK ------------------------------------------------------ L TD G ----- 987
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1235 vmathgvkgtrtt 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 pge 1052
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 -- 1350
Cdd:PRK00566 1053 lvdrsefeeenrkliaegkepa 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 1130
....*....
gi 2412574953 1351 IP M ni GTGL 1359
Cdd:PRK00566 1131 IP A -- 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 2412574953 1030 G S AVG A L C AQSIGEPGTQMTL K TFHFAGVASMN I TLG V PR I KEI I NA S kaistpiitaqldmdddadyarlvkgriektl 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 2412574953 1110 lgeiseyieevflpddcfilvklslerirllrlevnaetvrysictsklrvkpgdvavhgeavvcvtprenskssmyyvl 1189
Cdd:cd00630 --------------------------------------------------------------------------------
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1190 qflkedlpkvvvqgipevsravihideqsgkekfkllvegdnlravmathgvkgtrttsn 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 2412574953 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 2412574953 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
2.21e-59
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 225.14
E-value: 2.21e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 404 LRK LV rngp DVHPG AN f I QQRHMQMK R FLK Y gnrekmaqelk FG D IV E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPH 483
Cdd:PRK14906 460 MKR LV ---- ELEYA 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 2412574953 484 RTFRFNEC VCT PY NADFDGD E M NL H L P QTEE A K AEA L VLM GTKA N LVT P RN G E PL IAAI QD FLT G A Y L LT - LK D T F FDRA 562
Cdd:PRK14906 523 KAIKLHPL VCT AF NADFDGD Q M AV H V P LSTQ A Q AEA R VLM LSSN N IKS P AH G R PL TVPT QD MII G V Y Y LT t ER D G F EGEG 602
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 563 KACQIIASI L VGK D EKIKVR L PP ptilkpvtlwtgkqif SVIL R P S D D NP VR ANL rt KGKQYCGK GE DLC T NDSYVTIQN 642
Cdd:PRK14906 603 RTFADFDDA L NAY D ARADLD L QA ---------------- KIVV R L S R D MT VR GSY -- GDLEETKA GE RIE T TVGRIIFNQ 664
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 643 S ----- ELMCGS M D K GTL G sgsknnify I L LR D ---- WGQN E AADAMSRLARLAPV Y LSNR G FSIGIG D V T pgqg LLKA K 713
Cdd:PRK14906 665 V lpedy PYLNYK M V K KDI G --------- R L VN D ccnr YSTA E VEPILDGIKKTGFH Y ATRA G LTVSVY D A T ---- IPDD K 731
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 714 Y E L L NAGYK K CDEYI E ALNT G K L qqqpgct A E ETLEALILKELSVIRDHA G S A C L REL D KS N SPLT MA LC G SK G SFIN I S 793
Cdd:PRK14906 732 P E I L AEADE K VAAID E DYED G F L ------- S E RERHKQVVDIWTEATEEV G E A M L AGF D ED N PIYM MA DS G AR G NIKQ I R 804
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 794 Q MIACV G QQ A ISGSRVP D gfenrs LP hfekhsklpaakgf VANS F YS GL TPT E F F FH T MAG R E GLVDTA VK TA ET GY MQ R 873
Cdd:PRK14906 805 Q LAGMR G LM A DMKGEII D ------ LP -------------- IKAN F RE GL SVL E Y F IS T HGA R K GLVDTA LR TA DS GY LT R 864
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 874 RLV KSLE dlcsqy D LT VR S stgdiiqfiyggdg L D PAAM EG KDE PL -- EFKR V LD N IKA vypcqse R A L SKNELTLTT E A 951
Cdd:PRK14906 865 RLV DVAQ ------ D VI VR E -------------- E D CGTD EG VTY PL vk PKGD V DT N LIG ------- R C L LEDVCDPNG E V 917
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 952 IMKKNEFLCCQ D SFLQEIKTFIKG V SEKIKK T - RDK YG INDN gtteprv L Y QL D RI TR TQIEK fletcrdkymraqmep G 1030
Cdd:PRK14906 918 LLSAGDYIESM D DLKRLVEAGVTK V QIRTLM T c HAE YG VCQK ------- C Y GW D LA TR RPVNI ---------------- G 974
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1031 S AVG ALC AQSIGEPGTQ M T LK TFH FA GVA SMN IT L G V PR IK E IIN A S K AISTPII taqldmddd A DYA rlvk G RIEK T ll 1110
Cdd:PRK14906 975 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 ---- G TLQI T -- 1039
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1111 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 ----- NSKSSM 1185
Cdd:PRK14906 1040 G DKT E KTLTIHDQ D G ---------- NS R EYV -- V S A RVQFMPGVEDGVE V RV G QQITR G S ---- V N P HD llrlt DPNTTL 1103
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1186 Y Y VLQFLKE dlp KV V V QG I p EVSRAV I HIDEQSGKE K FKLLVE GD NL ---- R A V mathgvkgtrttsn N T YE V E K T lgie 1261
Cdd:PRK14906 1104 R Y IVSQVQD --- VY V S QG V - DINDKH I EVIARQMLR K VAVTNP GD SD ylpg R Q V -------------- N R YE F E D T ---- 1161
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1262 aartti I N EI qytmvnhgmsidrrhvm L L SDLMTYK G E -- V LGIT RFG LA km KE S V L ML ASF EK T ADH L F DAA YF G QK D S 1339
Cdd:PRK14906 1162 ------ A N NL ----------------- I L EGKQPPV G Q pl L LGIT KAS LA -- TD S W L SA ASF QE T TKV L T DAA IE G KV D H 1216
1130 1140
....*....|....*....|
gi 2412574953 1340 VC G VS E CI I M G I P MNI GTGL 1359
Cdd:PRK14906 1217 LA 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
5.61e-54
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain]
Cd Length: 659
Bit Score: 201.21
E-value: 5.61e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - R K L VRN G pdvhp 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 2412574953 424 rhmq M K RFL kygnr E KMAQ E L kf G DI V E r HL I D G DV VL F NR Q P S LH K L S I M A HLAKVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:cd01609 302 ---- A K KMI ----- E RKDP E V -- W DI L E - EV I K G HP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 369
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 584 P pptilkpvtlwt G KQ IF SV IL RP sddnpvra N L R tkgkqycgkgedlctnds YVTI qnselmcg 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 2412574953 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 2412574953 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 2412574953 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
4.38e-52
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain]
Cd Length: 1165
Bit Score: 201.16
E-value: 4.38e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 345 LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P ekvnkanin F L - RKL VRN G pdvhp 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 2412574953 424 rhmq M K RFL kygnr E KMAQ E LK fg DI V E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPHRTFRFNEC VCT PY NADFDGD 503
Cdd:COG0086 387 ---- A K KMV ----- E REEP E VW -- DI L E E - V I KEHP VL L NR A P T LH R L G I Q A FEPVLIEGKAIQLHPL VCT AF NADFDGD 454
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 576 DEK IKVR LPPPTILKPVTLW T -- G KQIFSV IL r P SD dnpvranlrtkgkqycgkgedlctndsy V TIQ N SE lmcgs 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 2412574953 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 2412574953 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 2412574953 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 2412574953 887 dltvrsstgd I IQFIYG G -- D G LD - P A AM EG KD -- EPL E f K R V L DNIK A -- V YPCQSERA L SKNELTLTT E AIMK knefl 959
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 ed V VDPGTGEV L VPAGTLIDE E VAEI ----- 837
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 960 ccqdsflqeiktf I KGVSEKIK K T R dkygindngtteprvlyqldri TRTQI E KFLET C RDK Y M R -- A QMEP --- G S AVG 1034
Cdd:COG0086 838 ------------- I EEAGIDSV K V R ---------------------- SVLTC E TRGGV C AKC Y G R dl A RGHL vni G E AVG 882
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1035 ALC AQSIGEPGTQ M T LK TFH FA G V AS mnitlgv PRIK E IINAS KA ISTPIITAQLDMDDDADYARL V KGRI E KTLLGEIS 1114
Cdd:COG0086 883 VIA AQSIGEPGTQ L T MR TFH IG G A AS ------- RAAE E SSIEA KA GGIVRLNNLKVVVNEEGKGVV V SRNS E LVIVDDGG 955
....*.
gi 2412574953 1115 EYI EE V 1120
Cdd:COG0086 956 RRE EE Y 961
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
528-703
4.74e-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: 177.05
E-value: 4.74e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 607 P sddnpv RA N LRT K G K QYC gkg EDLC T NDSYV T I Q N S EL MC G 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 IS G VI DK K T V G - K S LGSLIH I IYKEY G PE E T A KFLD RL QK L 141
170
....*....|....*..
gi 2412574953 687 APV YL SNR GFSIGI G D V 703
Cdd:pfam04983 142 GFR YL TKS GFSIGI D D I 158
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
246-1060
1.72e-50
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 197.45
E-value: 1.72e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 398 kani NF L R KL VRN G P dvhpg A NFIQ Q R hmqmkrflkygnr EK M AQE l K FGDIV 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 Y ----- A TTLK Q A ------------- KR 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 2412574953 476 HLA K VKPHRTFRFNEC VC TPY NADFDGD E M NL H L P QTE EA K AE AL VLM GTKA N LVT P RN G EPLIAAI QD FLT G A Y L L T L - 554
Cdd:PRK09603 1826 FHP K LIDGKAIQLHPL VC SAF NADFDGD Q M AV H V P LSQ EA I AE CK VLM LSSM N ILL P AS G KAVAIPS QD MVL G L Y Y L S L e 1905
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 632 ctndsyvtiqnselmcgsm 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 2412574953 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 2412574953 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 2412574953 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 2412574953 932 Y P CQS E RA L S kn EL TL TT E AIM KK neflccqdsf LQ E -- IK TFI ---------- KGV SE K I kktrdk YG I N dng TT E PRV 999
Cdd:PRK09603 2215 D P ITN E IL L Y -- AD TL ID E EGA KK ---------- VV E ag IK SIT irtpvtckap KGV CA K C ------ YG L N --- LG E GKM 2273
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2412574953 1000 L Y qldritrtqiekfletcrdkymraqme PG S AVG ALC AQSIGEPGTQ M TL K TFH FA G V AS 1060
Cdd:PRK09603 2274 S Y --------------------------- PG E AVG VVA AQSIGEPGTQ L TL R TFH VG G T AS 2307
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
246-1359
1.39e-48
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 190.99
E-value: 1.39e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 324 ELSGIPLNMAPKKWTRGFVQR LKGKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P EKVN K ANI nf 403
Cdd:PRK14844 1743 RRNALVNKAGAVGYKKSISDM LKGKQGRFR Q NL L GKRVD Y SGR S VI VVG P T L KLNQCGL P KRM A LE L FK P FVYS K LKM -- 1820
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 404 lrklvrngpdvhpganfiqqrh MQ M KRFL K YGNREKM A QELKFG D IV E R h L I DGDV VL F NR Q P S LH K L S I M A HLAKVKPH 483
Cdd:PRK14844 1821 ---------------------- YG M APTI K FASKLIR A EKPEVW D ML E E - V I KEHP VL L NR A P T LH R L G I Q A FEPILIEG 1877
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 632 C tn DSYV T IQNS elmcgsmdkgtlgsgsk NN 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 VKEI ----------------- TS 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 2412574953 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 2412574953 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 2412574953 866 A ET GY MQ RRLV KSLED - LCSQY D lt VRSST G DIIQ fiyggdgldp A AM EG KD eplefkr VLDNIKA V YPCQS eral SK N E 944
Cdd:PRK14844 2212 A NS GY LT RRLV DVSQN c IVTKH D -- CKTKN G LVVR ---------- A TV EG ST ------- IVASLES V VLGRT ---- AA N D 2268
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 945 L -- TL T T E AIM K KN E FL cc QDSFLQE I K tf I K G V sekikktr D KYG I NDNG T T E -- P R V LY qldritrtqiekf L ETC RD 1020
Cdd:PRK14844 2269 I yn PV T K E LLV K AG E LI -- DEDKVKQ I N -- I A G L -------- D VVK I RSPL T C E is P G V CS ------------- L CYG RD 2323
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1021 KYMRAQMEP G S AVG ALC AQS I GEPGTQ M T LK TFH FA GV ----------- AS M N I -------------------------- 1063
Cdd:PRK14844 2324 LATGKIVSI G E AVG VIA AQS V GEPGTQ L T MR TFH IG GV mtrgvessnii AS I N A kiklnnsniiidkngnkivisrscev 2403
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1064 ---- T LG VPRI K E -------- IINASKAI ------------ ST PIIT AQL ------ D MD D DA ------ D YARLVKGRIE K 1107
Cdd:PRK14844 2404 vlid S LG SEKL K H svpygakl YVDEGGSV kigdkvaewdpy TL PIIT EKT gtvsyq D LK D GI sitevm D ESTGISSKVV K 2483
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1108 -- T L LGEISEYIEEVF L P DD cfilvklsle RIRLLR L EVNA E TVRYSICTSK L R V KP G D v A VH GEA V VCV TPRE NS K S -- 1183
Cdd:PRK14844 2484 dw K L YSGGANLRPRIV L L DD ---------- NGKVMT L ASGV E ACYFIPIGAV L N V QD G Q - K VH AGD V ITR TPRE SV K T rd 2552
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1184 --- SMYY V LQFLKEDL PK -- VV V QG I P ------------ EV S RAVIHI DEQ S ------- GKE K FKLLV EGD NL R avmath 1239
Cdd:PRK14844 2553 itg GLPR V IELFEARR PK eh AI V SE I D gyvafsekdrrg KR S ILIKPV DEQ I spveylv SRS K HVIVN EGD FV R ------ 2626
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1240 gv KG TRTTSNNT -- YEVEKT LG I EA ARTTI I N EIQ YTMVNH G MS ID RR H VMLLSDL M TY K G E VL ---------------- 1301
Cdd:PRK14844 2627 -- KG DLLMDGDP dl HDILRV LG L EA LAHYM I S EIQ QVYRLQ G VR ID NK H LEVILKQ M LQ K V E IT dpgdtmylvgesidkl 2704
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 GT 1357
Cdd:PRK14844 2705 evdrendamsnsgkrpahylpilq 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 GT 2782
..
gi 2412574953 1358 GL 1359
Cdd:PRK14844 2783 GL 2784
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
729-834
1.43e-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: 1.43e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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
1.71e-33
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 138.73
E-value: 1.71e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 345 LK GKQGRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF P EKVNK aninflrk L V R N G P dvhpg A N F I QQ r 424
Cdd:PRK02625 339 IE GKQGRFR Q NL L GKRVD Y SGR S VI VVG P K L KMHQCGL P KEM A IE L FQ P FVIHR -------- L I R Q G I ----- V N N I KA - 404
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 425 hmq M K RFLKYGNR E KM aqelkfg DIV E R h L I D G DV VL F NR Q P S LH K L S I M A HLAKVKPH R TFRFNEC VC TPY NADFDGD E 504
Cdd:PRK02625 405 --- A K KLIQRADP E VW ------- QVL E E - V I E G HP VL L NR A P T LH R L G I Q A FEPILVEG R AIQLHPL VC PAF NADFDGD Q 473
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 2412574953 505 M NL H L P QTE EA K AEA LV LM GTKA N LVT P RN GEP LIAAI QD FLT G A Y L LT 553
Cdd:PRK02625 474 M AV H V P LSL EA Q AEA RL LM LASN N ILS P AT GEP IVTPS QD MVL G C Y Y LT 522
rpoC1
CHL00018 RNA polymerase beta' subunit
315-554
2.41e-33
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 138.50
E-value: 2.41e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 315 LQ C A L -- YINSELS G I P LNMAPK K WTRG F VQRLK GK Q GRFR G NL S GKRVD F SGR T VI SPD P N L RIDEVAV P VHV A KI L TF 392
Cdd:CHL00018 328 LQ E A V da LLDNGIR G Q P MRDGHN K PYKS F SDVIE GK E GRFR E NL L GKRVD Y SGR S VI VVG P S L SLHQCGL P REI A IE L FQ 407
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 393 P ekvnkanin F L - R K L V R NGPDVHPG A -- NF I QQRHMQMKRF L K ygnrekmaqelkfgdiver HLID G DV VL F NR Q P S LH 469
Cdd:CHL00018 408 P --------- F V i R G L I R QHLASNIR A ak SK I REKEPIVWEI L Q ------------------- EVMQ G HP VL L NR A P T LH 459
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 470 K L S I M A HLAKVKPH R TFRFNEC VC TPY NADFDGD E M NL H L P QTE EA K AEA LV LM GTKA NL VT P RN G E P LIAAI QD F L T G A 549
Cdd:CHL00018 460 R L G I Q A FQPILVEG R AICLHPL VC KGF NADFDGD Q M AV H V P LSL EA Q AEA RL LM FSHM NL LS P AI G D P ISVPS QD M L L G L 539
....*
gi 2412574953 550 Y L LT L 554
Cdd:CHL00018 540 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
3.94e-18
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: 91.07
E-value: 3.94e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 2412574953 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 cs 884
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 -- 206
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 885 qydltvrsstgd I IQFIYG G D -- GLDPA AM EGK D EPLEFK - R V L D nikavypcqse R ALSKNE L TLTT E A I MK KN E flcc 961
Cdd:TIGR02388 207 ------------ I VREEDC G T er SIVVR AM TEG D KKISLG d R L L G ----------- R LVAEDV L HPEG E V I VP KN T ---- 259
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 962 qdsflqeiktfik GVSEKIK KT rdkyg I NDN G TT E PR V LYQ L dritrt QI E KFLET CR DK Y MRA ----- QMEP G S AVG AL 1036
Cdd:TIGR02388 260 ------------- AIDPDLA KT ----- I ETA G IS E VV V RSP L ------ TC E AARSV CR KC Y GWS lahah LVDL G E AVG II 315
410 420
....*....|....*....|..
gi 2412574953 1037 C AQSIGEPGTQ M T LK TFH FA GV 1058
Cdd:TIGR02388 316 A 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
1.06e-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: 74.49
E-value: 1.06e-14
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 2412574953 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
2.10e-14
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 78.88
E-value: 2.10e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 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 E --- PL E 920
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 vli PL G 236
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 921 f K R V L D nikavypcqse R A L SKNELTLTT E A I MKK N eflccqdsfl QE I K tfi KGVSE KI K K T rdkygindn G TT E PR V L 1000
Cdd:PRK02597 237 - D R L L G ----------- R V L AEDVVDPEG E V I AER N ---------- TA I D --- PDLAK KI E K A --------- G VE E VM V R 282
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2412574953 1001 YQ L dritrt QI E KFLET CR DK Y ---- MRAQM - EP G S AVG ALC AQSIGEPGTQ M T LK TFH FA GV 1058
Cdd:PRK02597 283 SP L ------ TC 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 ...
1172-1363
2.18e-10
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain]
Cd Length: 381
Bit Score: 64.36
E-value: 2.18e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1172 VV C V T --- PR E N SKSS MY y V L QF L KE ---- D L PKV V VQ G IPEV ----------- S RAVIHIDEQ S GKEKFK L L V ------ 1227
Cdd:cd02737 152 GP 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 tveesc 230
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 1299
Cdd:cd02737 231 kkt 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 310
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 1300 VL 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 311 FV 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
7.39e-10
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 63.80
E-value: 7.39e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 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 2412574953 915 KDEP L EFK --- RVL - D N I K avypcqseralsknelt LTTEA I MKK N eflcc QD --- SFLQEIK TF - IKGV S ekikktrdk 986
Cdd:CHL00117 236 IERI L IQT lig RVL a D D I Y ----------------- IGSRC I ATR N ----- QD igi GLANRFI TF r AQPI S --------- 284
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2412574953 987 ygindngtteprvlyqldri T R TQI ekfle TCR D ky MRA -- Q M ------------ E P G S AVG ALCA QSIGEPGTQ M TL K T 1052
Cdd:CHL00117 285 -------------------- I R SPL ----- TCR S -- TSW ic Q L cygwslahgdlv E L G E AVG IIAG QSIGEPGTQ L TL R T 337
....*.
gi 2412574953 1053 FH FA GV 1058
Cdd:CHL00117 338 FH TG GV 343
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1004-1050
2.31e-06
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 52.20
E-value: 2.31e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 2412574953 1004 D RI T RTQI E KFLETCRDK Y MR A QM EP GS AVG ALC AQSIGEPGTQM T L 1050
Cdd:PRK14898 31 D GV T EEMV E EIIDEVVSA Y LN A LV EP YE AVG IVA AQSIGEPGTQM S L 77
Blast search parameters
Data Source:
Precalculated data, version = cdd.v.3.21
Preset Options: Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
