RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16766
(621 letters)
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 159 bits (406), Expect = 2e-44
Identities = 68/193 (35%), Positives = 88/193 (45%), Gaps = 24/193 (12%)
Query: 403 MFIRSLVVPPNNLRPL-SMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLS 461
M + L VPP LRP ++ E L + I+ +N LL
Sbjct: 3 MILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIK------------RNNRLKRLLE 50
Query: 462 EALKGIRGDTLNNKLQNSWHELQYNVDLLMD-AKLNINKTTGAHQIDGLKQMLDGKTGMI 520
I ++N LQ VD L+D L + L Q L GK G
Sbjct: 51 LGAPSII-------IRNEKRLLQEAVDTLIDNEGLPRANQKSGRPLKSLSQRLKGKEGRF 103
Query: 521 RQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGP 580
RQN++GKRV+F+ RSVITPDP L ++ +GVP E A LT+P VTP N+ LRK+V NGP
Sbjct: 104 RQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP 163
Query: 581 NVYPGANMIQNED 593
GA I
Sbjct: 164 ---NGAKYIIRGK 173
Score = 87.6 bits (218), Expect = 5e-19
Identities = 35/98 (35%), Positives = 50/98 (51%), Gaps = 9/98 (9%)
Query: 17 RSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED 76
RSVITPDP L ++ +GVP E A LT+P VTP N+ LRK+V NGP GA I
Sbjct: 117 RSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP---NGAKYIIR-- 171
Query: 77 GSVVRISSSQAVQRESLAKRLITPEDQQHRAIMKEKII 114
G + + ++S + D R ++ ++
Sbjct: 172 GKKTNLKLA----KKSKIANHLKIGDIVERHVIDGDVV 205
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 136 bits (346), Expect = 1e-33
Identities = 63/169 (37%), Positives = 90/169 (53%), Gaps = 32/169 (18%)
Query: 467 IRGDTLNNKLQNS-------------WHELQYNVDLLMDAKLNINKTTGA----HQ---- 505
IR +N +L+ + W LQY+V D N+ G H+
Sbjct: 245 IR---INQRLKENIEAGAPQLIIEDLWELLQYHVTTYFD-----NEIPGIPPARHRSGRP 296
Query: 506 IDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVT 565
+ L Q L GK G R N+ GKRVNF+ R+VI+PDP L+I+ +GVP AK LT P VT
Sbjct: 297 LKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVT 356
Query: 566 PWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLAKRL 614
WN+ LR+ V+NGP +PGAN + DG ++++ +E LA++L
Sbjct: 357 EWNIEELREYVLNGPEKHPGANYVIRPDGRRIKLT---DKNKEELAEKL 402
Score = 101 bits (255), Expect = 2e-22
Identities = 37/84 (44%), Positives = 54/84 (64%), Gaps = 3/84 (3%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+PDP L+I+ +GVP AK LT P VT WN+ LR+ V+NGP +PGAN +
Sbjct: 322 FSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVI 381
Query: 74 NEDGSVVRISSSQAVQRESLAKRL 97
DG ++++ +E LA++L
Sbjct: 382 RPDGRRIKLT---DKNKEELAEKL 402
Score = 83.0 bits (206), Expect = 2e-16
Identities = 34/92 (36%), Positives = 55/92 (59%), Gaps = 1/92 (1%)
Query: 132 QEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHI 191
+E++++SV K+ + T++ G+ I GGL D +G I + G C TCG +C GH GHI
Sbjct: 20 EEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVI-DPGLRCKTCGGRAGECPGHFGHI 78
Query: 192 ELPVPVINTLFFRDVQLLLKLSCFLCHKINIP 223
EL PVI+ F + + LL+ +C C ++ +
Sbjct: 79 ELARPVIHVGFAKLIYKLLRATCRECGRLKLT 110
>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 = 129 bits (326), Expect = 3e-31
Identities = 60/145 (41%), Positives = 85/145 (58%), Gaps = 6/145 (4%)
Query: 473 NNKLQNSWHELQYNVDLLMDAKL-NINKTT--GAHQIDGLKQMLDGKTGMIRQNMMGKRV 529
+++ W LQY+V D +L I + L Q L GK G R N+ GKRV
Sbjct: 257 QLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRV 316
Query: 530 NFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMI 589
NF+ R+VI+PDP ++I+ +GVP + AK LT P VTPWN+ LR+ V+NGP+ +PGAN +
Sbjct: 317 NFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYV 376
Query: 590 QNEDGSVVRISSSQAVQRESLAKRL 614
DG ++I +E LA+RL
Sbjct: 377 IRPDGRRIKIRD---ENKEELAERL 398
Score = 93.6 bits (233), Expect = 8e-20
Identities = 39/84 (46%), Positives = 56/84 (66%), Gaps = 3/84 (3%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+PDP ++I+ +GVP + AK LT P VTPWN+ LR+ V+NGP+ +PGAN +
Sbjct: 318 FSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVI 377
Query: 74 NEDGSVVRISSSQAVQRESLAKRL 97
DG ++I +E LA+RL
Sbjct: 378 RPDGRRIKIRD---ENKEELAERL 398
Score = 84.4 bits (209), Expect = 6e-17
Identities = 41/124 (33%), Positives = 68/124 (54%), Gaps = 5/124 (4%)
Query: 132 QEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHI 191
+E++++SVV+V + T++ G+ I GGL D +G I E G C TCG +C GH GHI
Sbjct: 15 EEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVI-EPGLRCKTCGGKVGECPGHFGHI 73
Query: 192 ELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVTQAKDLEET 251
EL PV++ F +++ +L+ +C C +I + ++ +I L + DL T
Sbjct: 74 ELARPVVHVGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKE----EGGDLAST 129
Query: 252 LFNE 255
L +
Sbjct: 130 LIEK 133
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2. 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 2, contains the active site. The
invariant motif -NADFDGD- binds the active site
magnesium ion.
Length = 165
Score = 115 bits (290), Expect = 6e-30
Identities = 41/75 (54%), Positives = 51/75 (68%)
Query: 526 GKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPG 585
GKRV+F+GRSVITPDP L +D +GVP+E A LT P VT N+ LRK+V NGPNV PG
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPG 60
Query: 586 ANMIQNEDGSVVRIS 600
A I+ G+ +
Sbjct: 61 AKYIKRIKGAKRDLE 75
Score = 97.7 bits (244), Expect = 1e-23
Identities = 35/67 (52%), Positives = 43/67 (64%)
Query: 17 RSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED 76
RSVITPDP L +D +GVP+E A LT P VT N+ LRK+V NGPNV PGA I+
Sbjct: 9 RSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPGAKYIKRIK 68
Query: 77 GSVVRIS 83
G+ +
Sbjct: 69 GAKRDLE 75
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 116 bits (292), Expect = 6e-27
Identities = 76/269 (28%), Positives = 114/269 (42%), Gaps = 67/269 (24%)
Query: 360 EQGYVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIR-------SLVVPP 412
E+ + + E + +L E ++D ELI D R + +VPP
Sbjct: 170 EEPTIFIEKTEIEEHRLLPIE--IRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPP 227
Query: 413 NNLRPLSMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTL 472
RP S+I+ + + DL + I+
Sbjct: 228 LTARP----------------------------SIILETGERSEDDLTHILVDIIK---A 256
Query: 473 NNKLQNS-------------WHELQYNVDLLMDAKLNINKTTG---AHQ------IDGLK 510
N KL+ S LQY+ D N T G AH + L
Sbjct: 257 NQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFD-----NATAGIPQAHHKGSGRPLKSLF 311
Query: 511 QMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVT 570
Q L GK G R N++GKRV+F+ R+VI+PDP ++ID +GVP A LT P V N+
Sbjct: 312 QRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIE 371
Query: 571 LLRKMVINGPNVYPGANMIQNEDGSVVRI 599
++++VINGP+ +PGAN I+ DG+ +R+
Sbjct: 372 KMKELVINGPDEFPGANAIRKGDGTKIRL 400
Score = 79.7 bits (196), Expect = 2e-15
Identities = 31/69 (44%), Positives = 47/69 (68%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+PDP ++ID +GVP A LT P V N+ ++++VINGP+ +PGAN I+
Sbjct: 332 FSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIR 391
Query: 74 NEDGSVVRI 82
DG+ +R+
Sbjct: 392 KGDGTKIRL 400
Score = 70.4 bits (172), Expect = 2e-12
Identities = 33/91 (36%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 133 EVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHIE 192
+ +++ ++ +P ++ G + GGL D +G I E G C TCGN C GH GHIE
Sbjct: 21 DARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTI-EPGQKCLTCGNLAANCPGHFGHIE 79
Query: 193 LPVPVINTLFFRDVQLLLKLSCFLCHKINIP 223
L PVI+ F +++ LL +C C K+ +P
Sbjct: 80 LAEPVIHIAFIDNIKDLLNSTCHKCAKLKLP 110
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 112 bits (282), Expect = 8e-26
Identities = 64/212 (30%), Positives = 87/212 (41%), Gaps = 44/212 (20%)
Query: 403 MFIRSLVVPPNNLRPLSMEQMPPVEHSR------NKLYQSILYSCGSLKSVIMAMKNKEQ 456
M + L VPP +LRP ++ R N LY+ ++ LK
Sbjct: 184 MILTVLPVPPPDLRPSI-----QLDGGRFAESDLNDLYRRVINRNNRLK----------- 227
Query: 457 SDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGK 516
LL A I ++N LQ VD L D + T G + L Q L GK
Sbjct: 228 -RLLELAAPII--------VRNEKRMLQEAVDALFDNRRPRAVT-GGRPLKSLSQRLKGK 277
Query: 517 TGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMV 576
G RQN++GKRV+++GRSVI+ P L ++ GVP + A L P VT N+ LR
Sbjct: 278 QGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT-- 335
Query: 577 INGPNVYPGANMIQNEDGSVVRISSSQAVQRE 608
GA + R+ V RE
Sbjct: 336 --------GAKYAKRMVER--RLPEVWDVLRE 357
Score = 89.6 bits (223), Expect = 1e-18
Identities = 34/137 (24%), Positives = 53/137 (38%), Gaps = 17/137 (12%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTK 183
+K + +E++ +V P T N GGL+D + ++ CT CG
Sbjct: 7 IKFGLASPEEIRS-WSGEVKKPETINYRTKPERGGLFDERIFGP-DKDYECT-CGKYKRI 63
Query: 184 CKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYVT 243
C G GHIEL PV + FF+ + LL ++C C ++ +A V
Sbjct: 64 CPGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCE--------------RVLYFEAYVVL 109
Query: 244 QAKDLEETLFNEENLRL 260
+ L NE
Sbjct: 110 GTDLEKIQLLNETEYVY 126
Score = 54.2 bits (131), Expect = 2e-07
Identities = 23/75 (30%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 17 RSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED 76
RSVI+ P L ++ GVP + A L P VT N+ LR GA +
Sbjct: 295 RSVISVGPNLKLNQCGVPKKMALELFKPFVVTELNIEGLRT----------GAKYAKRMV 344
Query: 77 GSVVRISSSQAVQRE 91
R+ V RE
Sbjct: 345 ER--RLPEVWDVLRE 357
>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 = 95.4 bits (238), Expect = 2e-21
Identities = 79/405 (19%), Positives = 128/405 (31%), Gaps = 87/405 (21%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHT-IPGGLYDLAMGPISERGDPCTTCGNNYT 182
++ + +E+++ SV +V P T+N PGGL D MG I ++ C TCG T
Sbjct: 7 IQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGTI-KKKSICETCGVEVT 65
Query: 183 KCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKLLDAGYV 242
+C GH GHIEL PV + FF+ + +L+ C LC +
Sbjct: 66 ECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSL---------------------- 103
Query: 243 TQAKDLEETLFNEENLRLHPAQLVQLVDSHVQSILAHGTKICDINDYKGGEELRSAFVAQ 302
E + + + P + L IC G
Sbjct: 104 ---LLNESVKYFFLKVVIDPKGKNSKKRLKKINNLCKKKSICSKCGEDNGG--------- 151
Query: 303 VLSRHVKRKCIFCATPINAISYQQRKIIKSFKIDKDNLDQSLDKSLNKSSNQIIRKREQG 362
+ A + K K + + L + + +RK
Sbjct: 152 ----------------LKAFEGCGKYQPKISKDGAEAIKALLKNIEIEELKEKLRK---- 191
Query: 363 YVMASEVEADFKKLWTNEHLFLKCLIPVLDTTKELIATDIMFIRSLVVPPNNLRPL-SME 421
+ +V FKK+ + E + P + + +I + L VPP +RP ++
Sbjct: 192 -LNPEKVLQIFKKI-SKEDEEILGFNPSGNRPEWMI------LTVLPVPPPCIRPSVQLD 243
Query: 422 QMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLSEALKGIRGDTLNNKLQNSWH 481
E + I+ LK +L E ++
Sbjct: 244 GGRFAEDDLTHKLRDIIKRNNRLKK------------MLEEGAPSHI-------IREEKR 284
Query: 482 ELQYNVDLLMD---AKLNINKTTGAHQIDGLKQMLDGKTGMIRQN 523
LQ +V L D + + Q L GK G R N
Sbjct: 285 LLQEHVATLFDNDIPGQPPALQKSGRPLKSISQRLKGKEGRFRGN 329
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 71.1 bits (175), Expect = 8e-13
Identities = 57/219 (26%), Positives = 91/219 (41%), Gaps = 44/219 (20%)
Query: 395 KELIATDI----MFIRSLVVPPNNLRPL-SMEQMPPVEHSRNKLYQSILYSCGSLKSVIM 449
K I T+I M + L V P LRP+ ++ + N+LY+ ++Y +L
Sbjct: 252 KHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLT---- 307
Query: 450 AMKNKEQSDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDG- 508
S L + KL LQ VD L+D N G DG
Sbjct: 308 --DLLTTSRSTPGEL--VMCQK---KL------LQEAVDALLD-----NGIRGQPMRDGH 349
Query: 509 ------LKQMLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPV 562
+++GK G R+N++GKRV+++GRSVI P L++ G+P E A L P
Sbjct: 350 NKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPF 409
Query: 563 PVTPWNVTLLRKMVING--PNVYPGANMIQNEDGSVVRI 599
++R ++ N+ + I+ ++ V I
Sbjct: 410 --------VIRGLIRQHLASNIRAAKSKIREKEPIVWEI 440
Score = 30.6 bits (70), Expect = 2.8
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 10/68 (14%)
Query: 17 RSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVING--PNVYPGANMIQN 74
RSVI P L++ G+P E A L P ++R ++ N+ + I+
Sbjct: 381 RSVIVVGPSLSLHQCGLPREIAIELFQPF--------VIRGLIRQHLASNIRAAKSKIRE 432
Query: 75 EDGSVVRI 82
++ V I
Sbjct: 433 KEPIVWEI 440
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 66.5 bits (162), Expect = 4e-11
Identities = 35/88 (39%), Positives = 51/88 (57%), Gaps = 2/88 (2%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTTGAHQ--IDGLKQMLDGKTGMIRQNMMGKRVNFAG 533
++N LQ VD+L D + N GA++ + L +++ GK G RQN++GKRV+F+G
Sbjct: 1681 VRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSG 1740
Query: 534 RSVITPDPYLNIDSIGVPLEFAKTLTYP 561
RSVI P L +D G+P A L P
Sbjct: 1741 RSVIVVGPNLKMDECGLPKNMALELFKP 1768
>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 = 63.8 bits (155), Expect = 2e-10
Identities = 40/126 (31%), Positives = 64/126 (50%), Gaps = 8/126 (6%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTTGAHQ--IDGLKQMLDGKTGMIRQNMMGKRVNFAG 533
++N LQ VD L+D GA+ + L +++GK G RQN++GKRV+++G
Sbjct: 293 VRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSG 352
Query: 534 RSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED 593
RSVI P L + G+P E A L P + L+R+ ++N N+ +IQ D
Sbjct: 353 RSVIVVGPKLKMHQCGLPKEMAIELFQPFVIH----RLIRQGIVN--NIKAAKKLIQRAD 406
Query: 594 GSVVRI 599
+ +
Sbjct: 407 DEIWSV 412
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 62.8 bits (153), Expect = 3e-10
Identities = 40/116 (34%), Positives = 60/116 (51%), Gaps = 8/116 (6%)
Query: 483 LQYNVDLLMDAKLNINKTTGAHQ--IDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPD 540
LQ VD L+D GA+ + L +++GK G RQN++GKRV+++GRSVI
Sbjct: 307 LQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVG 366
Query: 541 PYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSV 596
P L + G+P E A L P + L+R+ ++N N+ +IQ D V
Sbjct: 367 PKLKMHQCGLPKEMAIELFQPFVIH----RLIRQGIVN--NIKAAKKLIQRADPEV 416
Score = 28.9 bits (65), Expect = 8.5
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 17 RSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED 76
RSVI P L + G+P E A L P + L+R+ ++N N+ +IQ D
Sbjct: 360 RSVIVVGPKLKMHQCGLPKEMAIELFQPFVIH----RLIRQGIVN--NIKAAKKLIQRAD 413
Query: 77 GSV 79
V
Sbjct: 414 PEV 416
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 62.7 bits (152), Expect = 5e-10
Identities = 51/163 (31%), Positives = 75/163 (46%), Gaps = 23/163 (14%)
Query: 403 MFIRSLVVPPNNLRPL-SMEQMPPVEHSRNKLYQSILYSCGSLKSVIMAMKNKEQSDLLS 461
M + ++ + P +LRPL S+E P N Y++I+ +N LLS
Sbjct: 1669 MILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIIN------------RNNRLRKLLS 1716
Query: 462 EALKGIRGDTLNNKLQNSWHELQYNVDLLMD-AKLN--INKTTGAHQIDGLKQMLDGKTG 518
I ++N LQ VD L D ++ N +NK + ML GK G
Sbjct: 1717 LNPPEI-------MIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKKSISDMLKGKQG 1769
Query: 519 MIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYP 561
RQN++GKRV+++GRSVI P L ++ G+P A L P
Sbjct: 1770 RFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP 1812
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 61.4 bits (149), Expect = 1e-09
Identities = 33/81 (40%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 483 LQYNVDLLMDAKLNINKTTG--AHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPD 540
LQ VD L D TG + L ML GK G RQN++GKRV+++GRSVI
Sbjct: 377 LQEAVDSLFDNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVG 436
Query: 541 PYLNIDSIGVPLEFAKTLTYP 561
P+L + G+P A L P
Sbjct: 437 PHLKLHQCGLPSAMALELFKP 457
>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 = 59.3 bits (144), Expect = 4e-09
Identities = 37/118 (31%), Positives = 55/118 (46%), Gaps = 12/118 (10%)
Query: 483 LQYNVDLLMD--AKLNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFAGRSVITPD 540
LQ VD L D + + L ML GK G RQN++GKRV+++GRSVI
Sbjct: 281 LQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVG 340
Query: 541 PYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVING--PNVYPGANMIQNEDGSV 596
P L + G+P + A L P ++++++ N+ MI+ ED V
Sbjct: 341 PELKMYQCGLPKKMALELFKPF--------IIKRLIDRELAANIKSAKKMIEQEDPEV 390
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 53.1 bits (129), Expect = 4e-07
Identities = 22/44 (50%), Positives = 30/44 (68%)
Query: 512 MLDGKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFA 555
ML GK G RQN++GKRV+++GRSVI P L + G+P + A
Sbjct: 320 MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA 363
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 29.3 bits (66), Expect = 5.7
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 100 PEDQQHRAI---MKEKIITRQEVV--PEILKLKYYTDQEVKQLSV 139
P DQ+ + I + E +I R++V+ P I +YTD VK L V
Sbjct: 271 PSDQRGQTINDPLLESLINREDVILTPHI---AFYTDAAVKNLIV 312
>gnl|CDD|107380 cd06385, PBP1_NPR_A, Ligand-binding domain of type A natriuretic
peptide receptor. Ligand-binding domain of type A
natriuretic peptide receptor (NPR-A). NPR-A is one of
three known single membrane-spanning natriuretic peptide
receptors that regulate blood volume, blood pressure,
ventricular hypertrophy, pulmonary hypertension, fat
metabolism, and long bone growth. In mammals there are
three natriuretic peptides: ANP, BNP, and CNP. NPR-A is
highly expressed in kidney, adrenal, terminal ileum,
adipose, aortic, and lung tissues. The rank order of
NPR-A activation by natriuretic peptides is
ANP>BNP>>CNP. Single allele-inactivating mutations in
the promoter of human NPR-A are associated with
hypertension and heart failure.
Length = 405
Score = 28.9 bits (65), Expect = 8.2
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 16/59 (27%)
Query: 112 KIITRQEVVPEILKLKYYTDQEVKQ-LSVVKVFSPITFN-----SLGHTIPGGLYDLAM 164
KI+T +E P+ + E K+ LS +K + FN SL + I GG YD M
Sbjct: 271 KILTYKE--PQ--------NPEYKEFLSDLKTDAKEMFNFTVEDSLMNIIAGGFYDGVM 319
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
0.319 0.135 0.395
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: 31,319,904
Number of extensions: 3064633
Number of successful extensions: 2380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2369
Number of HSP's successfully gapped: 39
Length of query: 621
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 518
Effective length of database: 6,369,140
Effective search space: 3299214520
Effective search space used: 3299214520
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: 62 (27.5 bits)