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DNA-directed RNA polymerase I subunit RPA1 [Homo sapiens]
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 ...
16-1004
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: 1306.40
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 16 SF GM YSAEE LK KLSVK S ITNP RYL DSLG N P SAN GLYD L ALGP A D SKEV CSTC VQDFS NC S GH L GHIELPL T VYNPL L FD K 95
Cdd:cd01435 1 SF SF YSAEE IR KLSVK E ITNP VTF DSLG H P VPG GLYD P ALGP L D KDDI CSTC GLNYL NC P GH F GHIELPL P VYNPL F FD L 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 96 LY L LLRGSC LN CH MLTCPRAVIH L LLCQ L RV L EV G A L QAVY EL E rilnrfleenpdpsaseireeleqytteivqnnllg 175
Cdd:cd01435 81 LY K LLRGSC FY CH RFRISKWEVK L FVAK L KL L DK G L L VEAA EL D ------------------------------------ 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 176 sqgahvknvcesksklialfwkahmnakrcphcktgrsvvrkehnskltitfpamvhrtagqkdseplgieeaqigkrgy 255
Cdd:cd01435 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 256 ltptsarehlsalwknegfflnylfsgmdddgmesr 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 V 335
Cdd:cd01435 125 ------------------------------------ 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 N 168
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 336 VL IR K LLA L M A Q EQKL peevatpttdeekdsliaidr S F L STLP G QSLID KL Y N I W IR LQS H VN IV FDS EMDKLM - MDKY 414
Cdd:cd01435 169 QQ IR 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 227
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 415 PGI R 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 494
Cdd:cd01435 228 PGI K 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 307
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 495 SMVIN 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 RA R I LP E EK V 574
Cdd:cd01435 308 NAIED 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 387
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 575 LRLHYANCK 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 H Y M 654
Cdd:cd01435 388 LRLHYANCK 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 Q 467
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 655 E LVY RG L T ----- DK V GR V KLL S P S ILKP F PLWTGKQV V ST L L I N I IP EDHIP LNLSGK A K ITG K AW vketprsv P G FNP 729
Cdd:cd01435 468 Q LVY AA L R plfts DK D GR I KLL P P A ILKP K PLWTGKQV I ST I L K N L IP GNAPL LNLSGK K K TKK K VG -------- G G KWG 539
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 730 DSMC ESQVIIR 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 809
Cdd:cd01435 540 GGSE ESQVIIR 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 618
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 810 V KR QR I IEESTHC G PQ A VRAA L N L peaasydevrgkwqdahlgkdqrdfnmidlkfke EV N HYSNE I N KAC M P F GL HRQ F 889
Cdd:cd01435 619 E KR RK I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P K GL LKP F 664
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 890 PEN S 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 FFHCM 969
Cdd:cd01435 665 PEN N 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 FFHCM 744
970 980 990
....*....|....*....|....*....|....*
gi 103471997 970 AGREGL V DTAVKTSRSGYLQRC I IKHLEGL V V Q YD 1004
Cdd:cd01435 745 AGREGL 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 ...
958-1670
4.47e-170
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: 524.61
E-value: 4.47e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 958 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 1037
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 103471997 1038 P F LASNY E VIM K SQH L HEV L SRADPKKALHHFRAIKKW qskhpntllrrgaflsysqkiqeavkalklesenrngrspgt 1117
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1118 qemlrmwyeldeesrrkyqkkaaacpdps LSVWRPDIYF A SVSE T FETKVDDY S QEWAAQTEKSYEKSELSLDR L RTLLQ 1197
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1198 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 1276
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 103471997 1277 RV K SLKKQLTR V C LG E V LQKIDVQESFCMEEKQNKFQ V YQLRFQ F LPHAYYQQ E KCLR PE DI L RFMET R FF K L L ME SIKK 1356
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 103471997 1357 knnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeere 1436
Cdd:pfam04998 --------------------------------------------------------------------------------
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1437 geenddedmqeernphregarktqeqdeevglgteedpslpalltq PR K PTHSQEPQGPEAM E R R VQ A VR EI HP FI DDYQ 1516
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 103471997 1517 YDTEESLWCQVT V KLPL M KINFDMSS LV V SL AHGAVIYATK GI T R C L L NE TTNN K N E KEL VL N TEG I NL PELFKYAEVL D 1596
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 103471997 1597 LR R LY SNDIH A I ANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI RSNSSPLQ 1670
Cdd:pfam04998 443 AG R IL SNDIH E I LEIL 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 ...
16-1004
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: 1306.40
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 16 SF GM YSAEE LK KLSVK S ITNP RYL DSLG N P SAN GLYD L ALGP A D SKEV CSTC VQDFS NC S GH L GHIELPL T VYNPL L FD K 95
Cdd:cd01435 1 SF SF YSAEE IR KLSVK E ITNP VTF DSLG H P VPG GLYD P ALGP L D KDDI CSTC GLNYL NC P GH F GHIELPL P VYNPL F FD L 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 96 LY L LLRGSC LN CH MLTCPRAVIH L LLCQ L RV L EV G A L QAVY EL E rilnrfleenpdpsaseireeleqytteivqnnllg 175
Cdd:cd01435 81 LY K LLRGSC FY CH RFRISKWEVK L FVAK L KL L DK G L L VEAA EL D ------------------------------------ 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 176 sqgahvknvcesksklialfwkahmnakrcphcktgrsvvrkehnskltitfpamvhrtagqkdseplgieeaqigkrgy 255
Cdd:cd01435 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 256 ltptsarehlsalwknegfflnylfsgmdddgmesr 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 V 335
Cdd:cd01435 125 ------------------------------------ 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 N 168
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 336 VL IR K LLA L M A Q EQKL peevatpttdeekdsliaidr S F L STLP G QSLID KL Y N I W IR LQS H VN IV FDS EMDKLM - MDKY 414
Cdd:cd01435 169 QQ IR 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 227
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 415 PGI R 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 494
Cdd:cd01435 228 PGI K 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 307
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 495 SMVIN 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 RA R I LP E EK V 574
Cdd:cd01435 308 NAIED 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 387
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 575 LRLHYANCK 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 H Y M 654
Cdd:cd01435 388 LRLHYANCK 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 Q 467
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 655 E LVY RG L T ----- DK V GR V KLL S P S ILKP F PLWTGKQV V ST L L I N I IP EDHIP LNLSGK A K ITG K AW vketprsv P G FNP 729
Cdd:cd01435 468 Q LVY AA L R plfts DK D GR I KLL P P A ILKP K PLWTGKQV I ST I L K N L IP GNAPL LNLSGK K K TKK K VG -------- G G KWG 539
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 730 DSMC ESQVIIR 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 809
Cdd:cd01435 540 GGSE ESQVIIR 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 618
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 810 V KR QR I IEESTHC G PQ A VRAA L N L peaasydevrgkwqdahlgkdqrdfnmidlkfke EV N HYSNE I N KAC M P F GL HRQ F 889
Cdd:cd01435 619 E KR RK I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P K GL LKP F 664
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 890 PEN S 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 FFHCM 969
Cdd:cd01435 665 PEN N 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 FFHCM 744
970 980 990
....*....|....*....|....*....|....*
gi 103471997 970 AGREGL V DTAVKTSRSGYLQRC I IKHLEGL V V Q YD 1004
Cdd:cd01435 745 AGREGL 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 ...
958-1670
4.47e-170
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: 524.61
E-value: 4.47e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 958 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 1037
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 103471997 1038 P F LASNY E VIM K SQH L HEV L SRADPKKALHHFRAIKKW qskhpntllrrgaflsysqkiqeavkalklesenrngrspgt 1117
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1118 qemlrmwyeldeesrrkyqkkaaacpdps LSVWRPDIYF A SVSE T FETKVDDY S QEWAAQTEKSYEKSELSLDR L RTLLQ 1197
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1198 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 1276
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 103471997 1277 RV K SLKKQLTR V C LG E V LQKIDVQESFCMEEKQNKFQ V YQLRFQ F LPHAYYQQ E KCLR PE DI L RFMET R FF K L L ME SIKK 1356
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 103471997 1357 knnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeere 1436
Cdd:pfam04998 --------------------------------------------------------------------------------
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1437 geenddedmqeernphregarktqeqdeevglgteedpslpalltq PR K PTHSQEPQGPEAM E R R VQ A VR EI HP FI DDYQ 1516
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 103471997 1517 YDTEESLWCQVT V KLPL M KINFDMSS LV V SL AHGAVIYATK GI T R C L L NE TTNN K N E KEL VL N TEG I NL PELFKYAEVL D 1596
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 103471997 1597 LR R LY SNDIH A I ANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI RSNSSPLQ 1670
Cdd:pfam04998 443 AG R IL SNDIH E I LEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
4-1025
5.58e-165
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 524.42
E-value: 5.58e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 4 S KN M PWR R LQG I S FG MY S A EE LK K L SV KS I TNPRYL D SL G N P SAN GL Y D LA LG PA D SKEV C S TC VQDFSN C S GH L GHIEL 83
Cdd:PRK08566 1 S MM M IPK R IGS I K FG LL S P EE IR K M SV TK I ITADTY D DD G Y P IDG GL M D PR LG VI D PGLR C K TC GGRAGE C P GH F GHIEL 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 84 PLT V YNPLLFDKL Y L LLR GS C LN C hmltcpravihlllcqlrvlevgalqavyel E R IL nrf L E E N pdpsas EI R E E LE Q 163
Cdd:PRK08566 81 ARP V IHVGFAKLI Y K LLR AT C RE C ------------------------------- G R LK --- L T E E ------ EI E E Y LE K 120
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 164 YTT eivqnnllgsqgah V K NVCESKSK LI ALFW K AHMNAKR CPHC KT grsvvrkehn SKLT I T F pamvhrtag Q K dse P L 243
Cdd:PRK08566 121 LER -------------- L K EWGSLADD LI KEVK K EAAKRMV CPHC GE ---------- KQYK I K F --------- E K --- P T 164
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 244 GIE E AQIGKRGY LTP TSA RE H L SAL wknegfflnylfsg M D D D GMESRF NP S V ----- FF L DF L V VPP SRY RP VSR L gdq 318
Cdd:PRK08566 165 TFY E ERKEGLVK LTP SDI RE R L EKI -------------- P D E D LELLGI NP E V arpew MV L TV L P VPP VTV RP SIT L --- 227
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 319 mf TN GQ TVNLQAVM K D V VL IR kllalma QE Q K L P E -- E VAT P ttdeekdsliaidrsflstlpg Q SL I DK L yni W IR LQ S 396
Cdd:PRK08566 228 -- ET GQ RSEDDLTH K L V DI IR ------- IN Q R L K E ni E AGA P ---------------------- Q LI I ED L --- W EL LQ Y 273
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 397 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 I G I P MVF 462
Cdd:PRK08566 274 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 V G V P EAI 345
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 463 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 pkpqgtk IV C RH V 542
Cdd:PRK08566 346 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 ------- IV E RH L 412
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 543 KN GDI L L L NRQP T LHR P SI Q AHR A R I LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQY L V P K 622
Cdd:PRK08566 413 ID GDI V L F NRQP S LHR M SI M AHR V R V LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQ T E EA RAEA RI L MLVQEHI L S P R 491
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 623 D G Q P LA G L IQDH m V SGA SMT TR - GCF FT R E HYME L VYRG ltd KVGRVKLLS P S I LKPF P L WTGKQ VV S TL L inii P E D hi 701
Cdd:PRK08566 492 Y 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 ---- P K D -- 561
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 702 p LNL SG KAKI TGKAWVKE tprsvpgfnp DSM CE -- SQ V I I RE G E LL C GV L DK AHY G SSAYGLVHCCYEI YG G E TSGKV L T 779
Cdd:PRK08566 562 - LNL EF KAKI CSGCDECK ---------- KED CE hd AY V V I KN G K LL E GV I DK KAI G AEQGSILDRIVKE YG P E RARRF L D 630
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 780 CLA RL FTAYLQ L y RGFT L G VE D ILVKPK A DVKRQR IIEE sthcgpq A VRAALN L P EA ----------------------- 836
Cdd:PRK08566 631 SVT RL AIRFIM L - RGFT T G ID D EDIPEE A KEEIDE IIEE ------- A EKRVEE L I EA yengeleplpgrtleetlemkim 702
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 837 ASYDEV R --- G KWQDAH LG kdqrdfnmidlkfkeevnhysneinkacmpfglhrqf PE N SLQM M VQS GA K GS TV N TM Q IS 913
Cdd:PRK08566 703 QVLGKA R dea G EIAEKY LG ------------------------------------- LD N PAVI M ART GA R GS ML N LT Q MA 745
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 914 CLL GQ IELE G 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 993
Cdd:PRK08566 746 ACV GQ QSVR G 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 825
1050 1060 1070
....*....|....*....|....*....|..
gi 103471997 994 KH L EG L V V Q YD L TVRD SD G SV VQF L YGEDG L D 1025
Cdd:PRK08566 826 NA L QD L K V E YD G TVRD TR G NI VQF K YGEDG V D 857
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1199-1716
3.55e-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: 476.30
E-value: 3.55e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1199 K WQ RSL C EPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM V AS A NIKTP M M SV P VL N T K K A l K R V 1278
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 103471997 1279 KS LKK Q L T RV C L GE V LQ K ID V Q E sfcmeekqnkfqvyqlrfqflphayyqqekclrpedi LRFMET R F FK L L ME sikkkn 1358
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 103471997 1359 nkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeerege 1438
Cdd:cd02735 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1439 enddedmqeernphregarktqeqdeevglgteedpslpalltqprkpthsqepqgpeamerrvqavreihpfiddyqyd 1518
Cdd:cd02735 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1519 tees L WC Q VT V KLPL MKINFDMS 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 1598
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 103471997 1599 R L Y S NDIHA IA 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 1678
Cdd:cd02735 192 R I Y T NDIHA ML 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 103471997 1679 Q FLK Q AT ML G SH D E L R SPS AC LVVGK V V R GGTGLF E L K 1716
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
RPOLA_N
smart00663 RNA polymerase I subunit A N-terminus;
297-638
8.92e-108
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 345.27
E-value: 8.92e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 297 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 vatpttdeekdsliaidrsfl 375
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 103471997 376 stlpgqslidklyni WIR LQ SH V NIVF D S E - MDKLMM --- DKYPGIR Q I L EK KEG L FR KHMM GKRVD YA ARSVI C PD MYI 451
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 103471997 452 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 531
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 103471997 532 pqgtk IV C RHV KN GD IL L L NRQPTLHR P SIQAHR A R I L p E E K VL RL HYAN C KA YNADFDGDEMN A H F PQS ELG RAEA YV L 611
Cdd:smart00663 194 ----- IV E RHV ID GD VV L F NRQPTLHR M SIQAHR V R V L - E G K TI RL NPLV C SP YNADFDGDEMN L H V PQS LEA RAEA RE L 267
330 340
....*....|....*....|....*..
gi 103471997 612 ACTDQQY L V PK D G Q P LA G L IQD HMVSG 638
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 ...
434-614
1.33e-87
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: 282.27
E-value: 1.33e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 434 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 513
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 103471997 514 QREAVAKQL ltpatgapkpqgtk IV C RHV KN GD IL L L NRQP T LHR P SI QA HR A R I LP e E K VL RL HYANCKA YNADFDGDE 593
Cdd:pfam00623 81 LDKELEIGD -------------- IV E RHV ID GD VV L F NRQP S LHR L SI MG HR V R V LP - G K TF RL NLSVTTP YNADFDGDE 145
170 180
....*....|....*....|.
gi 103471997 594 MN A H F PQSE LG RAEA YV L ACT 614
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 ...
1172-1715
1.46e-47
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: 175.24
E-value: 1.46e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1172 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 1251
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 103471997 1252 LM v A SANIK TP M M SVPVL - NTK K ALKRVKSLK K QLTRVC L GE V LQK I DV qesfcmeekqnkf QVYQLRFQFLPHAYYQQ E 1330
Cdd:TIGR02389 88 VD - A RKTPS TP S M TIYLE d EYE K DREKAEEVA K KIEATK L ED V AKD I SI ------------- DLADMTVIIELDEEQLK E 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1331 KCLRPE D I lrfmetrffkll MES IKK KNNKA safrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegda 1410
Cdd:TIGR02389 154 RGITVD D V ------------ EKA IKK AKLGK ------------------------------------------------- 172
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1411 dasdakrkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdee V GLGTEEDPSLPALLTQ P R kpthsq 1490
Cdd:TIGR02389 173 ------------------------------------------------------- V IEIDMDNNTITIKPGN P S ------ 191
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1491 epqg PEAMERRVQAVREI H pfiddyqydteeslwcqvtvklplmkinfdmsslvvslahgav I YAT KGI T R CLL nettn N 1570
Cdd:TIGR02389 192 ---- LKELRKLKEKIKNL H ------------------------------------------- I KGI KGI K R VVI ----- R 219
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1571 K NEK E L V LN TEG I NL P E LF K YAE V l D LR R LYS NDIH A IA NTY GIEAA LRV I EK EIK DVFAVY G IA VD P RHL S LVAD Y M CF 1650
Cdd:TIGR02389 220 K EGD E Y V IY TEG S NL K E VL K LEG V - D KT R TTT NDIH E IA 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 103471997 1651 E G VYKPLN R F GI RSN - S S P L QQMT FE TSFQF L KQ A TML G SH DEL RSPSACLV VG KVVRG GTG LFE L 1715
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
1159-1715
1.63e-46
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 172.72
E-value: 1.63e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1159 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 1231
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 103471997 1232 H F AG RG E M NVTLG I PRL R EI l MV A SANIK TPMM SVPVL - NTKKALKRVKSLKKQLTRVC L GEVLQK I D V Q esfcmeekqn 1310
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 103471997 1311 kfq VYQLRFQFLPHAYYQQEKC L RPE D ILRFM E trff K LLMESIKKKN N K asafrnvntrratqrdldnagelgrsrgeq 1390
Cdd:PRK04309 152 --- LANMTIIIELDEEMLEDRG L TVD D VKEAI E ---- K KKGGEVEIEG N T ------------------------------ 194
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1391 egdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdeevglgt 1470
Cdd:PRK04309 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1471 eedpslpa L LTQ P RK P THS qepqgpe AMERRVQAV R E I H pfiddyqydteeslwcqvtvklplmkinfdmsslvvslahg 1550
Cdd:PRK04309 195 -------- L IIS P KE P SYR ------- ELRKLAEKI R N I K ----------------------------------------- 218
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1551 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 A I ANTY GIEAA LRV I EK EIK DVFA 1630
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 E I EEVL GIEAA RNA I IE EIK NTLE 290
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1631 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 KVVRG G 1709
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 103471997 1710 TG LF EL 1715
Cdd:PRK04309 371 TG DV EL 376
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
394-1252
2.08e-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: 176.78
E-value: 2.08e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 394 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 468
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 103471997 469 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 546
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 103471997 547 i L LLNR Q PTLHR PS IQA HRARIL 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 626
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 103471997 627 LAGLI QD h MV S G asmttrgcfftrehymel V Y RGL T D K V G RVK llspsilkpfplwt GKQVV S TLLIN I IPE D HIPLN L S 706
Cdd:TIGR02386 481 IVTPS QD - MV L G ------------------ L Y YLT T E K P G AKG -------------- EGKIF S NVDEA I RAY D NGKVH L H 527
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 707 GKAKITGKAWVK ET prs VP G --- FN p DSMC E SQVI I REG E llcg V L D K AHYG S sayg L VHCC YE IY G G E TSGKV L TCLAR 783
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 103471997 784 L FTA Y LQLY r G F T LGVE DI L V KP kadv KRQR I IE E sthcgpqavraalnlpeaa SYD EV RGKWQDAHL G K --- DQ R DFNM 860
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 103471997 861 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 935
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 103471997 936 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 1013
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 103471997 1014 vvqflyg E D G LDI pktqflqpkqfpflasny E V I MKSQH l HEVL S RA D pk KALHHFR A IKKWQSKHPNTLLRRGAFLS -- 1091
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 103471997 1092 YSQ KI QEA - VKAL K L esenrng RS PG T Q E MLR mwyeldeesrrkyqkka AA C pdpslsvwrpdiyfasvsetfetkvddy 1170
Cdd:TIGR02386 827 IAE KI ENS g IEKV K V ------- RS VL T C E SEH ----------------- GV C ---------------------------- 854
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1171 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 1247
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 103471997 1248 LR E IL 1252
Cdd:TIGR02386 913 VK E LF 917
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
424-990
1.11e-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: 145.30
E-value: 1.11e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 424 K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq AVIN gpnvhpgas MVINEDGS 503
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 103471997 504 R T AL SA VD M TQ RE avakqlltpatgap K P QGTK I VCRHV K NGDI LL l NR Q PTLHR PS IQA HRA r I L P E E K VLR LH YAN C K 583
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 103471997 584 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 TREHYME 655
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 103471997 656 LV Y R - G LT D KVG R V K LLSPSILKP fplw T GK Q V VS T L liniipedhiplnlsgkakit G KAW V K E - T P RS VP GF N pdsmc 733
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 103471997 734 es QVI iregellcgvl D 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 812
Cdd:COG0086 575 -- QVI ----------- N 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 103471997 813 Q R I I EE ST hcgp QA V raalnlpeaasy D E VRGKWQDAHLGKDQ R DFNM ID L kfkee VNHY S N E INKAC M P f GLHR Q fpe N 892
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 103471997 893 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 964
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 103471997 965 F FHCMAG R E GL V DTA V KT SR SGYL Q R 990
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 ...
16-1004
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: 1306.40
E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 16 SF GM YSAEE LK KLSVK S ITNP RYL DSLG N P SAN GLYD L ALGP A D SKEV CSTC VQDFS NC S GH L GHIELPL T VYNPL L FD K 95
Cdd:cd01435 1 SF SF YSAEE IR KLSVK E ITNP VTF DSLG H P VPG GLYD P ALGP L D KDDI CSTC GLNYL NC P GH F GHIELPL P VYNPL F FD L 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 96 LY L LLRGSC LN CH MLTCPRAVIH L LLCQ L RV L EV G A L QAVY EL E rilnrfleenpdpsaseireeleqytteivqnnllg 175
Cdd:cd01435 81 LY K LLRGSC FY CH RFRISKWEVK L FVAK L KL L DK G L L VEAA EL D ------------------------------------ 124
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 176 sqgahvknvcesksklialfwkahmnakrcphcktgrsvvrkehnskltitfpamvhrtagqkdseplgieeaqigkrgy 255
Cdd:cd01435 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 256 ltptsarehlsalwknegfflnylfsgmdddgmesr 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 V 335
Cdd:cd01435 125 ------------------------------------ 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 N 168
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 336 VL IR K LLA L M A Q EQKL peevatpttdeekdsliaidr S F L STLP G QSLID KL Y N I W IR LQS H VN IV FDS EMDKLM - MDKY 414
Cdd:cd01435 169 QQ IR 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 227
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 415 PGI R 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 494
Cdd:cd01435 228 PGI K 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 307
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 495 SMVIN 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 RA R I LP E EK V 574
Cdd:cd01435 308 NAIED 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 387
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 575 LRLHYANCK 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 H Y M 654
Cdd:cd01435 388 LRLHYANCK 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 Q 467
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 655 E LVY RG L T ----- DK V GR V KLL S P S ILKP F PLWTGKQV V ST L L I N I IP EDHIP LNLSGK A K ITG K AW vketprsv P G FNP 729
Cdd:cd01435 468 Q LVY AA L R plfts DK D GR I KLL P P A ILKP K PLWTGKQV I ST I L K N L IP GNAPL LNLSGK K K TKK K VG -------- G G KWG 539
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 730 DSMC ESQVIIR 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 809
Cdd:cd01435 540 GGSE ESQVIIR 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 618
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 810 V KR QR I IEESTHC G PQ A VRAA L N L peaasydevrgkwqdahlgkdqrdfnmidlkfke EV N HYSNE I N KAC M P F GL HRQ F 889
Cdd:cd01435 619 E KR RK I LRKAKKL G LE A AAEF L G L ---------------------------------- KL N KVTSS I I KAC L P K GL LKP F 664
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 890 PEN S 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 FFHCM 969
Cdd:cd01435 665 PEN N 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 FFHCM 744
970 980 990
....*....|....*....|....*....|....*
gi 103471997 970 AGREGL V DTAVKTSRSGYLQRC I IKHLEGL V V Q YD 1004
Cdd:cd01435 745 AGREGL I DTAVKTSRSGYLQRC L IKHLEGL K V N YD 779
RNAP_archeal_A'
cd02582 A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
11-1029
3.11e-178
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: 559.17
E-value: 3.11e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 11 R LQ GI S FG MY S A EE LK K L SV KS I TN P RYL D SL G N P SAN GL Y D LA LG PADSKEV C S TC VQDFSN C S GH L GHIEL PLT V YNP 90
Cdd:cd02582 3 R IK GI K FG LL S P EE IR K M SV VE I IT P DTY D ED G Y P IEG GL M D PR LG VIEPGLR C K TC GNTAGE C P GH F GHIEL ARP V IHV 82
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 91 LLFDKL Y L LLR GS C LN C HMLTC P RAV I hlllcqlrvlevgalqavyelerilnrfleenpdpsa SEIR E ELEQY tteivq 170
Cdd:cd02582 83 GFAKHI Y D LLR AT C RS C GRILL P EEE I ------------------------------------- EKYL E RIRRL ------ 119
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 171 nnllgsqgah VKNVC E SKSKL I ALFW K AHMNA K R CPHC KTGRSVVRK E HNSKLTITFPAMVHR tagqkdseplgieeaqi 250
Cdd:cd02582 120 ---------- KEKWP E LVKRV I EKVK K KAKKR K V CPHC GAPQYKIKL E KPTTFYEEKEEGEVK ----------------- 172
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 251 gkrgy LTP TSA RE H L SAL wknegfflnylfsg M D D D GMESRFN P SV ----- FF L DF L V VPP SRY RP VSR L gdqmf TN G QT 325
Cdd:cd02582 173 ----- LTP SEI RE R L EKI -------------- P D E D LELLGID P KT arpew MV L TV L P VPP VTV RP SIT L ----- ET G ER 228
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 326 VN lqavm K D vv L IR KL LALMAQE Q K L P E -- E VAT P ttdeekdsliaidrsflstlpg Q SL I DK L yni W IR LQ S HV NIV FD 403
Cdd:cd02582 229 SE ----- D D -- L TH KL VDIIRIN Q R L K E ni E AGA P ---------------------- Q LI I ED L --- W DL LQ Y HV TTY FD 276
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 404 S E M dklmmdky PGI R -------------- Q I L EK KEG L FR KHMM GKRV DYA AR S VI C PD MYINT NE I G I P MVF A TK LT Y P 469
Cdd:cd02582 277 N E I -------- PGI P parhrsgrplktla Q R L KG KEG R FR GNLS GKRV NFS AR T VI S PD PNLSI NE V G V P EDI A KE LT V P 348
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 470 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 K IV C RH VKN GDI L L 549
Cdd:cd02582 349 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 ------- W IV E RH LID GDI V L 415
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 550 L NRQP T LHR P SI Q AHR A R I LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQSE LG RAEA YV L ACTDQQY L V P KD G Q P LA G 629
Cdd:cd02582 416 F NRQP S LHR M SI M AHR V R V LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQSE EA RAEA RE L MLVQEHI L S P RY G G P II G 494
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 630 L IQD H m V SGA SMT TR - GCF FT R E HYME L VYRGLT D kvgr VK L LS P S IL K P F PLWTGKQ VV S TL L inii P E D hip LN LS GK 708
Cdd:cd02582 495 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 ---- P K D --- LN FE GK 562
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 709 AK ITGK awvketprsv PGFNP D SM C E -- SQ V I I RE G E LL C GV L DK AHY G SSAY G - L V H CCYEI YG G E TSGKV L TCLA RL F 785
Cdd:cd02582 563 AK VCSG ---------- CSECK D ED C P nd GY V V I KN G K LL E GV I DK KAI G AEQP G s L L H RIAKE YG N E VARRF L DSVT RL A 632
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 786 TAYLQ L Y r GFT L G VE D ILVKPK A DVKRQR II E E sthcgpq A VRAALN L P E aa S Y DE ----- VR G K wqdahl GKDQ rdfn M 860
Cdd:cd02582 633 IRFIE L R - GFT I G ID D EDIPEE A RKEIEE II K E ------- A EKKVYE L I E -- Q Y KN gelep LP G R ------ TLEE ---- T 692
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 861 IDL 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 R R PPLMASGKS LP C F E 939
Cdd:cd02582 693 LEM 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 E R INRGYRNRT LP H F K 767
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 940 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 YD L TVRDS D G SVV QF L Y 1019
Cdd:cd02582 768 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 YD G TVRDS R G NII QF K Y 847
1050
....*....|
gi 103471997 1020 GEDG L D IP K T 1029
Cdd:cd02582 848 GEDG V D PA K S 857
RNA_pol_Rpb1_5
pfam04998 RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
958-1670
4.47e-170
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: 524.61
E-value: 4.47e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 958 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 1037
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 103471997 1038 P F LASNY E VIM K SQH L HEV L SRADPKKALHHFRAIKKW qskhpntllrrgaflsysqkiqeavkalklesenrngrspgt 1117
Cdd:pfam04998 81 E F SDLKL E DKF K NDL L DDL L LLSEFSLSYKKEILVRDS ------------------------------------------ 118
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1118 qemlrmwyeldeesrrkyqkkaaacpdps LSVWRPDIYF A SVSE T FETKVDDY S QEWAAQTEKSYEKSELSLDR L RTLLQ 1197
Cdd:pfam04998 119 ----------------------------- KLGRDRLSKE A QERA T LLFELLLK S GLESKRVRSELTCNSKAFVC L LCYGR 169
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1198 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 1276
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 103471997 1277 RV K SLKKQLTR V C LG E V LQKIDVQESFCMEEKQNKFQ V YQLRFQ F LPHAYYQQ E KCLR PE DI L RFMET R FF K L L ME SIKK 1356
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 103471997 1357 knnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeere 1436
Cdd:pfam04998 --------------------------------------------------------------------------------
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1437 geenddedmqeernphregarktqeqdeevglgteedpslpalltq PR K PTHSQEPQGPEAM E R R VQ A VR EI HP FI DDYQ 1516
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 103471997 1517 YDTEESLWCQVT V KLPL M KINFDMSS LV V SL AHGAVIYATK GI T R C L L NE TTNN K N E KEL VL N TEG I NL PELFKYAEVL D 1596
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 103471997 1597 LR R LY SNDIH A I ANTY GIEAA LRVIEK EI KD V FAVY GI AVDP RHL S L V AD Y M CFE G VYKPLN R F GI RSNSSPLQ 1670
Cdd:pfam04998 443 AG R IL SNDIH E I LEIL GIEAA RNALLN EI RN V YRFQ GI YIND RHL E L I AD Q M TRK G YIMAIG R H GI NKAELSAL 516
PRK08566
PRK08566 DNA-directed RNA polymerase subunit A'; Validated
4-1025
5.58e-165
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain]
Cd Length: 882
Bit Score: 524.42
E-value: 5.58e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 4 S KN M PWR R LQG I S FG MY S A EE LK K L SV KS I TNPRYL D SL G N P SAN GL Y D LA LG PA D SKEV C S TC VQDFSN C S GH L GHIEL 83
Cdd:PRK08566 1 S MM M IPK R IGS I K FG LL S P EE IR K M SV TK I ITADTY D DD G Y P IDG GL M D PR LG VI D PGLR C K TC GGRAGE C P GH F GHIEL 80
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 84 PLT V YNPLLFDKL Y L LLR GS C LN C hmltcpravihlllcqlrvlevgalqavyel E R IL nrf L E E N pdpsas EI R E E LE Q 163
Cdd:PRK08566 81 ARP V IHVGFAKLI Y K LLR AT C RE C ------------------------------- G R LK --- L T E E ------ EI E E Y LE K 120
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 164 YTT eivqnnllgsqgah V K NVCESKSK LI ALFW K AHMNAKR CPHC KT grsvvrkehn SKLT I T F pamvhrtag Q K dse P L 243
Cdd:PRK08566 121 LER -------------- L K EWGSLADD LI KEVK K EAAKRMV CPHC GE ---------- KQYK I K F --------- E K --- P T 164
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 244 GIE E AQIGKRGY LTP TSA RE H L SAL wknegfflnylfsg M D D D GMESRF NP S V ----- FF L DF L V VPP SRY RP VSR L gdq 318
Cdd:PRK08566 165 TFY E ERKEGLVK LTP SDI RE R L EKI -------------- P D E D LELLGI NP E V arpew MV L TV L P VPP VTV RP SIT L --- 227
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 319 mf TN GQ TVNLQAVM K D V VL IR kllalma QE Q K L P E -- E VAT P ttdeekdsliaidrsflstlpg Q SL I DK L yni W IR LQ S 396
Cdd:PRK08566 228 -- ET GQ RSEDDLTH K L V DI IR ------- IN Q R L K E ni E AGA P ---------------------- Q LI I ED L --- W EL LQ Y 273
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 397 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 I G I P MVF 462
Cdd:PRK08566 274 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 V G V P EAI 345
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 463 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 pkpqgtk IV C RH V 542
Cdd:PRK08566 346 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 ------- IV E RH L 412
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 543 KN GDI L L L NRQP T LHR P SI Q AHR A R I LP e E K VL RL HY A N C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQY L V P K 622
Cdd:PRK08566 413 ID GDI V L F NRQP S LHR M SI M AHR V R V LP - G K TF RL NL A V C PP YNADFDGDEMN L H V PQ T E EA RAEA RI L MLVQEHI L S P R 491
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 623 D G Q P LA G L IQDH m V SGA SMT TR - GCF FT R E HYME L VYRG ltd KVGRVKLLS P S I LKPF P L WTGKQ VV S TL L inii P E D hi 701
Cdd:PRK08566 492 Y 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 ---- P K D -- 561
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 702 p LNL SG KAKI TGKAWVKE tprsvpgfnp DSM CE -- SQ V I I RE G E LL C GV L DK AHY G SSAYGLVHCCYEI YG G E TSGKV L T 779
Cdd:PRK08566 562 - LNL EF KAKI CSGCDECK ---------- KED CE hd AY V V I KN G K LL E GV I DK KAI G AEQGSILDRIVKE YG P E RARRF L D 630
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 780 CLA RL FTAYLQ L y RGFT L G VE D ILVKPK A DVKRQR IIEE sthcgpq A VRAALN L P EA ----------------------- 836
Cdd:PRK08566 631 SVT RL AIRFIM L - RGFT T G ID D EDIPEE A KEEIDE IIEE ------- A EKRVEE L I EA yengeleplpgrtleetlemkim 702
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 837 ASYDEV R --- G KWQDAH LG kdqrdfnmidlkfkeevnhysneinkacmpfglhrqf PE N SLQM M VQS GA K GS TV N TM Q IS 913
Cdd:PRK08566 703 QVLGKA R dea G EIAEKY LG ------------------------------------- LD N PAVI M ART GA R GS ML N LT Q MA 745
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 914 CLL GQ IELE G 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 993
Cdd:PRK08566 746 ACV GQ QSVR G 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 825
1050 1060 1070
....*....|....*....|....*....|..
gi 103471997 994 KH L EG L V V Q YD L TVRD SD G SV VQF L YGEDG L D 1025
Cdd:PRK08566 826 NA L QD L K V E YD G TVRD TR G NI VQF K YGEDG V D 857
RNAP_I_Rpa1_C
cd02735 Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
1199-1716
3.55e-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: 476.30
E-value: 3.55e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1199 K WQ RSL C EPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILM V AS A NIKTP M M SV P VL N T K K A l K R V 1278
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 103471997 1279 KS LKK Q L T RV C L GE V LQ K ID V Q E sfcmeekqnkfqvyqlrfqflphayyqqekclrpedi LRFMET R F FK L L ME sikkkn 1358
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 103471997 1359 nkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeerege 1438
Cdd:cd02735 --------------------------------------------------------------------------------
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1439 enddedmqeernphregarktqeqdeevglgteedpslpalltqprkpthsqepqgpeamerrvqavreihpfiddyqyd 1518
Cdd:cd02735 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1519 tees L WC Q VT V KLPL MKINFDMS 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 1598
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 103471997 1599 R L Y S NDIHA IA 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 1678
Cdd:cd02735 192 R I Y T NDIHA ML 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 103471997 1679 Q FLK Q AT ML G SH D E L R SPS AC LVVGK V V R GGTGLF E L K 1716
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
PRK14977
PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
7-1715
6.03e-154
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain]
Cd Length: 1321
Bit Score: 507.26
E-value: 6.03e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 7 MPWRRLQ GI S FG MY S AEELK K LSVKS IT N P RYL D SL G N P SAN GL Y D LA LG PADSKEV C S TC VQDFS NC S GH L GHIEL PLT 86
Cdd:PRK14977 4 LAVKAID GI I FG LI S PADAR K IGFAE IT A P EAY D ED G L P VQG GL L D GR LG TIEPGQK C L TC GNLAA NC P GH F GHIEL AEP 83
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 87 V YNPLLF D KLYL LL RGS C LN C HM L TC P RA vihlllcqlrvlevgalqavyelerilnrfleenp D PSASEIR EE LEQYTT 166
Cdd:PRK14977 84 V IHIAFI D NIKD LL NST C HK C AK L KL P QE ----------------------------------- D LNVFKLI EE AHAAAR 128
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 167 E I vqnnllg SQGAHVKNVC E SKSKLIALFW K AH mna K R CPHC kt G RSVVRK E H n SKL TI T fpamvhrtagqkdseplg IE 246
Cdd:PRK14977 129 D I ------- PEKRIDDEII E EVRDQVKVYA K KA --- K E CPHC -- G APQHEL E F - EEP TI F ------------------ IE 177
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 247 EAQ I GKR g Y L T P TSA R EHLSALWKNEGFFLNY lfsgmdd D GMES R fn P SVFF L DFLV VPP SRY RP vsrlgdqmftngq TV 326
Cdd:PRK14977 178 KTE I EEH - R L L P IEI R DIFEKIIDDDLELIGF ------- D PKKA R -- P EWAV L QAFL VPP LTA RP ------------- SI 234
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 327 N L Q - AVMKDVV L IRK L LALMAQE QKL P E -- EVAT P T tdeekdsliaidrsflstlpgq SLIDKL yni WIR LQ S H VNIV FD 403
Cdd:PRK14977 235 I L E t GERSEDD L THI L VDIIKAN QKL K E sk DAGA P P ---------------------- LIVEDE --- VDH LQ Y H TSTF FD 289
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 404 SEMDKLMMDKYP G IR ------- 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 476
Cdd:PRK14977 290 NATAGIPQAHHK G SG rplkslf 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 369
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 477 VQELRQA VINGP NVH PGA SMVINE DG SRTA L sav D MTQREA va K QL L TP A TGAPKP qg TK IV C RH VKN GDI LLL NRQP T L 556
Cdd:PRK14977 370 IEKMKEL VINGP DEF PGA NAIRKG DG TKIR L --- D FLEDKG -- K DA L RE A AEQLEI -- GD IV E RH LAD GDI VIF NRQP S L 442
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 557 H RP SI Q AHR ARI LP E e KVL RLH 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 HMV 636
Cdd:PRK14977 443 H KL SI L AHR VKV LP G - ATF RLH 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 FIT 521
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 637 SGASM T TRGCF F TREHYMELVYR - G L TD K vgrvk L LS P S I - L K PF P L WTGKQ VV S TL L inii P E D hip L N LS G K AK itgk 714
Cdd:PRK14977 522 AAYLI T KDDAL F DKNEASNIAML a G I TD P ----- L PE P A I k T K DG P A WTGKQ LF S LF L ---- P K D --- F N FE G I AK ---- 585
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 715 a W VKETPRSVP gf N P DSMCESQ V I I R EGEL LC GV L D KAHY G SSAYG --- L VHCCYEI YG GETSGKV L TCLARLFTAYLQL 791
Cdd:PRK14977 586 - W SAGKAGEAK -- D P SCLGDGY V L I K EGEL IS GV I D DNII G ALVEE pes L IDRIAKD YG EAVAIEF L NKILIIAKKEILH 662
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 792 Y r GF TL G VE D ILVKPK A dvk R Q R I IEESTHCGPQAVRAALNLPEAASYDEVR GK WQ dah L GKDQRDFNMIDLKFKE E VNH 871
Cdd:PRK14977 663 Y - GF SN G PG D LIIPDE A --- K Q E I EDDIQGMKDEVSDLIDQRKITRKITIYK GK EE --- L LRGMKEEEALEADIVN E LDK 735
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 872 Y ---- SNEI N K a C MP fglhrqf PE N SLQM M VQS GA K GS TV N TM QI SCL LGQ IELEG R RPPLMAS G K -------- S L PC F E 939
Cdd:PRK14977 736 A rdka GSSA N D - C ID ------- AD N AGKI M AKT GA R GS MA N LA QI AGA LGQ QKRKT R IGFVLTG G R lhegykdr A L SH F Q 807
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 940 PYEFT P R A G GFV TGRFLT G IKPP 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 1019
Cdd:PRK14977 808 EGDDN P D A H GFV KNNYRE G LNAA 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 887
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1020 GEDG L dipktqflqpkqfpflasnyevimksqhlhevlsra DP K K AL H H fraikkw QSKHPNTLLR rgaflsy S QKI qea 1099
Cdd:PRK14977 888 GEDG I ------------------------------------ DP Q K LD H G ------- EAFNLERIIE ------- K QKI --- 914
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1100 vkalklesenrngrspgtqemlrmwyeld E ESRRKYQ K kaaacpdpslsvwrpdiyfasvs ETF E TKVDD Y SQEWA A QTE 1179
Cdd:PRK14977 915 ----------------------------- E DRGKGAS K ----------------------- DEI E ELAKE Y TKTFN A NLP 942
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1180 K SY ---- EKS EL SL D R L RTL --- 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 1252
Cdd:PRK14977 943 K LL adai HGA EL KE D E L EAI cae 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 1021
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1253 MV A S A NIK TP M M SVPV ln TKKALKRVKSLKKQLTRVCLGE V LQK I DVQES fcmeekqnkfqvyqlrfqflph AYYQQE K C 1332
Cdd:PRK14977 1022 VD A R A KPS TP T M DIYL -- DDECKEDIEKAIEIARNLKELK V RAL I ADSAI ---------------------- DNANEI K L 1077
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1333 LR P EDILR fmetrffkllmesikk K N NKASAF R NVNTRR A TQRDLDNAG EL grsrgeqegdeeeeghivdaeaeegdada 1412
Cdd:PRK14977 1078 IK P DKRAL ---------------- E N GCIPME R FAEIEA A LAKGKKFEM EL ----------------------------- 1112
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1413 sdakrkekqeeevdyeseeeeeregeenddedmqeernphr E GARKTQEQD E E vglg TEE D PS L PA L LTQPR K pthsqep 1492
Cdd:PRK14977 1113 ----------------------------------------- E DDLIILDLV E A ---- ADR D KP L AT L IAIRN K ------- 1140
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1493 qgpe AMERR V QA V RE I hpfiddyqydte E SL W C qvtvklplmkinfdmsslvvslahgaviyatkgitrclln E TTNNKN 1572
Cdd:PRK14977 1141 ---- ILDKP V KG V PD I ------------ E RA W V ---------------------------------------- E LVEKDG 1164
1610 1620 1630 1640 1650 1660 1670 1680
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1573 EK E LVLN T E G I NL PELFKYAEV l D LRRLYS ND IHA IA N T Y GIEAA LRV I EK E IKDVFAVY G IA VD P R HLS LVAD Y MC FE G 1652
Cdd:PRK14977 1165 RD E WIIQ T S G S NL AAVLEMKCI - D IANTIT ND CFE IA G T L GIEAA RNA I FN E LASILEDQ G LE VD N R YIM LVAD I MC SR G 1243
1690 1700 1710 1720 1730 1740 1750
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1653 VYKP -- L NRF G I R SN ----- S SPL QQMT FE TSFQFLKQ A TML G SHDELRSPSAC L VV G KVVRG G T G LFE L 1715
Cdd:PRK14977 1244 TIEA ig L QAA G V R HG fagek D SPL AKAA FE ITTHTIAH A ALG G EIEKIKGILDA L IM G QNIPI G S G KVD L 1313
RNAP_III_RPC1_N
cd02583 Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
21-1008
9.87e-152
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: 486.29
E-value: 9.87e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 21 S A E ELKK LS VKSI TN PR - Y LDSLGN P SAN G LY D LA LG PA D SKEV C S TC VQDFSN C S GH L G H I E L P L T V YN pllfdklyll 99
Cdd:cd02583 2 S P E DIIR LS EVEV TN RN l Y DIETRK P LPY G VL D PR LG TS D KDGI C E TC GLNLAD C V GH F G Y I K L E L P V FH ---------- 71
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 100 lrgsclnchmltcpravihlllcqlrvle V G ALQ A VYE ler IL N ------- R F L EEN pdpsaseir EE LEQYTTEIVQN N 172
Cdd:cd02583 72 ----------------------------- I G YFK A IIN --- IL Q cicktcs R V L LPE --------- EE KRKFLKRLRRP N 110
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 173 L -- L GSQGAHV K NVCES K sklialfwkahm NAKR CPHC ktgrsvvrk EHNS K L titfpamvhrtag Q K D seplgieeaqi 250
Cdd:cd02583 111 L dn L QKKALKK K ILEKC K ------------ KVRK CPHC --------- GLLK K A ------------- Q E D ----------- 145
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 251 gkrgy L T P TSAREHLSALWKNEGFF L nylfs G M DDDG mesr FN P SVFF L DFLV VPP SRY RP VSRLGDQMF TN -- GQ TV N L 328
Cdd:cd02583 146 ----- L N P LKVLNLFKNIPPEDVEL L ----- L M NPLA ---- GR P ENLI L TRIP VPP LCI RP SVVMDEKSG TN ed DL TV K L 211
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 329 qavm KDVVLIRKLLA lm AQEQ K lpeevatpttdeekdsliaidrsflstlp G QS l ID K LYNI W IR LQ SHVNIVFD SE MDK 408
Cdd:cd02583 212 ---- SEIIFLNDVIK -- KHLE K ----------------------------- G AK - TQ K IMED W DF LQ LQCALYIN SE LPG 255
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 409 L --- M MD K Y P -- G IR Q I L EK K E G L FR KHMM GKRVD YAA R S VI C PD MYINTNEI G I P MVF A TK LTYP QP VT PW N VQE LR QA 483
Cdd:cd02583 256 L pls M QP K K P ir G FC Q R L KG K Q G R FR GNLS GKRVD FSG R T VI S PD PNLRIDQV G V P EHV A KI LTYP ER VT RY N IEK LR KL 335
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 484 V I NGP N VHPGA SM VI NE DG SRT - A L SAVD mtq R EAV A KQ L ltpatgapkpqgt KI --- V C RH VKN GDI L L L NRQP T LHR P 559
Cdd:cd02583 336 V L NGP D VHPGA NF VI KR DG GKK k F L KYGN --- R RKI A RE L ------------- KI gdi V E RH LED GDI V L F NRQP S LHR L 399
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 560 SI Q AHRA RIL P e EKVL R LHYAN C KA YNADFDGDEMN A H F PQ S E LG RAEA YV L ACTDQQYLV P KD G Q PL AGLI QD HMVSGA 639
Cdd:cd02583 400 SI M AHRA KVM P - WRTF R FNECV C TP YNADFDGDEMN L H V PQ T E EA RAEA LE L MGVKNNLVT P RN G E PL IAAT QD FLTASY 478
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 640 SM T TRGC FF T R EHYME L V y RGLT D KVGRVK L LS P S ILKP FP LWTGKQ VV S t LL INIIPEDHIPL NL SG K A K ITG K awvke 719
Cdd:cd02583 479 LL T SKDV FF D R AQFCQ L C - SYML D GEIKID L PP P A ILKP VE LWTGKQ IF S - LL LRPNKKSPVLV NL EA K E K SYT K ----- 551
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 720 tprsvpgf NPDS MC -- ESQ V I IR EG ELLCG V LDK AHY GS SAYGLVH cc Y EI --- YG G E TSGKVLTC LA R L FTAY L QL y RG 794
Cdd:cd02583 552 -------- KSPD MC pn DGY V V IR NS ELLCG R LDK STL GS GSKNSLF -- Y VL lrd YG P E AAAAAMNR LA K L SSRW L SN - RG 620
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 795 F TL G VE D il V K P KADVKRQR ii EE S thcgpqa V RAALNLPEAASYDEVR GK WQ d AHL G KDQRD fn MIDL K FKE E VNHYSN 874
Cdd:cd02583 621 F SI G ID D -- V T P SKELLKKK -- EE L ------- V DNGYAKCDEYIKQYKK GK LE - LQP G CTAEQ -- TLEA K ISG E LSKIRE 686
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 875 EIN KAC MPF g LH rqf PE NS LQM M VQS 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 TG 953
Cdd:cd02583 687 DAG KAC LKE - LH --- KS NS PLI M ALC 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 AN 761
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*
gi 103471997 954 R F LT G IK P P EFFFH C M A GREGLVDTAVKT SRS GY L QR CII K H LE G L V VQYD L TVR 1008
Cdd:cd02583 762 S F YS G LT P T EFFFH T M S GREGLVDTAVKT 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 ...
13-1004
1.03e-143
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: 462.39
E-value: 1.03e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 13 QGIS FG MY S AE E LKKL SV KS I TN P RYLDSL G N P SAN GL Y D LAL G PA D SKEV C S TC VQ D FSN C S GH L GHIEL PLT V YN pll 92
Cdd:cd02733 1 KRVQ FG IL S PD E IRAM SV AE I EH P ETYENG G G P KLG GL N D PRM G TI D RNSR C Q TC GG D MKE C P GH F GHIEL AKP V FH --- 77
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 93 fdklylllrgscln CHM LT cpr AVIHL L L C QLRVL evga L Q A vyel ER I L NR F leenpdpsa SE I RE E leqytteivqnn 172
Cdd:cd02733 78 -------------- IGF LT --- KILKI L R C VCKRE ---- L S A ---- ER V L EI F --------- KR I SD E ------------ 111
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 173 llgsqgahvknvcesksklialfwkahmnakrcphcktgrsvvrkehnskltitfpamvhrtagqk D SEP LG ieeaqigk 252
Cdd:cd02733 112 ------------------------------------------------------------------ D CRI LG -------- 117
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 253 rgy LT P TSA R ehlsalwknegfflnylfsgmdddgmesrfn P SVFF L DF L V VPP SRY RP VSRLG dq MFTNGQ --- T VN L Q 329
Cdd:cd02733 118 --- FD P KFS R ------------------------------- P DWMI L TV L P VPP PAV RP SVVMD -- GSARSE ddl T HK L A 161
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 330 AVM K dvvlirklla LMA Q EQKLPEEV A tpttdeekdsliaidrsflstlp GQSL I DKLYNI wir LQ S HV NIVF D S E --- M 406
Cdd:cd02733 162 DII K ---------- ANN Q LKRQEQNG A ----------------------- PAHI I EEDEQL --- LQ F HV ATYM D N E ipg L 205
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 407 DKLMMDK --- YPG IRQ I L EK KEG LF R KHM MGKRVD YA AR S VI C PD MYINTNEI G I P MVF A TK LT Y P QP VTP W N VQE L RQA 483
Cdd:cd02733 206 PQATQKS 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 F P EI VTP F N IDR L QEL 285
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 484 V I NGPN VH PGA SMV I NE DG S R TA L SAVDM tqrea VAKQL L TPAT gapkpqgtk IV C RH VKN GD IL L L NRQP T LH RP S IQA 563
Cdd:cd02733 286 V R NGPN EY PGA KYI I RD DG E R ID L RYLKK ----- ASDLH L QYGY --------- IV E RH LQD GD VV L F NRQP S LH KM S MMG 351
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 564 HR ARI LP e EKVL RL HYANCKA YNADFDGDEMN A H F PQS ELG RAE AYV L ACTDQ Q YLV P KDGQ P LA G LI QD HMVSGASM T T 643
Cdd:cd02733 352 HR VKV LP - YSTF RL NLSVTTP YNADFDGDEMN L H V PQS LET RAE LKE L MMVPR Q IVS P QSNK P VM G IV QD TLLGVRKL T K 430
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 644 R GC F FTREHY M E L VY r G L T D KV G RVKL ls P S ILKP F PLWTGKQ VV S T llin IIP e DHIP L NL S GKAKITG K A W vketprs 723
Cdd:cd02733 431 R DT F LEKDQV M N L LM - W L P D WD G KIPQ -- P A ILKP K PLWTGKQ IF S L ---- IIP - KINN L IR S SSHHDGD K K W ------- 495
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 724 vpg FN P D smc ESQ VII RE GELL C G V L D K AHY G S S AY GL V H CCYEI YG G E TSGKVLTCLA R LFTAY L q L YR GF TL G VE D IL 803
Cdd:cd02733 496 --- IS P G --- DTK VII EN GELL S G I L C K KTV G A S SG GL I H VIWLE YG P E AARDFIGNIQ R VVNNW L - L HN GF SI G IG D TI 568
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 804 VKPKADV K R Q RI I EESTH cgpqavraalnlpeaasyd E V RGKWQD A HL G KDQRDF - NMIDLK F KEE VN hys NEI NKA CMP 882
Cdd:cd02733 569 ADKETMK K I Q ET I KKAKR ------------------- D V IKLIEK A QN G ELEPQP g KTLRES F ENK VN --- RIL NKA RDK 626
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 883 F 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 EPYEFT P RAG GFV TGRF L T G I 959
Cdd:cd02733 627 A 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 IKDDYG P ESR GFV ENSY L R G L 706
970 980 990 1000
....*....|....*....|....*....|....*....|....*
gi 103471997 960 K P P EFFFH C M A GREGL V DTAVKT SRS GY L QR CII K HL E GLV V Q YD 1004
Cdd:cd02733 707 T P Q EFFFH A M G GREGL I DTAVKT AET GY I QR RLV K AM E DVM V K YD 751
RNAP_largest_subunit_N
cd00399 Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
389-1004
1.18e-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: 362.91
E-value: 1.18e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 389 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 463
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 103471997 464 TK L typqpvtpwnvqelrqavingpnvhpgasmvinedgsrtalsavdmtqreavakqlltpatgapkpqgtkivcrhvk 543
Cdd:cd00399 187 LT L ----------------------------------------------------------------------------- 189
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 544 N GD IL L L NRQP T LH RP SI Q AHR A R I LP E e KVL RL HYAN C KA YNADFDGDEMN A H F PQSE LG RAEA YV L ACTDQQY L V P KD 623
Cdd:cd00399 190 D GD PV L F NRQP S LH KL SI M AHR V 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 103471997 624 G Q PL A GL I QD H m VS GA SMT T R G cfftrehymelvyrgltdkvgrvkllspsilkpfplwtg KQ V VS TL L iniipedhipl 703
Cdd:cd00399 269 G E PL I GL S QD T - LL GA YLL T L G --------------------------------------- KQ I VS AA L ----------- 297
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 704 nlsgkakitgkawvketprsvpgfnpdsmcesqviiregellcgvldkahygss AY GL V H CCYEIY G G E TSG K V L TC L A R 783
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 103471997 784 LFTAY L QL y R GF TL G VE D ILVKPKADVKRQRI IEE sthcgpq A VRAALNLP EA ASYDEVR gkwqdah LGKDQRDFNMIDL 863
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 103471997 864 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 943
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 103471997 944 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 1004
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;
297-638
8.92e-108
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain]
Cd Length: 295
Bit Score: 345.27
E-value: 8.92e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 297 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 vatpttdeekdsliaidrsfl 375
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 103471997 376 stlpgqslidklyni WIR LQ SH V NIVF D S E - MDKLMM --- DKYPGIR Q I L EK KEG L FR KHMM GKRVD YA ARSVI C PD MYI 451
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 103471997 452 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 531
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 103471997 532 pqgtk IV C RHV KN GD IL L L NRQPTLHR P SIQAHR A R I L p E E K VL RL HYAN C KA YNADFDGDEMN A H F PQS ELG RAEA YV L 611
Cdd:smart00663 194 ----- IV E RHV ID GD VV L F NRQPTLHR M SIQAHR V R V L - E G K TI RL NPLV C SP YNADFDGDEMN L H V PQS LEA RAEA RE L 267
330 340
....*....|....*....|....*..
gi 103471997 612 ACTDQQY L V PK D G Q P LA G L IQD HMVSG 638
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 ...
434-614
1.33e-87
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: 282.27
E-value: 1.33e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 434 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 513
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 103471997 514 QREAVAKQL ltpatgapkpqgtk IV C RHV KN GD IL L L NRQP T LHR P SI QA HR A R I LP e E K VL RL HYANCKA YNADFDGDE 593
Cdd:pfam00623 81 LDKELEIGD -------------- IV E RHV ID GD VV L F NRQP S LHR L SI MG HR V R V LP - G K TF RL NLSVTTP YNADFDGDE 145
170 180
....*....|....*....|.
gi 103471997 594 MN A H F PQSE LG RAEA YV L ACT 614
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 ...
1199-1716
4.16e-56
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: 201.28
E-value: 4.16e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1199 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 1277
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 103471997 1278 V K SLKKQ L TRVC L GE V LQKIDVQ ----- ESFCM EE KQNKFQV Y qlr F Q F l P HAYYQ Q EKC lr PEDI LR FMET R ---- FF K 1348
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 103471997 1349 L L ME S I K KK NNK as A F RN - V N trra TQRDL DNA GE L G - R S R geqegdeeeegh I VDAEA E egdadasdakrkekqeeevd 1426
Cdd:cd02584 171 L S ME Q I A KK IKE -- E F KD d L N ---- VIFSD DNA EK L V i R I R ------------ I INDDE E -------------------- 212
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1427 yeseeeeeregeenddedmqeernphregar K TQEQDEE V G L GTE E D pslp AL L TQP rkpthsq EPQ G P E AMER rvqavr 1506
Cdd:cd02584 213 ------------------------------- K EEDSEDD V F L KKI E S ---- NM L SDM ------- TLK G I E GIRK ------ 244
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1507 eihpfiddyqydteeslwcqvtvklplmkinfdmsslvvslahga V IYATKGITR c LLN ET TNN K NEK E L VL N T E G I NL P 1586
Cdd:cd02584 245 --------------------------------------------- V FIREENKKK - VDI ET GEF K KRE E W VL E T D G V NL R 278
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1587 E LFKYAE V l D LR R LY SNDI HA I ANTY GIEAA LRVIE KE IKD V FAVY G IA V DP RHL S L VA D Y M CFE G VYKPLN R F GI - R SN 1665
Cdd:cd02584 279 E VLSHPG V - D PT R TT SNDI VE I FEVL 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 QD 357
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|.
gi 103471997 1666 SS PL QQMT FE TSFQF L KQ A TML G SH D E L RSP S ACLVV G KVVRG GTG L F E L K 1716
Cdd:cd02584 358 TG 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_A''
cd06528 A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
1179-1715
1.31e-52
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: 189.77
E-value: 1.31e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1179 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 1255
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 103471997 1256 SANIK TP M M SVPV - LNT K KALKRVKSLKKQLTRVC L GEVLQK I DVQ esfcmeekqnkfq VYQL R FQFLPHAYYQQEKCLR 1334
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 103471997 1335 PE D I L RFM E trffkllme SI KK K nnkasafrnvntrratqrdldnagelgrsrgeqegdeeeeghivd AEA EEGD ADASD 1414
Cdd:cd06528 154 VD D V L KAI E --------- KL KK G --------------------------------------------- KVG EEGD VTLIV 179
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1415 A K rkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdeevglgt E E D PS LPA L ltqprkpthsqepqg 1494
Cdd:cd06528 180 L K ------------------------------------------------------ A E E PS IKE L --------------- 190
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1495 peamerrv QAVR E ihpfiddyqydteeslwcqvtvklplm KI nfdmsslvvsla HGAV I YAT KGI T R CLLN ettnn K N E K 1574
Cdd:cd06528 191 -------- RKLA E --------------------------- KI ------------ LNTK I KGI KGI K R VIVR ----- K E E D 218
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1575 E L V LN TEG I NL PELF K YAE V l D LR R LYS N D IH A I ANTY GIEAA LRV I EK EIK DVFAVY G IA VD P RH LS LVAD Y M CFE G VY 1654
Cdd:cd06528 219 E Y V IY TEG S NL KAVL K VEG V - D PT R TTT N N IH E I EEVL 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 103471997 1655 KPLN R F GI RSN - S S P L QQMT FE TSFQF L KQ A TML G SH DELR SPSACLV VG KVVRG GTG LF EL 1715
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
RNAP_IV_RPD1_N
cd10506 Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
339-1008
8.45e-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: 196.86
E-value: 8.45e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 339 RKL L A L m AQ EQ K LPE E V a T P TTDEEK ds L IAIDRS FL ST LP ---- GQSLIDKLY niwi RLQSHVNIV FD SEMD --- KL MM 411
Cdd:cd10506 116 LPI L S L - AQ VK K ILK E I - D P KLIAKG -- L PRQEGL FL KC LP vppn CHRVTEFTH ---- GFSTGSRLI FD ERTR ayk KL VD 187
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 412 DKYPGIRQILE KK E GL -- FRKHMM GKR VDYAA RSV ICP D M Y INT NEIGIP MVF A TK LT YPQP V TP WN VQE L RQAVINGP n 489
Cdd:cd10506 188 FIGTANESAAS KK S GL kw MKDLLL GKR SGHSF RSV VVG D P Y LEL NEIGIP CEI A ER LT VSER V SS WN RER L QEYCDLTL - 266
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 490 vhpgas 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 HRARI L 569
Cdd:cd10506 267 ------ 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 LSVKV L 326
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 570 P 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 C F FT 649
Cdd:cd10506 327 P 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 V F LD 406
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 650 REHYME L VYRGLT dkvgrv K L LS P S I L K PF ---- PLWTGKQ VVST LL inii P E D hip L NL S G kakitgkawvketprsv P 725
Cdd:cd10506 407 KAQMQQ L QMLCPS ------ Q L PP P A I I K SP psng PLWTGKQ LFQM LL ---- P T D --- L DY S F ----------------- P 456
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 726 GFN pdsmcesq V I I RE GEL L c GVLDKAHYGSSAY G LV - HCCYEIYG G ETSG k V L TCLAR L FTAY L QL y RGF TLGVE D ILV 804
Cdd:cd10506 457 SNL -------- V F I SD GEL I - SSSGGSSWLRDSE G NL f SILVKHGP G KALD - F L DSAQG L LCEW L SM - RGF SVSLS D LYL 525
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 805 KPKA d VK RQ RI IEE s THC G PQAVRA A L N L ---------- PEAA S YD E VR - GKWQDAHLGKD Q RDFNMIDL --- K FK EEVN 870
Cdd:cd10506 526 SSDS - YS RQ KM IEE - ISL G LREAEI A C N I kqllvdsrkd FLSG S GE E ND v SSDVERVIYER Q KSAALSQA svs A FK QVFR 603
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 871 HYS 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 LMASG 932
Cdd:cd10506 604 DIQ 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 RVIEK 674
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 103471997 933 KSLP 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 1008
Cdd:cd10506 675 DGSE 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
RNA_pol_rpoA2
TIGR02389 DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
1172-1715
1.46e-47
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: 175.24
E-value: 1.46e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1172 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 1251
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 103471997 1252 LM v A SANIK TP M M SVPVL - NTK K ALKRVKSLK K QLTRVC L GE V LQK I DV qesfcmeekqnkf QVYQLRFQFLPHAYYQQ E 1330
Cdd:TIGR02389 88 VD - A RKTPS TP S M TIYLE d EYE K DREKAEEVA K KIEATK L ED V AKD I SI ------------- DLADMTVIIELDEEQLK E 153
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1331 KCLRPE D I lrfmetrffkll MES IKK KNNKA safrnvntrratqrdldnagelgrsrgeqegdeeeeghivdaeaeegda 1410
Cdd:TIGR02389 154 RGITVD D V ------------ EKA IKK AKLGK ------------------------------------------------- 172
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1411 dasdakrkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdee V GLGTEEDPSLPALLTQ P R kpthsq 1490
Cdd:TIGR02389 173 ------------------------------------------------------- V IEIDMDNNTITIKPGN P S ------ 191
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1491 epqg PEAMERRVQAVREI H pfiddyqydteeslwcqvtvklplmkinfdmsslvvslahgav I YAT KGI T R CLL nettn N 1570
Cdd:TIGR02389 192 ---- LKELRKLKEKIKNL H ------------------------------------------- I KGI KGI K R VVI ----- R 219
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1571 K NEK E L V LN TEG I NL P E LF K YAE V l D LR R LYS NDIH A IA NTY GIEAA LRV I EK EIK DVFAVY G IA VD P RHL S LVAD Y M CF 1650
Cdd:TIGR02389 220 K EGD E Y V IY TEG S NL K E VL K LEG V - D KT R TTT NDIH E IA 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 103471997 1651 E G VYKPLN R F GI RSN - S S P L QQMT FE TSFQF L KQ A TML G SH DEL RSPSACLV VG KVVRG GTG LFE L 1715
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
1159-1715
1.63e-46
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain]
Cd Length: 383
Bit Score: 172.72
E-value: 1.63e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1159 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 1231
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 103471997 1232 H F AG RG E M NVTLG I PRL R EI l MV A SANIK TPMM SVPVL - NTKKALKRVKSLKKQLTRVC L GEVLQK I D V Q esfcmeekqn 1310
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 103471997 1311 kfq VYQLRFQFLPHAYYQQEKC L RPE D ILRFM E trff K LLMESIKKKN N K asafrnvntrratqrdldnagelgrsrgeq 1390
Cdd:PRK04309 152 --- LANMTIIIELDEEMLEDRG L TVD D VKEAI E ---- K KKGGEVEIEG N T ------------------------------ 194
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1391 egdeeeeghivdaeaeegdadasdakrkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdeevglgt 1470
Cdd:PRK04309 --------------------------------------------------------------------------------
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1471 eedpslpa L LTQ P RK P THS qepqgpe AMERRVQAV R E I H pfiddyqydteeslwcqvtvklplmkinfdmsslvvslahg 1550
Cdd:PRK04309 195 -------- L IIS P KE P SYR ------- ELRKLAEKI R N I K ----------------------------------------- 218
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1551 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 A I ANTY GIEAA LRV I EK EIK DVFA 1630
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 E I EEVL GIEAA RNA I IE EIK NTLE 290
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1631 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 KVVRG G 1709
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 103471997 1710 TG LF EL 1715
Cdd:PRK04309 371 TG DV EL 376
rpoC_TIGR
TIGR02386 DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
394-1252
2.08e-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: 176.78
E-value: 2.08e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 394 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 468
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 103471997 469 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 546
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 103471997 547 i L LLNR Q PTLHR PS IQA HRARIL 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 626
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 103471997 627 LAGLI QD h MV S G asmttrgcfftrehymel V Y RGL T D K V G RVK llspsilkpfplwt GKQVV S TLLIN I IPE D HIPLN L S 706
Cdd:TIGR02386 481 IVTPS QD - MV L G ------------------ L Y YLT T E K P G AKG -------------- EGKIF S NVDEA I RAY D NGKVH L H 527
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 707 GKAKITGKAWVK ET prs VP G --- FN p DSMC E SQVI I REG E llcg V L D K AHYG S sayg L VHCC YE IY G G E TSGKV L TCLAR 783
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 103471997 784 L FTA Y LQLY r G F T LGVE DI L V KP kadv KRQR I IE E sthcgpqavraalnlpeaa SYD EV RGKWQDAHL G K --- DQ R DFNM 860
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 103471997 861 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 935
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 103471997 936 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 1013
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 103471997 1014 vvqflyg E D G LDI pktqflqpkqfpflasny E V I MKSQH l HEVL S RA D pk KALHHFR A IKKWQSKHPNTLLRRGAFLS -- 1091
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 103471997 1092 YSQ KI QEA - VKAL K L esenrng RS PG T Q E MLR mwyeldeesrrkyqkka AA C pdpslsvwrpdiyfasvsetfetkvddy 1170
Cdd:TIGR02386 827 IAE KI ENS g IEKV K V ------- RS VL T C E SEH ----------------- GV C ---------------------------- 854
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1171 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 1247
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 103471997 1248 LR E IL 1252
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 ...
617-802
1.46e-41
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: 150.47
E-value: 1.46e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 617 QY L V P KD G Q P LA G LI QD HMVSGASM T TRGC FF T RE HY M E L VYR G ltdkvgr VK L LS P S ILKP F - PLWTGKQ VV S T LL I N i 695
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 103471997 696 ipedhi PL N LS GK A K ITGK awvketprsvpgfn PDSMCE S Q V I I RE GEL LC GV L DK AHY G S S AYG L V H CC Y EI YG G E TSG 775
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 103471997 776 K V L TC L AR L FTA YL QLY r GF TL G VE DI 802
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; ...
420-1011
2.09e-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: 148.44
E-value: 2.09e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 420 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 497
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 103471997 498 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 HRA r I L P E E K VLR L 577
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 103471997 578 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 RGCFFTREHYM elv 657
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 KERKGDKGEGI --- 430
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 658 yrg LTDK VGRV kllspsilkpfplwtgkqvvst LLIN I I PE DHIPL N LS - G K AKI tgkawvketprsvpgfnpdsmces Q 736
Cdd:cd01609 431 --- IETT VGRV ---------------------- IFNE I L PE GLPFI N KT l K K KVL ------------------------ K 461
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 737 VI I R E gellcgvldkahygssayglvhc CY EI YG G E TSGKV L TCLAR L ftaylqlyr GF -------- TLGVE DI L V K P ka 808
Cdd:cd01609 462 KL I N E ----------------------- 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 103471997 809 dv KRQR II E E ST hcgp QA V raalnlpeaasy D E VRGKWQDAH L GKDQ R DFNM I DL -- KFK E E V nhy SNEIN K AC mpfglh 886
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 ------ 560
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 887 RQF 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 964
Cdd:cd01609 561 DKD 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 618
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 103471997 965 F FHCMAG R E GL V DTA V KT SR SGYL Q R ciikhle G LV - V QY D LT V RDS D 1011
Cdd:cd01609 619 F ISTHGA R K GL A DTA L KT AD SGYL T R ------- R LV d V AQ D VI V TEE D 659
RpoC
COG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
424-990
1.11e-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: 145.30
E-value: 1.11e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 424 K E G L FR KHMM GKRVDY AA RSVI CPDMYINTNEI G I P MVF A TK L TY P qpvtpwnvqelrq AVIN gpnvhpgas MVINEDGS 503
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 103471997 504 R T AL SA VD M TQ RE avakqlltpatgap K P QGTK I VCRHV K NGDI LL l NR Q PTLHR PS IQA HRA r I L P E E K VLR LH YAN C K 583
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 103471997 584 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 TREHYME 655
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 103471997 656 LV Y R - G LT D KVG R V K LLSPSILKP fplw T GK Q V VS T L liniipedhiplnlsgkakit G KAW V K E - T P RS VP GF N pdsmc 733
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 103471997 734 es QVI iregellcgvl D 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 812
Cdd:COG0086 575 -- QVI ----------- N 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 103471997 813 Q R I I EE ST hcgp QA V raalnlpeaasy D E VRGKWQDAHLGKDQ R DFNM ID L kfkee VNHY S N E INKAC M P f GLHR Q fpe N 892
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 103471997 893 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 964
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 103471997 965 F FHCMAG R E GL V DTA V KT SR SGYL Q R 990
Cdd:COG0086 739 F ISTHGA R K GL A DTA L KT AD SGYL T R 764
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1199-1299
2.98e-34
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: 134.27
E-value: 2.98e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1199 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 1278
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
....*....|....*....|.
gi 103471997 1279 KSL K KQLTRVC LGEV LQK I DV 1299
Cdd:cd02736 79 RIV K GRIEKTY LGEV ASY I EE 99
PRK14897
PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
1169-1711
6.59e-34
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain]
Cd Length: 509
Bit Score: 138.40
E-value: 6.59e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1169 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 1248
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 103471997 1249 R EI l MV A SANIK TP M M SV pvlntkkalkrvk S LKK qltrvclgevlqki D VQ E S fcm EEK qnkfqvyqlrfqflphayyq 1328
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 103471997 1329 qekclrpedilrfmetrffkl LM E SI KK KN N KA - SAFRNVN T rratqrdld NAG E L grsrgeqegdeeeeghivdaeaee 1407
Cdd:PRK14897 252 --------------------- VR E VA KK IE N TT l IDVADII T --------- DIA E M ------------------------ 277
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1408 gdadasdakrkekqeeevdyeseeeeeregeenddedmqeernphregarktqeqdeevglgteedpslp ALLTQP rkpt 1487
Cdd:PRK14897 278 ---------------------------------------------------------------------- SVVVEL ---- 283
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1488 hsqepq GP E A M ER R VQAVRE I HPF I DDYQYD T E E SL wc QVTVK L PLMKIN F DMSS L VVSLAHGAV I YAT KGI T R CLLNE t 1567
Cdd:PRK14897 284 ------ DE E K M KE R LIEYDD I LAA I SKLTFK T V E ID -- DGIIR L KPQQPS F KKLY L LAEKVKSLT I KGI KGI K R AIARK - 354
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1568 tn NKN E KEL V LN T E G I NL PELFKYA EV l D LR R L Y S NDI HA IA NTY GIEAA LRV I EK E I K DVFAVY G IA VD P RH LS LVAD Y 1647
Cdd:PRK14897 355 -- END E RRW V IY T Q G S NL KDVLEID EV - D PT R T Y T NDI IE IA 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 103471997 1648 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 KVVRG GTG 1711
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
PRK09603
PRK09603 DNA-directed RNA polymerase subunit beta/beta';
394-1235
1.17e-31
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain]
Cd Length: 2890
Bit Score: 136.21
E-value: 1.17e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 394 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 468
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 103471997 469 P QPVTP wnvqelrqavingpnvhpgasmv IN E D G SR T A L - S A VD M TQ reavakqlltpatgapkp Q GTKI V -- C - RHVKN 544
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 103471997 545 G DIL LLNR Q PTLH RP SIQA HRARIL 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 624
Cdd:PRK09603 1807 G YPV LLNR A PTLH KQ SIQA FHPKLI - 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 103471997 625 QPL A GLI QD h MV S G --- A S MTTR G C ------ F FTREHYMELVYRGLT D KVGRVKL L SPS il KPFPLWT G KQVVSTL L ini 695
Cdd:PRK09603 1886 KAV A IPS QD - MV L G lyy L S LEKS G V kgehkl F SSVNEIITAIDTKEL D IHAKIRV L DQG -- NIIATSA G RMIIKSI L --- 1959
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 696 ip E D H IP LN L sgkakitgka W VK etprsvpgfnpdsmcesqviiregellcg VLD K AHY G S sayg LV HCCYEIY G GETSG 775
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 103471997 776 KV L TC L AR L FTA Y l QLYR G FTLGV EDI LV k PK adv KR Q RII E EST hcgpqavraalnlpea ASYDEVRGKW q D AH L GK DQ 855
Cdd:PRK09603 1995 TF L DN L KT L GFR Y - ATKA G ISISM EDI IT - PK --- DK Q KMV E KAK ---------------- VEVKKIQQQY - D QG L LT DQ 2052
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 856 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 935
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 103471997 936 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 hlegl V V Q YDLT V R D SD G S vv 1015
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 ----- V S Q NVKV V S D DC G T -- 2181
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1016 qflyg ED G LD I PK ---- TQFLQ P KQ fpflasny E V I MKSQH L HE V L sra DP KKA lhhfraikkwqskhp NT LL RRGAFL - 1090
Cdd:PRK09603 2182 ----- HE G IE I TD iavg SELIE P LE -------- E R I FGRVL L ED V I --- DP ITN --------------- EI LL YADTLI d 2230
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1091 - SYSQ K IQ EA - V K ALKL esenrng R S P G T Q emlrmwyeldeesrr K YQ K KAA A cpdpslsvwrpdiyfasvsetfetkvd 1168
Cdd:PRK09603 2231 e EGAK K VV EA g I K SITI ------- R T P V T C --------------- K AP K GVC A --------------------------- 2261
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 103471997 1169 dysqewaaqte K S Y eks E L S L D rlrtllqlkw QRSLCE PGEAVG LL AAQSIGEP S TQ M TL N TFH FA G 1235
Cdd:PRK09603 2262 ----------- K C Y --- G L N L G ---------- EGKMSY PGEAVG VV AAQSIGEP G TQ L TL R TFH VG G 2304
PRK00566
PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
424-1251
2.72e-31
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain]
Cd Length: 1156
Bit Score: 134.42
E-value: 2.72e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 424 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 499
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 103471997 500 EDGSR T AL SA VD M TQ RE avakqlltpatgapkpqg TKI V C rhvkng D I L --------- LLNR Q PTLHR PS IQA HRA r I L P 570
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 103471997 571 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 ------ 644
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 103471997 645 -- G CF F TREHYMELV Y R gltdk V G R V K L LSPSILK pfpl W T G K QV V S T ---- LLI N - I I PE DH iplnlsgkakitgkawv 717
Cdd:PRK00566 512 ge G MV F SSPEEALRA Y E ----- N G E V D L HARIKVR ---- I T S K KL V E T tvgr VIF N e I L PE GL ----------------- 565
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 718 ketprsvp G F npdsmcesqviireg ELLCGV L D K AHYGS sayg LVHCC Y EI YG GETSGKV L TCLAR L ftaylqlyr GF -- 795
Cdd:PRK00566 566 -------- P F --------------- INVNKP L K K KEISK ---- IINEV Y RR YG LKETVIF L DKIKD L --------- GF ky 609
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 796 ------ TL G VE DI LVK P kadv KRQR IIEE STH cgpqavraalnlp E A asy D E VRGKWQDAHLGKDQ R DFNM ID L -- K FKE 867
Cdd:PRK00566 610 atrsgi SI G ID DI VIP P ---- EKKE IIEE AEK ------------- E V --- A E IEKQYRRGLITDGE R YNKV ID I ws K ATD 669
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 868 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 cfepyef TP 945
Cdd:PRK00566 670 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 ------- TP 725
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 946 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 vvqflyg 1020
Cdd:PRK00566 726 ----- 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 103471997 1021 ED G LDIPK tqflqpkqfpf LASNY EVI MK sqh L H E - V L S R -- A DP kkalhhfra I kkwqs KH P N T --- LLRR G AFLS -- Y 1092
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 ee I 835
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1093 SQ KI Q EA - VKAL K L esenrng RS P gtqemlrmwye L DE E S R R kyqkka AA C pdpslsvwrpdiyfasvsetfetkvddys 1171
Cdd:PRK00566 836 AD KI E EA g IEEV K I ------- RS V ----------- L TC E T R H ------ GV C ----------------------------- 862
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1172 qewaaqt 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 PR LR E I 1251
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 PR VA E L 919
PRK14906
PRK14906 DNA-directed RNA polymerase subunit beta';
421-1254
2.92e-30
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain]
Cd Length: 1460
Bit Score: 131.15
E-value: 2.92e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 421 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 500
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 103471997 501 dgs RT A LS AVD mtqreavakqlltpa T GA PKPQG tki V CRH V KNGDIL LLNR Q PTLHR PS IQA HRA r I L P E E K VLR LH YA 580
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 103471997 581 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 h M VS G A smttrgcfftre H Y MELVYR G 660
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 - M II G V ------------ Y Y LTTERD G 597
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 661 LTDK v GR VKLLSPSI L KPFPLWTGKQVVSTLLIN i IPE D HIPLNLS G KAKI T GKAWVK ET PRSVPG FN pdsmces QV IIR 740
Cdd:PRK14906 598 FEGE - 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 103471997 741 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 820
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 103471997 821 hcgpqavraalnlpea ASYDEVRGKWQ D AH L GKDQ R DFNMI D L kfkee VNHYSN E INK A c M PF G LHRQ fpe N SLQ MM VQ S 900
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 103471997 901 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 980
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 103471997 981 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 1059
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 103471997 1060 a D PK KAL hhfraikkwqskhpntllrrgaflsysqkiqeavkalkle SE N RN GR S pgtqemlrmwy E L DEES rrkyqkka 1139
Cdd:PRK14906 892 - K PK GDV ---------------------------------------- DT N LI GR C ----------- L L EDVC -------- 911
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1140 aacp DP SLS V wrpdiy FA S VSETF E TK v DD YSQEWA A QTE K S yekselsld RL RTL LQLKWQRSL C EP ------------ 1207
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 103471997 1208 -- G E AVG LL AAQSIGEP S TQ M T LN TFH FA G RGEMNV T L G I PR LR E ILMV 1254
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
394-638
2.51e-28
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain]
Cd Length: 663
Bit Score: 123.09
E-value: 2.51e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 394 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 468
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 103471997 469 P qpvtpwnvqelrq A VI N G pnvhpgasm V I NEDGSRTALS A VDMTQR eavakqlltpatgap K PQGTKIVCRH V KN G DIL 548
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 103471997 549 LLNR Q PTLHR PS IQA HRA 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 628
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 103471997 629 GLI QD h M VS G 638
Cdd:CHL00018 530 VPS QD - M LL G 538
RNAP_III_Rpc1_C
cd02736 Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
1530-1713
4.22e-27
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: 113.47
E-value: 4.22e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1530 KL P L M K I N -- F DMS SL VVS L A h GA V IYATKGIT R CLL N ETTNNKNE K E LV lnt EG IN L PELFKYAE V l DLR R LY SN D I HA 1607
Cdd:cd02736 119 KL Q L S K S N ly F LLQ SL KRK L P - DV V VSGIPEVK R AVI N KDKKKGKY K L LV --- EG YG L RAVMNTPG V - IGT R TT SN H I ME 193
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1608 IANTY GIEAA 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 TSFQF L KQ A TM 1686
Cdd:cd02736 194 VEKVL GIEAA 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 KTTDH L FN A AL 273
170 180
....*....|....*....|....*..
gi 103471997 1687 L G SH D ELRSP S A C LVV GK VVRG GTGLF 1713
Cdd:cd02736 274 H G RK D SIEGV S E C IIM GK PMPI GTGLF 300
PRK14844
PRK14844 DNA-directed RNA polymerase subunit beta/beta';
372-1002
5.60e-27
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain]
Cd Length: 2836
Bit Score: 120.88
E-value: 5.60e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 372 R SF LS TL P GQSL I DKLYNI wir LQ SH V NIV FD SEMDKLMMD K Y ------ PG I RQI L EK K E G L FR KHMM GKRVDY AA RSVI 445
Cdd:PRK14844 1712 R KL LS LN P PEIM I RNEKRM --- LQ EA V DSL FD NSRRNALVN K A gavgyk KS I SDM L KG K Q G R FR QNLL GKRVDY SG RSVI 1788
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 446 CPDMYINT N EI G I P MVF A TK L TY P qpvtpwnvqelrqavingpnvhpgasmvined GSRTA L SAVD M TQREAV A KQ L LT p 525
Cdd:PRK14844 1789 VVGPTLKL N QC G L P KRM A LE L FK P -------------------------------- FVYSK L KMYG M APTIKF A SK L IR - 1835
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 526 atg A P KP QGTKIVCRHV K NGDI LL l NR Q PTLHR PS IQA HRA r IL P E E K VLR LH YAN C K A Y NADFDGD E M NA H F P Q S ELGR 605
Cdd:PRK14844 1836 --- A E KP EVWDMLEEVI K EHPV 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 LEAQ 1910
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 606 A EA Y VL ACTDQQY L V P KD G Q P LAGLIQ D HMVSGASM T TR ---------- G C F FTR EH Y melvyrgltdkvgrvkl LS PSI 675
Cdd:PRK14844 1911 L EA R VL MMSTNNV L S P SN G R P IIVPSK D IVLGIYYL T LQ epkeddlpsf G A F CEV EH S ----------------- LS DGT 1973
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 676 L kpfplwtgk QVV S TLLINI ipe DH I pl N L SG KAKI tgkawvk E T PRSV PG fnpd SMCES Q VIIREGE L LCGVLDKAHYG 755
Cdd:PRK14844 1974 L --------- HIH S SIKYRM --- EY I -- N S SG ETHY ------- K T ICTT PG ---- RLILW Q IFPKHEN L GFDLINQVLTV 2028
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 756 SSAYGL V HCC Y EIY G ge T S GK V ltclar L F TAY L qlyrg FT LG vedilvkpkadvkrqri I E ES T HC G PQAV R AALNL PE 835
Cdd:PRK14844 2029 KEITSI V DLV Y RNC G -- Q S AT V ------ A F SDK L ----- MV LG ----------------- F E YA T FS G VSFS R CDMVI PE 2078
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 836 -- A ASY D EV RG ------- KW QD AHLGKDQ R DFNM ID l KFKEEVNHYS N EIN KA CMPFGLHRQF pe NS LQ MMV Q SGA K GST 906
Cdd:PRK14844 2079 tk A THV D HA RG eikkfsm QY QD GLITRSE R YNKV ID - EWSKCTDMIA N DML KA ISIYDGNSKY -- NS VY MMV N SGA R GST 2155
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 907 VNTM Q ISCLL G qielegrrpp LM AS gksl 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 SG 986
Cdd:PRK14844 2156 SQMK Q LAGMR G ---------- LM TK ---- P SG E II E - TP ----- IISN F RE G LNVF E Y F NSTHGA R K GL A DTA L KT AN SG 2215
650 660
....*....|....*....|....*....
gi 103471997 987 YL -------- Q R CI I ----- K HLE GLVV Q 1002
Cdd:PRK14844 2216 YL trrlvdvs Q N CI V tkhdc K TKN GLVV R 2244
RNA_pol_Rpb1_4
pfam05000 RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
839-951
1.09e-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: 105.91
E-value: 1.09e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 839 YD E VR GK WQ D AHLGKDQRD F NMIDLKFKEEVNHYSNE I NKACMP fglhrqf P E NS LQ MM VQ SGAKGS TV N TM QI SCLL GQ 918
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 103471997 919 IEL EG R R P P LMA SG KS LP C F EPYEFT P RAG GFV 951
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 ...
1604-1712
2.09e-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: 101.34
E-value: 2.09e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1604 D IH AIANTY 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 1682
Cdd:cd00630 49 S IH EMLEAL 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 103471997 1683 Q A TML G SH DEL RSP S ACLVV G KVVRG GTG L 1712
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 ...
1208-1256
9.72e-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: 9.72e-24
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 103471997 1208 GEAVG L LAAQSIGEP S TQMTL N TFHFAG RGE MNVTLG I PRL R EIL MV AS 1256
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
420-639
1.43e-22
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain]
Cd Length: 627
Bit Score: 104.83
E-value: 1.43e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 420 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 498
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 103471997 499 NE D GS rtalsavdmtqrea V AKQ L LTPAT G A P kpqgtkivcrhvkngdi L LLNR Q PTLHR PS IQA HRA r IL P E EKVLR LH 578
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 103471997 579 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 639
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
1558-1716
1.18e-21
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 102.66
E-value: 1.18e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1558 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 HA I ANTY GIEAA LRV I EK E IKDVFAVY G IA VD 1637
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 IE I QEVL GIEAA RNA I IN E MMNTLEQQ G LE VD 767
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1638 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 VVRG GTG LFE L K 1716
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 PIKL GTG CVD L R 847
RNA_pol_Rpb1_1
pfam04997 RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
10-429
2.32e-13
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595
Cd Length: 320
Bit Score: 73.09
E-value: 2.32e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 10 RRLQG I S FG MY S A EE LK K L SV KSI T N P R - Y LDSLGN P SAN GL Y D LAL G PA D SKEV C S TC VQDFSN C S GH L GHIEL PLT V Y 88
Cdd:pfam04997 2 KKIKE I Q FG IA S P EE IR K W SV GEV T K P E t Y NYGSLK P EEG GL L D ERM G TI D KDYE C E TC GKKKKD C P GH F GHIEL AKP V F 81
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 89 N pllfdklylllrgsclnchmltcprav I HLLLCQ L RV LE vgal QAVYELERI L nrfleenpdpsase IREELEQYTTEI 168
Cdd:pfam04997 82 H --------------------------- I GFFKKT L KI LE ---- CVCKYCSKL L -------------- LDPGKPKLFNKD 116
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 169 VQNNL L G -- SQ GA - HVKNV C ES K SK lialfwkahmnakr C P HC K t G RSV V RKEHNSKLTITFPAMVHRTAGQ K DS E PLG I 245
Cdd:pfam04997 117 KKRLG L E nl KM GA k AILEL C KK K DL -------------- C E HC G - G KNG V CGSQQPVSRKEGLKLKAAIKKS K EE E EKE I 181
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 246 eeaqigkrgy L T P TSAREHLSAL w KN E GF flny LFS G MDD dgme S RFN P SVFF L DF L V VPP SRY RP VSR L GDQMFTNGQ - 324
Cdd:pfam04997 182 ---------- L N P EKVLKIFKRI - SD E DV ---- EIL G FNP ---- S GSR P EWMI L TV L P VPP PCI RP SVQ L DGGRRAEDD l 242
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 325 T VN L QAVM K DVVLIR KLL A L M A QEQKLP EE vatpttdeekdsliaidrsflstlpgqslidklyni W IR LQ S HV NIV FD S 404
Cdd:pfam04997 243 T HK L RDII K RNNRLK KLL E L G A PSHIIR EE ------------------------------------ W RL LQ E HV ATL FD N 286
410 420 430
....*....|....*....|....*....|.
gi 103471997 405 E MDK ---- L MMD K Y P -- G I R Q I L EK KEG L FR 429
Cdd:pfam04997 287 E IPG lppa L QKS K R P lk S I S Q R L KG KEG R FR 317
RNAP_beta'_C
cd02655 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
1203-1252
4.36e-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: 4.36e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 103471997 1203 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 1252
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 ...
1593-1715
6.78e-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: 6.78e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1593 EVL D LR R LYSND I HA I ANTY GI E AA LRVIEKEIKDVFAVY G IA V DPR HL S LVAD Y M CFE G VYKP LN RF G IR ------ SN S 1666
Cdd:cd02737 250 DLI D WE R SMPYS I QQ I KSVL 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 103471997 1667 S P LQQMT F ETSFQ - FLK Q A TM l G SH D E L RSPSACLVV GK VVRG GTG - L FE L 1715
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
1203-1232
3.09e-09
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain]
Cd Length: 1364
Bit Score: 62.26
E-value: 3.09e-09
10 20 30
....*....|....*....|....*....|
gi 103471997 1203 S L C E P GEAVG LL A A QSIGEP S TQ M TL N TFH 1232
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 ...
890-1235
1.86e-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: 59.48
E-value: 1.86e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 890 P E NS LQ MM VQ SGA K G stv N TM Q ISC L L G qie LE G rrpp LMA SGKSLPCFE P YEFTP R A G GF VT grfltgikpp E FFFHCM 969
Cdd:TIGR02388 117 P L NS VY MM AF SGA R G --- N MS Q VRQ L V G --- MR G ---- LMA NPQGEIIDL P IKTNF R E G LT VT ---------- E YVISSY 176
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 970 AG R E GLVDTA VK T SR SGYL Q R CIIK hleglv V QY D LT VR DS D GSVVQ flygedgl D I PKTQFLQPKQFPF L AS nyevimk 1049
Cdd:TIGR02388 177 GA R K GLVDTA LR T AD SGYL T R RLVD ------ V SQ D VI VR EE D CGTER -------- S I VVRAMTEGDKKIS L GD ------- 235
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1050 sqhlh EV L S R ADPKKA LH hfraikkwqskhpntllrrgaflsysqkiqeavkalklesenrngrspgtqemlrmwyelde 1129
Cdd:TIGR02388 236 ----- RL L G R LVAEDV LH -------------------------------------------------------------- 248
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1130 esrrkyqkkaaac P DPSLS V WRPDIYFASVSE T F ET kvddysqewa A QTEKSYEK S E L SLDRL R TLLQLKWQR SL C ---- 1205
Cdd:TIGR02388 249 ------------- P EGEVI V PKNTAIDPDLAK T I ET ---------- A GISEVVVR S P L TCEAA R SVCRKCYGW SL A hahl 305
330 340 350
....*....|....*....|....*....|.
gi 103471997 1206 - EP GEAVG LL AAQSIGEP S TQ M T LN TFH FA G 1235
Cdd:TIGR02388 306 v DL GEAVG II AAQSIGEP G TQ L T MR TFH TG G 336
rpoC2
PRK02597 DNA-directed RNA polymerase subunit beta'; Provisional
890-1235
5.29e-08
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain]
Cd Length: 1331
Bit Score: 58.08
E-value: 5.29e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 890 P E NS LQ MM VQ SGA K G stv N TM Q ISC L L G qie LE G rrpp LMA S gksl P CF E ---- P YEFTP R A G GF VT grfltgikpp E FF 965
Cdd:PRK02597 118 P L NS VY MM AF SGA R G --- N MS Q VRQ L V G --- MR G ---- LMA N ---- P QG E iidl P IKTNF R E G LT VT ---------- E YV 173
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 966 FHCMAG R E GLVDTA VK T SR SGYL Q R ciikhle G LV - V QY D LT VR DS D ----- G S VV QFLYGE D GLD IP ktqflqpkqfpf 1039
Cdd:PRK02597 174 ISSYGA R K GLVDTA LR T AD SGYL T R ------- R LV d V SQ D VI VR EE D cgttr G I VV EAMDDG D RVL IP ------------ 234
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1040 lasnyevi MKSQH L HE VL SR adpkkalhhfraikkw QSKH P -- NTLLR R GAFLSY -- SQ KI QE A - V KALKL esenrng RS 1114
Cdd:PRK02597 235 -------- LGDRL L GR VL AE ---------------- DVVD P eg EVIAE R NTAIDP dl AK KI EK A g V EEVMV ------- RS 283
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 103471997 1115 P G T Q E ML R mwyeldeesrrkyqkkaaacpdpsl SV W R pdiyfasvsetfetkvddysqewaaqte K S Y EK S e L SLDR L RT 1194
Cdd:PRK02597 284 P L T C E AA R ------------------------- SV C R ---------------------------- K C Y GW S - L AHNH L VD 309
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 103471997 1195 L lqlkwqrslcep GEAVG LL AAQSIGEP S TQ M T LN TFH FA G 1235
Cdd:PRK02597 310 L ------------ GEAVG II AAQSIGEP G TQ L T MR TFH TG G 338
PRK14898
PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
1199-1228
1.18e-04
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain]
Cd Length: 858
Bit Score: 47.20
E-value: 1.18e-04
10 20 30
....*....|....*....|....*....|
gi 103471997 1199 KWQRS L C EP G EAVG LL AAQSIGEP S TQM T L 1228
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
