RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17068
(157 letters)
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 37.2 bits (87), Expect = 0.002
Identities = 15/71 (21%), Positives = 24/71 (33%), Gaps = 1/71 (1%)
Query: 44 DRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRG-YRE 102
D+ ++ G R R RD+ + NR R G RG R +R R+
Sbjct: 211 QGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRD 270
Query: 103 QNRGYRDQNAD 113
+ +
Sbjct: 271 RRGRRGGDGGN 281
Score = 33.7 bits (78), Expect = 0.029
Identities = 13/73 (17%), Positives = 23/73 (31%)
Query: 45 RDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYREQN 104
++ R RG R + + RE + R RG R + R R +
Sbjct: 216 EERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRR 275
Query: 105 RGYRDQNADIAIK 117
G + ++
Sbjct: 276 GGDGGNEREPELR 288
Score = 32.2 bits (74), Expect = 0.11
Identities = 11/63 (17%), Positives = 18/63 (28%)
Query: 44 DRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYREQ 103
+ + + R R D+ ++ G R R RD + R R
Sbjct: 190 RGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGD 249
Query: 104 NRG 106
G
Sbjct: 250 RDG 252
Score = 31.0 bits (71), Expect = 0.21
Identities = 14/72 (19%), Positives = 20/72 (27%)
Query: 42 HTDRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYR 101
DR + R G REQ E+ R RG R ++
Sbjct: 178 REDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRD 237
Query: 102 EQNRGYRDQNAD 113
+ R+ D
Sbjct: 238 ARGDDNREDRGD 249
Score = 31.0 bits (71), Expect = 0.24
Identities = 9/72 (12%), Positives = 20/72 (27%)
Query: 42 HTDRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYR 101
+ + R+ R ++ ++ G R R R+++
Sbjct: 181 RQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARG 240
Query: 102 EQNRGYRDQNAD 113
+ NR R
Sbjct: 241 DDNREDRGDRDG 252
Score = 29.9 bits (68), Expect = 0.51
Identities = 11/70 (15%), Positives = 23/70 (32%)
Query: 44 DRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYREQ 103
++R + + RD + R R ++ + G R +R R++
Sbjct: 176 GDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDR 235
Query: 104 NRGYRDQNAD 113
D N +
Sbjct: 236 RDARGDDNRE 245
Score = 28.3 bits (64), Expect = 1.7
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 44 DRDQNRGYHNQNRGYRNQIRGYRDQNHGY---REQNRGYREQNRGYRDHNRGYRE 95
R + R + + RG RD + G + R +R+++R R G E
Sbjct: 228 GRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNE 282
>gnl|CDD|133399 cd04772, HTH_TioE_rpt1, First Helix-Turn-Helix DNA binding domain
of the regulatory protein TioE. Putative
helix-turn-helix (HTH) regulatory protein, TioE, and
related proteins. TioE is part of the thiocoraline gene
cluster, which is involved in the biosynthesis of the
antitumor thiocoraline from the marine actinomycete,
Micromonospora. These proteins share the N-terminal DNA
binding domain with other transcription regulators of
the MerR superfamily that promote transcription by
reconfiguring the spacer between the -35 and -10
promoter elements. Proteins in this family are unique
within the MerR superfamily in that they are composed of
just two adjacent MerR-like N-terminal domains; this CD
contains the N-terminal or first repeat (rpt1) of these
tandem MerR-like domain proteins.
Length = 99
Score = 28.5 bits (64), Expect = 0.61
Identities = 17/84 (20%), Positives = 25/84 (29%), Gaps = 14/84 (16%)
Query: 60 NQIRGYRDQN---------HGYREQNRGYREQNRGYRDHNRGYREQKRGYREQNRGYRDQ 110
+R Y +GYR + R YR GY GYR R R
Sbjct: 15 QTVRNYESLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGY-----GYRVAQRIMRAV 69
Query: 111 NADIAIKTADTANKSAVNANNIKE 134
+A I + + ++
Sbjct: 70 HAGIVASALALVDAAHALLQRYRQ 93
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 28.3 bits (63), Expect = 1.9
Identities = 16/59 (27%), Positives = 21/59 (35%), Gaps = 1/59 (1%)
Query: 54 QNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYREQNRGYRDQNA 112
+G R YR G +Q + E RG + G + G QNR R N
Sbjct: 521 GGQGRRWNPNPYRQSGQGRSQQQQPQPE-ARGNQSRTPGPGRGQGGRGNQNRNQRSGNN 578
>gnl|CDD|223719 COG0646, MetH, Methionine synthase I (cobalamin-dependent),
methyltransferase domain [Amino acid transport and
metabolism].
Length = 311
Score = 27.3 bits (61), Expect = 4.1
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 88 DHNRGYREQKRGYREQNRGYRDQNADIA-IKTA-DTAN-KSAVNA-NNIKENSHENLPLL 143
D + E YREQ G D AD+ I+T DT N K+AV A + E LP++
Sbjct: 133 DFAVTFDELVEAYREQVEGLIDGGADLILIETIFDTLNAKAAVFAAREVFEELGVRLPVM 192
Query: 144 KSQ 146
S
Sbjct: 193 ISG 195
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 27.1 bits (61), Expect = 4.2
Identities = 6/45 (13%), Positives = 13/45 (28%)
Query: 67 DQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYREQNRGYRDQN 111
++ E+N EQ R R + + + +
Sbjct: 1 ERLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSEL 45
>gnl|CDD|235537 PRK05632, PRK05632, phosphate acetyltransferase; Reviewed.
Length = 684
Score = 27.0 bits (61), Expect = 4.8
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 109 DQNADIAIKTADTA 122
+Q A+IAI++AD+A
Sbjct: 537 EQLAEIAIQSADSA 550
>gnl|CDD|180772 PRK06948, PRK06948, ribonucleotide reductase-like protein;
Provisional.
Length = 595
Score = 27.1 bits (60), Expect = 4.8
Identities = 13/38 (34%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 51 YHNQNRGYRNQIRGYRDQNHGYR--EQNRGYREQNRGY 86
H R RG R +NH YR RG R Y
Sbjct: 482 EHRPVRAGAGGARGMRAENHAYRLFRSLRGERAALPDY 519
>gnl|CDD|182194 PRK10015, PRK10015, oxidoreductase; Provisional.
Length = 429
Score = 26.9 bits (59), Expect = 5.0
Identities = 14/53 (26%), Positives = 24/53 (45%)
Query: 104 NRGYRDQNADIAIKTADTANKSAVNANNIKENSHENLPLLKSQLSNSEAPKSM 156
N G+ + D+AI +A A + + A + S +L K +L S + M
Sbjct: 309 NLGFTVRGMDLAIASAQAAATTVIAAKERADFSASSLAQYKRELEQSCVMRDM 361
>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
Provisional.
Length = 474
Score = 27.0 bits (59), Expect = 5.4
Identities = 22/113 (19%), Positives = 42/113 (37%), Gaps = 22/113 (19%)
Query: 42 HTDRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGY-------------RD 88
H RD G+ + G R + Y Q+ ++ R ++ +
Sbjct: 115 HGGRDTEPGHAHIENGERKSPKSYNQQSRKK-HRDESLRNKHGRPSGPPAMSPGEHFDQT 173
Query: 89 HNRGYR---EQKRGYREQNRGYRDQNADI----AIKTADTANKSAVNANNIKE 134
H+ YR ++ R++ R D D AI+T A S ++ +++ E
Sbjct: 174 HDAEYRLRFNERDARRDRIRKEYDIPTDKITEQAIETLKIAGAS-ISIDSVLE 225
>gnl|CDD|235529 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated.
Length = 377
Score = 26.7 bits (59), Expect = 5.4
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 74 EQNRGYREQNRGYRDHNRGYREQKRGYREQNRGYRDQNADIAIKTADTANKSAVNANNIK 133
E R R R+ NRG R RG R Q G+ + I + T TA + V ++I+
Sbjct: 143 EAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVI-VDTLATARRQGVALDDIR 201
>gnl|CDD|221509 pfam12287, Caprin-1_C, Cytoplasmic
activation/proliferation-associated protein-1 C term.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 343 and 708 amino
acids in length. This family is the C terminal region of
caprin-1. Caprin-1 is a protein involved in regulating
cellular proliferation. In mutated phenotypes, the G1
phase of the cell cycle is greatly lengthened, impairing
normal proliferation. The C terminal region of caprin-1
contains RGG motifs which are characteristic of RNA
binding domains. It is possible that caprin-1 functions
through an RNA binding mechanism.
Length = 319
Score = 26.9 bits (59), Expect = 5.9
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 56 RGYRNQIRGYRDQNHGYREQNRGYR-----EQNRGY 86
R R I GYR ++G+R GYR N GY
Sbjct: 250 RNPRGMINGYRGPSNGFRGGYDGYRPPFSNTPNSGY 285
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 26.8 bits (59), Expect = 6.8
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 3/70 (4%)
Query: 44 DRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKRGYREQ 103
R ++G R R++ R R + R+ RG R ++R + R YR
Sbjct: 14 TRRSDKGRERSRRRSRSRDRSRRRR---DRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRD 70
Query: 104 NRGYRDQNAD 113
+R +
Sbjct: 71 DRRSGRNTKE 80
>gnl|CDD|227742 COG5455, COG5455, Predicted integral membrane protein [Function
unknown].
Length = 129
Score = 25.9 bits (57), Expect = 6.9
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 5/68 (7%)
Query: 42 HTDRDQNRGYHNQNRGYRNQIRGYRDQNHGYREQNRGYREQNRGYRDHNRGYREQKR-GY 100
H DRD+ +++ + + ++ RG R YR H R+ +R
Sbjct: 41 HLDRDRAWDRPRTVERRSYELKSVIAKFNRWK---RGDR-LPPMYRRHQYNIRDYRRYNL 96
Query: 101 REQNRGYR 108
R RG
Sbjct: 97 RAPPRGQH 104
>gnl|CDD|215138 PLN02248, PLN02248, cellulose synthase-like protein.
Length = 1135
Score = 26.5 bits (59), Expect = 8.1
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 85 GYRDHNRGYR 94
GYR HNRG+R
Sbjct: 842 GYRMHNRGWR 851
>gnl|CDD|185152 PRK15239, PRK15239, putative fimbrial protein StaA; Provisional.
Length = 197
Score = 25.8 bits (56), Expect = 8.7
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 110 QNADIAIKTADTANKSAVNANNIKENSHE 138
+ DIA+ D AN ++ N N+ E
Sbjct: 127 KAVDIAVHHVDDANALSLVKINDPSNTME 155
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
0.313 0.129 0.380
Gapped
Lambda K H
0.267 0.0650 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,637,667
Number of extensions: 654745
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 490
Number of HSP's successfully gapped: 47
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.1 bits)