RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3015
(1791 letters)
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, 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.
Length = 410
Score = 532 bits (1372), Expect = e-174
Identities = 203/310 (65%), Positives = 243/310 (78%), Gaps = 13/310 (4%)
Query: 1094 VTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPT--RISPWLLRIELDRKRMTDKKL 1151
VTA T IYYDPDPQNTVI ED+EFV Y+E PD D R+SPWLLRIELDRK+MTDKKL
Sbjct: 112 VTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKL 171
Query: 1152 TMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLR 1211
+ME I++KI F DDLN IF+DDNAEKLV+RIRI+N D+ K +D EDD+FL+
Sbjct: 172 SMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLK 224
Query: 1212 CIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKV 1271
IE+NMLSDMTL+GIE I + ++KK++ I E+GEFK +W+LETDG +L +V
Sbjct: 225 KIESNMLSDMTLKGIEGI---RKVFIREENKKKVDI-ETGEFKKREEWVLETDGVNLREV 280
Query: 1272 LSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMT 1331
LS VDP RT SNDI EIF+VLGIEA RK++ KE+ V+ F G YVNYRHLALLCDVMT
Sbjct: 281 LSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMT 340
Query: 1332 AKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRM 1391
+GHLMAITRHGINRQDTG LMRCSFEETVD+L++AAA E D ++GVSENI++GQL +
Sbjct: 341 QRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPI 400
Query: 1392 GTGCFDLLLD 1401
GTGCFDLLLD
Sbjct: 401 GTGCFDLLLD 410
Score = 227 bits (582), Expect = 2e-65
Identities = 78/115 (67%), Positives = 94/115 (81%), Gaps = 3/115 (2%)
Query: 773 LCKIIFVL---SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINR 829
+ +I VL + RK++ KE+ V+ F G YVNYRHLALLCDVMT +GHLMAITRHGINR
Sbjct: 296 IVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINR 355
Query: 830 QDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 884
QDTG LMRCSFEETVD+L++AAA E D ++GVSENI++GQL +GTGCFDLLLD
Sbjct: 356 QDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLLLD 410
Score = 179 bits (457), Expect = 8e-49
Identities = 81/154 (52%), Positives = 95/154 (61%), Gaps = 37/154 (24%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPT--RISPWLLRIELDRKRMTD 1586
L VTA T IYYDPDPQNTVI ED+EFV Y+E PD D R+SPWLLRIELDRK+M
Sbjct: 109 LKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKM-- 166
Query: 1587 KKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKL 1646
TDKKL+ME I++KI F DDLN IF+DDNAEKL
Sbjct: 167 --------------------------TDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKL 200
Query: 1647 VLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIE 1680
V+RIRI+N D+ K +D EDD+FL+ IE
Sbjct: 201 VIRIRIINDDEEKEED-------SEDDVFLKKIE 227
Score = 169 bits (430), Expect = 3e-45
Identities = 55/77 (71%), Positives = 65/77 (84%)
Query: 516 SVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETV 575
++ KE+ V+ F G YVNYRHLALLCDVMT +GHLMAITRHGINRQDTG LMRCSFEETV
Sbjct: 311 ALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETV 370
Query: 576 DVLMDAAAHAEADPMRG 592
D+L++AAA E D ++G
Sbjct: 371 DILLEAAAFGETDDLKG 387
Score = 48.4 bits (116), Expect = 3e-05
Identities = 16/31 (51%), Positives = 22/31 (70%), Gaps = 2/31 (6%)
Query: 988 YRLSSEAFEWLVGEIENRFQQAQVIA--CVG 1016
YRL+ EAF+W++GEIE RF ++ V VG
Sbjct: 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVG 31
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 336 bits (863), Expect = 2e-97
Identities = 145/386 (37%), Positives = 217/386 (56%), Gaps = 48/386 (12%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDS 130
+E+ +++L I + P+P I KP WTGKQ+FSL +P ++N+ ++
Sbjct: 518 TKEEALDLLRAAGIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDEC 577
Query: 131 GPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTV 190
D VV+++G LL G++ KK++G GS+L E G E RF ++ +
Sbjct: 578 KKED--CEHDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRL 635
Query: 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGI 250
+++L G + GI D ED+
Sbjct: 636 AIRFIMLRGFTTGIDD-------------------EDI---------------------- 654
Query: 251 GDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDAR 310
+ EI I++A++ V E+I+ N +LEP PG TL +T E ++ ++L AR
Sbjct: 655 -----PEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKAR 709
Query: 311 DKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPH 370
D+ G A+K L N M G++GS +N++Q+ ACVGQQ+V G+RI G+R RTLPH
Sbjct: 710 DEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPH 769
Query: 371 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430
F D G E+RGFV +SY +GLTP+EFFFHAMGGREGL+DTAV+T+++GY+QRRLI A++
Sbjct: 770 FKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQ 829
Query: 431 SVMVHYDCTVRNSVGQLIQLRYGEDG 456
+ V YD TVR++ G ++Q +YGEDG
Sbjct: 830 DLKVEYDGTVRDTRGNIVQFKYGEDG 855
Score = 139 bits (352), Expect = 5e-33
Identities = 50/74 (67%), Positives = 61/74 (82%)
Query: 1009 AQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAM 1068
Q+ ACVGQQ+V G+RI G+R RTLPHF D G E+RGFV +SY +GLTP+EFFFHAM
Sbjct: 742 TQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAM 801
Query: 1069 GGREGLIDTAVKTA 1082
GGREGL+DTAV+T+
Sbjct: 802 GGREGLVDTAVRTS 815
Score = 64.1 bits (157), Expect = 6e-10
Identities = 21/38 (55%), Positives = 30/38 (78%)
Query: 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDG 629
GY+QRRLI A++ + V YD TVR++ G ++Q +YGEDG
Sbjct: 818 GYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDG 855
Score = 63.0 bits (154), Expect = 1e-09
Identities = 20/38 (52%), Positives = 33/38 (86%)
Query: 28 PYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVM 65
P E+ +LG++P+ ARP+WM++TVLPVPP++VRP++ +
Sbjct: 190 PDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITL 227
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, 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.
Length = 867
Score = 308 bits (791), Expect = 3e-88
Identities = 141/377 (37%), Positives = 206/377 (54%), Gaps = 59/377 (15%)
Query: 86 DGKMPQPCILKPKPLWTGKQVFSLIIPGNVNM-----TRTHSTHPDDEDSGPYQWISPGD 140
G P+P I KPK WTGKQ+FS +P ++N + +E P D
Sbjct: 528 FGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEGRAKICSSDACKKEEC--------PHD 579
Query: 141 TKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQTVVNNWLLLEGH 200
VV+++G LL G++ KK++G G +LH E G E RF ++ + ++ L G
Sbjct: 580 AYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGF 639
Query: 201 SIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGIGDTIADPQTY 260
+ GI D D+ +
Sbjct: 640 TTGIDD-------------------IDI---------------------------PKEAK 653
Query: 261 LEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKS 320
EI+ I+KA++ V +I++ N +LEP PG T+ +T E ++ +L ARD+ G A+K
Sbjct: 654 EEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKY 713
Query: 321 LTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPES 380
L N+ M G++GS +NI+Q+ A VGQQ+V G RI G+R RTLPHF K D G ++
Sbjct: 714 LDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKA 773
Query: 381 RGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTV 440
RGFV +S+ GL P+E+FFHA GGREGL+DTAV+T+++GY+QRRLI A++ + V YD TV
Sbjct: 774 RGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTV 833
Query: 441 RNSVGQLIQLRYGEDGL 457
R++ G LIQ +YGEDG+
Sbjct: 834 RDTRGNLIQFKYGEDGV 850
Score = 127 bits (321), Expect = 2e-29
Identities = 47/86 (54%), Positives = 62/86 (72%), Gaps = 7/86 (8%)
Query: 1010 QVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMG 1069
Q+ A VGQQ+V G RI G+R RTLPHF K D G ++RGFV +S+ GL P+E+FFHA G
Sbjct: 737 QMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAG 796
Query: 1070 GREGLIDTAVKTAET-------VNVL 1088
GREGL+DTAV+T+++ +N L
Sbjct: 797 GREGLVDTAVRTSQSGYMQRRLINAL 822
Score = 62.8 bits (153), Expect = 1e-09
Identities = 22/46 (47%), Positives = 38/46 (82%)
Query: 28 PYEESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQE 73
P E++ +LG++PK ARP+WM++TVLPVPP++VRP++ + R+++
Sbjct: 186 PDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSED 231
Score = 61.7 bits (150), Expect = 3e-09
Identities = 26/55 (47%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 576 DVLMDAAAHAEADPMRGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGL 630
+ L+D A GY+QRRLI A++ + V YD TVR++ G LIQ +YGEDG+
Sbjct: 799 EGLVDTAVRT---SQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGV 850
>gnl|CDD|218366 pfam04990, RNA_pol_Rpb1_7, RNA polymerase Rpb1, domain 7. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase compared
to three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). This domain, domain 7,
represents a mobile module of the RNA polymerase. Domain
7 forms a substantial interaction with the lobe domain of
Rpb2 (pfam04561).
Length = 135
Score = 222 bits (568), Expect = 3e-67
Identities = 80/136 (58%), Positives = 109/136 (80%), Gaps = 5/136 (3%)
Query: 1091 LFQVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD--FDPTRISPWLLRIELDRKRMTD 1148
L VTA+T IYYDPDP+NTVI ED+E+V Y+E+PD DP+R+SPWLLR+ELDR++MTD
Sbjct: 3 LRSVTASTEIYYDPDPRNTVIEEDREWVESYFEIPDEDDDPSRLSPWLLRLELDREKMTD 62
Query: 1149 KKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDM 1208
KKLTM+ I++KI FGDDL+ I++DDNAEKLV+RIR+ + + K E+ D+ EDD+
Sbjct: 63 KKLTMKDIAQKIKQEFGDDLHVIYSDDNAEKLVIRIRVKDDEGEK---EDSVGDEDEDDV 119
Query: 1209 FLRCIEANMLSDMTLQ 1224
FL+ +E+NMLS +TL+
Sbjct: 120 FLKRLESNMLSSLTLR 135
Score = 193 bits (493), Expect = 3e-57
Identities = 74/154 (48%), Positives = 100/154 (64%), Gaps = 33/154 (21%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPD--FDPTRISPWLLRIELDRKRMTD 1586
L VTA+T IYYDPDP+NTVI ED+E+V Y+E+PD DP+R+SPWLLR+ELDR++M
Sbjct: 3 LRSVTASTEIYYDPDPRNTVIEEDREWVESYFEIPDEDDDPSRLSPWLLRLELDREKM-- 60
Query: 1587 KKLTMEAISEKINAGFGDDLNTPLSPTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKL 1646
TDKKLTM+ I++KI FGDDL+ I++DDNAEKL
Sbjct: 61 --------------------------TDKKLTMKDIAQKIKQEFGDDLHVIYSDDNAEKL 94
Query: 1647 VLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIE 1680
V+RIR+ + + K E+ D+ EDD+FL+ +E
Sbjct: 95 VIRIRVKDDEGEK---EDSVGDEDEDDVFLKRLE 125
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 236 bits (605), Expect = 1e-64
Identities = 95/398 (23%), Positives = 154/398 (38%), Gaps = 67/398 (16%)
Query: 73 EQMMNILMFLPIWDGKMPQPCILKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDEDSGP 132
+ I + D + I K L TGK + S I P ++ +T D
Sbjct: 467 TPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTT---DGRRIF 523
Query: 133 YQWIS-PGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVC-GRFYGNIQTV 190
+ + D V + +G L+ G++ KK + + E G EV + +
Sbjct: 524 NRGLPEDKDVLVKIVNGKLIKGVIDKKIVT---------IYREYGPEVASKALVKLLDKL 574
Query: 191 VNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGHSIGI 250
N + G G IGI
Sbjct: 575 KNLGIK---GIGGFG------------------------------------------IGI 589
Query: 251 GDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILNDAR 310
G D + E + +A+ V+++I + DL T N + + E L +A
Sbjct: 590 GR--KDIEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAI 647
Query: 311 DKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPH 370
+ + + G G+ +NISQ++ +GQQ V G++I
Sbjct: 648 IEEIKITLEEQGLDFV--DIRHMGLSGARMNISQIVQLIGQQGVMGEKISVL----ARAA 701
Query: 371 FIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAME 430
F E+ G E+S+L GLT +E+F H +GGR GL+DTA+KTA++GY+ RRL+ +
Sbjct: 702 FEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQ 761
Query: 431 SVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRID 468
++V D V + +G +IQ YGEDG R+
Sbjct: 762 DLIVQEDDCVTDGIGVVIQFEYGEDGEDLTERILGRVL 799
Score = 110 bits (277), Expect = 4e-24
Identities = 33/87 (37%), Positives = 49/87 (56%), Gaps = 7/87 (8%)
Query: 998 LVGEIENRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAG 1057
L G N +Q++ +GQQ V G++I F E+ G E+S+L G
Sbjct: 670 LSGARMNI---SQIVQLIGQQGVMGEKISVL----ARAAFEVTVKHLEAEGPGESSFLEG 722
Query: 1058 LTPSEFFFHAMGGREGLIDTAVKTAET 1084
LT +E+F H +GGR GL+DTA+KTA++
Sbjct: 723 LTENEYFGHPIGGRTGLVDTALKTADS 749
Score = 78.0 bits (193), Expect = 3e-14
Identities = 49/205 (23%), Positives = 88/205 (42%), Gaps = 4/205 (1%)
Query: 1198 EDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIA 1257
+ +DK ++ + S ++ ++ + + + I +
Sbjct: 544 KGVIDKKIVTIYREY-GPEVASKALVKLLDKLKNLGIKG-IGGFGIGIGRKDIEAEDEKD 601
Query: 1258 DWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLY 1317
+ ++E +G+ L +L + D RT N+I EI +VLGIEA+R ++ +E+ L+ GL
Sbjct: 602 EIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLD 661
Query: 1318 VN-YRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 1376
RH+ L M + I + G+ + L R +FE TV L +A E+ +
Sbjct: 662 FVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEVTVKHL-EAEGPGESSFL 720
Query: 1377 RGVSENIIMGQLPRMGTGCFDLLLD 1401
G++EN G TG D L
Sbjct: 721 EGLTENEYFGHPIGGRTGLVDTALK 745
Score = 58.8 bits (143), Expect = 2e-08
Identities = 36/154 (23%), Positives = 58/154 (37%), Gaps = 30/154 (19%)
Query: 517 VEKEMNTVLQFYGLYVN-YRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETV 575
+ +E+ L+ GL RH+ L M + I + G+ + L R +FE TV
Sbjct: 647 IIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAFEVTV 706
Query: 576 DVLMDAAAHAEADPMRG----------------------------YIQRRLIKAMESVMV 607
L +A E+ + G Y+ RRL+ + ++V
Sbjct: 707 KHL-EAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIV 765
Query: 608 HYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRID 641
D V + +G +IQ YGEDG R+
Sbjct: 766 QEDDCVTDGIGVVIQFEYGEDGEDLTERILGRVL 799
Score = 48.8 bits (117), Expect = 3e-05
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 30 EESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARN 71
++ +L RP+WM++TVLPVPP +RP++ + G
Sbjct: 171 VDAFLLS----GNRPEWMILTVLPVPPPDLRPSIQLDGGRFA 208
Score = 41.5 bits (98), Expect = 0.004
Identities = 28/104 (26%), Positives = 45/104 (43%), Gaps = 2/104 (1%)
Query: 782 VRKSVEKEMNTVLQFYGLYVN-YRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSF 840
+R ++ +E+ L+ GL RH+ L M + I + G+ + L R +F
Sbjct: 643 LRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKISVLARAAF 702
Query: 841 EETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 884
E TV L +A E+ + G++EN G TG D L
Sbjct: 703 EVTVKHL-EAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTALK 745
Score = 38.4 bits (90), Expect = 0.044
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 1495 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 1531
T I+TP P++ +QDT+ +T D L
Sbjct: 430 TQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPS 466
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 217 bits (554), Expect = 6e-57
Identities = 129/415 (31%), Positives = 198/415 (47%), Gaps = 58/415 (13%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCI-LKPKPLWTGKQVFSLIIPGNVNMTRTHSTHPDDED 129
++ + NI M I D +P+P I K P WTGKQ+FSL +P + N + +
Sbjct: 534 DKNEASNIAMLAGITD-PLPEPAIKTKDGPAWTGKQLFSLFLPKDFNFEGI-AKWSAGKA 591
Query: 130 SGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSG---SLLHICFLELGHEVCGRFYGN 186
GD V+++ G L+ G++ +G SL+ + G V F
Sbjct: 592 GEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGEAVAIEFLNK 651
Query: 187 IQTVVNNWLLLEGHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGH 246
I + +L G S G GD I + EI+ I+ K++V ++I
Sbjct: 652 ILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLID------------- 698
Query: 247 SIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRIL 306
Q + ++ I K KE+++ +++ + E + L
Sbjct: 699 -----------QRKITRKITIYKGKEELLRGMKE--------------EEALEADIVNEL 733
Query: 307 NDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVE--------GKR 358
+ ARDK G SA + N K M G++GS N++Q+ +GQQ + G R
Sbjct: 734 DKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGR 793
Query: 359 IPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 418
+ G++ R L HF + D P++ GFV+N+Y GL +EFFFHAMGGREGLID A +T ++
Sbjct: 794 LHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDS 853
Query: 419 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGL------CGEAVEHQRI 467
GY QRRL A+E + + YD TVR+ G +IQ ++GEDG+ GEA +RI
Sbjct: 854 GYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHGEAFNLERI 908
Score = 121 bits (304), Expect = 3e-27
Identities = 62/216 (28%), Positives = 110/216 (50%), Gaps = 22/216 (10%)
Query: 1199 DAVDKMEDDMFLRCIEA--NMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1256
D V+ + D L + A N + D ++G+ I + ++ L + D +
Sbjct: 1120 DLVEAADRDKPLATLIAIRNKILDKPVKGVPDIERAWVELVEKDGRD------------- 1166
Query: 1257 ADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGL 1316
+W+++T G++L VL + +D T +ND EI LGIEA R ++ E+ ++L+ GL
Sbjct: 1167 -EWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGL 1225
Query: 1317 YVNYRHLALLCDVMTAKGHLMAI------TRHGINRQDTGALMRCSFEETVDVLMDAAAH 1370
V+ R++ L+ D+M ++G + AI RHG + L + +FE T + AA
Sbjct: 1226 EVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALG 1285
Query: 1371 AEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 1406
E + ++G+ + +IMGQ +G+G DLL+D
Sbjct: 1286 GEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
Score = 91.6 bits (227), Expect = 3e-18
Identities = 54/181 (29%), Positives = 83/181 (45%), Gaps = 18/181 (9%)
Query: 1009 AQVIACVGQQNVE--------GKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTP 1060
AQ+ +GQQ + G R+ G++ R L HF + D P++ GFV+N+Y GL
Sbjct: 770 AQIAGALGQQKRKTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNA 829
Query: 1061 SEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYDP---DPQNTVIP----E 1113
+EFFFHAMGGREGLID A +T ++ L + + YD DP +I E
Sbjct: 830 AEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGE 889
Query: 1114 DQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFN 1173
D F+ RI + + D+ +E ++++ F +L +
Sbjct: 890 DGIDPQKLDHGEAFNLERIIEKQKIEDRGKGASKDE---IEELAKEYTKTFNANLPKLLA 946
Query: 1174 D 1174
D
Sbjct: 947 D 947
Score = 75.4 bits (185), Expect = 2e-13
Identities = 34/115 (29%), Positives = 62/115 (53%), Gaps = 6/115 (5%)
Query: 781 SVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAI------TRHGINRQDTGA 834
+ R ++ E+ ++L+ GL V+ R++ L+ D+M ++G + AI RHG +
Sbjct: 1207 AARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSP 1266
Query: 835 LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEKCK 889
L + +FE T + AA E + ++G+ + +IMGQ +G+G DLL+D
Sbjct: 1267 LAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
Score = 58.9 bits (142), Expect = 3e-08
Identities = 17/51 (33%), Positives = 35/51 (68%)
Query: 30 EESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILM 80
++ ++G DPK ARP+W ++ VPPL+ RP++++ R+++ + +IL+
Sbjct: 201 DDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILV 251
Score = 55.4 bits (133), Expect = 3e-07
Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 9/69 (13%)
Query: 578 LMDAAAHAEADPMRGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGL------C 631
L+D A E GY QRRL A+E + + YD TVR+ G +IQ ++GEDG+
Sbjct: 843 LIDKARRTEDS---GYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDH 899
Query: 632 GEAVEHQRI 640
GEA +RI
Sbjct: 900 GEAFNLERI 908
Score = 48.9 bits (116), Expect = 3e-05
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 6/79 (7%)
Query: 520 EMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAI------TRHGINRQDTGALMRCSFEE 573
E+ ++L+ GL V+ R++ L+ D+M ++G + AI RHG + L + +FE
Sbjct: 1215 ELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEI 1274
Query: 574 TVDVLMDAAAHAEADPMRG 592
T + AA E + ++G
Sbjct: 1275 TTHTIAHAALGGEIEKIKG 1293
Score = 32.3 bits (73), Expect = 2.8
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 1498 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANT----AIYYDPDPQ 1545
+I+P+ P++G +QD +TA +TK D DK A+ A DP P+
Sbjct: 502 NLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPE 553
>gnl|CDD|132725 cd06528, RNAP_A'', 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.
Length = 363
Score = 173 bits (442), Expect = 2e-47
Identities = 84/266 (31%), Positives = 134/266 (50%), Gaps = 40/266 (15%)
Query: 1137 LRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQD 1196
+ IELD + + D+ +T++ + + I + + + +VL+ +
Sbjct: 138 ITIELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----------E 183
Query: 1197 EEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1256
E + LR + A + + ++GI+ I +V I+ E E
Sbjct: 184 EPSIKE-------LRKL-AEKILNTKIKGIKGIKRV------------IVRKEEDE---- 219
Query: 1257 ADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGL 1316
+++ T+G++L VL VDP RT +N+I EI +VLGIEA R ++ E+ L+ GL
Sbjct: 220 --YVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGL 277
Query: 1317 YVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 1376
V+ RH+ L+ D+MT G + I RHGI + L R +FE TV L+DAA E D +
Sbjct: 278 DVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDEL 337
Query: 1377 RGVSENIIMGQLPRMGTGCFDLLLDA 1402
RGV ENII+GQ +GTG +L +D
Sbjct: 338 RGVIENIIVGQPIPLGTGDVELTMDP 363
Score = 103 bits (259), Expect = 2e-23
Identities = 44/103 (42%), Positives = 61/103 (59%)
Query: 783 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 842
R ++ E+ L+ GL V+ RH+ L+ D+MT G + I RHGI + L R +FE
Sbjct: 261 RNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEV 320
Query: 843 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDA 885
TV L+DAA E D +RGV ENII+GQ +GTG +L +D
Sbjct: 321 TVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMDP 363
Score = 69.2 bits (170), Expect = 5e-12
Identities = 32/76 (42%), Positives = 43/76 (56%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
E+ L+ GL V+ RH+ L+ D+MT G + I RHGI + L R +FE TV L
Sbjct: 266 NEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHL 325
Query: 579 MDAAAHAEADPMRGYI 594
+DAA E D +RG I
Sbjct: 326 LDAAVRGEVDELRGVI 341
Score = 30.7 bits (70), Expect = 7.3
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 1575 LRIELDRKRMTDKKLTMEAISEKINAGFG--------DDLNTPLSPTDKKLTMEAISEKI 1626
+ IELD + + D+ +T++ + + I L + + ++EKI
Sbjct: 138 ITIELDEEMLEDRGITVDDVLKAIEKLKKGKVGEEGDVTLIVLKAEEPSIKELRKLAEKI 197
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 173 bits (441), Expect = 6e-47
Identities = 86/268 (32%), Positives = 136/268 (50%), Gaps = 42/268 (15%)
Query: 1137 LRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQD 1196
+ IELD + + D+ LT++ + E I G ++ E L I
Sbjct: 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---------K 200
Query: 1197 EEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1256
E + LR + A + ++ ++GI+ I +V II E E
Sbjct: 201 EPSYRE-------LRKL-AEKIRNIKIKGIKGIKRV------------IIRKEGDE---- 236
Query: 1257 ADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGL 1316
+++ T+G++L +VL VD RT +N+I EI +VLGIEA R ++ +E+ L+ GL
Sbjct: 237 --YVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGL 294
Query: 1317 YVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 1376
V+ RH+ L+ D+MT G + I RHG++ + L R +FE TV L+DAA E D +
Sbjct: 295 DVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354
Query: 1377 RGVSENIIMGQLPRMGTGCFDLLLDAEK 1404
+GV+ENII+GQ +GTG +L +D
Sbjct: 355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
Score = 106 bits (267), Expect = 4e-24
Identities = 42/105 (40%), Positives = 64/105 (60%)
Query: 783 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 842
R ++ +E+ L+ GL V+ RH+ L+ D+MT G + I RHG++ + L R +FE
Sbjct: 278 RNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEV 337
Query: 843 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLDAEK 887
TV L+DAA E D ++GV+ENII+GQ +GTG +L +D
Sbjct: 338 TVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382
Score = 72.6 bits (179), Expect = 5e-13
Identities = 29/76 (38%), Positives = 44/76 (57%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E+ L+ GL V+ RH+ L+ D+MT G + I RHG++ + L R +FE TV L
Sbjct: 283 EEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHL 342
Query: 579 MDAAAHAEADPMRGYI 594
+DAA E D ++G
Sbjct: 343 LDAAVRGEVDELKGVT 358
Score = 31.4 bits (72), Expect = 5.4
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 1575 LRIELDRKRMTDKKLTMEAISEKINAGFGDD 1605
+ IELD + + D+ LT++ + E I G +
Sbjct: 157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGE 187
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, 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].
Length = 367
Score = 171 bits (436), Expect = 2e-46
Identities = 86/265 (32%), Positives = 138/265 (52%), Gaps = 39/265 (14%)
Query: 1137 LRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQD 1196
+ IELD +++ ++ +T++ + + I + I D N I I S +
Sbjct: 142 VIIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDGNT------ITIKPPKPSLKE- 194
Query: 1197 EEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1256
LR + + ++ ++GI+ I KR++I + G+
Sbjct: 195 -------------LRKL-KEKIKNLHIKGIKGI-------------KRVVIRKEGD---- 223
Query: 1257 ADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGL 1316
++++ T+G++L +VL VD RT +NDI EI +VLGIEA R ++ +E+ L+ GL
Sbjct: 224 -EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGL 282
Query: 1317 YVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 1376
V+ RHL L+ D+MT G + I RHGI+ + L R +FE TV L+DAA E D +
Sbjct: 283 DVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342
Query: 1377 RGVSENIIMGQLPRMGTGCFDLLLD 1401
GV ENII+GQ +GTG DL++D
Sbjct: 343 AGVIENIIVGQPIPLGTGDVDLVMD 367
Score = 106 bits (267), Expect = 3e-24
Identities = 45/102 (44%), Positives = 63/102 (61%)
Query: 783 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 842
R ++ +E+ L+ GL V+ RHL L+ D+MT G + I RHGI+ + L R +FE
Sbjct: 266 RNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEV 325
Query: 843 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLLD 884
TV L+DAA E D + GV ENII+GQ +GTG DL++D
Sbjct: 326 TVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLVMD 367
Score = 73.2 bits (180), Expect = 3e-13
Identities = 32/77 (41%), Positives = 45/77 (58%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E+ L+ GL V+ RHL L+ D+MT G + I RHGI+ + L R +FE TV L
Sbjct: 271 EEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHL 330
Query: 579 MDAAAHAEADPMRGYIQ 595
+DAA E D + G I+
Sbjct: 331 LDAAIRGEVDELAGVIE 347
>gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4. RNA
polymerases catalyze the DNA dependent polymerisation 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.
Length = 108
Score = 154 bits (392), Expect = 5e-44
Identities = 63/99 (63%), Positives = 70/99 (70%)
Query: 286 LEPTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQV 345
LE G TL +TFE +N ILN ARD G A KSL N++ M +G+KGS INISQ+
Sbjct: 10 LEDIWGMTLEETFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQI 69
Query: 346 IACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFV 384
C GQQNVEGKRIPFGF RTLPHF KDD GPESRGFV
Sbjct: 70 AGCRGQQNVEGKRIPFGFSGRTLPHFKKDDEGPESRGFV 108
Score = 82.4 bits (204), Expect = 2e-18
Identities = 33/47 (70%), Positives = 36/47 (76%)
Query: 1004 NRFQQAQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFV 1050
+ +Q+ C GQQNVEGKRIPFGF RTLPHF KDD GPESRGFV
Sbjct: 62 SIINISQIAGCRGQQNVEGKRIPFGFSGRTLPHFKKDDEGPESRGFV 108
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation 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.
Length = 447
Score = 162 bits (413), Expect = 1e-42
Identities = 93/430 (21%), Positives = 149/430 (34%), Gaps = 111/430 (25%)
Query: 956 EDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQV---- 1011
+ L +TLLF+ L+RS + +K V +S+A + ++++++ V
Sbjct: 97 DVLLLLSEFSLSTLLFEILLRSGIESKRVRSELTCNSKAGVCFLCYGRDKYRRSLVEPGE 156
Query: 1012 -----------------------IACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRG 1048
A V +NV +K+
Sbjct: 157 AVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPR-----------LKEI------I 199
Query: 1049 FVENSYLAGLTPSEFFFHAMGGREGLID---TAVKTAETVNVLVFLFQVTANTAIYYDPD 1105
V P I VK L+ L +VT IYYD D
Sbjct: 200 NV-AKNNK--KPVI-----TVLLIKNIVSDKARVKKQREEKTLLLLKKVTIIIVIYYDDD 251
Query: 1106 PQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFG 1165
++TVI +D+ +V Y+ +P+
Sbjct: 252 SESTVIKKDRIWVLAYFVIPEEV------------------------------------- 274
Query: 1166 DDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQG 1225
+ ++ I S K + + L
Sbjct: 275 --------AEEVALAIIIIGKRKSRK---------RKKNNLGVAKDEKGLEEEELLLLNK 317
Query: 1226 IEAIGKVYMHLPQTDSKKRIIITESGEFKAIADWLLETDGTSLMKVLSER-DVDPVRTFS 1284
I + + + K +WLL+T+G +L V+ + +D +T+S
Sbjct: 318 ILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYS 377
Query: 1285 NDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGI 1344
NDI E+ + LGIEA R S+ E+ V +F G+YVN RHLALL D+MT KG L+ ITR G+
Sbjct: 378 NDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGL 437
Query: 1345 NRQDT-GALM 1353
NR+ + LM
Sbjct: 438 NREKSSFILM 447
Score = 158 bits (402), Expect = 3e-41
Identities = 61/110 (55%), Positives = 75/110 (68%)
Query: 391 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVHYDCTVRNSVGQLIQL 450
GLTP EFFFH MGGREGLIDTAVKTAETGY+QRRL+KA+E ++V YD TVRNS G+++Q
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQF 60
Query: 451 RYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLRNVSSLRR 500
YGEDGL +E Q T+ S K E K++ D ++ L S
Sbjct: 61 LYGEDGLDPLKIEGQGRFTIEDSDLKLEKKFKIDLNDVLLLLSEFSLSTL 110
Score = 88.9 bits (221), Expect = 4e-18
Identities = 36/82 (43%), Positives = 51/82 (62%)
Query: 592 GYIQRRLIKAMESVMVHYDCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFE 651
GY+QRRL+KA+E ++V YD TVRNS G+++Q YGEDGL +E Q T+ S K E
Sbjct: 29 GYLQRRLVKALEDLVVQYDDTVRNSGGEIVQFLYGEDGLDPLKIEGQGRFTIEDSDLKLE 88
Query: 652 DKYRFDPSNERQLRRIFNEDVL 673
K++ D ++ L F+ L
Sbjct: 89 KKFKIDLNDVLLLLSEFSLSTL 110
Score = 87.3 bits (217), Expect = 2e-17
Identities = 53/233 (22%), Positives = 85/233 (36%), Gaps = 26/233 (11%)
Query: 611 CTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNE 670
+ V +I + Y +D V + V E+ + + +
Sbjct: 234 LLLLKKVTIIIVIYYDDDS--ESTVIKKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSR 291
Query: 671 DVLRELMGSGDVISELEKEMVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCE 730
+ +G LE+E K L I V ++ + + EKL +
Sbjct: 292 KRKKNNLGVAKDEKGLEEE-ELLLLNKILLVIPGIKVKYGVILTDGRVDPHTIL-EKLGK 349
Query: 731 DRE------ALREIFSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFLCKIIFVLSVRK 784
+ L+ + V+ E L+ L I + R
Sbjct: 350 EWLLKTEGNNLQAVMR--LQGVIDNDKTYSNDIR---------EMLKKL-GIE---AARD 394
Query: 785 SVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT-GALM 836
S+ E+ V +F G+YVN RHLALL D+MT KG L+ ITR G+NR+ + LM
Sbjct: 395 SILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGLNREKSSFILM 447
Score = 79.6 bits (197), Expect = 4e-15
Identities = 28/54 (51%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 515 TSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDT-GALM 567
S+ E+ V +F G+YVN RHLALL D+MT KG L+ ITR G+NR+ + LM
Sbjct: 394 DSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGLNREKSSFILM 447
Score = 74.6 bits (184), Expect = 2e-13
Identities = 45/137 (32%), Positives = 51/137 (37%), Gaps = 21/137 (15%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAET-------VNVLVFLFQVTANTAIYYDPDPQNT 1109
GLTP EFFFH MGGREGLIDTAVKTAET V L L + YD +T
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLV-------VQYD----DT 49
Query: 1110 VIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRK---RMTDKKLTMEAISEKINAGFGD 1166
V E V Y DP +I D K + +
Sbjct: 50 VRNSGGEIVQFLYGEDGLDPLKIEGQGRFTIEDSDLKLEKKFKIDLNDVLLLLSEFSLST 109
Query: 1167 DLNCIFNDDNAEKLVLR 1183
L I E +R
Sbjct: 110 LLFEILLRSGIESKRVR 126
Score = 38.4 bits (90), Expect = 0.032
Identities = 22/70 (31%), Positives = 35/70 (50%)
Query: 1529 LDKVTANTAIYYDPDPQNTVIPEDQEFVNVYYEMPDFDPTRISPWLLRIELDRKRMTDKK 1588
L KVT IYYD D ++TVI +D+ +V Y+ +P+ ++ ++ I + R K
Sbjct: 237 LKKVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRKRKKN 296
Query: 1589 LTMEAISEKI 1598
A EK
Sbjct: 297 NLGVAKDEKG 306
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, 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.
Length = 300
Score = 151 bits (385), Expect = 2e-40
Identities = 67/184 (36%), Positives = 98/184 (53%), Gaps = 22/184 (11%)
Query: 1216 NMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITES---GEFKAIADWLLETDGTSLMKVL 1272
L D+ + GI + KR +I + G++K L +G L V+
Sbjct: 136 RKLPDVVVSGIPEV-------------KRAVINKDKKKGKYK------LLVEGYGLRAVM 176
Query: 1273 SERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTA 1332
+ V RT SN I E+ +VLGIEA R ++ E+ ++ +G+ ++ RH+ LL D+MT
Sbjct: 177 NTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTF 236
Query: 1333 KGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMG 1392
KG ++ ITR GI + LM SFE+T D L +AA H D + GVSE IIMG+ +G
Sbjct: 237 KGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIG 296
Query: 1393 TGCF 1396
TG F
Sbjct: 297 TGLF 300
Score = 111 bits (280), Expect = 2e-26
Identities = 41/97 (42%), Positives = 60/97 (61%)
Query: 783 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 842
R ++ E+ ++ +G+ ++ RH+ LL D+MT KG ++ ITR GI + LM SFE+
Sbjct: 204 RSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEK 263
Query: 843 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCF 879
T D L +AA H D + GVSE IIMG+ +GTG F
Sbjct: 264 TTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
Score = 79.2 bits (196), Expect = 1e-15
Identities = 29/73 (39%), Positives = 44/73 (60%)
Query: 520 EMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 579
E+ ++ +G+ ++ RH+ LL D+MT KG ++ ITR GI + LM SFE+T D L
Sbjct: 210 EIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLF 269
Query: 580 DAAAHAEADPMRG 592
+AA H D + G
Sbjct: 270 NAALHGRKDSIEG 282
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation 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.
Length = 158
Score = 139 bits (352), Expect = 8e-38
Identities = 49/138 (35%), Positives = 75/138 (54%), Gaps = 13/138 (9%)
Query: 71 NQEQMMNILMFLPIWDGKMPQPCILKP-KPLWTGKQVFSLIIPGNVNMTRTHSTHPDDED 129
++E++M +LM+ + +P P ILKP KPLWTGKQ FS ++P +N T+ +
Sbjct: 33 DREEVMQLLMYGIV----LPHPAILKPIKPLWTGKQTFSRLLPNEINPKGKPKTNEETL- 87
Query: 130 SGPYQWISPGDTKVVVEHGSLLMGILCKKSLGTSSGSLLHICFLELGHEVCGRFYGNIQT 189
D+ V++ +G L+ G++ KK G S GSL+HI + E G E +F +Q
Sbjct: 88 -------CENDSYVLINNGELISGVIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQK 140
Query: 190 VVNNWLLLEGHSIGIGDT 207
+ +L G SIGI D
Sbjct: 141 LGFRYLTKSGFSIGIDDI 158
Score = 67.3 bits (165), Expect = 1e-12
Identities = 14/43 (32%), Positives = 25/43 (58%)
Query: 1498 QIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDKVTANTAIYY 1540
I++PQN +P++G QD + + +T+RD F D+ + Y
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMY 43
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 148 bits (375), Expect = 6e-36
Identities = 86/267 (32%), Positives = 139/267 (52%), Gaps = 38/267 (14%)
Query: 1137 LRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQD 1196
+++ELD + + D+ LT+E++ E I G ++ + VL ++
Sbjct: 623 IKVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYLKP---------- 665
Query: 1197 EEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAI 1256
+ + + + I + ++ L+GI I +V + + ++ E+
Sbjct: 666 KTPSYKAL-----RKRIPK--IKNIVLKGIPGIERVLVKKEEHEND--------EEY--- 707
Query: 1257 ADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGL 1316
+L T G++L +V VD RT +N+I EI +VLGIEA R ++ EM L+ GL
Sbjct: 708 ---VLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGL 764
Query: 1317 YVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPM 1376
V+ RHL L+ D+MTA G + I RHG+ + L R +FEETV L DAA H E D +
Sbjct: 765 EVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKL 824
Query: 1377 RGVSENIIMGQLPRMGTGCFDLLLDAE 1403
+GV EN+I+G+ ++GTGC DL +D E
Sbjct: 825 KGVIENVIVGKPIKLGTGCVDLRIDRE 851
Score = 102 bits (255), Expect = 1e-21
Identities = 70/201 (34%), Positives = 104/201 (51%), Gaps = 27/201 (13%)
Query: 695 SWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALRE--IFSSGESNVVLPCNL 752
S+K LR+ + ++ ++ G I +E+ K E+ E E +++ G NL
Sbjct: 669 SYKALRKRIPK--IKNIVLKG--IPGIERVLVKK-EEHENDEEYVLYTQGS-------NL 716
Query: 753 MEVIFILQRWKLWGNENLRFLCKIIF----VLSV---RKSVEKEMNTVLQFYGLYVNYRH 805
EV K+ G + R I VL + R ++ EM L+ GL V+ RH
Sbjct: 717 REVF------KIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRH 770
Query: 806 LALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSEN 865
L L+ D+MTA G + I RHG+ + L R +FEETV L DAA H E D ++GV EN
Sbjct: 771 LMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIEN 830
Query: 866 IIMGQLPRMGTGCFDLLLDAE 886
+I+G+ ++GTGC DL +D E
Sbjct: 831 VIVGKPIKLGTGCVDLRIDRE 851
Score = 73.4 bits (180), Expect = 9e-13
Identities = 36/79 (45%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 517 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 576
+ + MNT L+ GL V+ RHL L+ D+MTA G + I RHG+ + L R +FEETV
Sbjct: 752 INEMMNT-LEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEKGSVLARAAFEETVK 810
Query: 577 VLMDAAAHAEADPMRGYIQ 595
L DAA H E D ++G I+
Sbjct: 811 HLYDAAEHGEVDKLKGVIE 829
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 143 bits (362), Expect = 1e-35
Identities = 83/270 (30%), Positives = 135/270 (50%), Gaps = 40/270 (14%)
Query: 1130 TRISPWLLRIELDRKRMTDKKLTMEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNS 1189
T I+ + +ELD ++M ++ + + I I KL + ++
Sbjct: 272 TDIAEMSVVVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDD 314
Query: 1190 DDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITE 1249
+++ ++ + K+ +L A + +T++GI+ I + I E
Sbjct: 315 GIIRLKPQQPSFKKL----YLL---AEKVKSLTIKGIKGIKRA------------IARKE 355
Query: 1250 SGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNT 1309
+ E + W++ T G++L VL +VDP RT++NDI EI VLGIEA R ++ E
Sbjct: 356 NDERR----WVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKR 411
Query: 1310 VLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAA 1369
LQ GL V+ RH+ L+ D+MT G + AI RHGI+ + + L R +FE T L+ A
Sbjct: 412 TLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGI 471
Query: 1370 HAEADPMRGVSENIIMGQLPRMGTGCFDLL 1399
E D + GV+ENII+GQ +GTG L+
Sbjct: 472 LGEVDKLAGVAENIIVGQPITLGTGAVSLV 501
Score = 87.6 bits (217), Expect = 2e-17
Identities = 41/100 (41%), Positives = 58/100 (58%)
Query: 783 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 842
R ++ E LQ GL V+ RH+ L+ D+MT G + AI RHGI+ + + L R +FE
Sbjct: 402 RNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEI 461
Query: 843 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLL 882
T L+ A E D + GV+ENII+GQ +GTG L+
Sbjct: 462 TGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLV 501
Score = 64.1 bits (156), Expect = 4e-10
Identities = 29/76 (38%), Positives = 41/76 (53%)
Query: 520 EMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLM 579
E LQ GL V+ RH+ L+ D+MT G + AI RHGI+ + + L R +FE T L+
Sbjct: 408 EAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLL 467
Query: 580 DAAAHAEADPMRGYIQ 595
A E D + G +
Sbjct: 468 RAGILGEVDKLAGVAE 483
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, 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.
Length = 158
Score = 131 bits (332), Expect = 3e-35
Identities = 51/110 (46%), Positives = 69/110 (62%)
Query: 1286 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGIN 1345
I E+ + LGIEA R+++ +E+ VL G+ V+ RH+ L+ DVMT G L +TR G
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFR 108
Query: 1346 RQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
T LMR SFE+T L+DAAA E D + GVSENII+G+ +GTG
Sbjct: 109 ASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
Score = 115 bits (291), Expect = 1e-29
Identities = 44/97 (45%), Positives = 60/97 (61%)
Query: 782 VRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFE 841
R+++ +E+ VL G+ V+ RH+ L+ DVMT G L +TR G T LMR SFE
Sbjct: 62 ARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFE 121
Query: 842 ETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
+T L+DAAA E D + GVSENII+G+ +GTG
Sbjct: 122 KTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
Score = 89.0 bits (221), Expect = 3e-20
Identities = 33/74 (44%), Positives = 43/74 (58%)
Query: 519 KEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVL 578
+E+ VL G+ V+ RH+ L+ DVMT G L +TR G T LMR SFE+T L
Sbjct: 68 REIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHL 127
Query: 579 MDAAAHAEADPMRG 592
+DAAA E D + G
Sbjct: 128 LDAAAAGEKDELEG 141
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, 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.
Length = 309
Score = 116 bits (294), Expect = 2e-28
Identities = 43/123 (34%), Positives = 69/123 (56%), Gaps = 1/123 (0%)
Query: 1277 VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL 1336
+D R ++NDI + GIEA R+++ KE++ V + YG+ V+ RHL+L+ D MT +G
Sbjct: 188 LDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGY 247
Query: 1337 MAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCF 1396
R G+ + L + SFE T+ L A + + D + S +++G+ GTG F
Sbjct: 248 RPFNRIGMESSTSP-LQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLF 306
Query: 1397 DLL 1399
DLL
Sbjct: 307 DLL 309
Score = 94.6 bits (236), Expect = 1e-20
Identities = 34/100 (34%), Positives = 56/100 (56%), Gaps = 1/100 (1%)
Query: 783 RKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEE 842
R+++ KE++ V + YG+ V+ RHL+L+ D MT +G R G+ + L + SFE
Sbjct: 211 RRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESSTSP-LQKMSFET 269
Query: 843 TVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLL 882
T+ L A + + D + S +++G+ GTG FDLL
Sbjct: 270 TLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
Score = 64.5 bits (158), Expect = 1e-10
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 516 SVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETV 575
++ KE++ V + YG+ V+ RHL+L+ D MT +G R G+ + L + SFE T+
Sbjct: 213 AIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESSTSP-LQKMSFETTL 271
Query: 576 DVLMDAAAHAEAD 588
L A + + D
Sbjct: 272 AFLKKATLNGDID 284
>gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase compared
to three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). This domain, domain 6,
represents a mobile module of the RNA polymerase. Domain
6 forms part of the shelf module. This family appears to
be specific to the largest subunit of RNA polymerase II.
Length = 187
Score = 112 bits (283), Expect = 4e-28
Identities = 37/57 (64%), Positives = 47/57 (82%)
Query: 953 VAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQA 1009
V G+D LSK+A ENATLLF+ L+RSTL +K V E YRL+ EAF+W++GEIE+RF QA
Sbjct: 131 VRGDDPLSKEAQENATLLFKILLRSTLASKRVLEEYRLNKEAFDWVLGEIESRFNQA 187
Score = 100 bits (252), Expect = 6e-24
Identities = 41/128 (32%), Positives = 59/128 (46%), Gaps = 34/128 (26%)
Query: 630 LCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNEDVLRELMGSGDVISELEKE 689
+ G VE Q++DT+ LS FE KYR D + +
Sbjct: 1 MDGAFVEKQKLDTLKLSDAAFEKKYRVDLMDPDE-------------------------- 34
Query: 690 MVDHFSWKQLRRIFNEDVLRELMGSGDVISELEKEWEKLCEDREALRE-IFSSGESNVVL 748
L + +EDV++EL+G +V L++E+E+L EDR LRE IF G+S L
Sbjct: 35 -------GFLPGVLDEDVVKELLGDAEVQKLLDEEYEQLLEDRRLLREEIFPDGDSKWPL 87
Query: 749 PCNLMEVI 756
P NL +I
Sbjct: 88 PVNLQRII 95
Score = 49.0 bits (118), Expect = 3e-06
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 457 LCGEAVEHQRIDTVALSHKKFEDKYRFDPSNERPTLR 493
+ G VE Q++DT+ LS FE KYR D +
Sbjct: 1 MDGAFVEKQKLDTLKLSDAAFEKKYRVDLMDPDEGFL 37
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, 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].
Length = 1140
Score = 68.9 bits (169), Expect = 2e-11
Identities = 57/203 (28%), Positives = 90/203 (44%), Gaps = 32/203 (15%)
Query: 245 GHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFE--NQV 302
G +I D + + Y ++ A K+ + IQK +N L T R+ ++
Sbjct: 605 GTTISASDIVVPDEKYEILKEADKE-----VAKIQKFYNKGL-ITDEERYRKVVSIWSET 658
Query: 303 NRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFG 362
+ DA K KK ++N + M +G++G NISQ G + + K P G
Sbjct: 659 KDKVTDAMMK---LLKKDTYKFNPIFMMADSGARG---NISQFRQLAGMRGLMAK--PSG 710
Query: 363 FRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQ 422
+ IK +S+ GLT E+F G R+GL DTA+KTA++GY+
Sbjct: 711 ---DIIELPIK------------SSFREGLTVLEYFISTHGARKGLADTALKTADSGYLT 755
Query: 423 RRLIK-AMESVMVHYDCTVRNSV 444
RRL+ A + V+ DC +
Sbjct: 756 RRLVDVAQDVVVREEDCGTEEGI 778
Score = 48.5 bits (116), Expect = 4e-05
Identities = 38/150 (25%), Positives = 64/150 (42%), Gaps = 44/150 (29%)
Query: 1286 DICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHG-- 1343
D ++ ++ GI+AV++ + KE+ V + G+ +N +H+ ++ M K + IT G
Sbjct: 988 DPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRK---VRITDSGDS 1044
Query: 1344 -------INRQ-------------------------------DTGA-LMRCSFEETVDVL 1364
I+ +T + L SF+ET VL
Sbjct: 1045 NLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVL 1104
Query: 1365 MDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
DAA + D + G+ EN+I+G L GTG
Sbjct: 1105 TDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
Score = 46.2 bits (110), Expect = 2e-04
Identities = 19/39 (48%), Positives = 25/39 (64%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL DAA + D + G+ EN+I+G L GTG
Sbjct: 1096 SFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
Score = 39.6 bits (93), Expect = 0.020
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 1053 SYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 1084
S+ GLT E+F G R+GL DTA+KTA++
Sbjct: 720 SFREGLTVLEYFISTHGARKGLADTALKTADS 751
Score = 33.5 bits (77), Expect = 1.3
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 42 ARPDWMLVTVLPVPPLSVRPAVVMHG 67
RP+WM++ V+PV P +RP V + G
Sbjct: 214 NRPEWMVLDVIPVIPPELRPMVQLDG 239
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. RNA
polymerases catalyze the DNA dependent polymerisation 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.
Length = 330
Score = 65.8 bits (161), Expect = 5e-11
Identities = 21/51 (41%), Positives = 33/51 (64%)
Query: 30 EESIILGMDPKFARPDWMLVTVLPVPPLSVRPAVVMHGSARNQEQMMNILM 80
E+ ILG +P RP+WM++TVLPVPP +RP+V + G ++ + + L
Sbjct: 207 EDEEILGFNPSGNRPEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLR 257
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 58.7 bits (142), Expect = 3e-08
Identities = 39/140 (27%), Positives = 69/140 (49%), Gaps = 23/140 (16%)
Query: 301 QVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVG-QQNVEGKRI 359
QV I +A ++ G + E N + M +G++G+ I Q+ G +++G+ I
Sbjct: 762 QVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEII 821
Query: 360 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETG 419
LP ++ ++ GL+ E+F G R+GL+DTA++TA++G
Sbjct: 822 -------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRTADSG 860
Query: 420 YIQRRLIKAMESVMV-HYDC 438
Y+ RRL+ + V+V DC
Sbjct: 861 YLTRRLVDVAQDVIVREEDC 880
Score = 37.5 bits (87), Expect = 0.088
Identities = 18/39 (46%), Positives = 25/39 (64%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL DAA + D + G+ EN+I+G+ GTG
Sbjct: 1197 SFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
Score = 37.5 bits (87), Expect = 0.088
Identities = 18/39 (46%), Positives = 25/39 (64%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
SF+ET VL DAA + D + G+ EN+I+G+ GTG
Sbjct: 1197 SFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
Score = 34.8 bits (80), Expect = 0.53
Identities = 13/28 (46%), Positives = 21/28 (75%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAET 1084
GL+ E+F G R+GL+DTA++TA++
Sbjct: 832 GLSVLEYFISTHGARKGLVDTALRTADS 859
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, 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].
Length = 1227
Score = 54.9 bits (132), Expect = 4e-07
Identities = 38/125 (30%), Positives = 65/125 (52%), Gaps = 29/125 (23%)
Query: 325 NNLKAMVVAGSKGSNINISQVIACVGQQ----NVEGKRIPFGFRKRTLPHFIKDDYGPES 380
N++ M +G++G N+SQV VG + N +G+ I LP
Sbjct: 119 NSVYMMAFSGARG---NMSQVRQLVGMRGLMANPQGEII-------DLP----------- 157
Query: 381 RGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMV-HYDCT 439
++ ++ GLT +E+ + G R+GL+DTA++TA++GY+ RRL+ + V+V DC
Sbjct: 158 ---IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCG 214
Query: 440 VRNSV 444
S+
Sbjct: 215 TERSI 219
Score = 46.0 bits (109), Expect = 2e-04
Identities = 38/139 (27%), Positives = 62/139 (44%), Gaps = 40/139 (28%)
Query: 1295 GIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAK-------------GHL----- 1336
++ V++ + E+ V Q G+ ++ +H+ ++ MT+K G L
Sbjct: 1084 SLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQ 1143
Query: 1337 -------MAITRHGINRQDTGALM--------------RCSFEETVDVLMDAAAHAEADP 1375
MAIT G Q T L+ SF+ET VL +AA ++D
Sbjct: 1144 VEQVNEAMAIT-GGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDW 1202
Query: 1376 MRGVSENIIMGQLPRMGTG 1394
+RG+ EN+I+G+L GTG
Sbjct: 1203 LRGLKENVIIGRLIPAGTG 1221
Score = 44.5 bits (105), Expect = 7e-04
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 4/60 (6%)
Query: 819 LMAITRHGINRQDTGALMRC-SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
L+ IT+ +N T + + SF+ET VL +AA ++D +RG+ EN+I+G+L GTG
Sbjct: 1165 LLGITKASLN---TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1221
Score = 34.8 bits (80), Expect = 0.57
Identities = 13/35 (37%), Positives = 26/35 (74%)
Query: 1050 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 1084
++ ++ GLT +E+ + G R+GL+DTA++TA++
Sbjct: 158 IKTNFREGLTVTEYVISSYGARKGLVDTALRTADS 192
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 52.7 bits (126), Expect = 2e-06
Identities = 40/124 (32%), Positives = 62/124 (50%), Gaps = 21/124 (16%)
Query: 322 TEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESR 381
++YN++ MV +G++GS SQ+ G + + K P G T P
Sbjct: 2138 SKYNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIIS 2182
Query: 382 GFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMV-HYDCTV 440
F E GL E+F G R+GL DTA+KTA +GY+ RRL+ ++ +V +DC
Sbjct: 2183 NFRE-----GLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKT 2237
Query: 441 RNSV 444
+N +
Sbjct: 2238 KNGL 2241
Score = 51.9 bits (124), Expect = 4e-06
Identities = 48/193 (24%), Positives = 82/193 (42%), Gaps = 60/193 (31%)
Query: 1241 SKKRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVR 1300
S+ + +I G+F D L+ D DP D+ +I +VLG+EA+
Sbjct: 2612 SRSKHVIVNEGDFVRKGDLLM--------------DGDP------DLHDILRVLGLEALA 2651
Query: 1301 KSVEKEMNTVLQFYGLYVNYRHLALLC--------------------------------D 1328
+ E+ V + G+ ++ +HL ++ D
Sbjct: 2652 HYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDREND 2711
Query: 1329 VMTAKG----HLMAITRHGINR---QDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSE 1381
M+ G H + I + GI R + + + SF+ET VL +AA ++DP+ G+ E
Sbjct: 2712 AMSNSGKRPAHYLPILQ-GITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKE 2770
Query: 1382 NIIMGQLPRMGTG 1394
N+I+G+L GTG
Sbjct: 2771 NVIVGRLIPAGTG 2783
Score = 43.8 bits (103), Expect = 0.001
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 8/74 (10%)
Query: 811 DVMTAKG----HLMAITRHGINR---QDTGALMRCSFEETVDVLMDAAAHAEADPMRGVS 863
D M+ G H + I + GI R + + + SF+ET VL +AA ++DP+ G+
Sbjct: 2711 DAMSNSGKRPAHYLPILQ-GITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLK 2769
Query: 864 ENIIMGQLPRMGTG 877
EN+I+G+L GTG
Sbjct: 2770 ENVIVGRLIPAGTG 2783
Score = 31.9 bits (72), Expect = 4.9
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 43 RPDWMLVTVLPVPPLSVRPAVVM 65
RP+WM++T +P+ P +RP V +
Sbjct: 1665 RPEWMILTTIPILPPDLRPLVSL 1687
Score = 31.5 bits (71), Expect = 6.6
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 1052 NSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAI 1100
+++ GL E+F G R+GL DTA+KTA + + L V+ N +
Sbjct: 2182 SNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIV 2230
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 52.4 bits (127), Expect = 2e-06
Identities = 60/203 (29%), Positives = 95/203 (46%), Gaps = 44/203 (21%)
Query: 245 GHSIGIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFE---NQ 301
G SIGI D + P+ EI I++A+++V E I+K + L T N+
Sbjct: 614 GISIGIDDIVIPPEKK-EI---IEEAEKEVAE-IEKQYRRGL---------ITDGERYNK 659
Query: 302 VNRILNDARDKTGGSAKKSLTEY----NNLKAMVVAGSKGSNINISQVIACVG-QQNVEG 356
V I + A D+ + K+L++ N + M +G++GS I Q+ G G
Sbjct: 660 VIDIWSKATDEVAKAMMKNLSKDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSG 719
Query: 357 KRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTA 416
+ I P IK +++ GLT E+F G R+GL DTA+KTA
Sbjct: 720 EIIE-------TP--IK------------SNFREGLTVLEYFISTHGARKGLADTALKTA 758
Query: 417 ETGYIQRRLIK-AMESVMVHYDC 438
++GY+ RRL+ A + ++ DC
Sbjct: 759 DSGYLTRRLVDVAQDVIVREDDC 781
Score = 44.7 bits (107), Expect = 6e-04
Identities = 20/39 (51%), Positives = 28/39 (71%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL +AA + DP+RG+ EN+I+G+L GTG
Sbjct: 1098 SFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTG 1136
Score = 44.7 bits (107), Expect = 6e-04
Identities = 20/39 (51%), Positives = 28/39 (71%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
SF+ET VL +AA + DP+RG+ EN+I+G+L GTG
Sbjct: 1098 SFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTG 1136
Score = 35.8 bits (84), Expect = 0.30
Identities = 15/26 (57%), Positives = 18/26 (69%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTA 1082
GLT E+F G R+GL DTA+KTA
Sbjct: 733 GLTVLEYFISTHGARKGLADTALKTA 758
Score = 31.2 bits (72), Expect = 7.6
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 43 RPDWMLVTVLPVPPLSVRPAV 63
+P+WM++ VLPV P +RP V
Sbjct: 223 KPEWMILDVLPVIPPDLRPLV 243
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 52.3 bits (126), Expect = 3e-06
Identities = 40/120 (33%), Positives = 62/120 (51%), Gaps = 29/120 (24%)
Query: 330 MVVAGSKGSNINISQVIACVGQQ----NVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVE 385
M +G++G N+SQV VG + N +G+ I LP IK + F E
Sbjct: 125 MAFSGARG---NMSQVRQLVGMRGLMANPQGEII-------DLP--IKTN-------FRE 165
Query: 386 NSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVH-YDCTVRNSV 444
GLT +E+ + G R+GL+DTA++TA++GY+ RRL+ + V+V DC +
Sbjct: 166 -----GLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGI 220
Score = 42.7 bits (101), Expect = 0.002
Identities = 19/39 (48%), Positives = 28/39 (71%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 877
SF+ET VL +AA ++D +RG+ EN+I+G+L GTG
Sbjct: 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
Score = 42.7 bits (101), Expect = 0.002
Identities = 19/39 (48%), Positives = 28/39 (71%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1394
SF+ET VL +AA ++D +RG+ EN+I+G+L GTG
Sbjct: 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
Score = 33.0 bits (76), Expect = 1.8
Identities = 13/27 (48%), Positives = 21/27 (77%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAE 1083
GLT +E+ + G R+GL+DTA++TA+
Sbjct: 166 GLTVTEYVISSYGARKGLVDTALRTAD 192
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, 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.
Length = 381
Score = 49.7 bits (119), Expect = 9e-06
Identities = 32/130 (24%), Positives = 53/130 (40%), Gaps = 6/130 (4%)
Query: 1277 VDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHL 1336
+D R+ I +I VLGI+A + + + + + G V HL L+ D MT G
Sbjct: 252 IDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEF 311
Query: 1337 MAITRHGINRQDTGA-----LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRM 1391
+ + G Q F + + AA +D + GV + G+ +
Sbjct: 312 VGLNAKGYKAQRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPV 371
Query: 1392 GTGC-FDLLL 1400
GTG F++L
Sbjct: 372 GTGSKFEILW 381
Score = 37.0 bits (86), Expect = 0.079
Identities = 26/113 (23%), Positives = 42/113 (37%), Gaps = 14/113 (12%)
Query: 777 IFVLSVRKSVEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGA-- 834
FV + +V +VL+ HL L+ D MT G + + G Q
Sbjct: 277 QFVQRLESAVSMTGKSVLR--------EHLLLVADSMTYSGEFVGLNAKGYKAQRRSLKI 328
Query: 835 ---LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC-FDLLL 883
F + + AA +D + GV + G+ +GTG F++L
Sbjct: 329 SAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSKFEILW 381
>gnl|CDD|132721 cd02655, RNAP_beta'_C, 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.
Length = 204
Score = 46.8 bits (112), Expect = 3e-05
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 801 VNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 860
N R L L + L+ IT+ +N + + SF+ET VL +AA + D +R
Sbjct: 129 ENKRLLLLGKKPAKYEPVLLGITKASLNTE--SFISAASFQETTKVLTEAAIEGKIDWLR 186
Query: 861 GVSENIIMGQLPRMGTGC 878
G+ EN+I+G+L GTG
Sbjct: 187 GLKENVILGRLIPAGTGL 204
Score = 46.8 bits (112), Expect = 3e-05
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 1318 VNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMR 1377
N R L L + L+ IT+ +N + + SF+ET VL +AA + D +R
Sbjct: 129 ENKRLLLLGKKPAKYEPVLLGITKASLNTE--SFISAASFQETTKVLTEAAIEGKIDWLR 186
Query: 1378 GVSENIIMGQLPRMGTGC 1395
G+ EN+I+G+L GTG
Sbjct: 187 GLKENVILGRLIPAGTGL 204
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 48.8 bits (116), Expect = 4e-05
Identities = 54/201 (26%), Positives = 86/201 (42%), Gaps = 32/201 (15%)
Query: 249 GIGDTIADPQTYLEIQMAIKKAKEDVIEVIQKAHNMDLEPTPGNTLRQTFENQVNRILND 308
GI ++ D T + Q ++KAK +V + IQ+ ++ L Q N++ +
Sbjct: 2012 GISISMEDIITPKDKQKMVEKAKVEVKK-IQQQYDQGL------LTDQERYNKIIDTWTE 2064
Query: 309 ARDKTGGSAKKSLTE----YNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFR 364
DK ++ + +N++ M +G++GS I Q+ A G P G
Sbjct: 2065 VNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTK-----PDGSI 2119
Query: 365 KRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRR 424
T P F E GL E+F G R+GL DTA+KTA GY+ R+
Sbjct: 2120 IET----------PIISNFKE-----GLNVLEYFNSTHGARKGLADTALKTANAGYLTRK 2164
Query: 425 LIKAMESV-MVHYDCTVRNSV 444
LI ++V +V DC +
Sbjct: 2165 LIDVSQNVKVVSDDCGTHEGI 2185
Score = 40.7 bits (95), Expect = 0.010
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 802 NYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 861
N R +AL + A+ L+ ITR I + SF+ET VL +A+ + D +
Sbjct: 2799 NARVIALKGEPAIAEPVLLGITRAAIGSDSI--ISAASFQETTKVLTEASIAMKKDFLED 2856
Query: 862 VSENIIMGQLPRMGTGCF 879
+ EN+++G++ +GTG +
Sbjct: 2857 LKENVVLGRMIPVGTGMY 2874
Score = 40.7 bits (95), Expect = 0.010
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 1319 NYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 1378
N R +AL + A+ L+ ITR I + SF+ET VL +A+ + D +
Sbjct: 2799 NARVIALKGEPAIAEPVLLGITRAAIGSDSI--ISAASFQETTKVLTEASIAMKKDFLED 2856
Query: 1379 VSENIIMGQLPRMGTGCF 1396
+ EN+++G++ +GTG +
Sbjct: 2857 LKENVVLGRMIPVGTGMY 2874
Score = 38.4 bits (89), Expect = 0.049
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 43 RPDWMLVTVLPVPPLSVRPAVVMHG 67
RP+WM++TVLPV P +RP V + G
Sbjct: 1622 RPEWMMLTVLPVLPPDLRPLVALDG 1646
Score = 32.2 bits (73), Expect = 3.5
Identities = 18/47 (38%), Positives = 24/47 (51%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTAETVNVLVFLFQVTANTAIYYD 1103
GL E+F G R+GL DTA+KTA + L V+ N + D
Sbjct: 2131 GLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSD 2177
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 46.5 bits (111), Expect = 2e-04
Identities = 22/53 (41%), Positives = 37/53 (69%), Gaps = 2/53 (3%)
Query: 391 GLTPSEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKAMESVMVH-YDC-TVR 441
GL+ +E+ G R+G++DTAV+TA+ GY+ RRL++ ++ ++V DC T R
Sbjct: 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTR 224
Score = 37.6 bits (88), Expect = 0.073
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 839 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 878
SF+ET VL AA D ++G+ EN+I+G L GTG
Sbjct: 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
Score = 37.6 bits (88), Expect = 0.073
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 1356 SFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTGC 1395
SF+ET VL AA D ++G+ EN+I+G L GTG
Sbjct: 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
Score = 32.2 bits (74), Expect = 3.1
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 1057 GLTPSEFFFHAMGGREGLIDTAVKTA 1082
GL+ +E+ G R+G++DTAV+TA
Sbjct: 172 GLSLTEYIISCYGARKGVVDTAVRTA 197
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 44.4 bits (106), Expect = 3e-04
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 1489 VENIHVTPRQIITPQNNRPVMGIVQDTLTAVR 1520
+ + P I++P+N +P++G +QD L +
Sbjct: 264 ARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
Score = 43.3 bits (103), Expect = 6e-04
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 45 DWMLVTVLPVPPLSVRPAVVMHGSARNQ 72
+WM++TVLPVPP +RP+V + G +
Sbjct: 1 EWMILTVLPVPPPCLRPSVQLDGGRFAE 28
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 36.3 bits (84), Expect = 0.19
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 42 ARPDWMLVTVLPVPPLSVRPAVVMHG 67
+RP+WM++ V+PV P +RP V + G
Sbjct: 240 SRPEWMVLDVIPVIPPDLRPMVQLDG 265
>gnl|CDD|219837 pfam08430, Fork_head_N, Forkhead N-terminal region. The region
described in this family is found towards the N-terminus
of various eukaryotic fork head/HNF-3-related
transcription factors (which contain the pfam00250
domain). These proteins play key roles in embryogenesis,
maintenance of differentiated cell states, and
tumorigenesis.
Length = 137
Score = 33.8 bits (77), Expect = 0.29
Identities = 11/51 (21%), Positives = 13/51 (25%), Gaps = 3/51 (5%)
Query: 898 TGMMGGPAGMFFGSAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPG 948
GM G G GS MS M + A+ A
Sbjct: 61 NGMSPGYGGA--GSPMGMMGMSS-MGTSLSPSGTMGAMGPMPAGSGGSLSP 108
>gnl|CDD|240312 PTZ00202, PTZ00202, tuzin; Provisional.
Length = 550
Score = 35.1 bits (81), Expect = 0.36
Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 575 VDVLMDAAAHAEADPMRGYIQRRLIKAMESVMVHY--DCTVRNSVGQLIQLRYGEDGLCG 632
+D L+ A Y ++L+KAM + + D +R +V +L Y E
Sbjct: 453 LDELLAAVRQRRVSA-AEYTNQKLLKAMRQLQAAWAGDPQLRAAVKRLAAFPYDEG---- 507
Query: 633 EAVEHQRIDTVALSHKKFEDKYRFDPSNERQLRR 666
+H+ D +L D +DP + + R
Sbjct: 508 ---QHEGYDASSLRSPALRDIVLYDPVQDVWMFR 538
Score = 32.1 bits (73), Expect = 3.2
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 9/79 (11%)
Query: 418 TGYIQRRLIKAMESVMVHY--DCTVRNSVGQLIQLRYGEDGLCGEAVEHQRIDTVALSHK 475
Y ++L+KAM + + D +R +V +L Y E +H+ D +L
Sbjct: 468 AEYTNQKLLKAMRQLQAAWAGDPQLRAAVKRLAAFPYDEG-------QHEGYDASSLRSP 520
Query: 476 KFEDKYRFDPSNERPTLRN 494
D +DP + RN
Sbjct: 521 ALRDIVLYDPVQDVWMFRN 539
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 34.6 bits (79), Expect = 0.53
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 42 ARPDWMLVTVLPVPPLSVRPAVVMHG 67
+RP+WM++ V+PV P +RP V + G
Sbjct: 233 SRPEWMVLDVIPVIPPDLRPMVQLDG 258
>gnl|CDD|218431 pfam05099, TerB, Tellurite resistance protein TerB. This family
contains the TerB tellurite resistance proteins from a a
number of bacteria.
Length = 140
Score = 32.6 bits (75), Expect = 0.82
Identities = 12/80 (15%), Positives = 25/80 (31%), Gaps = 22/80 (27%)
Query: 634 AVEHQRIDTVALSHKKFEDKYRFDPSNERQLRRIFNEDVLRELMGSGDVISELEKEMVDH 693
E Q I + ++ DP L + E E+E D
Sbjct: 42 EEERQAIRRL------LRSRFGLDPEEAAALIELAE---------------EAEQEAPDL 80
Query: 694 FSW-KQLRRIFNEDVLRELM 712
+ + + ++ F+ + L+
Sbjct: 81 YEFTRAIKDHFDYEQRLALL 100
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 33.7 bits (78), Expect = 1.0
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 42 ARPDWMLVTVLPVPPLSVRPAVVMHG 67
P+WM++ +LPV P +RP + + G
Sbjct: 259 IEPEWMVLCLLPVLPPELRPIIQLDG 284
>gnl|CDD|215251 PLN02457, PLN02457, phenylalanine ammonia-lyase.
Length = 706
Score = 33.5 bits (77), Expect = 1.3
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 11/68 (16%)
Query: 1252 EFKAIADWLLETDGTSLMKVLSER-DVDPVRTFSNDICEIF---QVLG--IEAVR---KS 1302
E AI + +L DG+S MK + + DP++ D + Q LG IE +R KS
Sbjct: 306 EAAAIMEHIL--DGSSYMKAAKKLHETDPLQKPKQDRYALRTSPQWLGPQIEVIRAATKS 363
Query: 1303 VEKEMNTV 1310
+E+E+N+V
Sbjct: 364 IEREINSV 371
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 32.7 bits (75), Expect = 1.5
Identities = 12/52 (23%), Positives = 14/52 (26%), Gaps = 1/52 (1%)
Query: 899 GMMGGPAG-MFFGSAATPSSMSPQMTPWAQSTPAYNALMSPGAAMTPGGPGF 949
GM GG A + A P W P+ PG F
Sbjct: 85 GMFGGGAPRPPPAAPAVQPPAPPARPGWGSGGPSQQGAGQQPGYAQPGPGSF 136
>gnl|CDD|234300 TIGR03662, Chlor_Arch_YYY, Chlor_Arch_YYY domain. Members of this
highly hydrophobic probable integral membrane family
belong to two classes. In one, a single copy of the
region modeled by This model represents essentially the
full length of a strongly hydrophobic protein of about
700 to 900 residues (variable because of long inserts in
some). The domain architecture of the other class
consists of an additional N-terminal region, two copies
of the region represented by this model, and three to
four repeats of TPR, or tetratricopeptide repeat. The
unusual species range includes several Archaea, several
Chloroflexi, and Clostridium phytofermentans. An unusual
motif YYYxG is present, and we suggest the name
Chlor_Arch_YYY protein. The function is unknown.
Length = 723
Score = 31.6 bits (72), Expect = 4.7
Identities = 13/44 (29%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 754 EVIFILQRWKLWGNENLRFLCKIIFVLSVRKSVEKEMNTVLQFY 797
E + L L L +II+V MNTV +FY
Sbjct: 478 ETLLALGGLGLL------LLVEIIYVRDNIGGDYYRMNTVFKFY 515
>gnl|CDD|227605 COG5280, COG5280, Phage-related minor tail protein [Function
unknown].
Length = 634
Score = 31.3 bits (71), Expect = 5.2
Identities = 22/116 (18%), Positives = 34/116 (29%), Gaps = 13/116 (11%)
Query: 1146 MTDKKLTMEAISEKINAG--FGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDK 1203
D LT AI+ + G G +D L+ + I+ + SK Q+E
Sbjct: 324 FKDLGLTGGAITALMIKGNKSGAL-----TEDMLSDLMKALNIVGKELSKSQNEALPFGT 378
Query: 1204 MEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLP-QTDSKKRIIITESGEFKAIAD 1258
D + + + A LP D+ K I D
Sbjct: 379 KTTDKVKKGFDDISILSELATFFGAKA-----LPKVKDAIKAAAFATELLGTVIED 429
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(DH)-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 311
Score = 31.1 bits (71), Expect = 5.7
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 718 ISELEKEWEKLCEDREALREI---FSSGESNVVLPCNLMEVIFILQRWKLWGNENLRFL 773
+ EK E +EALR + E+ ++ CN +E+ + + +E L
Sbjct: 13 VELREKLAFSEEELKEALRRLLEKPGISEAVLLSTCNRVELYLVGDNFHKLADELEELL 71
>gnl|CDD|218108 pfam04487, CITED, CITED. CITED, CBP/p300-interacting
transactivator with ED-rich tail, are characterized by a
conserved 32-amino acid sequence at the C-terminus.
CITED proteins do not bind DNA directly and are thought
to function as transcriptional co-activators.
Length = 206
Score = 30.2 bits (68), Expect = 6.9
Identities = 15/70 (21%), Positives = 19/70 (27%), Gaps = 11/70 (15%)
Query: 894 IPLATGMMGGPAGMFFGSAATPS----SMSPQMTPWAQ----STPAYN-ALMSPGAAMTP 944
M PA M F ++ P PQ+ Q +T A G
Sbjct: 69 GGHPHQSM--PAYMMFNPSSKPQPFMLVPGPQLMASMQLQKLNTQYQGHAGAPAGHPGGG 126
Query: 945 GGPGFSPSVA 954
G F P
Sbjct: 127 GPQQFRPGAG 136
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 30.4 bits (69), Expect = 9.5
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 203 GIGDTIADPQTYLEIQMAIK-KAKEDVI--EVIQKAHNMDLEPTPGHSIGIGDTIADPQT 259
G GD DP + E + K K E E +++ HN + G + +
Sbjct: 73 GAGDEPPDPLSPGEQGLQRKLKELEREQKEEEVREKHNKKIIEKFGEDLE------EVYK 126
Query: 260 YLEIQMAIKKAKEDVIEVIQKA 281
+++ + +++ +E +E+++KA
Sbjct: 127 FMKGEAKVEEEEEKQMEILEKA 148
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.137 0.408
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 92,957,414
Number of extensions: 9513696
Number of successful extensions: 8347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 8292
Number of HSP's successfully gapped: 142
Length of query: 1791
Length of database: 10,937,602
Length adjustment: 111
Effective length of query: 1680
Effective length of database: 6,014,308
Effective search space: 10104037440
Effective search space used: 10104037440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 66 (29.0 bits)