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DNA-directed RNA polymerase I subunit RPA1 isoform X2 [Macaca mulatta]
Protein Classification
DNA-directed RNA polymerase I subunit RPA1 ( domain architecture ID 11546233 )
DNA-directed RNA polymerase I subunit RPA1 is the largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors
List of domain hits
Name
Accession
Description
Interval
E-value
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
156-896
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: 1196.61
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 156 H L F ALW K N E G ---- FF L NY L FS G MDDDGM E SR F NPSV FFLD F L V VPP S R Y RP V S R LGD QM F T N G Q T V N L QAVM KD VVL IR 231
Cdd:cd01435 93 H R F RIS K W E V klfv AK L KL L DK G LLVEAA E LD F GYDM FFLD V L L VPP N R F RP P S F LGD KV F E N P Q N V L L SKIL KD NQQ IR 172
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 232 K LLA L M A Q EQKL peevaapppdeekdsliaidr S F L STLP G QSFID KL Y N I W IR LQS H VN IV FDS EMDKLM - MDKY PGI R 310
Cdd:cd01435 173 D LLA S M R Q AESQ --------------------- S K L DLIS G KTNSE KL I N A W LQ LQS A VN EL FDS TKAPKS g KKSP PGI K 231
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 311 Q I LEKKEGLFR KH MMGKRV D YAARSVI C PD MY I N TNEIGIP M VFA T KLT Y P Q PVTP W NV Q ELRQAVINGP N V H PGA SMVI 390
Cdd:cd01435 232 Q L LEKKEGLFR MN MMGKRV N YAARSVI S PD PF I E TNEIGIP L VFA K KLT F P E PVTP F NV E ELRQAVINGP D V Y PGA NAIE 311
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 391 N EDG SRTA LSA VDMTQ R E A V AK Q LL TPATGAPKPQ G T K I V C RH VKN GD IL LLNRQPTLH R PSI Q AH HA R I LP E EK V LRLH 470
Cdd:cd01435 312 D EDG RLIL LSA LSEER R K A L AK L LL LLSSAKLLLN G P K K V Y RH LLD GD VV LLNRQPTLH K PSI M AH KV R V LP G EK T LRLH 391
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 471 YANCK A YNADFDGDEMN A HFPQSEL G RAEAY VL A C TD Q QYLVP K DG Q PL A GLIQDH M VSG ASM T T R GC FFTRE Q Y ME LVY 550
Cdd:cd01435 392 YANCK S YNADFDGDEMN L HFPQSEL A RAEAY YI A S TD N QYLVP T DG K PL R GLIQDH V VSG VLL T S R DT FFTRE E Y QQ LVY 471
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 551 RG L T ----- DK V GR V KL F PP S ILKP L PLWTGKQV L ST L L I N I IP EDHIP LNLSGK A K ITG K AW vketprsv P G FNPDSMC 625
Cdd:cd01435 472 AA L R plfts DK D GR I KL L PP A ILKP K PLWTGKQV I ST I L K N L IP GNAPL LNLSGK K K TKK K VG -------- G G KWGGGSE 543
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 626 ESQV V IR E GELL C GVLDK AHY G S SAYGLVH CC YE I YGGET S GK V L TC L A RLFTAYLQ l Y RGFT L G V ED I L VK PKAD V KR Q 705
Cdd:cd01435 544 ESQV I IR N GELL T GVLDK SQF G A SAYGLVH AV YE L YGGET A GK L L SA L G RLFTAYLQ - M RGFT C G I ED L L LT PKAD E KR R 622
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 706 R I IEESTHC G PR A VRAA L N L peatsydevqgkwqdahlgkdqrdfnmidlkfke EV N HYSNE I N KAC M P F GL HRQ FPEN S 785
Cdd:cd01435 623 K I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P K GL LKP FPEN N 668
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 786 LQ M MVQSGAKGS T VN TM QISCLLGQ I ELEGRR P PLM A SGK S LP C F E PY EFT PRAGGF V T G RFLTGI K P P E F FFHCMAGRE 865
Cdd:cd01435 669 LQ L MVQSGAKGS M VN AS QISCLLGQ Q ELEGRR V PLM V SGK T LP S F P PY DTS PRAGGF I T D RFLTGI R P Q E Y FFHCMAGRE 748
730 740 750
....*....|....*....|....*....|.
gi 1622858458 866 GL V DTAVKTSRSGYLQRC I IKHLEGL V V Q YD 896
Cdd:cd01435 749 GL I DTAVKTSRSGYLQRC L IKHLEGL K V N YD 779
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
850-1562
4.90e-167
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: 514.60
E-value: 4.90e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 850 G IK P P EFFFH C M A GREGL V DTAVKT SR SGYLQR CII K H LE G LVV Q YD L TVR D S D G SV VQFLYGEDGLD IP K TQFLQPKQF 929
Cdd:pfam04998 1 G LT P Q EFFFH T M G GREGL I DTAVKT AE SGYLQR RLV K A LE D LVV T YD D TVR N S G G EI VQFLYGEDGLD PL K IEKQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 930 P F LASNY E VIM K SQH L HEV L SRADPKKALRHFRAIKKW qskhpntllrrgaflsysqkiqaavkalnlesenrngrspgt 1009
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1010 qemlrmwyeldeesrrkyqkkaatcpdps LSVWRPDIYF A SVSE T FETKVDDY S QEWAAQTEKSYEKSELSLDR L RTLLQ 1089
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1090 L KW Q R SL CE PGEAVG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM V a S A NIK T P MMS V PVLNTK - KA L K 1168
Cdd:pfam04998 170 L LY Q Q SL IN PGEAVG II AAQSIGEP G TQMTLNTFHFAG VASK NVTLG V PRL K EI IN V - S K NIK S P SLT V YLFDEV g RE L E 248
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1169 RV K SLKKQLTR V C LG E V LQKIDVQESFRMEEKQNKFR V YQLRFQ F LPHAYYQQ E KCLR PE DI L RFMET R FF K L L ME SIKK 1248
Cdd:pfam04998 249 KA K KVYGAIEK V T LG S V VESGEILYDPDPFNTPIISD V KGVVKF F DIIDEVTN E EEID PE TG L LILVI R LL K I L NK SIKK 328
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1249 knnkasafrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeere 1328
Cdd:pfam04998 --------------------------------------------------------------------------------
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1329 geenndedtqeernphregaretqerdeevgsgteedpalpalltq PR K PTHSQEPQGPEAV E R R VQ A VR EI HS FI DDYQ 1408
Cdd:pfam04998 329 ---------------------------------------------- VV K SEVIPRSIRNKVD E G R DI A IG EI TA FI IKIS 362
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1409 YDTEESLWCQVT V KLPL M KINFDMGS LV V SL AHGAVIYATK GI T R C L L NE TTNN K N E KEL VL N TEG I NL PELFKYAEVL D 1488
Cdd:pfam04998 363 KKIRQDTGGLRR V DELF M EEDPKLAI LV A SL LGNITLRGIP GI K R I L V NE DDKG K V E PDW VL E TEG V NL LRVLLVPGFV D 442
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622858458 1489 LR R LY SNDIH AMANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI RSNSSPLQ 1562
Cdd:pfam04998 443 AG R IL SNDIH EILEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
Name
Accession
Description
Interval
E-value
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
156-896
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: 1196.61
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 156 H L F ALW K N E G ---- FF L NY L FS G MDDDGM E SR F NPSV FFLD F L V VPP S R Y RP V S R LGD QM F T N G Q T V N L QAVM KD VVL IR 231
Cdd:cd01435 93 H R F RIS K W E V klfv AK L KL L DK G LLVEAA E LD F GYDM FFLD V L L VPP N R F RP P S F LGD KV F E N P Q N V L L SKIL KD NQQ IR 172
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 232 K LLA L M A Q EQKL peevaapppdeekdsliaidr S F L STLP G QSFID KL Y N I W IR LQS H VN IV FDS EMDKLM - MDKY PGI R 310
Cdd:cd01435 173 D LLA S M R Q AESQ --------------------- S K L DLIS G KTNSE KL I N A W LQ LQS A VN EL FDS TKAPKS g KKSP PGI K 231
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 311 Q I LEKKEGLFR KH MMGKRV D YAARSVI C PD MY I N TNEIGIP M VFA T KLT Y P Q PVTP W NV Q ELRQAVINGP N V H PGA SMVI 390
Cdd:cd01435 232 Q L LEKKEGLFR MN MMGKRV N YAARSVI S PD PF I E TNEIGIP L VFA K KLT F P E PVTP F NV E ELRQAVINGP D V Y PGA NAIE 311
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 391 N EDG SRTA LSA VDMTQ R E A V AK Q LL TPATGAPKPQ G T K I V C RH VKN GD IL LLNRQPTLH R PSI Q AH HA R I LP E EK V LRLH 470
Cdd:cd01435 312 D EDG RLIL LSA LSEER R K A L AK L LL LLSSAKLLLN G P K K V Y RH LLD GD VV LLNRQPTLH K PSI M AH KV R V LP G EK T LRLH 391
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 471 YANCK A YNADFDGDEMN A HFPQSEL G RAEAY VL A C TD Q QYLVP K DG Q PL A GLIQDH M VSG ASM T T R GC FFTRE Q Y ME LVY 550
Cdd:cd01435 392 YANCK S YNADFDGDEMN L HFPQSEL A RAEAY YI A S TD N QYLVP T DG K PL R GLIQDH V VSG VLL T S R DT FFTRE E Y QQ LVY 471
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 551 RG L T ----- DK V GR V KL F PP S ILKP L PLWTGKQV L ST L L I N I IP EDHIP LNLSGK A K ITG K AW vketprsv P G FNPDSMC 625
Cdd:cd01435 472 AA L R plfts DK D GR I KL L PP A ILKP K PLWTGKQV I ST I L K N L IP GNAPL LNLSGK K K TKK K VG -------- G G KWGGGSE 543
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 626 ESQV V IR E GELL C GVLDK AHY G S SAYGLVH CC YE I YGGET S GK V L TC L A RLFTAYLQ l Y RGFT L G V ED I L VK PKAD V KR Q 705
Cdd:cd01435 544 ESQV I IR N GELL T GVLDK SQF G A SAYGLVH AV YE L YGGET A GK L L SA L G RLFTAYLQ - M RGFT C G I ED L L LT PKAD E KR R 622
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 706 R I IEESTHC G PR A VRAA L N L peatsydevqgkwqdahlgkdqrdfnmidlkfke EV N HYSNE I N KAC M P F GL HRQ FPEN S 785
Cdd:cd01435 623 K I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P K GL LKP FPEN N 668
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 786 LQ M MVQSGAKGS T VN TM QISCLLGQ I ELEGRR P PLM A SGK S LP C F E PY EFT PRAGGF V T G RFLTGI K P P E F FFHCMAGRE 865
Cdd:cd01435 669 LQ L MVQSGAKGS M VN AS QISCLLGQ Q ELEGRR V PLM V SGK T LP S F P PY DTS PRAGGF I T D RFLTGI R P Q E Y FFHCMAGRE 748
730 740 750
....*....|....*....|....*....|.
gi 1622858458 866 GL V DTAVKTSRSGYLQRC I IKHLEGL V V Q YD 896
Cdd:cd01435 749 GL I DTAVKTSRSGYLQRC L IKHLEGL K V N YD 779
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
850-1562
4.90e-167
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: 514.60
E-value: 4.90e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 850 G IK P P EFFFH C M A GREGL V DTAVKT SR SGYLQR CII K H LE G LVV Q YD L TVR D S D G SV VQFLYGEDGLD IP K TQFLQPKQF 929
Cdd:pfam04998 1 G LT P Q EFFFH T M G GREGL I DTAVKT AE SGYLQR RLV K A LE D LVV T YD D TVR N S G G EI VQFLYGEDGLD PL K IEKQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 930 P F LASNY E VIM K SQH L HEV L SRADPKKALRHFRAIKKW qskhpntllrrgaflsysqkiqaavkalnlesenrngrspgt 1009
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1010 qemlrmwyeldeesrrkyqkkaatcpdps LSVWRPDIYF A SVSE T FETKVDDY S QEWAAQTEKSYEKSELSLDR L RTLLQ 1089
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1090 L KW Q R SL CE PGEAVG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM V a S A NIK T P MMS V PVLNTK - KA L K 1168
Cdd:pfam04998 170 L LY Q Q SL IN PGEAVG II AAQSIGEP G TQMTLNTFHFAG VASK NVTLG V PRL K EI IN V - S K NIK S P SLT V YLFDEV g RE L E 248
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1169 RV K SLKKQLTR V C LG E V LQKIDVQESFRMEEKQNKFR V YQLRFQ F LPHAYYQQ E KCLR PE DI L RFMET R FF K L L ME SIKK 1248
Cdd:pfam04998 249 KA K KVYGAIEK V T LG S V VESGEILYDPDPFNTPIISD V KGVVKF F DIIDEVTN E EEID PE TG L LILVI R LL K I L NK SIKK 328
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1249 knnkasafrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeere 1328
Cdd:pfam04998 --------------------------------------------------------------------------------
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1329 geenndedtqeernphregaretqerdeevgsgteedpalpalltq PR K PTHSQEPQGPEAV E R R VQ A VR EI HS FI DDYQ 1408
Cdd:pfam04998 329 ---------------------------------------------- VV K SEVIPRSIRNKVD E G R DI A IG EI TA FI IKIS 362
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1409 YDTEESLWCQVT V KLPL M KINFDMGS LV V SL AHGAVIYATK GI T R C L L NE TTNN K N E KEL VL N TEG I NL PELFKYAEVL D 1488
Cdd:pfam04998 363 KKIRQDTGGLRR V DELF M EEDPKLAI LV A SL LGNITLRGIP GI K R I L V NE DDKG K V E PDW VL E TEG V NL LRVLLVPGFV D 442
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622858458 1489 LR R LY SNDIH AMANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI RSNSSPLQ 1562
Cdd:pfam04998 443 AG R IL SNDIH EILEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1091-1608
1.03e-155
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: 475.91
E-value: 1.03e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1091 K WQ RSL C EPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM V AS A NIKTP M M SV P VL N T K K A l K R V 1170
Cdd:cd02735 1 K YM RSL V EPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM T AS K NIKTP S M TL P LK N G K S A - E R A 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1171 KS LKK Q L T RV C L GE V LQ K ID V Q E sfrmeekqnkfrvyqlrfqflphayyqqekclrpedi LRFMET R F FK L L ME sikkkn 1250
Cdd:cd02735 80 ET LKK R L S RV T L SD V VE K VE V T E ------------------------------------- ILKTIE R V FK K L LG ------ 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1251 nkasafrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeerege 1330
Cdd:cd02735 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1331 enndedtqeernphregaretqerdeevgsgteedpalpalltqprkpthsqepqgpeaverrvqavreihsfiddyqyd 1410
Cdd:cd02735 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1411 tees L WC Q VT V KLPL MKINFDMG S L V VS LA HG AVI YATK GITRC LLN E TTNNKNE K E LV l N TEG I NL PE L F K YAEV LD LR 1490
Cdd:cd02735 117 ---- K WC E VT I KLPL SSPKLLLL S I V EK LA RK AVI REIP GITRC FVV E EDKGGKT K Y LV - I TEG V NL AA L W K FSDI LD VN 191
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1491 R L Y S NDIHAM A NTYGIEAA L R V I E KEI KD VF A VYGIAVDPRHLSL V ADYM C FEG V Y K P L NR F G IR S NS SPLQ Q M T FET SF 1570
Cdd:cd02735 192 R I Y T NDIHAM L NTYGIEAA R R A I V KEI SN VF K VYGIAVDPRHLSL I ADYM T FEG G Y R P F NR I G ME S ST SPLQ K M S FET TL 271
490 500 510
....*....|....*....|....*....|....*...
gi 1622858458 1571 Q FLK Q AT ML G SH D E L R SPS AC LVVGK V V K GGTGLF E L K 1608
Cdd:cd02735 272 A FLK K AT LN G DI D N L S SPS SR LVVGK P V N GGTGLF D L L 309
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
281-917
4.23e-150
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 482.43
E-value: 4.23e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 281 NI W IR LQ S HV NIV FD S E M dklmmdky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT N 346
Cdd:PRK08566 266 DL W EL LQ Y HV TTY FD N E I -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI N 337
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 347 E I G I P MVF A TK LT Y P QP VT P WN VQ ELR QA V I NGP NV HPGA SM VI NE DG S R TA L SAVD mtq R E AV A KQ L ltp AT G A pkpqg 426
Cdd:PRK08566 338 E V G V P EAI A KE LT V P ER VT E WN IE ELR EY V L NGP EK HPGA NY VI RP DG R R IK L TDKN --- K E EL A EK L --- EP G W ----- 406
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 427 tk IV C RH VKN GDI L L L NRQP T LHR P SI Q AH HA R I LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACT 506
Cdd:PRK08566 407 -- IV E RH LID GDI V L F NRQP S LHR M SI M AH RV R V LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQ T E EA RAEA RI L MLV 483
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 507 DQQY L V P KD G Q P LA G L IQDH m V SGA SMT TR - GCF FT R E QYME L VYRG ltd KVGRVKLFP P S I LKPL P L WTGKQ VL S TL L i 585
Cdd:PRK08566 484 QEHI L S P RY G G P II G G IQDH - I SGA YLL TR k STL FT K E EALD L LRAA --- GIDELPEPE P A I ENGK P Y WTGKQ IF S LF L - 558
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 586 nii P E D hip LNL SG KAKI TGKAWVKE tprsvpgfnp DSM CE -- SQ VVI RE G E LL C GV L DK AHY G SSAYGLVHCCYEI YG G 663
Cdd:PRK08566 559 --- P K D --- LNL EF KAKI CSGCDECK ---------- KED CE hd AY VVI KN G K LL E GV I DK KAI G AEQGSILDRIVKE YG P 622
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 664 E TSGKV L TCLA RL FTAYLQ L y RGFT L G VE D ILVKPK A DVKRQR IIEE sthcgpravraalnlpeat SYDE V QG --- KWQD 740
Cdd:PRK08566 623 E RARRF L DSVT RL AIRFIM L - RGFT T G ID D EDIPEE A KEEIDE IIEE ------------------- AEKR V EE lie AYEN 682
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 741 AH L ---- G KDQRD fn MIDL K FKEEVNHYSN E INK - A CMPF G lhrqf PE N SLQM M VQS GA K GS TV N TM Q ISCLL GQ IELE G 815
Cdd:PRK08566 683 GE L eplp G RTLEE -- TLEM K IMQVLGKARD E AGE i A EKYL G ----- LD N PAVI M ART GA R GS ML N LT Q MAACV GQ QSVR G 755
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 816 R R PPLMASGKS LP C F E P YEFTPR A G GFV TGRFLT G IK P P EFFFH C M A GREGLVDTAV K TS R SGY L QR CI I KH L EG L V V Q Y 895
Cdd:PRK08566 756 E R IRRGYRDRT LP H F K P GDLGAE A R GFV RSSYKS G LT P T EFFFH A M G GREGLVDTAV R TS Q SGY M QR RL I NA L QD L K V E Y 835
650 660
....*....|....*....|..
gi 1622858458 896 D L TVRD SD G SV VQF L YGEDG L D 917
Cdd:PRK08566 836 D G TVRD TR G NI VQF K YGEDG V D 857
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
189-530
3.89e-107
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 342.96
E-value: 3.89e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 189 FF L DF L V VPP SRY RP VSR L GDQM F - TNGQ T VN L QAVM K DVVLIRK LL A L M A QEQKLPE E vaapppdeekdsliaidrsfl 267
Cdd:smart00663 3 MI L TV L P VPP PCL RP SVQ L DGGR F a EDDL T HL L RDII K RNNRLKR LL E L G A PSIIIRN E --------------------- 61
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 268 stlpgqsfidklyni WIR LQ SH V NIVF D S E - MDKLMM --- DKYPGIR Q I L EK KEG L FR KHMM GKRVD YA ARSVI C PD MYI 343
Cdd:smart00663 62 --------------- KRL LQ EA V DTLI D N E g LPRANQ ksg RPLKSLS Q R L KG KEG R FR QNLL GKRVD FS ARSVI T PD PNL 126
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 344 NT NE I G I P MVF A TK LT Y P QP VTP W N VQE LR QA V I NGP nvh P GA SMV I N ed G SR T A L SAVD mtq REAV A KQ L LTPA tgapk 423
Cdd:smart00663 127 KL NE V G V P KEI A LE LT F P EI VTP L N IDK LR KL V R NGP --- N GA KYI I R -- G KK T N L KLAK --- KSKI A NH L KIGD ----- 193
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 424 pqgtk IV C RHV KN GD IL L L NRQPTLHR P SIQAH HA R I L p E E K VL RL HYAN C KA YNADFDGDEMN A H F PQS ELG RAEA YV L 503
Cdd:smart00663 194 ----- IV E RHV ID GD VV L F NRQPTLHR M SIQAH RV R V L - E G K TI RL NPLV C SP YNADFDGDEMN L H V PQS LEA RAEA RE L 267
330 340
....*....|....*....|....*..
gi 1622858458 504 ACTDQQY L V PK D G Q P LA G L IQD HMVSG 530
Cdd:smart00663 268 MLVPNNI L S PK N G K P II G P IQD MLLGL 294
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
326-506
1.94e-86
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: 278.80
E-value: 1.94e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 326 GKRVD YA AR S VI C PD MYINTN E I G I P MV FA TK LT Y P QP VTP W N VQE LRQ A V I NGPNV H PGA SMV I NED G S R TA L SAVDMT 405
Cdd:pfam00623 1 GKRVD FS AR T VI S PD PNLKLD E V G V P IS FA KT LT F P EI VTP Y N IKR LRQ L V E NGPNV Y PGA NYI I RIN G A R RD L RYQKRR 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 406 QREAVAKQL ltpatgapkpqgtk IV C RHV KN GD IL L L NRQP T LHR P SI QA H HA R I LP e E K VL RL HYANCKA YNADFDGDE 485
Cdd:pfam00623 81 LDKELEIGD -------------- IV E RHV ID GD VV L F NRQP S LHR L SI MG H RV R V LP - G K TF RL NLSVTTP YNADFDGDE 145
170 180
....*....|....*....|.
gi 1622858458 486 MN A H F PQSE LG RAEA YV L ACT 506
Cdd:pfam00623 146 MN L H V PQSE EA RAEA EE L MLV 166
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1064-1607
5.94e-46
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: 170.23
E-value: 5.94e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1064 Q E WAAQTE K SYEKSELS LD RLRTLLQLKWQ RSL CE PGEAVG LL AAQSIGEP S TQMT LN TFH F AG RG E M NVTLG I PRL R EI 1143
Cdd:TIGR02389 8 K E LEETVK K REISDKEE LD EIIKRVEEEYL RSL ID PGEAVG IV AAQSIGEP G TQMT MR TFH Y AG VA E L NVTLG L PRL I EI 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1144 LM v A SANIK TP M M SVPVL - NTK K ALKRVKSLK K QLTRVC L GE V LQK I DVQ esfrmeekqnkfr VYQLRFQFLPHAYYQQ E 1222
Cdd:TIGR02389 88 VD - A RKTPS TP S M TIYLE d EYE K DREKAEEVA K KIEATK L ED V AKD I SID ------------- LADMTVIIELDEEQLK E 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1223 KCLRPE D I lrfmetrffkll MES IKK KNNKA safrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegda 1302
Cdd:TIGR02389 154 RGITVD D V ------------ EKA IKK AKLGK ------------------------------------------------- 172
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1303 dasdakrkekqeeevdyeseeeeeregeenndedtqeernphregaretqerdee V GSGTEEDPALPALLTQ P R kpthsq 1382
Cdd:TIGR02389 173 ------------------------------------------------------- V IEIDMDNNTITIKPGN P S ------ 191
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1383 epqg PEAVERRVQAVREI H sfiddyqydteeslwcqvtvklplmkinfdmgslvvslahgav I YAT KGI T R CLL nettn N 1462
Cdd:TIGR02389 192 ---- LKELRKLKEKIKNL H ------------------------------------------- I KGI KGI K R VVI ----- R 219
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1463 K NEK E L V LN TEG I NL P E LF K YAE V l D LR R LYS NDIH AM A NTY GIEAA LRV I EK EIK DVFAVY G IA VD P RHL S LVAD Y M CF 1542
Cdd:TIGR02389 220 K EGD E Y V IY TEG S NL K E VL K LEG V - D KT R TTT NDIH EI A EVL GIEAA RNA I IE EIK RTLEEQ G LD VD I RHL M LVAD L M TW 298
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622858458 1543 E G VYKPLN R F GI RSN - S S P L QQMT FE TSFQF L KQ A TML G SH DEL RSPSACLV VG KVVKG GTG LFE L 1607
Cdd:TIGR02389 299 D G EVRQIG R H GI SGE k A S V L ARAA FE VTVKH L LD A AIR G EV DEL KGVIENII VG QPIPL GTG DVD L 364
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1051-1607
4.35e-45
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 168.10
E-value: 4.35e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1051 VS ET F E T K VD D Y S Q E WAAQT ---- EKSY E KSE L SLDRLRTLLQL --- KWQ RSL C EPGEAVG LL AAQSIGEP S TQMT LN TF 1123
Cdd:PRK04309 3 SE ET L E E K LE D A S L E LPQKL keel REKL E ERK L TEEEVEEIIEE vvr EYL RSL V EPGEAVG VV AAQSIGEP G TQMT MR TF 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1124 H F AG RG E M NVTLG I PRL R EI l MV A SANIK TPMM SVPVL - NTKKALKRVKSLKKQLTRVC L GEVLQK I D V Q esfrmeekqn 1202
Cdd:PRK04309 83 H Y AG VA E I NVTLG L PRL I EI - VD A RKEPS TPMM TIYLK d EYAYDREKAEEVARKIEATT L ENLAKD I S V D ---------- 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1203 kfr VYQLRFQFLPHAYYQQEKC L RPE D ILRFM E trff K LLMESIKKKN N K asafrnvntrratqrdldnagesgrsrgeq 1282
Cdd:PRK04309 152 --- LANMTIIIELDEEMLEDRG L TVD D VKEAI E ---- K KKGGEVEIEG N T ------------------------------ 194
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1283 egdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeeregeenndedtqeernphregaretqerdeevgsgt 1362
Cdd:PRK04309 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1363 eedpalpa L LTQ P RK P THS qepqgpe AVERRVQAV R E I H sfiddyqydteeslwcqvtvklplmkinfdmgslvvslahg 1442
Cdd:PRK04309 195 -------- L IIS P KE P SYR ------- ELRKLAEKI R N I K ----------------------------------------- 218
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1443 av I YAT KGI T R CLLN ettnn K NEK E L V LN TEG I NL P E LF K YAE V l D LR R LYS N D IH AMANTY GIEAA LRV I EK EIK DVFA 1522
Cdd:PRK04309 219 -- I KGI KGI K R VIIR ----- K EGD E Y V IY TEG S NL K E VL K VEG V - D AT R TTT N N IH EIEEVL GIEAA RNA I IE EIK NTLE 290
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1523 VY G IA VD P RH LS LVAD Y M CFE G VYKPLN R F G IR - SNS S P L QQMT FE TSFQF L KQ A TML G SH DEL RSPSACLV VG KVVKG G 1601
Cdd:PRK04309 291 EQ G LD VD I RH IM LVAD M M TWD G EVRQIG R H G VS g EKA S V L ARAA FE VTVKH L LD A AVR G EV DEL KGVTENII VG QPIPL G 370
....*.
gi 1622858458 1602 TG LF EL 1607
Cdd:PRK04309 371 TG DV EL 376
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
286-1144
5.99e-44
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: 175.24
E-value: 5.99e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 286 LQ SH V NIV FD SEMDK --- LMMDKY P -- GIRQI L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L ty 360
Cdd:TIGR02386 281 LQ EA V DAL FD NGRRG kpv VGKNNR P lk SLSDM L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPELKMYQC G L P KKM A LE L -- 358
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 361 pqp VT P WNVQE L - RQAVI ng P N VHPGAS M VIN ED gsrtal SA V - D MT qr E A V A K Q lltpatgap K P qgtkivcrhvkngd 438
Cdd:TIGR02386 359 --- FK P FIIKR L i DRELA -- A N IKSAKK M IEQ ED ------ PE V w D VL -- E D V I K E --------- H P -------------- 402
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 439 i L LLNR Q PTLHR PS IQA HHARIL p E E K VL RLH YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V PKDG Q P 518
Cdd:TIGR02386 403 - V LLNR A PTLHR LG IQA FEPVLV - E G K AI RLH PLV C T A F NADFDGD Q M AV H V P L S PEAQ AEA RA L MLASNNI L N PKDG K P 480
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 519 LAGLI QD h MV sgasmtt R G CF ftreq Y MELVYR G ltd KV G RV K L F ppsilkplplwtgkqvl S TLLIN I IPE D HIPLN L S 598
Cdd:TIGR02386 481 IVTPS QD - MV ------- L G LY ----- Y LTTEKP G --- AK G EG K I F ----------------- S NVDEA I RAY D NGKVH L H 527
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 599 GKAKITGKAWVK ET prs VP G --- FN p DSMC E SQVV I REG E llcg V L D K AHYG S sayg L VHCC YE IY G G E TSGKV L TCLAR 675
Cdd:TIGR02386 528 ALIGVRTSGEIL ET --- TV G rvi FN - EILP E GFPY I NDN E ---- P L S K KEIS S ---- L IDLL YE VH G I E ETAEM L DKIKA 595
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 676 L FTA Y LQLY r G F T LGVE DI L V KP kadv KRQR I IE E sthcgpravraalnlpeat SYD EV QGKWQDAHL G K --- DQ R DFNM 752
Cdd:TIGR02386 596 L GFK Y ATKS - G T T ISAS DI V V PD ---- EKYE I LK E ------------------- ADK EV AKIQKFYNK G L itd EE R YRKV 651
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 753 IDL -- KF K EE V NH - YSNEIN K acmpfglh RQFPE N SLQ MM VQ SGA K G STVNTM Q ISCLL G qielegrrpp LMA -- SG KSL 827
Cdd:TIGR02386 652 VSI ws ET K DK V TD a MMKLLK K -------- DTYKF N PIF MM AD SGA R G NISQFR Q LAGMR G ---------- LMA kp SG DII 713
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 828 P cfepyef T P raggf VTGR F LT G IKPP E F F FHCMAG R E GL V DTA V KT SR SGYL Q R ciikhle G LV - V QY D LT VR DS D - G S 905
Cdd:TIGR02386 714 E ------- L P ----- IKSS F RE G LTVL E Y F ISTHGA R K GL A DTA L KT AD SGYL T R ------- R LV d V AQ D VV VR EE D c G T 774
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 906 vvqflyg E D G LDI pktqflqpkqfpflasny E V I MKSQH l HEVL S RA D pk KALRHFR A IKKWQSKHPNTLLRRGAFLS -- 983
Cdd:TIGR02386 775 ------- E E G IEV ------------------ E A I VEGKD - EIIE S LK D -- RIVGRYS A EDVYDPDTGKLIAEANTLIT ee 826
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 984 YSQ KI QAA - VKALNL esenrng RS PG T Q E MLR mwyeldeesrrkyqkka AT C pdpslsvwrpdiyfasvsetfetkvddy 1062
Cdd:TIGR02386 827 IAE KI ENS g IEKVKV ------- RS VL T C E SEH ----------------- GV C ---------------------------- 854
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1063 sqewaaqt E K S Y eks ELS L DRLR tllqlkwqrs L C E P GEAVG LL AAQSIGEP S TQ M T LN TFH --- F AG RGE m NV T L G I PR 1139
Cdd:TIGR02386 855 -------- Q K C Y --- GRD L ATGK ---------- L V E I GEAVG VI AAQSIGEP G TQ L T MR TFH tgg V AG ASG - DI T Q G L PR 912
....*
gi 1622858458 1140 LR E IL 1144
Cdd:TIGR02386 913 VK E LF 917
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
316-882
2.14e-34
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: 144.15
E-value: 2.14e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 316 K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq AVIN gpnvhpgas MVINEDGS 395
Cdd:COG0086 324 K Q G R FR QNLL GKRVDY SG RSVI VVGPELKLHQC G L P KKM A LE L FK P ------------- FIYR --------- KLEERGLA 381
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 396 R T AL SA VD M TQ RE avakqlltpatgap K P QGTK I VCRHV K NGDI LL l NR Q PTLHR PS IQA HHA r I L P E E K VLR LH YAN C K 475
Cdd:COG0086 382 T T IK SA KK M VE RE -------------- E P EVWD I LEEVI K EHPV LL - NR A PTLHR LG IQA FEP - V L I E G K AIQ LH PLV C T 445
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 476 A Y NADFDGD E M NA H F P Q S ELGRA EA YV L ACTDQQY L V P KD G Q P LAGLI QD h MV S G ASMT TR -------- G CF F TREQYME 547
Cdd:COG0086 446 A F NADFDGD Q M AV H V P L S LEAQL EA RL L MLSTNNI L S P AN G K P IIVPS QD - MV L G LYYL TR eregakge G MI F ADPEEVL 524
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 548 LV Y R - G LT D KVG R V K LFPPSILKP lplw T GK Q V LS T L liniipedhiplnlsgkakit G KAW V K E - T P RS VP GF N pdsmc 625
Cdd:COG0086 525 RA Y E n G AV D LHA R I K VRITEDGEQ ---- V GK I V ET T V --------------------- G RYL V N E i L P QE VP FY N ----- 574
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 626 esqvviregellc G V LD K A H YGS sayg LVHCC Y EIY G GETSGKV L TC L AR L ft AYLQLY R - G FTL G VE D IL V k PK A dvk R 704
Cdd:COG0086 575 ------------- Q V IN K K H IEV ---- IIRQM Y RRC G LKETVIF L DR L KK L -- GFKYAT R a G ISI G LD D MV V - PK E --- K 631
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 705 Q R I I EE ST hcgp RA V raalnlpeatsy D E VQGKWQDAHLGKDQ R DFNM ID L kfkee VNHY S N E INKAC M P f GLHR Q fpe N 784
Cdd:COG0086 632 Q E I F EE AN ---- KE V ------------ K E IEKQYAEGLITEPE R YNKV ID G ----- WTKA S L E TESFL M A - AFSS Q --- N 686
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 785 SLQ MM VQ SGA K GS T vntmqiscll G Q IE - L E G R R p P LMA -- SG kslpcf EPY E f TP ----- R A G gfvtgrfl T G IK pp E F 856
Cdd:COG0086 687 TTY MM AD SGA R GS A ---------- D Q LR q L A G M R - G LMA kp SG ------ NII E - TP igsnf R E G -------- L G VL -- E Y 738
570 580
....*....|....*....|....*.
gi 1622858458 857 F FHCMAG R E GL V DTA V KT SR SGYL Q R 882
Cdd:COG0086 739 F ISTHGA R K GL A DTA L KT AD SGYL T R 764
Name
Accession
Description
Interval
E-value
RNAP_I_RPA1_N
cd01435 Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
156-896
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: 1196.61
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 156 H L F ALW K N E G ---- FF L NY L FS G MDDDGM E SR F NPSV FFLD F L V VPP S R Y RP V S R LGD QM F T N G Q T V N L QAVM KD VVL IR 231
Cdd:cd01435 93 H R F RIS K W E V klfv AK L KL L DK G LLVEAA E LD F GYDM FFLD V L L VPP N R F RP P S F LGD KV F E N P Q N V L L SKIL KD NQQ IR 172
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 232 K LLA L M A Q EQKL peevaapppdeekdsliaidr S F L STLP G QSFID KL Y N I W IR LQS H VN IV FDS EMDKLM - MDKY PGI R 310
Cdd:cd01435 173 D LLA S M R Q AESQ --------------------- S K L DLIS G KTNSE KL I N A W LQ LQS A VN EL FDS TKAPKS g KKSP PGI K 231
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 311 Q I LEKKEGLFR KH MMGKRV D YAARSVI C PD MY I N TNEIGIP M VFA T KLT Y P Q PVTP W NV Q ELRQAVINGP N V H PGA SMVI 390
Cdd:cd01435 232 Q L LEKKEGLFR MN MMGKRV N YAARSVI S PD PF I E TNEIGIP L VFA K KLT F P E PVTP F NV E ELRQAVINGP D V Y PGA NAIE 311
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 391 N EDG SRTA LSA VDMTQ R E A V AK Q LL TPATGAPKPQ G T K I V C RH VKN GD IL LLNRQPTLH R PSI Q AH HA R I LP E EK V LRLH 470
Cdd:cd01435 312 D EDG RLIL LSA LSEER R K A L AK L LL LLSSAKLLLN G P K K V Y RH LLD GD VV LLNRQPTLH K PSI M AH KV R V LP G EK T LRLH 391
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 471 YANCK A YNADFDGDEMN A HFPQSEL G RAEAY VL A C TD Q QYLVP K DG Q PL A GLIQDH M VSG ASM T T R GC FFTRE Q Y ME LVY 550
Cdd:cd01435 392 YANCK S YNADFDGDEMN L HFPQSEL A RAEAY YI A S TD N QYLVP T DG K PL R GLIQDH V VSG VLL T S R DT FFTRE E Y QQ LVY 471
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 551 RG L T ----- DK V GR V KL F PP S ILKP L PLWTGKQV L ST L L I N I IP EDHIP LNLSGK A K ITG K AW vketprsv P G FNPDSMC 625
Cdd:cd01435 472 AA L R plfts DK D GR I KL L PP A ILKP K PLWTGKQV I ST I L K N L IP GNAPL LNLSGK K K TKK K VG -------- G G KWGGGSE 543
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 626 ESQV V IR E GELL C GVLDK AHY G S SAYGLVH CC YE I YGGET S GK V L TC L A RLFTAYLQ l Y RGFT L G V ED I L VK PKAD V KR Q 705
Cdd:cd01435 544 ESQV I IR N GELL T GVLDK SQF G A SAYGLVH AV YE L YGGET A GK L L SA L G RLFTAYLQ - M RGFT C G I ED L L LT PKAD E KR R 622
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 706 R I IEESTHC G PR A VRAA L N L peatsydevqgkwqdahlgkdqrdfnmidlkfke EV N HYSNE I N KAC M P F GL HRQ FPEN S 785
Cdd:cd01435 623 K I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P K GL LKP FPEN N 668
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 786 LQ M MVQSGAKGS T VN TM QISCLLGQ I ELEGRR P PLM A SGK S LP C F E PY EFT PRAGGF V T G RFLTGI K P P E F FFHCMAGRE 865
Cdd:cd01435 669 LQ L MVQSGAKGS M VN AS QISCLLGQ Q ELEGRR V PLM V SGK T LP S F P PY DTS PRAGGF I T D RFLTGI R P Q E Y FFHCMAGRE 748
730 740 750
....*....|....*....|....*....|.
gi 1622858458 866 GL V DTAVKTSRSGYLQRC I IKHLEGL V V Q YD 896
Cdd:cd01435 749 GL I DTAVKTSRSGYLQRC L IKHLEGL K V N YD 779
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
850-1562
4.90e-167
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: 514.60
E-value: 4.90e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 850 G IK P P EFFFH C M A GREGL V DTAVKT SR SGYLQR CII K H LE G LVV Q YD L TVR D S D G SV VQFLYGEDGLD IP K TQFLQPKQF 929
Cdd:pfam04998 1 G LT P Q EFFFH T M G GREGL I DTAVKT AE SGYLQR RLV K A LE D LVV T YD D TVR N S G G EI VQFLYGEDGLD PL K IEKQGRFTI 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 930 P F LASNY E VIM K SQH L HEV L SRADPKKALRHFRAIKKW qskhpntllrrgaflsysqkiqaavkalnlesenrngrspgt 1009
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1010 qemlrmwyeldeesrrkyqkkaatcpdps LSVWRPDIYF A SVSE T FETKVDDY S QEWAAQTEKSYEKSELSLDR L RTLLQ 1089
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1090 L KW Q R SL CE PGEAVG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM V a S A NIK T P MMS V PVLNTK - KA L K 1168
Cdd:pfam04998 170 L LY Q Q SL IN PGEAVG II AAQSIGEP G TQMTLNTFHFAG VASK NVTLG V PRL K EI IN V - S K NIK S P SLT V YLFDEV g RE L E 248
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1169 RV K SLKKQLTR V C LG E V LQKIDVQESFRMEEKQNKFR V YQLRFQ F LPHAYYQQ E KCLR PE DI L RFMET R FF K L L ME SIKK 1248
Cdd:pfam04998 249 KA K KVYGAIEK V T LG S V VESGEILYDPDPFNTPIISD V KGVVKF F DIIDEVTN E EEID PE TG L LILVI R LL K I L NK SIKK 328
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1249 knnkasafrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeere 1328
Cdd:pfam04998 --------------------------------------------------------------------------------
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1329 geenndedtqeernphregaretqerdeevgsgteedpalpalltq PR K PTHSQEPQGPEAV E R R VQ A VR EI HS FI DDYQ 1408
Cdd:pfam04998 329 ---------------------------------------------- VV K SEVIPRSIRNKVD E G R DI A IG EI TA FI IKIS 362
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1409 YDTEESLWCQVT V KLPL M KINFDMGS LV V SL AHGAVIYATK GI T R C L L NE TTNN K N E KEL VL N TEG I NL PELFKYAEVL D 1488
Cdd:pfam04998 363 KKIRQDTGGLRR V DELF M EEDPKLAI LV A SL LGNITLRGIP GI K R I L V NE DDKG K V E PDW VL E TEG V NL LRVLLVPGFV D 442
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622858458 1489 LR R LY SNDIH AMANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI RSNSSPLQ 1562
Cdd:pfam04998 443 AG R IL SNDIH EILEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
50-921
3.07e-160
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: 509.10
E-value: 3.07e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 50 Q EE L E Q Y TAE I vq NN L LGSQGAH VK N V cesksk LTA V FW KA h MNA K R CPHC KTGRSVVRK E HNSKLTITFPAMVHR tagq 129
Cdd:cd02582 106 E EE I E K Y LER I -- RR L KEKWPEL VK R V ------ IEK V KK KA - KKR K V CPHC GAPQYKIKL E KPTTFYEEKEEGEVK ---- 172
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 130 kdseplgieeaqmgkrgy LTP TSA RE H L falwknegfflnylf SGMD D DGM E S - RFN P SV ----- FF L DF L V VPP SRY RP 203
Cdd:cd02582 173 ------------------ LTP SEI RE R L --------------- EKIP D EDL E L l GID P KT arpew MV L TV L P VPP VTV RP 219
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 204 VSR L gdqmf TN G QTVN lqavm K D vv L IR KL LALMAQE Q K L P E -- E VA AP ppdeekdsliaidrsflstlpg Q SF I DK L yn 281
Cdd:cd02582 220 SIT L ----- ET G ERSE ----- D D -- L TH KL VDIIRIN Q R L K E ni E AG AP ---------------------- Q LI I ED L -- 263
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 282 i W IR LQ S HV NIV FD S E M dklmmdky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT NE 347
Cdd:cd02582 264 - W DL LQ Y HV TTY FD N E I -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI NE 334
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 348 I G I P MVF A TK LT Y P QP VT P WN VQEL R QA V I NGP NVH PGA SM VI NE DG S R TA L SA V D mtq RE AV A KQ L ltp AT G apkpqgt 427
Cdd:cd02582 335 V G V P EDI A KE LT V P ER VT E WN IEKM R KL V L NGP DKW PGA NY VI RP DG R R IR L RY V N --- RE EL A ER L --- EP G ------- 401
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 428 K IV C RH VKN GDI L L L NRQP T LHR P SI Q AH HA R I LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQSE LG RAEA YV L ACTD 507
Cdd:cd02582 402 W IV E RH LID GDI V L F NRQP S LHR M SI M AH RV R V LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQSE EA RAEA RE L MLVQ 480
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 508 QQY L V P KD G Q P LA G L IQD H m V SGA SMT TR - GCF FT R E QYME L VYRGLT D kvgr VK L FP P S IL K P L PLWTGKQ VL S TL L in 586
Cdd:cd02582 481 EHI L S P RY G G P II G G IQD Y - I SGA YLL TR k TTL FT K E EALQ L LSAAGY D ---- GL L PE P A IL E P K PLWTGKQ LF S LF L -- 553
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 587 ii P E D hip LN LS GKAK ITGK awvketprsv PGFNP D SM C E -- SQ VVI RE G E LL C GV L DK AHY G SSAY G - L V H CCYEI YG G 663
Cdd:cd02582 554 -- P K D --- LN FE GKAK VCSG ---------- CSECK D ED C P nd GY VVI KN G K LL E GV I DK KAI G AEQP G s L L H RIAKE YG N 618
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 664 E TSGKV L TCLA RL FTAYLQ L Y r GFT L G VE D ILVKPK A DVKRQR II E E sthcgpravraalnlpeat SYDE V QG --- KWQD 740
Cdd:cd02582 619 E VARRF L DSVT RL AIRFIE L R - GFT I G ID D EDIPEE A RKEIEE II K E ------------------- AEKK V YE lie QYKN 678
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 741 AH L ---- G KDQRD fn MIDL K FKEEVNHYSN E IN K - A CMPFG lhrqf P E N SLQM M VQS GA K GS TV N TM Q ISCL LGQ IELE G 815
Cdd:cd02582 679 GE L eplp G RTLEE -- TLEM K IMQVLGKARD E AG K v A SKYLD ----- P F N NAVI M ART GA R GS ML N LT Q MAAC LGQ QSVR G 751
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 816 R R PPLMASGKS LP C F E P YEFT P R A G GFV TGR F LT G IK P P EFFFH C M A GREGLVDTAV K TS R SGY L QR CI I KH L EG L V V Q Y 895
Cdd:cd02582 752 E R INRGYRNRT LP H F K P GDLG P E A R GFV RSS F RD G LS P T EFFFH A M G GREGLVDTAV R TS Q SGY M QR RL I NA L QD L Y V E Y 831
890 900
....*....|....*....|....*.
gi 1622858458 896 D L TVRDS D G SVV QF L YGEDG L D IP K T 921
Cdd:cd02582 832 D G TVRDS R G NII QF K YGEDG V D PA K S 857
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1091-1608
1.03e-155
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: 475.91
E-value: 1.03e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1091 K WQ RSL C EPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM V AS A NIKTP M M SV P VL N T K K A l K R V 1170
Cdd:cd02735 1 K YM RSL V EPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM T AS K NIKTP S M TL P LK N G K S A - E R A 79
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1171 KS LKK Q L T RV C L GE V LQ K ID V Q E sfrmeekqnkfrvyqlrfqflphayyqqekclrpedi LRFMET R F FK L L ME sikkkn 1250
Cdd:cd02735 80 ET LKK R L S RV T L SD V VE K VE V T E ------------------------------------- ILKTIE R V FK K L LG ------ 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1251 nkasafrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeerege 1330
Cdd:cd02735 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1331 enndedtqeernphregaretqerdeevgsgteedpalpalltqprkpthsqepqgpeaverrvqavreihsfiddyqyd 1410
Cdd:cd02735 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1411 tees L WC Q VT V KLPL MKINFDMG S L V VS LA HG AVI YATK GITRC LLN E TTNNKNE K E LV l N TEG I NL PE L F K YAEV LD LR 1490
Cdd:cd02735 117 ---- K WC E VT I KLPL SSPKLLLL S I V EK LA RK AVI REIP GITRC FVV E EDKGGKT K Y LV - I TEG V NL AA L W K FSDI LD VN 191
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1491 R L Y S NDIHAM A NTYGIEAA L R V I E KEI KD VF A VYGIAVDPRHLSL V ADYM C FEG V Y K P L NR F G IR S NS SPLQ Q M T FET SF 1570
Cdd:cd02735 192 R I Y T NDIHAM L NTYGIEAA R R A I V KEI SN VF K VYGIAVDPRHLSL I ADYM T FEG G Y R P F NR I G ME S ST SPLQ K M S FET TL 271
490 500 510
....*....|....*....|....*....|....*...
gi 1622858458 1571 Q FLK Q AT ML G SH D E L R SPS AC LVVGK V V K GGTGLF E L K 1608
Cdd:cd02735 272 A FLK K AT LN G DI D N L S SPS SR LVVGK P V N GGTGLF D L L 309
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
281-917
4.23e-150
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 482.43
E-value: 4.23e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 281 NI W IR LQ S HV NIV FD S E M dklmmdky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT N 346
Cdd:PRK08566 266 DL W EL LQ Y HV TTY FD N E I -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI N 337
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 347 E I G I P MVF A TK LT Y P QP VT P WN VQ ELR QA V I NGP NV HPGA SM VI NE DG S R TA L SAVD mtq R E AV A KQ L ltp AT G A pkpqg 426
Cdd:PRK08566 338 E V G V P EAI A KE LT V P ER VT E WN IE ELR EY V L NGP EK HPGA NY VI RP DG R R IK L TDKN --- K E EL A EK L --- EP G W ----- 406
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 427 tk IV C RH VKN GDI L L L NRQP T LHR P SI Q AH HA R I LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACT 506
Cdd:PRK08566 407 -- IV E RH LID GDI V L F NRQP S LHR M SI M AH RV R V LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQ T E EA RAEA RI L MLV 483
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 507 DQQY L V P KD G Q P LA G L IQDH m V SGA SMT TR - GCF FT R E QYME L VYRG ltd KVGRVKLFP P S I LKPL P L WTGKQ VL S TL L i 585
Cdd:PRK08566 484 QEHI L S P RY G G P II G G IQDH - I SGA YLL TR k STL FT K E EALD L LRAA --- GIDELPEPE P A I ENGK P Y WTGKQ IF S LF L - 558
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 586 nii P E D hip LNL SG KAKI TGKAWVKE tprsvpgfnp DSM CE -- SQ VVI RE G E LL C GV L DK AHY G SSAYGLVHCCYEI YG G 663
Cdd:PRK08566 559 --- P K D --- LNL EF KAKI CSGCDECK ---------- KED CE hd AY VVI KN G K LL E GV I DK KAI G AEQGSILDRIVKE YG P 622
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 664 E TSGKV L TCLA RL FTAYLQ L y RGFT L G VE D ILVKPK A DVKRQR IIEE sthcgpravraalnlpeat SYDE V QG --- KWQD 740
Cdd:PRK08566 623 E RARRF L DSVT RL AIRFIM L - RGFT T G ID D EDIPEE A KEEIDE IIEE ------------------- AEKR V EE lie AYEN 682
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 741 AH L ---- G KDQRD fn MIDL K FKEEVNHYSN E INK - A CMPF G lhrqf PE N SLQM M VQS GA K GS TV N TM Q ISCLL GQ IELE G 815
Cdd:PRK08566 683 GE L eplp G RTLEE -- TLEM K IMQVLGKARD E AGE i A EKYL G ----- LD N PAVI M ART GA R GS ML N LT Q MAACV GQ QSVR G 755
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 816 R R PPLMASGKS LP C F E P YEFTPR A G GFV TGRFLT G IK P P EFFFH C M A GREGLVDTAV K TS R SGY L QR CI I KH L EG L V V Q Y 895
Cdd:PRK08566 756 E R IRRGYRDRT LP H F K P GDLGAE A R GFV RSSYKS G LT P T EFFFH A M G GREGLVDTAV R TS Q SGY M QR RL I NA L QD L K V E Y 835
650 660
....*....|....*....|..
gi 1622858458 896 D L TVRD SD G SV VQF L YGEDG L D 917
Cdd:PRK08566 836 D G TVRD TR G NI VQF K YGEDG V D 857
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
174-900
3.93e-142
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: 458.55
E-value: 3.93e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 174 G M DDDG mesr FN P SVFF L DFLV VPP SRY RP VSRLGDQMF TN -- GQ TV N L qavm KDVVLIRKLLA lm AQEQ K lpeevaapp 251
Cdd:cd02583 167 L M NPLA ---- GR P ENLI L TRIP VPP LCI RP SVVMDEKSG TN ed DL TV K L ---- SEIIFLNDVIK -- KHLE K --------- 227
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 252 pdeekdsliaidrsflstlp G QS f ID K LYNI W IR LQ SHVNIVFD SE MDK L --- M MD K Y P -- G IR Q I L EK K E G L FR KHMM G 326
Cdd:cd02583 228 -------------------- G AK - TQ K IMED W DF LQ LQCALYIN SE LPG L pls M QP K K P ir G FC Q R L KG K Q G R FR GNLS G 286
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 327 KRVD YAA R S VI C PD MYINTNEI G I P MVF A TK LTYP QP VT PW N VQE LR QA V I NGP N VHPGA SM VI NE DG SRT - A L SAVD mt 405
Cdd:cd02583 287 KRVD FSG R T VI S PD PNLRIDQV G V P EHV A KI LTYP ER VT RY N IEK LR KL V L NGP D VHPGA NF VI KR DG GKK k F L KYGN -- 364
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 406 q R EAV A KQ L ltpatgapkpqgt KI --- V C RH VKN GDI L L L NRQP T LHR P SI Q AH H A RIL P e EKVL R LHYAN C KA YNADFD 482
Cdd:cd02583 365 - R RKI A RE L ------------- KI gdi V E RH LED GDI V L F NRQP S LHR L SI M AH R A KVM P - WRTF R FNECV C TP YNADFD 429
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 483 GDEMN A H F PQ S E LG RAEA YV L ACTDQQYLV P KD G Q PL AGLI QD HMVSGASM T TRGC FF T R E Q YME L V y RGLT D KVGRVK L 562
Cdd:cd02583 430 GDEMN L H V PQ T E EA RAEA LE L MGVKNNLVT P RN G E PL IAAT QD FLTASYLL T SKDV FF D R A Q FCQ L C - SYML D GEIKID L 508
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 563 F PP S ILKP LP LWTGKQ VL S t LL INIIPEDHIPL NL SG K A K ITG K awvketprsvpgf NPDS MC -- ESQ VVIR EG ELLCG V 640
Cdd:cd02583 509 P PP A ILKP VE LWTGKQ IF S - LL LRPNKKSPVLV NL EA K E K SYT K ------------- KSPD MC pn DGY VVIR NS ELLCG R 574
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 641 LDK AHY GS SAYGLVH cc Y EI --- YG G E TSGKVLTC LA R L FTAY L QL y RGF TL G VE D il V K P KADVKRQR -- IIEE sthcg 715
Cdd:cd02583 575 LDK STL GS GSKNSLF -- Y VL lrd YG P E AAAAAMNR LA K L SSRW L SN - RGF SI G ID D -- V T P SKELLKKK ee LVDN ----- 644
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 716 pravraalnlpeat S Y DEVQGKWQDAHL GK DQRDF -- NMID --- L K FKE E VNHYSNEIN KAC MPF g LH rqf PE NS LQM M V 790
Cdd:cd02583 645 -------------- G Y AKCDEYIKQYKK GK LELQP gc TAEQ tle A K ISG E LSKIREDAG KAC LKE - LH --- KS NS PLI M A 706
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 791 QS G A KGS TV N TM Q - I S C l L GQ IELE G R R P P LMASGKS LP C F EPYEF TP R A G GFV TGR F LT G IK P P EFFFH C M A GREGLVD 869
Cdd:cd02583 707 LC G S KGS NI N IS Q m I A C - V GQ QIIS G K R I P NGFEDRT LP H F PRNSK TP A A K GFV ANS F YS G LT P T EFFFH T M S GREGLVD 785
730 740 750
....*....|....*....|....*....|.
gi 1622858458 870 TAVKT SRS GY L QR CII K H LE G L V VQYD L TVR 900
Cdd:cd02583 786 TAVKT AET GY M QR RLM K A LE D L S VQYD G TVR 816
RNAP_II_RPB1_N
cd02733 Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
286-896
2.40e-139
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: 448.91
E-value: 2.40e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 286 LQ S HV NIVF D S E --- MDKLMMDK --- YPG IRQ I L EK KEG LF R KHM MGKRVD YA AR S VI C PD MYINTNEI G I P MVF A TK LT 359
Cdd:cd02733 190 LQ F HV ATYM D N E ipg LPQATQKS grp LKS IRQ R L KG KEG RI R GNL MGKRVD FS AR T VI T PD PNLELDQV G V P RSI A MN LT 269
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 360 Y P QP VTP W N VQE L RQA V I NGPN VH PGA SMV I NE DG S R TA L SAVDM tqrea VAKQL L TPAT gapkpqgtk IV C RH VKN GD I 439
Cdd:cd02733 270 F P EI VTP F N IDR L QEL V R NGPN EY PGA KYI I RD DG E R ID L RYLKK ----- ASDLH L QYGY --------- IV E RH LQD GD V 335
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 440 L L L NRQP T LH RP S IQA H HARI LP e EKVL RL HYANCKA YNADFDGDEMN A H F PQS ELG RAE AYV L ACTDQ Q YLV P KDGQ P L 519
Cdd:cd02733 336 V L F NRQP S LH KM S MMG H RVKV LP - YSTF RL NLSVTTP YNADFDGDEMN L H V PQS LET RAE LKE L MMVPR Q IVS P QSNK P V 414
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 520 A G LI QD HMVSGASM T T R GC F FTRE Q Y M E L VY r G L T D KV G RVK lf P P S ILKP L PLWTGKQ VL S T llin IIP e DHIP L NL S G 599
Cdd:cd02733 415 M G IV QD TLLGVRKL T K R DT F LEKD Q V M N L LM - W L P D WD G KIP -- Q P A ILKP K PLWTGKQ IF S L ---- IIP - KINN L IR S S 486
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 600 KAKITG K A W vketprsvpg FN P D smc ESQ V V I RE GELL C G V L D K AHY G S S AY GL V H CCYEI YG G E TSGKVLTCLA R LFTA 679
Cdd:cd02733 487 SHHDGD K K W ---------- IS P G --- DTK V I I EN GELL S G I L C K KTV G A S SG GL I H VIWLE YG P E AARDFIGNIQ R VVNN 553
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 680 Y L q L YR GF TL G VE D ILVKPKADV K R Q RI I EESTH cgpravraalnlpeatsyd E V QGKWQD A HL G KDQRDF - NMIDLK F K 758
Cdd:cd02733 554 W L - L HN GF SI G IG D TIADKETMK K I Q ET I KKAKR ------------------- D V IKLIEK A QN G ELEPQP g KTLRES F E 613
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 759 EE VN hys NEI NKA CMPF G LHR Q F --- PE N SLQM MV QS G A KGS TV N TM QI SCLL GQ IEL EG R R P P LMASGKS LP C F EPYEF 835
Cdd:cd02733 614 NK VN --- RIL NKA RDKA G KSA Q K sls ED N NFKA MV TA G S KGS FI N IS QI IACV GQ QNV EG K R I P FGFRRRT LP H F IKDDY 690
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622858458 836 T P RAG GFV TGRF L T G IK P P EFFFH C M A GREGL V DTAVKT SRS GY L QR CII K HL E GLV V Q YD 896
Cdd:cd02733 691 G P ESR GFV ENSY L R G LT P Q EFFFH A M G GREGL I DTAVKT AET GY I QR RLV K AM E DVM V K YD 751
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
4-1607
1.87e-135
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 454.10
E-value: 1.87e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 4 CP RAVI H LL L CQ l R V LEVGALQAVYE L E ---- RILNRFLEENA D PSASEIQ EE LEQYTAE I vqnnllg SQGAHVKNVC E S 79
Cdd:PRK14977 71 CP GHFG H IE L AE - P V IHIAFIDNIKD L L nstc HKCAKLKLPQE D LNVFKLI EE AHAAARD I ------- PEKRIDDEII E E 142
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 80 KSKLTA V FW K AH mna K R CPHC kt G RSVVRK E H n SKL TI T fpamvhrtagqkdseplg IE EAQMGKR g Y L T P TSA R EHLFA 159
Cdd:PRK14977 143 VRDQVK V YA K KA --- K E CPHC -- G APQHEL E F - EEP TI F ------------------ IE KTEIEEH - R L L P IEI R DIFEK 197
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 160 LWKNEGFFLNY lfsgmdd D GMES R fn P SVFF L DFLV VPP SRY RP vsrlgdqmftngq TVN L Q - AVMKDVV L IRK L LALMA 238
Cdd:PRK14977 198 IIDDDLELIGF ------- D PKKA R -- P EWAV L QAFL VPP LTA RP ------------- SII L E t GERSEDD L THI L VDIIK 255
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 239 QE QKL P E -- EVA APP pdeekdsliaidrsflstlpgq SFIDKL yni WIR LQ S H VNIV FD SEMDKLMMDKYP G IR ------ 310
Cdd:PRK14977 256 AN QKL K E sk DAG APP ---------------------- LIVEDE --- VDH LQ Y H TSTF FD NATAGIPQAHHK G SG rplksl 310
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 311 - Q I L EK KEG L FR KHMM GKRVD YA AR S VI C PD MY I NTN E I G I P MVF A T KLT Y P QP V TPW N VQELRQA VINGP NVH PGA SMV 389
Cdd:PRK14977 311 f Q R L KG KEG R FR GNLI GKRVD FS AR T VI S PD PM I DID E V G V P EAI A M KLT I P EI V NEN N IEKMKEL VINGP DEF PGA NAI 390
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 390 INE DG SRTA L sav D MTQREA va K QL L TP A TGAPKP qg TK IV C RH VKN GDI LLL NRQP T LH RP SI Q AH HARI LP E e KVL RL 469
Cdd:PRK14977 391 RKG DG TKIR L --- D FLEDKG -- K DA L RE A AEQLEI -- GD IV E RH LAD GDI VIF NRQP S LH KL SI L AH RVKV LP G - ATF RL 462
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 470 H Y A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQYLV P KD G Q P LA G LI QD HMVSGASM T TRGCF F TREQYMELV 549
Cdd:PRK14977 463 H P A V C PP YNADFDGDEMN L H V PQ I E DA RAEA IE L MGVKDNLIS P RT G G P II G AL QD FITAAYLI T KDDAL F DKNEASNIA 542
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 550 YR - G L TD KVGR vklf P PSIL K PL P L WTGKQ VL S TL L inii P E D hip L N LS G K AK itgka W VKETPRSVP gf N P DSMCESQ 628
Cdd:PRK14977 543 ML a G I TD PLPE ---- P AIKT K DG P A WTGKQ LF S LF L ---- P K D --- F N FE G I AK ----- W SAGKAGEAK -- D P SCLGDGY 604
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 629 V V I R EGEL LC GV L D KAHY G SSAYG --- L VHCCYEI YG GETSGKV L TCLARLFTAYLQL Y r GF TL G VE D ILVKPK A dvk R Q 705
Cdd:PRK14977 605 V L I K EGEL IS GV I D DNII G ALVEE pes L IDRIAKD YG EAVAIEF L NKILIIAKKEILH Y - GF SN G PG D LIIPDE A --- K Q 680
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 706 R I IEESTHCGPRAVRAALNLPEATSYDEVQ GK WQ dah L GKDQRDFNMIDLKFKE E VNHY ---- SNEI N K a C MP fglhrqf 781
Cdd:PRK14977 681 E I EDDIQGMKDEVSDLIDQRKITRKITIYK GK EE --- L LRGMKEEEALEADIVN E LDKA rdka GSSA N D - C ID ------- 749
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 782 PE N SLQM M VQS GA K GS TV N TM QI SCL LGQ IELEG R RPPLMAS G K -------- S L PC F EPYEFT P R A G GFV TGRFLT G IKP 853
Cdd:PRK14977 750 AD N AGKI M AKT GA R GS MA N LA QI AGA LGQ QKRKT R IGFVLTG G R lhegykdr A L SH F QEGDDN P D A H GFV KNNYRE G LNA 829
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 854 P EFFFH C M A GREGL V D T A VK T SR SGY L QR CIIKH LE GLVVQ YD L TVRD SD G SVV QF LY GEDG L D IP K tqflqpkqfpfla 933
Cdd:PRK14977 830 A EFFFH A M G GREGL I D K A RR T ED SGY F QR RLANA LE DIRLE YD E TVRD PH G HII QF KF GEDG I D PQ K ------------- 896
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 934 snyevimksqhlhev L SRADP kkalrhfraikkwqs KHPNTLLR rgaflsy S QKI qaavkalnlesenrngrspgtqeml 1013
Cdd:PRK14977 897 --------------- L DHGEA --------------- FNLERIIE ------- K QKI ------------------------- 914
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1014 rmwyeld E ESRRKYQ K kaatcpdpslsvwrpdiyfasvs ETF E TKVDD Y SQEWA A QTE K SY ---- EKS EL SL D R L RTL -- 1087
Cdd:PRK14977 915 ------- E DRGKGAS K ----------------------- DEI E ELAKE Y TKTFN A NLP K LL adai HGA EL KE D E L EAI ca 964
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1088 - LQLKWQRSLC EPG E A V G LLA AQSI G EP S TQMTL N TFH F AG RGE M N VT L G IP R LR E i L MV A S A NIK TP M M SV pvlntkk A 1166
Cdd:PRK14977 965 e GKEGFEKAKV EPG Q A I G IIS AQSI A EP G TQMTL R TFH A AG IKA M D VT H G LE R FI E - L VD A R A KPS TP T M DI ------- Y 1036
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1167 L KR vksl KKQLTRVCLG E VLQKI dvqesfrmee K QN K F R VYQLRFQF lph AYYQQE K CLR P EDILR fmetrffkllmesi 1246
Cdd:PRK14977 1037 L DD ---- ECKEDIEKAI E IARNL ---------- K EL K V R ALIADSAI --- DNANEI K LIK P DKRAL -------------- 1085
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1247 kk K N NKASAF R NVNTRR A TQRDLDNAG E SGRSR geqegdeedegh I VDAEA E EG D A D asdakrkekqeeevdyeseeeee 1326
Cdd:PRK14977 1086 -- E N GCIPME R FAEIEA A LAKGKKFEM E LEDDL ------------ I ILDLV E AA D R D ----------------------- 1128
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1327 regeenndedtqeernphregaretqerdeevgsgteedpalpalltqprkpthsqepqgpeave RRVQAVRE I HSF I D D 1406
Cdd:PRK14977 1129 ----------------------------------------------------------------- KPLATLIA I RNK I L D 1143
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1407 yqydteeslwcq VT VK lplmkinfdmgslvvslahgaviy ATKG I T R CLL n E TTNNKNEK E LVLN T E G I NL PELFKYAEV 1486
Cdd:PRK14977 1144 ------------ KP VK ------------------------ GVPD I E R AWV - E LVEKDGRD E WIIQ T S G S NL AAVLEMKCI 1186
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1487 l D LRRLYS ND IHAM A N T Y GIEAA LRV I EK E IKDVFAVY G IA VD P R HLS LVAD Y MC FE G VYKP -- L NRF G I R SN ----- S S 1559
Cdd:PRK14977 1187 - D IANTIT ND CFEI A G T L GIEAA RNA I FN E LASILEDQ G LE VD N R YIM LVAD I MC SR G TIEA ig L QAA G V R HG fagek D S 1265
1610 1620 1630 1640
....*....|....*....|....*....|....*....|....*...
gi 1622858458 1560 PL QQMT FE TSFQFLKQ A TML G SHDELRSPSAC L VV G KVVKG G T G LFE L 1607
Cdd:PRK14977 1266 PL AKAA FE ITTHTIAH A ALG G EIEKIKGILDA L IM G QNIPI G S G KVD L 1313
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
281-896
1.21e-110
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: 362.14
E-value: 1.21e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 281 NI W IR LQ S HV NIVF D SEMDKL --- MMDKY P -- GIR Q I L EK KEG L FR KHM MGKRVD YAA RSVI C PD MYINTNEI G I P MVF A 355
Cdd:cd00399 107 ER W RL LQ E HV DTYL D NGIAGQ pqt QKSGR P lr SLA Q R L KG KEG R FR GNL MGKRVD FSG RSVI S PD PNLRLDQV G V P KSI A 186
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 356 TK L typqpvtpwnvqelrqavingpnvhpgasmvinedgsrtalsavdmtqreavakqlltpatgapkpqgtkivcrhvk 435
Cdd:cd00399 187 LT L ----------------------------------------------------------------------------- 189
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 436 N GD IL L L NRQP T LH RP SI Q AH HA R I LP E e KVL RL HYAN C KA YNADFDGDEMN A H F PQSE LG RAEA YV L ACTDQQY L V P KD 515
Cdd:cd00399 190 D GD PV L F NRQP S LH KL SI M AH RV R V LP G - STF RL NPLV C SP YNADFDGDEMN L H V PQSE EA RAEA RE L MLVPNNI L S P QN 268
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 516 G Q PL A GL I QD H m VS GA SMT T R G cfftreqymelvyrgltdkvgrvklfppsilkplplwtg KQ VL S TL L iniipedhipl 595
Cdd:cd00399 269 G E PL I GL S QD T - LL GA YLL T L G --------------------------------------- KQ IV S AA L ----------- 297
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 596 nlsgkakitgkawvketprsvpgfnpdsmcesqvviregellcgvldkahygss AY GL V H CCYEIY G G E TSG K V L TC L A R 675
Cdd:cd00399 298 ------------------------------------------------------ PG GL L H TVTREL G P E KAA K L L SN L Q R 323
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 676 LFTAY L QL y R GF TL G VE D ILVKPKADVKRQRI IEE sthcgpr A VRAALNLP EA TSYDEVQ gkwqdah LGKDQRDFNMIDL 755
Cdd:cd00399 324 VGFVF L TT - S GF SV G IG D VIDDGVIPEEKTEL IEE ------- A KKKVDEVE EA FQAGLLT ------- AQEGMTLEESLED 388
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 756 KFKEEV N HYSNEINK A CMPF g L HRQFPE NS LQM M VQ SGAKGS TV N TM Q I S CLL GQ IEL EG R R P P LMA S GKS LP C F EPYEF 835
Cdd:cd00399 389 NILDFL N EARDKAGS A ASVN - L DLVSKF NS IYV M AM SGAKGS FI N IR Q M S ACV GQ QSV EG K R I P RGF S DRT LP H F SKDDY 467
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622858458 836 T P R A G GF VTGR FL T G IK P P E F FFH C M A GREGLVDTAVKT SR SGYLQR CII K H LE G LVV Q YD 896
Cdd:cd00399 468 S P E A K GF IRNS FL E G LT P L E Y FFH A M G GREGLVDTAVKT AE SGYLQR RLV K A LE D LVV H YD 528
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
189-530
3.89e-107
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 342.96
E-value: 3.89e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 189 FF L DF L V VPP SRY RP VSR L GDQM F - TNGQ T VN L QAVM K DVVLIRK LL A L M A QEQKLPE E vaapppdeekdsliaidrsfl 267
Cdd:smart00663 3 MI L TV L P VPP PCL RP SVQ L DGGR F a EDDL T HL L RDII K RNNRLKR LL E L G A PSIIIRN E --------------------- 61
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 268 stlpgqsfidklyni WIR LQ SH V NIVF D S E - MDKLMM --- DKYPGIR Q I L EK KEG L FR KHMM GKRVD YA ARSVI C PD MYI 343
Cdd:smart00663 62 --------------- KRL LQ EA V DTLI D N E g LPRANQ ksg RPLKSLS Q R L KG KEG R FR QNLL GKRVD FS ARSVI T PD PNL 126
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 344 NT NE I G I P MVF A TK LT Y P QP VTP W N VQE LR QA V I NGP nvh P GA SMV I N ed G SR T A L SAVD mtq REAV A KQ L LTPA tgapk 423
Cdd:smart00663 127 KL NE V G V P KEI A LE LT F P EI VTP L N IDK LR KL V R NGP --- N GA KYI I R -- G KK T N L KLAK --- KSKI A NH L KIGD ----- 193
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 424 pqgtk IV C RHV KN GD IL L L NRQPTLHR P SIQAH HA R I L p E E K VL RL HYAN C KA YNADFDGDEMN A H F PQS ELG RAEA YV L 503
Cdd:smart00663 194 ----- IV E RHV ID GD VV L F NRQPTLHR M SIQAH RV R V L - E G K TI RL NPLV C SP YNADFDGDEMN L H V PQS LEA RAEA RE L 267
330 340
....*....|....*....|....*..
gi 1622858458 504 ACTDQQY L V PK D G Q P LA G L IQD HMVSG 530
Cdd:smart00663 268 MLVPNNI L S PK N G K P II G P IQD MLLGL 294
RNA_pol_Rpb1_2
pfam00623 RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
326-506
1.94e-86
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: 278.80
E-value: 1.94e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 326 GKRVD YA AR S VI C PD MYINTN E I G I P MV FA TK LT Y P QP VTP W N VQE LRQ A V I NGPNV H PGA SMV I NED G S R TA L SAVDMT 405
Cdd:pfam00623 1 GKRVD FS AR T VI S PD PNLKLD E V G V P IS FA KT LT F P EI VTP Y N IKR LRQ L V E NGPNV Y PGA NYI I RIN G A R RD L RYQKRR 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 406 QREAVAKQL ltpatgapkpqgtk IV C RHV KN GD IL L L NRQP T LHR P SI QA H HA R I LP e E K VL RL HYANCKA YNADFDGDE 485
Cdd:pfam00623 81 LDKELEIGD -------------- IV E RHV ID GD VV L F NRQP S LHR L SI MG H RV R V LP - G K TF RL NLSVTTP YNADFDGDE 145
170 180
....*....|....*....|.
gi 1622858458 486 MN A H F PQSE LG RAEA YV L ACT 506
Cdd:pfam00623 146 MN L H V PQSE EA RAEA EE L MLV 166
RNAP_II_Rpb1_C
cd02584 Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
1091-1608
6.09e-54
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: 194.73
E-value: 6.09e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1091 KWQ RSL CE PGE A VG LL AAQSIGEP S TQMTLNTFHFAG RGEM NVTLG I PRL R EI LM VA S a NIKTP MMS V PVLN - TK K ALKR 1169
Cdd:cd02584 18 RFN RSL VH PGE M VG TI AAQSIGEP A TQMTLNTFHFAG VSAK NVTLG V PRL K EI IN VA K - NIKTP SLT V YLEP g FA K DEEK 96
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1170 V K SLKKQ L TRVC L GE V LQKIDVQ ----- ESFRM EE KQNKFRV Y qlr F Q F l P HAYYQ Q EKC lr PEDI LR FMET R ---- FF K 1240
Cdd:cd02584 97 A K KIQSR L EHTT L KD V TAATEIY ydpdp QNTVI EE DKEFVES Y --- F E F - P DEDVE Q DRL -- SPWL LR IELD R kkmt DK K 170
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1241 L L ME S I K KK NNK as A F RN - V N trra TQRDL DNA g E SGRS R GE qegdeedegh I VDAEA E EGDADAS D AKR K ekqeeevdy 1319
Cdd:cd02584 171 L S ME Q I A KK IKE -- E F KD d L N ---- VIFSD DNA - E KLVI R IR ---------- I INDDE E KEEDSED D VFL K --------- 224
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1320 eseeeeeregeenndedtqeernphrega RETQERD eevgsgte E D PA L palltqprkpthsqep Q G P E AVER rvqavre 1399
Cdd:cd02584 225 ----------------------------- KIESNML -------- S D MT L ---------------- K G I E GIRK ------- 244
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1400 ihsfiddyqydteeslwcqvtvklplmkinfdmgslvvslahga V IYATKGITR c LLN ET TNN K NEK E L VL N T E G I NL P E 1479
Cdd:cd02584 245 -------------------------------------------- V FIREENKKK - VDI ET GEF K KRE E W VL E T D G V NL R E 279
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1480 LFKYAE V l D LR R LY SNDI HAMANTY GIEAA LRVIE KE IKD V FAVY G IA V DP RHL S L VA D Y M CFE G VYKPLN R F GI - R SNS 1558
Cdd:cd02584 280 VLSHPG V - D PT R TT SNDI VEIFEVL GIEAA RKALL KE LRN V ISFD G SY V NY RHL A L LC D V M TQR G HLMAIT R H GI n R QDT 358
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1559 S PL QQMT FE TSFQF L KQ A TML G SH D E L RSP S ACLVV G KVVKG GTG L F E L K 1608
Cdd:cd02584 359 G PL MRCS FE ETVDI L LE A AAF G ET D D L KGV S ENIML G QLAPI GTG C F D L L 408
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
231-900
6.13e-52
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: 197.24
E-value: 6.13e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 231 RKL L A L m AQ EQ K LPE E VA app P DEEKDS L IAIDRS FL ST LP ----------- GQS F IDKLYN I WIRLQSHVN ivfdsemd 299
Cdd:cd10506 116 LPI L S L - AQ VK K ILK E ID --- P KLIAKG L PRQEGL FL KC LP vppnchrvtef THG F STGSRL I FDERTRAYK -------- 183
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 300 KL MMDKYPGIRQILE KK E GL -- FRKHMM GKR VDYAA RSV ICP D M Y INT NEIGIP MVF A TK LT YPQP V TP WN VQE L RQAVI 377
Cdd:cd10506 184 KL VDFIGTANESAAS KK S GL kw MKDLLL GKR SGHSF RSV VVG D P Y LEL NEIGIP CEI A ER LT VSER V SS WN RER L QEYCD 263
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 378 NGP nvhpgas MVINED G S R TA lsavdmt Q R EAVAKQLL T PAT G apkpqgt KIVC R HVKN GD IL L L NR Q P TL H RP S IQ A HH 457
Cdd:cd10506 264 LTL ------- LLKGVI G V R RN ------- G R LVGVRSHN T LQI G ------- DVIH R PLVD GD VV L V NR P P SI H QH S LI A LS 322
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 458 ARI LP EEK V LRLHYAN C KAYNA DFDGD EMNAHF PQS ELG RAE AYV L ACTDQ Q YLVPKD GQ P L AG L I QD HMVSGAS MT T RG 537
Cdd:cd10506 323 VKV LP TNS V VSINPLC C SPFRG DFDGD CLHGYI PQS LQA RAE LEE L VALPK Q LISSQS GQ N L LS L T QD SLLAAHL MT E RG 402
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 538 C F FTRE Q YME L VYRGLTDKV grvklf PP S I L K - P L --- PLWTGKQ VLST LL inii P E D hip L NL S G kakitgkawvketp 613
Cdd:cd10506 403 V F LDKA Q MQQ L QMLCPSQLP ------ PP A I I K s P P sng PLWTGKQ LFQM LL ---- P T D --- L DY S F -------------- 455
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 614 rsv P GFN pdsmcesq V V I RE GEL L c GVLDKAHYGSSAY G LV - HCCYEIYG G ETSG k V L TCLAR L FTAY L QL y RGF TLGVE 692
Cdd:cd10506 456 --- P SNL -------- V F I SD GEL I - SSSGGSSWLRDSE G NL f SILVKHGP G KALD - F L DSAQG L LCEW L SM - RGF SVSLS 521
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 693 D ILVKPKA d VK RQ RI IEE s THC G P R AVRA A L N L ---------- PEAT S YD E VQ - GKWQDAHLGKD Q RDFNMIDL --- K FK 758
Cdd:cd10506 522 D LYLSSDS - YS RQ KM IEE - ISL G L R EAEI A C N I kqllvdsrkd FLSG S GE E ND v SSDVERVIYER Q KSAALSQA svs A FK 599
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 759 EEVNHYS N EIN K - A CM pfglhrqfp E NSL QM M VQS G A KGS TVNTM Q I S CL LG - Q IE L EG --- R R P ------------- P L 820
Cdd:cd10506 600 QVFRDIQ N LVY K y A SK --------- D NSL LA M IKA G S KGS LLKLV Q Q S GC LG l Q LS L VK lsy R I P rqlscaawnsqks P R 670
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 821 MASGKSLP C F E P Y E ftpr AG G F V TGR FL T G IK P P E F F F H CMAG R EGLVDTAVKT sr S G Y L Q R CIIKHLEGLV V Q YD L TVR 900
Cdd:cd10506 671 VIEKDGSE C T E S Y I ---- PY G V V ESS FL D G LN P L E C F V H SITS R DSSFSSNADL -- P G T L F R KLMFFMRDIY V A YD G TVR 744
RNAP_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1071-1607
2.77e-50
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: 182.84
E-value: 2.77e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1071 E KSYEKSE L S L DRLRTLLQL --- KWQ RSL C EPGEAVG LL AAQSIGEP S TQMTL N TFH F AG RG E M NVTLG I PRL R EI LM v A 1147
Cdd:cd06528 8 E EVLKEHG L T L SEAEEIIKE vlr EYL RSL I EPGEAVG IV AAQSIGEP G TQMTL R TFH Y AG VA E I NVTLG L PRL I EI VD - A 86
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1148 SANIK TP M M SVPV - LNT K KALKRVKSLKKQLTRVC L GEVLQK I DVQ esfrmeekqnkfr VYQL R FQFLPHAYYQQEKCLR 1226
Cdd:cd06528 87 RKEPS TP T M TIYL e EEY K YDREKAEEVARKIEETT L ENLAED I SID ------------- LFNM R ITIELDEEMLEDRGIT 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1227 PE D I L RFM E trffkllme SI KK K nnkasafrnvntrratqrdldnagesgrsrgeqegdeedeghivd AEA EEGD ADA sd 1306
Cdd:cd06528 154 VD D V L KAI E --------- KL KK G --------------------------------------------- KVG EEGD VTL -- 177
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1307 akrkekqeeevdyeseeeeeregeenndedtqeernphregaretqerdeevgsgteedpalpa LLTQPRK P T hsqepqg 1386
Cdd:cd06528 178 ---------------------------------------------------------------- IVLKAEE P S ------- 186
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1387 PEAVERRVQAVREIH sfiddyqydteeslwcqvtvklplmkinfdmgslvvslahgav I YAT KGI T R CLLN ettnn K N E K 1466
Cdd:cd06528 187 IKELRKLAEKILNTK ------------------------------------------- I KGI KGI K R VIVR ----- K E E D 218
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1467 E L V LN TEG I NL PELF K YAE V l D LR R LYS N D IH AMANTY GIEAA LRV I EK EIK DVFAVY G IA VD P RH LS LVAD Y M CFE G VY 1546
Cdd:cd06528 219 E Y V IY TEG S NL KAVL K VEG V - D PT R TTT N N IH EIEEVL GIEAA RNA I IN EIK RTLEEQ G LD VD I RH IM LVAD I M TYD G EV 297
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622858458 1547 KPLN R F GI RSN - S S P L QQMT FE TSFQF L KQ A TML G SH DELR SPSACLV VG KVVKG GTG LF EL 1607
Cdd:cd06528 298 RQIG R H GI AGE k P S V L ARAA FE VTVKH L LD A AVR G EV DELR GVIENII VG QPIPL GTG DV EL 359
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1064-1607
5.94e-46
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: 170.23
E-value: 5.94e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1064 Q E WAAQTE K SYEKSELS LD RLRTLLQLKWQ RSL CE PGEAVG LL AAQSIGEP S TQMT LN TFH F AG RG E M NVTLG I PRL R EI 1143
Cdd:TIGR02389 8 K E LEETVK K REISDKEE LD EIIKRVEEEYL RSL ID PGEAVG IV AAQSIGEP G TQMT MR TFH Y AG VA E L NVTLG L PRL I EI 87
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1144 LM v A SANIK TP M M SVPVL - NTK K ALKRVKSLK K QLTRVC L GE V LQK I DVQ esfrmeekqnkfr VYQLRFQFLPHAYYQQ E 1222
Cdd:TIGR02389 88 VD - A RKTPS TP S M TIYLE d EYE K DREKAEEVA K KIEATK L ED V AKD I SID ------------- LADMTVIIELDEEQLK E 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1223 KCLRPE D I lrfmetrffkll MES IKK KNNKA safrnvntrratqrdldnagesgrsrgeqegdeedeghivdaeaeegda 1302
Cdd:TIGR02389 154 RGITVD D V ------------ EKA IKK AKLGK ------------------------------------------------- 172
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1303 dasdakrkekqeeevdyeseeeeeregeenndedtqeernphregaretqerdee V GSGTEEDPALPALLTQ P R kpthsq 1382
Cdd:TIGR02389 173 ------------------------------------------------------- V IEIDMDNNTITIKPGN P S ------ 191
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1383 epqg PEAVERRVQAVREI H sfiddyqydteeslwcqvtvklplmkinfdmgslvvslahgav I YAT KGI T R CLL nettn N 1462
Cdd:TIGR02389 192 ---- LKELRKLKEKIKNL H ------------------------------------------- I KGI KGI K R VVI ----- R 219
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1463 K NEK E L V LN TEG I NL P E LF K YAE V l D LR R LYS NDIH AM A NTY GIEAA LRV I EK EIK DVFAVY G IA VD P RHL S LVAD Y M CF 1542
Cdd:TIGR02389 220 K EGD E Y V IY TEG S NL K E VL K LEG V - D KT R TTT NDIH EI A EVL GIEAA RNA I IE EIK RTLEEQ G LD VD I RHL M LVAD L M TW 298
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622858458 1543 E G VYKPLN R F GI RSN - S S P L QQMT FE TSFQF L KQ A TML G SH DEL RSPSACLV VG KVVKG GTG LFE L 1607
Cdd:TIGR02389 299 D G EVRQIG R H GI SGE k A S V L ARAA FE VTVKH L LD A AIR G EV DEL KGVIENII VG QPIPL GTG DVD L 364
PRK04309
PRK04309 DNA-directed RNA polymerase subunit A''; Validated
1051-1607
4.35e-45
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 168.10
E-value: 4.35e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1051 VS ET F E T K VD D Y S Q E WAAQT ---- EKSY E KSE L SLDRLRTLLQL --- KWQ RSL C EPGEAVG LL AAQSIGEP S TQMT LN TF 1123
Cdd:PRK04309 3 SE ET L E E K LE D A S L E LPQKL keel REKL E ERK L TEEEVEEIIEE vvr EYL RSL V EPGEAVG VV AAQSIGEP G TQMT MR TF 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1124 H F AG RG E M NVTLG I PRL R EI l MV A SANIK TPMM SVPVL - NTKKALKRVKSLKKQLTRVC L GEVLQK I D V Q esfrmeekqn 1202
Cdd:PRK04309 83 H Y AG VA E I NVTLG L PRL I EI - VD A RKEPS TPMM TIYLK d EYAYDREKAEEVARKIEATT L ENLAKD I S V D ---------- 151
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1203 kfr VYQLRFQFLPHAYYQQEKC L RPE D ILRFM E trff K LLMESIKKKN N K asafrnvntrratqrdldnagesgrsrgeq 1282
Cdd:PRK04309 152 --- LANMTIIIELDEEMLEDRG L TVD D VKEAI E ---- K KKGGEVEIEG N T ------------------------------ 194
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1283 egdeedeghivdaeaeegdadasdakrkekqeeevdyeseeeeeregeenndedtqeernphregaretqerdeevgsgt 1362
Cdd:PRK04309 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1363 eedpalpa L LTQ P RK P THS qepqgpe AVERRVQAV R E I H sfiddyqydteeslwcqvtvklplmkinfdmgslvvslahg 1442
Cdd:PRK04309 195 -------- L IIS P KE P SYR ------- ELRKLAEKI R N I K ----------------------------------------- 218
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1443 av I YAT KGI T R CLLN ettnn K NEK E L V LN TEG I NL P E LF K YAE V l D LR R LYS N D IH AMANTY GIEAA LRV I EK EIK DVFA 1522
Cdd:PRK04309 219 -- I KGI KGI K R VIIR ----- K EGD E Y V IY TEG S NL K E VL K VEG V - D AT R TTT N N IH EIEEVL GIEAA RNA I IE EIK NTLE 290
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1523 VY G IA VD P RH LS LVAD Y M CFE G VYKPLN R F G IR - SNS S P L QQMT FE TSFQF L KQ A TML G SH DEL RSPSACLV VG KVVKG G 1601
Cdd:PRK04309 291 EQ G LD VD I RH IM LVAD M M TWD G EVRQIG R H G VS g EKA S V L ARAA FE VTVKH L LD A AVR G EV DEL KGVTENII VG QPIPL G 370
....*.
gi 1622858458 1602 TG LF EL 1607
Cdd:PRK04309 371 TG DV EL 376
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
286-1144
5.99e-44
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: 175.24
E-value: 5.99e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 286 LQ SH V NIV FD SEMDK --- LMMDKY P -- GIRQI L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L ty 360
Cdd:TIGR02386 281 LQ EA V DAL FD NGRRG kpv VGKNNR P lk SLSDM L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPELKMYQC G L P KKM A LE L -- 358
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 361 pqp VT P WNVQE L - RQAVI ng P N VHPGAS M VIN ED gsrtal SA V - D MT qr E A V A K Q lltpatgap K P qgtkivcrhvkngd 438
Cdd:TIGR02386 359 --- FK P FIIKR L i DRELA -- A N IKSAKK M IEQ ED ------ PE V w D VL -- E D V I K E --------- H P -------------- 402
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 439 i L LLNR Q PTLHR PS IQA HHARIL p E E K VL RLH YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V PKDG Q P 518
Cdd:TIGR02386 403 - V LLNR A PTLHR LG IQA FEPVLV - E G K AI RLH PLV C T A F NADFDGD Q M AV H V P L S PEAQ AEA RA L MLASNNI L N PKDG K P 480
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 519 LAGLI QD h MV sgasmtt R G CF ftreq Y MELVYR G ltd KV G RV K L F ppsilkplplwtgkqvl S TLLIN I IPE D HIPLN L S 598
Cdd:TIGR02386 481 IVTPS QD - MV ------- L G LY ----- Y LTTEKP G --- AK G EG K I F ----------------- S NVDEA I RAY D NGKVH L H 527
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 599 GKAKITGKAWVK ET prs VP G --- FN p DSMC E SQVV I REG E llcg V L D K AHYG S sayg L VHCC YE IY G G E TSGKV L TCLAR 675
Cdd:TIGR02386 528 ALIGVRTSGEIL ET --- TV G rvi FN - EILP E GFPY I NDN E ---- P L S K KEIS S ---- L IDLL YE VH G I E ETAEM L DKIKA 595
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 676 L FTA Y LQLY r G F T LGVE DI L V KP kadv KRQR I IE E sthcgpravraalnlpeat SYD EV QGKWQDAHL G K --- DQ R DFNM 752
Cdd:TIGR02386 596 L GFK Y ATKS - G T T ISAS DI V V PD ---- EKYE I LK E ------------------- ADK EV AKIQKFYNK G L itd EE R YRKV 651
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 753 IDL -- KF K EE V NH - YSNEIN K acmpfglh RQFPE N SLQ MM VQ SGA K G STVNTM Q ISCLL G qielegrrpp LMA -- SG KSL 827
Cdd:TIGR02386 652 VSI ws ET K DK V TD a MMKLLK K -------- DTYKF N PIF MM AD SGA R G NISQFR Q LAGMR G ---------- LMA kp SG DII 713
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 828 P cfepyef T P raggf VTGR F LT G IKPP E F F FHCMAG R E GL V DTA V KT SR SGYL Q R ciikhle G LV - V QY D LT VR DS D - G S 905
Cdd:TIGR02386 714 E ------- L P ----- IKSS F RE G LTVL E Y F ISTHGA R K GL A DTA L KT AD SGYL T R ------- R LV d V AQ D VV VR EE D c G T 774
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 906 vvqflyg E D G LDI pktqflqpkqfpflasny E V I MKSQH l HEVL S RA D pk KALRHFR A IKKWQSKHPNTLLRRGAFLS -- 983
Cdd:TIGR02386 775 ------- E E G IEV ------------------ E A I VEGKD - EIIE S LK D -- RIVGRYS A EDVYDPDTGKLIAEANTLIT ee 826
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 984 YSQ KI QAA - VKALNL esenrng RS PG T Q E MLR mwyeldeesrrkyqkka AT C pdpslsvwrpdiyfasvsetfetkvddy 1062
Cdd:TIGR02386 827 IAE KI ENS g IEKVKV ------- RS VL T C E SEH ----------------- GV C ---------------------------- 854
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1063 sqewaaqt E K S Y eks ELS L DRLR tllqlkwqrs L C E P GEAVG LL AAQSIGEP S TQ M T LN TFH --- F AG RGE m NV T L G I PR 1139
Cdd:TIGR02386 855 -------- Q K C Y --- GRD L ATGK ---------- L V E I GEAVG VI AAQSIGEP G TQ L T MR TFH tgg V AG ASG - DI T Q G L PR 912
....*
gi 1622858458 1140 LR E IL 1144
Cdd:TIGR02386 913 VK E LF 917
RNA_pol_Rpb1_3
pfam04983 RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
509-694
4.70e-42
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: 151.63
E-value: 4.70e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 509 QY L V P KD G Q P LA G LI QD HMVSGASM T TRGC FF T RE QY M E L VYR G ltdkvgr VK L FP P S ILKP L - PLWTGKQ VL S T LL I N i 587
Cdd:pfam04983 1 NI L S P QN G K P II G PS QD MVLGAYLL T REDT FF D RE EV M Q L LMY G ------- IV L PH P A ILKP I k PLWTGKQ TF S R LL P N - 72
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 588 ipedhi PL N LS GK A K ITGK awvketprsvpgfn PDSMCE S Q V V I RE GEL LC GV L DK AHY G S S AYG L V H CC Y EI YG G E TSG 667
Cdd:pfam04983 73 ------ EI N PK GK P K TNEE -------------- DLCEND S Y V L I NN GEL IS GV I DK KTV G K S LGS L I H II Y KE YG P E ETA 132
170 180
....*....|....*....|....*..
gi 1622858458 668 K V L TC L AR L FTA YL QLY r GF TL G VE DI 694
Cdd:pfam04983 133 K F L DR L QK L GFR YL TKS - GF SI G ID DI 158
RNAP_beta'_N
cd01609 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
312-903
1.21e-36
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: 148.82
E-value: 1.21e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 312 I L EK K E G L FR KHMM GKRVDY AA RSVI C -- P DMYIN tn EI G I P MVF A TK L typqp VT P WNVQ EL rqavingpnvhpgasmv 389
Cdd:cd01609 235 M L KG K Q G R FR QNLL GKRVDY SG RSVI V vg P ELKLH -- QC G L P KEM A LE L ----- FK P FVIR EL ----------------- 290
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 390 I NEDGSRTAL SA VD M TQ R E avakqlltpatgap K P QGTK I V c RH V KN G DIL LLNR Q PTLHR PS IQA HHA r I L P E E K VLR L 469
Cdd:cd01609 291 I ERGLAPNIK SA KK M IE R K -------------- D P EVWD I L - EE V IK G HPV LLNR A PTLHR LG IQA FEP - V L I E G K AIQ L 354
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 470 H YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA Y VL ACTDQQY L V P KD G Q P LAGLI QD h MV S G ASMT T RGCF ftr EQYM E LV 549
Cdd:cd01609 355 H PLV C T A F NADFDGD Q M AV H V P L S LEAQ AEA R VL MLSSNNI L S P AS G K P IVTPS QD - MV L G LYYL T KERK --- GDKG E GI 430
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 550 yrg LTDK VGRV klfppsilkplplwtgkqvlst LLIN I I PE D hiplnlsgkakitgkawvketprs V P GF N P dsmcesqv 629
Cdd:cd01609 431 --- IETT VGRV ---------------------- IFNE I L PE G ------------------------ L P FI N K -------- 453
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 630 VIREGE L lcgvldkahygssa YG L VHC CY EI YG G E TSGKV L TCLAR L ftaylqlyr GF -------- TLGVE DI L V K P kad 701
Cdd:cd01609 454 TLKKKV L -------------- KK L INE CY DR YG L E ETAEL L DDIKE L --------- GF kyatrsgi SISID DI V V P P --- 507
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 702 v KRQR II E E ST hcgp RA V raalnlpeatsy D E VQGKWQDAH L GKDQ R DFNM I DL -- KFK E E V nhy SNEIN K AC mpfglh R 779
Cdd:cd01609 508 - EKKE II K E AE ---- EK V ------------ K E IEKQYEKGL L TEEE R YNKV I EI wt EVT E K V --- ADAMM K NL ------ D 561
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 780 QF P E N SLQ MM VQ SGA K GS TVNTM Q ISCLL G qielegrrpp LMA -- SGK SLP cfepyef T P raggf VTGR F LT G IKPP E F F 857
Cdd:cd01609 562 KD P F N PIY MM AD SGA R GS KSQIR Q LAGMR G ---------- LMA kp SGK IIE ------- L P ----- IKSN F RE G LTVL E Y F 619
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 1622858458 858 FHCMAG R E GL V DTA V KT SR SGYL Q R ciikhle G LV - V QY D LT V RDS D 903
Cdd:cd01609 620 ISTHGA R K GL A DTA L KT AD SGYL T R ------- R LV d V AQ D VI V TEE D 659
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1091-1605
4.35e-35
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: 136.58
E-value: 4.35e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1091 K WQ R SLC EPG E AVG LL AAQSIGEP S TQMTL N TFHFAG RGE MN V TLG I PR LR EI l MV AS A NI K TP MMSVPVL N t KKAL K RV 1170
Cdd:cd02736 1 K YM R AKV EPG T AVG AI AAQSIGEP G TQMTL K TFHFAG VAS MN I TLG V PR IK EI - IN AS K NI S TP IITAKLE N - DRDE K SA 78
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1171 KSL K KQLTRVC LGEV LQK I DV qesfrmeekqnkfrvyqlrfqflphayyqqek CLR P E D I lr FME trf F KL LMES I K K - K 1249
Cdd:cd02736 79 RIV K GRIEKTY LGEV ASY I EE -------------------------------- VYS P D D C -- YIL --- I KL DKKI I E K l Q 121
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1250 NN K ASAFRNVNTRR atq R D L DNAGE SG rsrgeqegdeedeghivdaeaeegdad ASDA KR kekqeeevdyeseeeeereg 1329
Cdd:cd02736 122 LS K SNLYFLLQSLK --- R K L PDVVV SG --------------------------- IPEV KR -------------------- 151
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1330 eenndedtqeernphregaretqerdeevgsgteedpalpalltqprkpthsqepqgpe AV errvqavre I HSFIDDYQ Y 1409
Cdd:cd02736 152 ----------------------------------------------------------- AV --------- I NKDKKKGK Y 163
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1410 dtee S L WCQVTVKLPL M KINFDM G SLVV S lahgaviyatkgitrcllnett N NKN E kel V LNTE GI nlpelfkyaevldl 1489
Cdd:cd02736 164 ---- K L LVEGYGLRAV M NTPGVI G TRTT S ---------------------- N HIM E --- V EKVL GI -------------- 200
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1490 rrlysndihamantygi EAA LRV I EK EI KDVFAVY G IAV DPRH LS L V AD Y M C F E G VYKPLN RFGI RSNS - S P L QQMT FE T 1568
Cdd:cd02736 201 ----------------- EAA RST I IN EI QYTMKSH G MSI DPRH IM L L AD L M T F K G EVLGIT RFGI AKMK e S V L MLAS FE K 263
490 500 510
....*....|....*....|....*....|....*..
gi 1622858458 1569 SFQF L KQ A TML G SH D ELRSP S A C LVV GK VVKG GTGLF 1605
Cdd:cd02736 264 TTDH L FN A ALH G RK D SIEGV S E C IIM GK PMPI GTGLF 300
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
316-882
2.14e-34
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: 144.15
E-value: 2.14e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 316 K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq AVIN gpnvhpgas MVINEDGS 395
Cdd:COG0086 324 K Q G R FR QNLL GKRVDY SG RSVI VVGPELKLHQC G L P KKM A LE L FK P ------------- FIYR --------- KLEERGLA 381
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 396 R T AL SA VD M TQ RE avakqlltpatgap K P QGTK I VCRHV K NGDI LL l NR Q PTLHR PS IQA HHA r I L P E E K VLR LH YAN C K 475
Cdd:COG0086 382 T T IK SA KK M VE RE -------------- E P EVWD I LEEVI K EHPV LL - NR A PTLHR LG IQA FEP - V L I E G K AIQ LH PLV C T 445
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 476 A Y NADFDGD E M NA H F P Q S ELGRA EA YV L ACTDQQY L V P KD G Q P LAGLI QD h MV S G ASMT TR -------- G CF F TREQYME 547
Cdd:COG0086 446 A F NADFDGD Q M AV H V P L S LEAQL EA RL L MLSTNNI L S P AN G K P IIVPS QD - MV L G LYYL TR eregakge G MI F ADPEEVL 524
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 548 LV Y R - G LT D KVG R V K LFPPSILKP lplw T GK Q V LS T L liniipedhiplnlsgkakit G KAW V K E - T P RS VP GF N pdsmc 625
Cdd:COG0086 525 RA Y E n G AV D LHA R I K VRITEDGEQ ---- V GK I V ET T V --------------------- G RYL V N E i L P QE VP FY N ----- 574
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 626 esqvviregellc G V LD K A H YGS sayg LVHCC Y EIY G GETSGKV L TC L AR L ft AYLQLY R - G FTL G VE D IL V k PK A dvk R 704
Cdd:COG0086 575 ------------- Q V IN K K H IEV ---- IIRQM Y RRC G LKETVIF L DR L KK L -- GFKYAT R a G ISI G LD D MV V - PK E --- K 631
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 705 Q R I I EE ST hcgp RA V raalnlpeatsy D E VQGKWQDAHLGKDQ R DFNM ID L kfkee VNHY S N E INKAC M P f GLHR Q fpe N 784
Cdd:COG0086 632 Q E I F EE AN ---- KE V ------------ K E IEKQYAEGLITEPE R YNKV ID G ----- WTKA S L E TESFL M A - AFSS Q --- N 686
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 785 SLQ MM VQ SGA K GS T vntmqiscll G Q IE - L E G R R p P LMA -- SG kslpcf EPY E f TP ----- R A G gfvtgrfl T G IK pp E F 856
Cdd:COG0086 687 TTY MM AD SGA R GS A ---------- D Q LR q L A G M R - G LMA kp SG ------ NII E - TP igsnf R E G -------- L G VL -- E Y 738
570 580
....*....|....*....|....*.
gi 1622858458 857 F FHCMAG R E GL V DTA V KT SR SGYL Q R 882
Cdd:COG0086 739 F ISTHGA R K GL A DTA L KT AD SGYL T R 764
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
286-1127
7.81e-34
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 143.14
E-value: 7.81e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 286 LQ SH V NIV FD SEMDKLMM --- D K Y P -- GIRQ I LEK K E G L FR KHMM GKRVD YAA RSVI CPDMYINTN E I G I P MVF A TK L TY 360
Cdd:PRK09603 1688 LQ EA V DVL FD NGRSTNAV kga N K R P lk SLSE I IKG K Q G R FR QNLL GKRVD FSG RSVI VVGPNLKMD E C G L P KNM A LE L FK 1767
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 361 P QPVTP wnvqelrqavingpnvhpgasmv IN E D G SR T A L - S A VD M TQ reavakqlltpatgapkp Q GTKI V -- C - RHVKN 436
Cdd:PRK09603 1768 P HLLSK ----------------------- LE E R G YA T T L k Q A KR M IE ------------------ Q KSNE V we C l QEITE 1806
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 437 G DIL LLNR Q PTLH RP SIQA H H ARIL p EE K VLR LH YAN C K A Y NADFDGD E M NA H F P Q S ELGR AE AY VL ACTDQQY L V P KD G 516
Cdd:PRK09603 1807 G YPV LLNR A PTLH KQ SIQA F H PKLI - DG K AIQ LH PLV C S A F NADFDGD Q M AV H V P L S QEAI AE CK VL MLSSMNI L L P AS G 1885
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 517 QPL A GLI QD h MV S G --- A S MTTR G C ------ F FTREQYMELVYRGLT D KVGRVKLFPPS il KPLPLWT G KQVLSTL L ini 587
Cdd:PRK09603 1886 KAV A IPS QD - MV L G lyy L S LEKS G V kgehkl F SSVNEIITAIDTKEL D IHAKIRVLDQG -- NIIATSA G RMIIKSI L --- 1959
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 588 ip E D H IP LN L sgkakitgka W VK etprsvpgfnpdsmcesqvviregellcg VLD K AHY G S sayg LV HCCYEIY G GETSG 667
Cdd:PRK09603 1960 -- P D F IP TD L ---------- W NR ----------------------------- PMK K KDI G V ---- LV DYVHKVG G IGITA 1994
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 668 KV L TC L AR L FTA Y l QLYR G FTLGV EDI LV k PK adv KR Q RII E EST hcgpravraalnlpea TSYDEV Q GKW q D AH L GK DQ 747
Cdd:PRK09603 1995 TF L DN L KT L GFR Y - ATKA G ISISM EDI IT - PK --- DK Q KMV E KAK ---------------- VEVKKI Q QQY - D QG L LT DQ 2052
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 748 RDF N M I d LKFKE EVN hys NEIN K AC M PFGLHRQFPE NS LQ MM VQ SGA K GS TVNTM Q I S CLL G qielegrrpp LM AS gksl 827
Cdd:PRK09603 2053 ERY N K I - IDTWT EVN --- DKMS K EM M TAIAKDKEGF NS IY MM AD SGA R GS AAQIR Q L S AMR G ---------- LM TK ---- 2114
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 828 P CFEPY E f TP raggf VTGR F LT G IKPP E F F FHCMAG R E GL V DTA V KT SRS GYL Q R CI I K hleglvvqydltvrdsdgsvv 907
Cdd:PRK09603 2115 P DGSII E - TP ----- IISN F KE G LNVL E Y F NSTHGA R K GL A DTA L KT ANA GYL T R KL I D --------------------- 2167
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 908 qflygedgldipktqflqpkqfpf LAS N YE V IMKSQHL HE VLSRA D pkkalrhfraikkwqskhpntl LRR G AF L -- SYS 985
Cdd:PRK09603 2168 ------------------------ VSQ N VK V VSDDCGT HE GIEIT D ---------------------- IAV G SE L ie PLE 2201
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 986 QK I QAA V KA lnlesen RNGRS P G T Q E M L rm W Y E --- L DEE SRR K YQKKAAT cpdpslsvwrpdiyfasv S E T FE T K V DDY 1062
Cdd:PRK09603 2202 ER I FGR V LL ------- EDVID P I T N E I L -- L Y A dtl I DEE GAK K VVEAGIK ------------------ S I T IR T P V TCK 2254
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622858458 1063 SQE wa AQTE K S Y eks E L S L D rlrtllqlkw QRSLCE PGEAVG LL AAQSIGEP S TQ M TL N TFH FA G 1127
Cdd:PRK09603 2255 APK -- GVCA K C Y --- G L N L G ---------- EGKMSY PGEAVG VV AAQSIGEP G TQ L TL R TFH VG G 2304
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1061-1603
5.98e-32
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 132.24
E-value: 5.98e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1061 DYSQ E W aaq TEKS YE KS els L D R L R T llql KWQ R SLCE P G EAVG LL AAQSIGEP S TQMT LN TFH F AG RG EMNVTLG I PRL 1140
Cdd:PRK14897 153 MKKK E L --- SDDE YE EI --- L R R I R E ---- EYE R ARVD P Y EAVG IV AAQSIGEP G TQMT MR TFH Y AG VA EMNVTLG L PRL 222
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1141 R EI l MV A SANIK TP M M SV pvlntkkalkrvk S LKK qltrvclgevlqki D VQ E S frm EEK qnkfrvyqlrfqflphayyq 1220
Cdd:PRK14897 223 I EI - VD A RKKPS TP T M TI ------------- Y LKK -------------- D YR E D --- EEK -------------------- 251
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1221 qekclrpedilrfmetrffkl LM E SI KK KN N KA - SAFRNVN T rratqr D L dnagesgrsrgeqegdeedeghivdaeaee 1299
Cdd:PRK14897 252 --------------------- VR E VA KK IE N TT l IDVADII T ------ D I ------------------------------ 274
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1300 gd A DA S DAKRKEK qeeevdyeseeeeeregeenndedtqeernphrega RETQ ER DE E V gsgteedpalpalltqprkpt 1379
Cdd:PRK14897 275 -- A EM S VVVELDE ------------------------------------ EKMK ER LI E Y --------------------- 295
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1380 hsqepqgp EAVERRVQAVREIHSF IDD yqydteeslwcq VTVK L PLMKIN F DMGS L VVSLAHGAV I YAT KGI T R CLLNE t 1459
Cdd:PRK14897 296 -------- DDILAAISKLTFKTVE IDD ------------ GIIR L KPQQPS F KKLY L LAEKVKSLT I KGI KGI K R AIARK - 354
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1460 tn NKN E KEL V LN T E G I NL PELFKYA EV l D LR R L Y S NDI HAM A NTY GIEAA LRV I EK E I K DVFAVY G IA VD P RH LS LVAD Y 1539
Cdd:PRK14897 355 -- END E RRW V IY T Q G S NL KDVLEID EV - D PT R T Y T NDI IEI A TVL GIEAA RNA I IH E A K RTLQEQ G LN VD I RH IM LVAD M 431
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622858458 1540 M C F E G VY K PLN R F GI RS - N SS P L QQMT FE TSFQF L KQ A TM LG SH D E L RSPSACLV VG KVVKG GTG 1603
Cdd:PRK14897 432 M T F D G SV K AIG R H GI SG e K SS V L ARAA FE ITGKH L LR A GI LG EV D K L AGVAENII VG QPITL GTG 496
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
316-1143
3.26e-31
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 134.04
E-value: 3.26e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 316 K E G L FR KHMM GKRVDY AA RSVI C -- P D -- MY intn EI G I P MVF A TK L typqp VT P WNVQE L rqavingpnvhpgasmv IN 391
Cdd:PRK00566 324 K Q G R FR QNLL GKRVDY SG RSVI V vg P E lk LH ---- QC G L P KKM A LE L ----- FK P FIMKK L ----------------- VE 377
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 392 EDGSR T AL SA VD M TQ RE avakqlltpatgapkpqg TKI V C rhvkng D I L --------- LLNR Q PTLHR PS IQA HHA r I L P 462
Cdd:PRK00566 378 RGLAT T IK SA KK M VE RE ------------------ DPE V W ------ D V L eevikehpv LLNR A PTLHR LG IQA FEP - V L I 432
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 463 E E K VLR LH YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA Y VL ACTDQQY L V P KD G Q P LAGLI QD h MV S G ASMT TR ------ 536
Cdd:PRK00566 433 E G K AIQ LH PLV C T A F NADFDGD Q M AV H V P L S LEAQ AEA R VL MLSSNNI L S P AN G K P IIVPS QD - MV L G LYYL TR eregak 511
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 537 -- G CF F TREQYMELV Y R ---- G L TDKVG rvklfppsilkp LPLWTG K Q V LS T --- LLI N - I I PE DH iplnlsgkakitgk 606
Cdd:PRK00566 512 ge G MV F SSPEEALRA Y E ngev D L HARIK ------------ VRITSK K L V ET T vgr VIF N e I L PE GL -------------- 565
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 607 awvketprsvp G F npdsmcesqvvireg ELLCGV L D K AHYGS sayg LVHCC Y EI YG GETSGKV L TCLAR L ftaylqlyr G 686
Cdd:PRK00566 566 ----------- P F --------------- INVNKP L K K KEISK ---- IINEV Y RR YG LKETVIF L DKIKD L --------- G 606
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 687 F -------- TL G VE DI LVK P kadv KRQR IIEE STH cgpravraalnlp E A tsy D E VQGKWQDAHLGKDQ R DFNM ID L -- K 756
Cdd:PRK00566 607 F kyatrsgi SI G ID DI VIP P ---- EKKE IIEE AEK ------------- E V --- A E IEKQYRRGLITDGE R YNKV ID I ws K 666
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 757 FKE EV nhy SNEIN K A c MP fgl HR Q FPE N SLQ MM VQ SGA K G stv NTM QI SC L L G qie LE G rrpp LMA -- SG KSLP cfepye 834
Cdd:PRK00566 667 ATD EV --- AKAMM K N - LS --- KD Q ESF N PIY MM AD SGA R G --- SAS QI RQ L A G --- MR G ---- LMA kp SG EIIE ------ 723
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 835 f TP raggf VTGR F LT G IKPP E F F F -- H cma G - R E GL V DTA V KT SR SGYL Q R ciikhle G LV - V QY D LT VR DS D - G S vvqf 909
Cdd:PRK00566 724 - TP ----- IKSN F RE G LTVL E Y F I st H --- G a R K GL A DTA L KT AD SGYL T R ------- R LV d V AQ D VI VR ED D c G T ---- 783
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 910 lyg ED G LDIPK tqflqpkqfpf LASNY EVI MK sqh L H E - V L S R -- A DP kkalrhfra I kkwqs KH P N T --- LLRR G AFLS 983
Cdd:PRK00566 784 --- DR G IEVTA ----------- IIEGG EVI EP --- L E E r I L G R vl A ED --------- V ----- VD P E T gev IVPA G TLID 832
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 984 -- YSQ KI QA A ---- VK A lnlesenrng RS P gtqemlrmwye L DE E S R R kyqkka AT C pdpslsvwrpdiyfasvsetfet 1057
Cdd:PRK00566 833 ee IAD KI EE A giee VK I ---------- RS V ----------- L TC E T R H ------ GV C ----------------------- 862
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1058 kvddysqewaaqt E K S Y EKS e L S ldrlrtllqlkw QRS L CEP GEAVG LL AAQSIGEP S TQ M T LN TFH FA G rge MNV T L G I 1137
Cdd:PRK00566 863 ------------- A K C Y GRD - L A ------------ TGK L VNI GEAVG VI AAQSIGEP G TQ L T MR TFH TG G --- VDI T G G L 913
....*.
gi 1622858458 1138 PR LR E I 1143
Cdd:PRK00566 914 PR VA E L 919
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
313-1146
5.48e-29
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 126.91
E-value: 5.48e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 313 L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L T yp Q P VTPWNVQ EL RQ A V ingp N V hpgasmvine 392
Cdd:PRK14906 409 L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPHLKLHQC G L P SAM A LE L F -- K P FVMKRLV EL EY A A ---- N I ---------- 472
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 393 dgs RT A LS AVD mtqreavakqlltpa T GA PKPQG tki V CRH V KNGDIL LLNR Q PTLHR PS IQA HHA r I L P E E K VLR LH YA 472
Cdd:PRK14906 473 --- KA A KR AVD --------------- R GA SYVWD --- V LEE V IQDHPV LLNR A PTLHR LG IQA FEP - V L V E G K AIK LH PL 530
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 473 N C K A Y NADFDGD E M NA H F P Q S ELGR AEA Y VL ACTDQQYLV P KD G Q PL AGLI QD HMVSGASM TT RGCF F TR E qymelvyrg 552
Cdd:PRK14906 531 V C T A F NADFDGD Q M AV H V P L S TQAQ AEA R VL MLSSNNIKS P AH G R PL TVPT QD MIIGVYYL TT ERDG F EG E --------- 601
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 553 ltdkv GR VKLFPPSI L KPLPLWTGKQVLSTLLIN i IPE D HIPLNLS G KAKI T GKAWVK ET PRSVPG FN pdsmces QV VIR 632
Cdd:PRK14906 602 ----- GR TFADFDDA L NAYDARADLDLQAKIVVR - LSR D MTVRGSY G DLEE T KAGERI ET TVGRII FN ------- QV LPE 668
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 633 EGEL L CGVLD K AHY G S sayg LV HC C YEI Y GGETSGKV L TCLARLFTA Y LQL y R G F T LG V E D ILVKPKAD vkrq R I IE E ST 712
Cdd:PRK14906 669 DYPY L NYKMV K KDI G R ---- LV ND C CNR Y STAEVEPI L DGIKKTGFH Y ATR - A G L T VS V Y D ATIPDDKP ---- E I LA E AD 739
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 713 hcgpravraalnlpea TSYDEVQGKWQ D AH L GKDQ R DFNMI D L kfkee VNHYSN E INK A c M PF G LHRQ fpe N SLQ MM VQ S 792
Cdd:PRK14906 740 ---------------- EKVAAIDEDYE D GF L SERE R HKQVV D I ----- WTEATE E VGE A - M LA G FDED --- N PIY MM AD S 794
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 793 GA K G STVNTM Q ISCLL G qielegrrpp LMA SG K SLPCFE P yeftpraggf VTGR F LT G IKPP E F F FHCMAG R E GLVDTA V 872
Cdd:PRK14906 795 GA R G NIKQIR Q LAGMR G ---------- LMA DM K GEIIDL P ---------- IKAN F RE G LSVL E Y F ISTHGA R K GLVDTA L 854
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 873 K T SR SGYL Q R CIIK hleglv V QY D LT VR DS D - G S vvqflyg ED G LDI P ktqflqpkqfpflasnyevimksqh L H evlsr 951
Cdd:PRK14906 855 R T AD SGYL T R RLVD ------ V AQ D VI VR EE D c G T ------- DE G VTY P ------------------------- L V ----- 891
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 952 a D PK KAL rhfraikkwqskhpntllrrgaflsysqkiqaavkalnle SE N RN GR S pgtqemlrmwy E L DEES rrkyqkka 1031
Cdd:PRK14906 892 - K PK GDV ---------------------------------------- DT N LI GR C ----------- L L EDVC -------- 911
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1032 atcp DP SLS V wrpdiy FA S VSETF E TK v DD YSQEWA A QTE K S yekselsld RL RTL LQLKWQRSL C EP ------------ 1099
Cdd:PRK14906 912 ---- DP NGE V ------ LL S AGDYI E SM - DD LKRLVE A GVT K V --------- QI RTL MTCHAEYGV C QK cygwdlatrrpv 971
810 820 830 840
....*....|....*....|....*....|....*....|....*....
gi 1622858458 1100 -- G E AVG LL AAQSIGEP S TQ M T LN TFH FA G RGEMNV T L G I PR LR E ILMV 1146
Cdd:PRK14906 972 ni G T AVG II AAQSIGEP G TQ L T MR TFH SG G VAGDDI T Q G L PR VA E LFEA 1020
rpoC1
CHL00018 RNA polymerase beta' subunit
286-530
2.12e-28
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 123.09
E-value: 2.12e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 286 LQ SH V NIVF D SEM - DKL M M D ---- K Y PGIRQIL E K KEG L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY 360
Cdd:CHL00018 328 LQ EA V DALL D NGI r GQP M R D ghnk P Y KSFSDVI E G KEG R FR ENLL GKRVDY SG RSVI VVGPSLSLHQC G L P REI A IE L FQ 407
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 361 P qpvtpwnvqelrq A VI N G pnvhpgasm V I NEDGSRTALS A VDMTQR eavakqlltpatgap K PQGTKIVCRH V KN G DIL 440
Cdd:CHL00018 408 P ------------- F VI R G --------- L I RQHLASNIRA A KSKIRE --------------- K EPIVWEILQE V MQ G HPV 450
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 441 LLNR Q PTLHR PS IQA HHA r IL P E EKVLR LH YAN CK AY NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V P KD G Q P LA 520
Cdd:CHL00018 451 LLNR A PTLHR LG IQA FQP - IL V E GRAIC LH PLV CK GF NADFDGD Q M AV H V P L S LEAQ AEA RL L MFSHMNL L S P AI G D P IS 529
250
....*....|
gi 1622858458 521 GLI QD h M VS G 530
Cdd:CHL00018 530 VPS QD - M LL G 538
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
286-894
1.40e-26
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 119.34
E-value: 1.40e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 286 LQ SH V NIV FD SEMDKLMMD K Y ------ PG I RQI L EK K E G L FR KHMM GKRVDY AA RSVI CPDMYINT N EI G I P MVF A TK L T 359
Cdd:PRK14844 1731 LQ EA V DSL FD NSRRNALVN K A gavgyk KS I SDM L KG K Q G R FR QNLL GKRVDY SG RSVI VVGPTLKL N QC G L P KRM A LE L F 1810
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 360 Y P qpvtpwnvqelrqavingpnvhpgasmvined GSRTA L SAVD M TQREAV A KQ L LT patg A P KP QGTKIVCRHV K NGDI 439
Cdd:PRK14844 1811 K P -------------------------------- FVYSK L KMYG M APTIKF A SK L IR ---- A E KP EVWDMLEEVI K EHPV 1854
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 440 LL l NR Q PTLHR PS IQA HHA r IL P E E K VLR LH YAN C K A Y NADFDGD E M NA H F P Q S ELGRA EA Y VL ACTDQQY L V P KD G Q P L 519
Cdd:PRK14844 1855 LL - NR A PTLHR LG IQA FEP - IL I E G K AIQ LH PLV C T A F NADFDGD Q M AV H V P I S LEAQL EA R VL MMSTNNV L S P SN G R P I 1932
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 520 agliqdh M V SGASMTTRGCFF T REQYM E lvyrgltdkvgrvklfppsil KP LP LW - TGKQ V LST L LINII ped HI PLNLS 598
Cdd:PRK14844 1933 ------- I V PSKDIVLGIYYL T LQEPK E --------------------- DD LP SF g AFCE V EHS L SDGTL --- HI HSSIK 1981
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 599 GKAKIT --- G KAWV K e T PRSV PG fnpd SMCES Q VVIREGE L LCGVLDKAHYGSSAYGL V HCC Y EIY G ge T S GK V ltclar 675
Cdd:PRK14844 1982 YRMEYI nss G ETHY K - T ICTT PG ---- RLILW Q IFPKHEN L GFDLINQVLTVKEITSI V DLV Y RNC G -- Q S AT V ------ 2048
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 676 L F TAY L qlyrg FT LG vedilvkpkadvkrqri I E ES T HC G PRAV R AALNL PE -- AT SY D EVQ G ------- KW QD AHLGKD 746
Cdd:PRK14844 2049 A F SDK L ----- MV LG ----------------- F E YA T FS G VSFS R CDMVI PE tk AT HV D HAR G eikkfsm QY QD GLITRS 2106
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 747 Q R DFNM ID l KFKEEVNHYS N EIN KA CMPFGLHRQF pe NS LQ MMV Q SGA K GST VNTM Q ISCLL G qielegrrpp LM AS gks 826
Cdd:PRK14844 2107 E R YNKV ID - EWSKCTDMIA N DML KA ISIYDGNSKY -- NS VY MMV N SGA R GST SQMK Q LAGMR G ---------- LM TK --- 2170
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 827 l P CF E PY E f TP raggf VTGR F LT G IKPP E F F FHCMAG R E GL V DTA V KT SR SGYL -------- Q R CI I ----- K HLE GLVV 893
Cdd:PRK14844 2171 - P SG E II E - TP ----- IISN F RE G LNVF E Y F NSTHGA R K GL A DTA L KT AN SGYL trrlvdvs Q N CI V tkhdc K TKN GLVV 2243
.
gi 1622858458 894 Q 894
Cdd:PRK14844 2244 R 2244
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
731-843
1.96e-26
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: 105.14
E-value: 1.96e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 731 YD E VQ GK WQ D AHLGKDQRD F NMIDLKFKEEVNHYSNE I NKACMP fglhrqf P E NS LQ MM VQ SGAKGS TV N TM QI SCLL GQ 810
Cdd:pfam05000 3 DA E RY GK LE D IWGMTLEES F EALINNILNKARDPAGN I ASKSLD ------- P N NS IY MM AD SGAKGS II N IS QI AGCR GQ 75
90 100 110
....*....|....*....|....*....|...
gi 1622858458 811 IEL EG R R P P LMA SG KS LP C F EPYEFT P RAG GFV 843
Cdd:pfam05000 76 QNV EG K R I P FGF SG RT LP H F KKDDEG P ESR GFV 108
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1496-1604
3.20e-25
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: 103.27
E-value: 3.20e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1496 D IH A M ANTY GIEAA LRV I EK EI KD V F A VY G IA VD P RH LS L V AD Y M CFE G VYKPLN R F G - IR S NS SPL QQMT FE TSFQF L K 1574
Cdd:cd00630 49 S IH E M LEAL GIEAA RET I IR EI QK V L A SQ G VS VD R RH IE L I AD V M TYS G GLRGVT R S G f RA S KT SPL MRAS FE KTTKH L L 128
90 100 110
....*....|....*....|....*....|
gi 1622858458 1575 Q A TML G SH DEL RSP S ACLVV G KVVKG GTG L 1604
Cdd:cd00630 129 D A AAA G EK DEL EGV S ENIIL G RPAPL GTG S 158
RNAP_largest_subunit_C
cd00630 Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
1100-1148
9.07e-24
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: 99.41
E-value: 9.07e-24
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1622858458 1100 GEAVG L LAAQSIGEP S TQMTL N TFHFAG RGE MNVTLG I PRL R EIL MV AS 1148
Cdd:cd00630 1 GEAVG V LAAQSIGEP G TQMTL R TFHFAG VAS MNVTLG L PRL K EIL NA AS 49
rpoC1
PRK02625 DNA-directed RNA polymerase subunit gamma; Provisional
312-531
1.76e-22
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 104.44
E-value: 1.76e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 312 I L E K K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L typqp VT P WNVQE L - RQ AVI N gp N VHPGASMVI 390
Cdd:PRK02625 338 I I E G K Q G R FR QNLL GKRVDY SG RSVI VVGPKLKMHQC G L P KEM A IE L ----- FQ P FVIHR L i RQ GIV N -- N IKAAKKLIQ 410
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 391 NE D GS rtalsavdmtqrea V AKQ L LTPAT G A P kpqgtkivcrhvkngdi L LLNR Q PTLHR PS IQA HHA r IL P E EKVLR LH 470
Cdd:PRK02625 411 RA D PE -------------- V WQV L EEVIE G H P ----------------- V LLNR A PTLHR LG IQA FEP - IL V E GRAIQ LH 458
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622858458 471 YAN C K A Y NADFDGD E M NA H F P Q S ELGR AEA YV L ACTDQQY L V P KD G Q P LAGLI QD h MV S G A 531
Cdd:PRK02625 459 PLV C P A F NADFDGD Q M AV H V P L S LEAQ AEA RL L MLASNNI L S P AT G E P IVTPS QD - MV L G C 518
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1450-1608
1.70e-21
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 101.89
E-value: 1.70e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1450 GI T R C L LNETTNNKN E k E L VL N T E G I NL P E L FK y A E VL D LR R LYS N D I HAMANTY GIEAA LRV I EK E IKDVFAVY G IA VD 1529
Cdd:PRK14898 690 GI E R V L VKKEEHEND E - E Y VL Y T Q G S NL R E V FK - I E GV D TS R TTT N N I IEIQEVL GIEAA RNA I IN E MMNTLEQQ G LE VD 767
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1530 P RHL S LVAD Y M CFE G VY KP LN R F G IRSNS - S P L QQMT FE TSFQF L KQ A TML G SH D E L RSPSACLV VGK VV K G GTG LFE L K 1608
Cdd:PRK14898 768 I RHL M LVAD I M TAD G EV KP IG R H G VAGEK g S V L ARAA FE ETVKH L YD A AEH G EV D K L KGVIENVI VGK PI K L GTG CVD L R 847
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1095-1144
4.07e-12
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: 67.17
E-value: 4.07e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1095 S L C E P GEAVG LL AAQSIGEP S TQ M T LN TFH FA G RGE m NV T L G I PR LR E IL 1144
Cdd:cd02655 1 K L V E L GEAVG II AAQSIGEP G TQ L T MR TFH TG G VAT - DI T Q G L PR VE E LF 49
RNAP_IV_NRPD1_C
cd02737 Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
1485-1607
5.81e-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: 63.21
E-value: 5.81e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622858458 1485 EVL D LR R LYSND I HAMANTY GI E AA LRVIEKEIKDVFAVY G IA V DPR HL S LVAD Y M CFE G VYKP LN RF G IR ------ SN S 1558
Cdd:cd02737 250 DLI D WE R SMPYS I QQIKSVL GI D AA FEQFVQRLESAVSMT G KS V LRE HL L LVAD S M TYS G EFVG LN AK G YK aqrrsl KI S 329
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1622858458 1559 S P LQQMT F ETSFQ - FLK Q A TM l G SH D E L RSPSACLVV GK VVKG GTG - L FE L 1607
Cdd:cd02737 330 A P FTEAC F SSPIK c FLK A A KK - G AS D S L SGVLDACAW GK EAPV GTG s K FE I 379
rpoC2
CHL00117 RNA polymerase beta'' subunit; Reviewed
1095-1124
2.86e-09
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 62.26
E-value: 2.86e-09
10 20 30
....*....|....*....|....*....|
gi 1622858458 1095 S L C E P GEAVG LL A A QSIGEP S TQ M TL N TFH 1124
Cdd:CHL00117 310 D L V E L GEAVG II A G QSIGEP G TQ L TL R TFH 339
rpoC2_cyan
TIGR02388 DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
1067-1127
4.70e-08
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: 58.32
E-value: 4.70e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622858458 1067 A A QTEKSYEK S E L SLDRL R TLLQLKWQR SL C ----- EP GEAVG LL AAQSIGEP S TQ M T LN TFH FA G 1127
Cdd:TIGR02388 271 T A GISEVVVR S P L TCEAA R SVCRKCYGW SL A hahlv DL GEAVG II AAQSIGEP G TQ L T MR TFH TG G 336
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
1100-1127
5.95e-08
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 58.08
E-value: 5.95e-08
10 20
....*....|....*....|....*...
gi 1622858458 1100 GEAVG LL AAQSIGEP S TQ M T LN TFH FA G 1127
Cdd:PRK02597 311 GEAVG II AAQSIGEP G TQ L T MR TFH TG G 338
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1091-1120
1.10e-04
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 47.20
E-value: 1.10e-04
10 20 30
....*....|....*....|....*....|
gi 1622858458 1091 KWQRS L C EP G EAVG LL AAQSIGEP S TQM T L 1120
Cdd:PRK14898 48 AYLNA L V EP Y EAVG IV AAQSIGEP G TQM 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
