RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3023
(392 letters)
>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 = 306 bits (787), Expect = e-103
Identities = 141/359 (39%), Positives = 188/359 (52%), Gaps = 51/359 (14%)
Query: 10 LRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRSSRCQ 67
L+ +K++QFGI SP+EIR+ SV E + PET +P+ GGL+D R G I + S C+
Sbjct: 1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNYGSLKPEPGGLLDERMGTIKKKSICE 58
Query: 68 TCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLK 127
TC +TECPGHFGHI+LAKPVFH+GF K + ILRCVC CS LL++ S V+
Sbjct: 59 TCGVEVTECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSLLLNESVKYFFLKVVI 118
Query: 128 TKG--QSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNI 185
S++R I +LCK K+IC E + GCG+YQP I
Sbjct: 119 DPKGKNSKKRLKKINNLCKKKSICSKCGEDNGGLK-------------AFEGCGKYQPKI 165
Query: 186 RRSG-LDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEW 244
+ G + A K++ + ++K+ +L + I + D
Sbjct: 166 SKDGAEAIKALLKNIEIEELKEKLRKLNPEKVLQIFK----------KISKE--DEEILG 213
Query: 245 KHVNEDSQEKK-----------------IPLTGKGVLLDDLTHKLADIIKCNNELIRNES 287
N + + L G DDLTHKL DIIK NN L +
Sbjct: 214 --FNPSGNRPEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLE 271
Query: 288 SGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNL 346
GA +H+I E ++LQ HVATL DND+PG P A+QKSG+PLK+I RLKGKEGR RGNL
Sbjct: 272 EGAPSHIIREEKRLLQEHVATLFDNDIPGQPPALQKSGRPLKSISQRLKGKEGRFRGNL 330
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 211 bits (541), Expect = 3e-66
Identities = 81/135 (60%), Positives = 98/135 (72%), Gaps = 2/135 (1%)
Query: 256 IPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMP 315
+ L G DDLTH L DIIK NN L R GA + +I ++LQ V TL DN+
Sbjct: 19 VQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE-- 76
Query: 316 GLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRS 375
GLPRA QKSG+PLK++ RLKGKEGR R NL+GKRVDFSAR+VITPDPNL++++VGVP+
Sbjct: 77 GLPRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKE 136
Query: 376 IAQNMTFPEIVTPFN 390
IA +TFPEIVTP N
Sbjct: 137 IALELTFPEIVTPLN 151
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 200 bits (511), Expect = 3e-57
Identities = 73/127 (57%), Positives = 96/127 (75%)
Query: 266 DDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSG 325
DDLTHKL DII+ N L N +GA +I + ++LQ+HV T DN++PG+P A +SG
Sbjct: 235 DDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSG 294
Query: 326 KPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI 385
+PLK + RLKGKEGR RGNL GKRV+FSARTVI+PDPNL I++VGVP +IA+ +T PE
Sbjct: 295 RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPER 354
Query: 386 VTPFNMD 392
VT +N++
Sbjct: 355 VTEWNIE 361
Score = 147 bits (373), Expect = 1e-38
Identities = 57/107 (53%), Positives = 73/107 (68%), Gaps = 5/107 (4%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQTCAG 71
+ ++FG+LSP+EIR+MSVT+ I +T + G P GGLMDPR GVID RC+TC G
Sbjct: 9 IGSIKFGLLSPEEIRKMSVTK--IITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGG 66
Query: 72 NMTECPGHFGHIDLAKPVFHVGFVTKTI-KILRCVCFYCSKLLVSPS 117
ECPGHFGHI+LA+PV HVGF K I K+LR C C +L ++
Sbjct: 67 RAGECPGHFGHIELARPVIHVGFA-KLIYKLLRATCRECGRLKLTEE 112
>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 = 189 bits (483), Expect = 2e-53
Identities = 75/127 (59%), Positives = 97/127 (76%)
Query: 266 DDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSG 325
DDLTHKL DII+ N L N +GA +I + ++LQ+HVAT DN++PG+P A +SG
Sbjct: 231 DDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSG 290
Query: 326 KPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI 385
+PLK + RLKGKEGR RGNL GKRV+FSARTVI+PDPN+ I++VGVP IA+ +T PE
Sbjct: 291 RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPER 350
Query: 386 VTPFNMD 392
VTP+N+D
Sbjct: 351 VTPWNID 357
Score = 134 bits (338), Expect = 3e-34
Identities = 53/105 (50%), Positives = 72/105 (68%), Gaps = 3/105 (2%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQTCAG 71
+ ++FG+LSP+EIR+MSV E + +T + G P GGLMDPR GVI+ RC+TC G
Sbjct: 4 IGSIKFGLLSPEEIRKMSVVE--VVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGG 61
Query: 72 NMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSP 116
+ ECPGHFGHI+LA+PV HVGF + KILR C C ++ ++
Sbjct: 62 KVGECPGHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITLTE 106
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 162 bits (411), Expect = 7e-44
Identities = 53/127 (41%), Positives = 75/127 (59%), Gaps = 5/127 (3%)
Query: 266 DDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSG 325
DL +I NN L R A ++ +MLQ V L DN PRA+ G
Sbjct: 210 SDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDN---RRPRAVTG-G 264
Query: 326 KPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI 385
+PLK++ RLKGK+GR R NL+GKRVD+S R+VI+ PNL+++Q GVP+ +A + P +
Sbjct: 265 RPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELFKPFV 324
Query: 386 VTPFNMD 392
VT N++
Sbjct: 325 VTELNIE 331
Score = 139 bits (352), Expect = 6e-36
Identities = 54/200 (27%), Positives = 74/200 (37%), Gaps = 38/200 (19%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQTCAG 71
+ ++FG+ SP+EIR E +K PET+ +P+ GGL D R D+ C TC
Sbjct: 4 IFDIKFGLASPEEIRS-WSGE--VKKPETINYRTKPERGGLFDERIFGPDKDYEC-TCGK 59
Query: 72 NMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQ 131
CPG FGHI+LA PV H+ F +L C C ++L VVL T +
Sbjct: 60 YKRICPGGFGHIELAAPVAHIWFFKSIPSLLDMTCRDCERVLYF-----EAYVVLGTDLE 114
Query: 132 SRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLD 191
K + + E E CG I D
Sbjct: 115 ------------KIQLLNE--TEYVY--------------DSFCAHCGAEAIKILLEKPD 146
Query: 192 LTAEWKHVNEDSQEKKIPLT 211
L E + + K L
Sbjct: 147 LETEREEETLSPTKVKKLLK 166
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 152 bits (386), Expect = 2e-40
Identities = 70/128 (54%), Positives = 93/128 (72%), Gaps = 1/128 (0%)
Query: 266 DDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQK-S 324
DDLTH L DIIK N +L ++ +GA ++ + + LQ+H +T DN G+P+A K S
Sbjct: 244 DDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKGS 303
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPE 384
G+PLK++ RLKGKEGR RGNL+GKRVDFSARTVI+PDP + ID+VGVP +IA +T PE
Sbjct: 304 GRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPE 363
Query: 385 IVTPFNMD 392
IV N++
Sbjct: 364 IVNENNIE 371
Score = 112 bits (280), Expect = 1e-26
Identities = 44/121 (36%), Positives = 64/121 (52%), Gaps = 7/121 (5%)
Query: 9 PLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQ 67
++ + + FG++SP + R++ E I PE E G P GGL+D R G I+ +C
Sbjct: 5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCL 62
Query: 68 TCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLK 127
TC CPGHFGHI+LA+PV H+ F+ +L C C+KL + P+ V K
Sbjct: 63 TCGNLAANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKL----PQEDLNVFK 118
Query: 128 T 128
Sbjct: 119 L 119
>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 = 91.9 bits (229), Expect = 4e-22
Identities = 29/43 (67%), Positives = 35/43 (81%)
Query: 348 GKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFN 390
GKRVDFS R+VITPDPNL++D+VGVP +A +T PEIVT N
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLN 43
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 89.2 bits (221), Expect = 5e-19
Identities = 50/127 (39%), Positives = 71/127 (55%), Gaps = 9/127 (7%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL + +I NN L R GA ++ +MLQ V +L DN G P
Sbjct: 343 LNDLYRR---VINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRP-VTGPG 398
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPE 384
+PLK++ LKGK+GR R NL+GKRVD+S R+VI P+L++ Q G+P ++A E
Sbjct: 399 NRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMAL-----E 453
Query: 385 IVTPFNM 391
+ PF M
Sbjct: 454 LFKPFVM 460
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 86.9 bits (216), Expect = 2e-18
Identities = 43/106 (40%), Positives = 59/106 (55%), Gaps = 5/106 (4%)
Query: 275 IIKCNNELIR-NESSGAATHVIAENIK-MLQFHVATLTDNDMPGLPRAMQKS-GKPLKAI 331
+I NN L +S + + K +LQ V L DN + G P M+ KP K+
Sbjct: 299 VIYRNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALLDNGIRGQP--MRDGHNKPYKSF 356
Query: 332 KARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIA 377
++GKEGR R NL+GKRVD+S R+VI P+L + Q G+PR IA
Sbjct: 357 SDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIA 402
>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 = 85.9 bits (213), Expect = 6e-18
Identities = 50/114 (43%), Positives = 68/114 (59%), Gaps = 6/114 (5%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIK-MLQFHVATLTDNDMPGLPRAMQK 323
L+DL + +I NN L R GA +I N K MLQ V L DN G P + K
Sbjct: 247 LNDLYRR---VINRNNRLKRLLELGAPE-IIVRNEKRMLQEAVDALFDNGRRGKP-VVGK 301
Query: 324 SGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIA 377
+ +PLK++ LKGK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A
Sbjct: 302 NNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMA 355
Score = 35.8 bits (83), Expect = 0.040
Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 22/100 (22%)
Query: 15 KVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR---------------Q 57
++ I SPD IR S G +K PET+ +P+ GL + +
Sbjct: 1 AIKISIASPDTIRNWS--YGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYK 58
Query: 58 GVIDRSSRCQTCAGNMTECP---GHFGHIDLAKPVFHVGF 94
+ + C+ C +TE GHI+LA PV H+ +
Sbjct: 59 KIRYKGVVCERCGVEVTESKVRRERMGHIELAAPVAHIWY 98
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 82.4 bits (205), Expect = 7e-17
Identities = 42/106 (39%), Positives = 56/106 (52%), Gaps = 23/106 (21%)
Query: 274 DIIKCNNELIRNESSGAATHVIAENIK-MLQFHVATLTDNDMPGLPRAMQKSGK-PLKAI 331
+II +RNE K MLQ V L DN G R + PLK++
Sbjct: 279 EII------VRNE-------------KRMLQEAVDALFDNGRRG--RPVTGPNNRPLKSL 317
Query: 332 KARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIA 377
LKGK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A
Sbjct: 318 SDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMA 363
Score = 31.2 bits (72), Expect = 1.1
Identities = 29/115 (25%), Positives = 43/115 (37%), Gaps = 48/115 (41%)
Query: 14 KKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR--------------- 56
++ G+ SP++IR S G +K PET+ +P+ GL R
Sbjct: 8 DAIKIGLASPEKIRSWS--YGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKY 65
Query: 57 -----QGVIDRSSRCQTCAGNMTECPG-----------HFGHIDLAKPVFHVGFV 95
+G+I C+ C G GHI+LA PV H+ F
Sbjct: 66 KRVRYKGII-----CERC--------GVEVTRSKVRRERMGHIELAAPVAHIWFF 107
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 80.0 bits (197), Expect = 6e-16
Identities = 47/133 (35%), Positives = 74/133 (55%), Gaps = 3/133 (2%)
Query: 256 IPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMP 315
+ L G + D+ +I N L R GA ++ +MLQ V L DN
Sbjct: 1642 VALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRS 1701
Query: 316 GLPRAMQKSGK-PLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPR 374
A++ + K PLK++ +KGK+GR R NL+GKRVDFS R+VI PNL++D+ G+P+
Sbjct: 1702 T--NAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPK 1759
Query: 375 SIAQNMTFPEIVT 387
++A + P +++
Sbjct: 1760 NMALELFKPHLLS 1772
>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 = 76.5 bits (188), Expect = 4e-15
Identities = 43/122 (35%), Positives = 69/122 (56%), Gaps = 4/122 (3%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL + +I NN L R + A ++ +MLQ V L DN G + +
Sbjct: 266 LNDLYRR---VINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRT-VVGAN 321
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPE 384
+PLK++ ++GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 322 NRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPF 381
Query: 385 IV 386
++
Sbjct: 382 VI 383
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 75.9 bits (187), Expect = 6e-15
Identities = 48/126 (38%), Positives = 70/126 (55%), Gaps = 11/126 (8%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIK-MLQFHVATLTDNDMPGLPRAMQK 323
L+DL + +I NN L R + A +I N K MLQ V L DN G +
Sbjct: 273 LNDLYRR---VINRNNRLARLQEI-LAPEIIVRNEKRMLQEAVDALIDNGRRG-RTVVGA 327
Query: 324 SGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+ +PLK++ ++GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A
Sbjct: 328 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMA-----I 382
Query: 384 EIVTPF 389
E+ PF
Sbjct: 383 ELFQPF 388
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 73.1 bits (179), Expect = 9e-14
Identities = 45/127 (35%), Positives = 65/127 (51%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
+ DL H II NN L + S +I +MLQ V +L DN +
Sbjct: 1694 VSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGA 1753
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPE 384
K+I LKGK+GR R NL+GKRVD+S R+VI P L+++Q G+P+ +A + P
Sbjct: 1754 VGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPF 1813
Query: 385 IVTPFNM 391
+ + M
Sbjct: 1814 VYSKLKM 1820
Score = 31.1 bits (70), Expect = 1.1
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 18/99 (18%)
Query: 15 KVQFGILSPDEIRRMS------VTEGGIKFPETMEGGR--PKLGGLMDPRQGVIDRSSR- 65
+V I SP+ I+RMS V+ + + +GG PK+ G ++ + + + +
Sbjct: 1450 EVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKR 1509
Query: 66 ------CQTCAGNMTECP---GHFGHIDLAKPVFHVGFV 95
C+ C +T GHI+LA PV H+ F+
Sbjct: 1510 RHRGRICEKCGVEVTSSKVRRERMGHIELASPVAHIWFL 1548
>gnl|CDD|221906 pfam13057, DUF3919, Protein of unknown function (DUF3919). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 251 and 262 amino
acids in length. There is a conserved YLNG sequence
motif.
Length = 228
Score = 29.6 bits (67), Expect = 2.5
Identities = 26/108 (24%), Positives = 42/108 (38%), Gaps = 17/108 (15%)
Query: 251 SQEKKIPLTG--KGVLLDDL--THKLADIIKCNNELIRNESSGAATHV-------IAENI 299
K PL K LLD L L++II NE+I +++ + I +I
Sbjct: 93 GDNGKSPLINRLKNYLLDYLYTPSNLSNIINSANEVIIFDNNNNGKKLGSSDKELIKNSI 152
Query: 300 KMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLM 347
K L+ +TDN + + +P I + KE N++
Sbjct: 153 KKLK----KITDNK--EIQKLTNSKEEPKYHITIYIDNKEENKSENII 194
>gnl|CDD|152995 pfam12561, TagA, ToxR activated gene A lipoprotein. This domain
family is found in bacteria, and is approximately 140
amino acids in length. The family is found in
association with pfam10462. There is a conserved GAG
sequence motif. This family is a bacterial lipoprotein.
Length = 135
Score = 28.1 bits (63), Expect = 3.9
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 145 GKNICEGGDEMDINKDGAEDP 165
IC GGDE+ + +G +
Sbjct: 65 SNYICTGGDEITWSINGQRNR 85
>gnl|CDD|179117 PRK00770, PRK00770, deoxyhypusine synthase-like protein;
Provisional.
Length = 384
Score = 28.6 bits (64), Expect = 6.2
Identities = 24/80 (30%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 66 CQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKI---LRCVCFYCSKLLVSPSHPKVR 122
T +G MT P FG + P+ GF+ I L Y L + HP V
Sbjct: 55 GLTLSGAMT--PAGFG-VSALAPLIEAGFIDWIISTGANLYHDLHYALGLPLFAGHPFVD 111
Query: 123 DVVLKTKGQSRRRQAFI-YD 141
DV L+ +G R YD
Sbjct: 112 DVKLREEGIIRIYDIIFDYD 131
>gnl|CDD|223071 PHA03392, egt, ecdysteroid UDP-glucosyltransferase; Provisional.
Length = 507
Score = 28.8 bits (65), Expect = 6.3
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 14/89 (15%)
Query: 229 YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNE-- 286
Y PN+ RS W+ +NE E + L + LAD N+L++ +
Sbjct: 186 YYPNLWRSKFGNLNVWETINEIYTELR---------LYNEFSLLADE---QNKLLKQQFG 233
Query: 287 SSGAATHVIAENIKMLQFHVATLTDNDMP 315
+ +++L +V + DN+ P
Sbjct: 234 PDTPTIRELRNRVQLLFVNVHPVFDNNRP 262
>gnl|CDD|235800 PRK06436, PRK06436, glycerate dehydrogenase; Provisional.
Length = 303
Score = 27.9 bits (62), Expect = 9.6
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 137 AFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKK---QGHGGCGRYQPNIRRS-GLDL 192
AF L KNICE M L NK G+GG GR + ++ G+++
Sbjct: 89 AFALLLAWAKNICENNYNMKNGNFKQSPTKLLYNKSLGILGYGGIGRRVALLAKAFGMNI 148
Query: 193 TA 194
A
Sbjct: 149 YA 150
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 0.137 0.415
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: 19,907,585
Number of extensions: 1900674
Number of successful extensions: 1330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1311
Number of HSP's successfully gapped: 36
Length of query: 392
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 293
Effective length of database: 6,546,556
Effective search space: 1918140908
Effective search space used: 1918140908
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 (21.7 bits)
S2: 60 (26.7 bits)