RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4197
(124 letters)
>gnl|CDD|220325 pfam09637, Med18, Med18 protein. Med18 is one subunit of Mediator,
a head-module multiprotein complex, that stimulates
basal RNA polymerase II (Pol II) transcription. Med18
consists of an eight-stranded beta-barrel with a central
pore and three flanking helices. It complexes with Med8
and Med20 proteins by forming a heterodimer of two-fold
symmetry with Med20 and binding the C-terminal
alpha-helix region of Med8 across the top of its barrel.
This complex creates a multipartite TBP-binding site
that can be modulated by transcriptional activators.
Length = 243
Score = 107 bits (270), Expect = 4e-30
Identities = 46/123 (37%), Positives = 64/123 (52%), Gaps = 9/123 (7%)
Query: 5 DKARPTIVRSSIDVA-CSCTVVEFLTEMGCRMDFEYISRGYMFRKGRMKILVSKIFKMSQ 63
RP VR+ I+ S ++++FL E+G R D+EYI++G F KG + I +SK+FK+
Sbjct: 118 GNNRPVTVRTIIESDLPSGSLLQFLKELGYRFDYEYITKGVRFFKGDIVITLSKVFKIPD 177
Query: 64 GKPSDSGV---EPISQSYLVELSILAPGGQDVIGEDM-----KAFAEQLKPLVQLEKIDY 115
DS S SYLVE SI P G D+ + EQLK LV+LE D
Sbjct: 178 EGQEDSSPLELLDPSGSYLVEASINVPKGTDIEAMNKAVAELLKLKEQLKGLVELEIPDR 237
Query: 116 KRL 118
+
Sbjct: 238 LSM 240
>gnl|CDD|169406 PRK08366, vorA, 2-ketoisovalerate ferredoxin oxidoreductase subunit
alpha; Reviewed.
Length = 390
Score = 36.1 bits (83), Expect = 0.002
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 5/57 (8%)
Query: 58 IFKMSQGKPSDSGVEPISQSYLVELSILAPGGQDVIGEDMKAFAEQLKPLVQLEKID 114
+F ++G ++ PI ++Y+V L GG+D D+KA AE +K +++ K+D
Sbjct: 329 LFTEAKGALYNTDARPIMKNYIVGL-----GGRDFTVNDVKAIAEDMKKVIEKGKLD 380
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 27.8 bits (62), Expect = 1.6
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 82 LSILAPGG--QDVIGEDMKAFAEQLKP-LVQL 110
L+ AP Q + E ++AFAEQL P VQL
Sbjct: 294 LTQFAPAAAQQSLYSEQIRAFAEQLSPEQVQL 325
>gnl|CDD|234950 PRK01390, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 460
Score = 27.5 bits (62), Expect = 1.8
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 20/62 (32%)
Query: 57 KIFKMSQGKPSDSGVEP-------ISQSYLVELSILAPGGQDVIGEDMKAFAEQLKPLVQ 109
+I+ ++ GKP + G+E I+++YL IGE +AFA L V
Sbjct: 355 RIYWIAGGKPKEGGIESLAPFFPRIAKAYL-------------IGEAAEAFAATLGGAVP 401
Query: 110 LE 111
E
Sbjct: 402 FE 403
>gnl|CDD|221568 pfam12419, DUF3670, SNF2 Helicase protein. This domain family is
found in bacteria, archaea and eukaryotes, and is
approximately 140 amino acids in length. The family is
found in association with pfam00271, pfam00176. Most of
the proteins in this family are annotated as SNF2
helicases but there is little accompanying literature to
confirm this.
Length = 141
Score = 26.4 bits (59), Expect = 2.8
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 77 SYLVELSILAPGGQDVIGEDMKAFAEQLKPLVQL 110
+ EL++ GGQ++ E+ + AE PLV+L
Sbjct: 72 DFDWELAL---GGQELTEEEFEELAESKSPLVRL 102
>gnl|CDD|149801 pfam08855, DUF1825, Domain of unknown function (DUF1825). This
uncharacterized family of proteins are principally found
in cyanobacteria.
Length = 108
Score = 26.2 bits (58), Expect = 3.3
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 95 EDMKAFAEQLKPLVQLEKIDYKRLPLS 121
E K E+++ L+ ++I YKRL LS
Sbjct: 37 EGKKDHIEKMEELIDRQRIFYKRLELS 63
>gnl|CDD|129414 TIGR00314, cdhA, CO dehydrogenase/acetyl-CoA synthase complex,
epsilon subunit. Acetyl-CoA decarbonylase/synthase
(ACDS) is a multienzyme complex. Carbon monoxide
dehydrogenase is a synonym. The ACDS complex carries out
an unusual reaction involving the reversible cleavage
and synthesis of acetyl-CoA in methanogens. The model
contains the prosite signature for 4Fe-4S ferredoxins
[C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462
of the model [Energy metabolism, Chemoautotrophy].
Length = 784
Score = 26.3 bits (58), Expect = 5.7
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 1 MGVGDKARPTIVRSSIDVACSCTVVEFLTEMGCRMDFE 38
G+ DK++P I+ +V + ++L E G + E
Sbjct: 226 FGIIDKSKPVILVIGHNVMPGRPIADYLEENGMEDEVE 263
>gnl|CDD|222272 pfam13628, DUF4142, Domain of unknown function (DUF4142). This is
a bacterial family of unknown function.
Length = 137
Score = 25.6 bits (57), Expect = 6.5
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 85 LAPGGQDVIGEDMKAFAEQLKPLVQ 109
A G D ++KAFA + P +Q
Sbjct: 107 YAASGDD---PELKAFAAKTLPTLQ 128
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 26.0 bits (58), Expect = 7.3
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 12/44 (27%)
Query: 2 GVGDKARPTIVR-------SSI-DVA----CSCTVVEFLTEMGC 33
G+G+ +IV S D+ S T++E L E+G
Sbjct: 1380 GLGENVAKSIVEAREEGEFLSKEDLRKRTKVSKTLIEKLDELGV 1423
>gnl|CDD|237572 PRK13962, PRK13962, bifunctional phosphoglycerate
kinase/triosephosphate isomerase; Provisional.
Length = 645
Score = 25.8 bits (57), Expect = 8.0
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 10/68 (14%)
Query: 44 YMFRKGRMKILVSKIFKMSQGKPSDS-GVEPISQSYLVEL----SILAPGGQDVIGEDMK 98
Y+ G ILVS + + +G+ + P+++ L EL I A DVIG+D K
Sbjct: 47 YLLDHGAKVILVSHLGR-PKGEFDPKFSMAPVAKR-LSELLGKEVIFAK---DVIGDDAK 101
Query: 99 AFAEQLKP 106
QLK
Sbjct: 102 KAVAQLKE 109
>gnl|CDD|203422 pfam06304, DUF1048, Protein of unknown function (DUF1048). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 92
Score = 24.6 bits (54), Expect = 9.0
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 90 QDVIGEDMKAFAEQL 104
+V GED+ AF ++L
Sbjct: 57 LEVTGEDVAAFCDEL 71
>gnl|CDD|161761 TIGR00200, cinA_nterm, competence/damage-inducible protein CinA
N-terminal domain. cinA is a DNA damage- or
competence-inducible protein that is polycistronic with
recA in a number of species [DNA metabolism, DNA
replication, recombination, and repair].
Length = 413
Score = 25.6 bits (56), Expect = 9.2
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 8/62 (12%)
Query: 48 KGRMKILVSKIFKMSQGKPSDSGVEPISQSYLVELSILAPGGQDVIGEDMKAFAEQLKPL 107
+G + + K +E + L I GQ VIGED + Q+
Sbjct: 216 RGEVPLRELK--LTGPESEQQRAMEKL------WLDIKRVAGQSVIGEDTEGLPAQISRE 267
Query: 108 VQ 109
+Q
Sbjct: 268 LQ 269
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 0.138 0.393
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,199,707
Number of extensions: 530514
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 420
Number of HSP's successfully gapped: 25
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
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: 53 (24.1 bits)