RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12021
(106 letters)
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 29.1 bits (66), Expect = 0.056
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 82 YQCPQCPYRASQKATLKTHMAIKH 105
Y+C CPY S L+ H+ + H
Sbjct: 1 YKCSHCPYS-STPKKLERHLKLHH 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.3 bits (65), Expect = 0.36
Identities = 24/90 (26%), Positives = 29/90 (32%), Gaps = 26/90 (28%)
Query: 40 INWPTVRQYNSG--MFPCEV--CGKKYKYKWGLSRHKRDECGQEPK-------------- 81
I+ P+ + C V C KKYK + GL H Q K
Sbjct: 335 IDTPSRMLKVKDGKPYKCPVEGCNKKYKNQNGLKYHML-HGHQNQKLHENPSPEKMNIFS 393
Query: 82 -----YQCPQCPYRASQKATLKTHMAIKHS 106
Y+C C R LK H KHS
Sbjct: 394 AKDKPYRCEVCDKRYKNLNGLKYH--RKHS 421
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 25.3 bits (55), Expect = 1.4
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 82 YQCPQCPYRASQKATLKTHMAIKH 105
++CP C S K LK H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 25.3 bits (55), Expect = 1.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 53 FPCEVCGKKYKYKWGLSRHKR 73
F C +CGK + K L RH R
Sbjct: 1 FKCPLCGKSFSSKDALKRHLR 21
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 1.6
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 82 YQCPQCPYRASQKATLKTHMAI 103
Y+CP+C K+ L+ HM
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
Score = 24.0 bits (52), Expect = 5.0
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 53 FPCEVCGKKYKYKWGLSRHKR 73
+ C CGK +K K L H R
Sbjct: 1 YRCPECGKVFKSKSALREHMR 21
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 25.0 bits (55), Expect = 1.9
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 68 LSRHKRDECGQEPKYQCPQCPYRASQ 93
L RH R G++P Y+CP C S
Sbjct: 2 LRRHMRTHTGEKP-YKCPVCGKSFSS 26
>gnl|CDD|200253 TIGR03225, benzo_boxB, benzoyl-CoA oxygenase, B subunit. Members
of this protein family are BoxB, the B subunit of
benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts
in an aerobic pathway of benzoate catabolism via
coenzyme A ligation [Energy metabolism, Other].
Length = 471
Score = 27.1 bits (60), Expect = 2.0
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 16 ITETCIVIRSLGVDKSLDTNVLNFINWPTVRQY 48
I TC V++ LG D L I+ PT+++Y
Sbjct: 254 IQRTCQVMKELGTDDPYRIRALGVIDLPTIQKY 286
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 27.0 bits (61), Expect = 2.4
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 8/20 (40%)
Query: 54 PCEVC-GKKY-------KYK 65
PC+VC GK+Y KYK
Sbjct: 763 PCDVCKGKRYNRETLEVKYK 782
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 26.5 bits (58), Expect = 2.6
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 49 NSGMFPCEVCGKKYKYKWGLSRHKRDEC 76
N G+ C +C ++ K + RH EC
Sbjct: 178 NEGLVQCPICQQRMPEK-AVERHLDSEC 204
>gnl|CDD|237428 PRK13564, PRK13564, anthranilate synthase component I; Provisional.
Length = 520
Score = 25.9 bits (58), Expect = 4.6
Identities = 7/7 (100%), Positives = 7/7 (100%)
Query: 19 TCIVIRS 25
TCIVIRS
Sbjct: 464 TCIVIRS 470
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 26.0 bits (57), Expect = 5.2
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 5/43 (11%)
Query: 26 LGVDKSLDTNVLNFINW-----PTVRQYNSGMFPCEVCGKKYK 63
LG ++ L FIN+ +R+ + E CG Y+
Sbjct: 460 LGSNEELIRWFKAFINYSEPEKEPLRETRKDLEKFEKCGPSYR 502
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 23.5 bits (51), Expect = 6.1
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 55 CEVCGKKYKYKWGLSRHKR 73
C CGK + K L RH R
Sbjct: 2 CPDCGKSFSRKSNLKRHLR 20
>gnl|CDD|238698 cd01407, SIR2-fam, SIR2 family of proteins includes silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation, where the
acetyl group from the lysine epsilon-amino group is
transferred to the ADP-ribose moiety of NAD+, producing
nicotinamide and the novel metabolite
O-acetyl-ADP-ribose. Sir2 proteins, also known as
sirtuins, are found in all eukaryotes and many archaea
and prokaryotes and have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
The most-studied function, gene silencing, involves the
inactivation of chromosome domains containing key
regulatory genes by packaging them into a specialized
chromatin structure that is inaccessible to DNA-binding
proteins. The oligomerization state of Sir2 appears to
be organism-dependent, sometimes occurring as a monomer
and sometimes as a multimer.
Length = 218
Score = 25.2 bits (56), Expect = 7.8
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 55 CEVCGKKYKYKWGLSRHKRDECGQEPKYQCPQC 87
C CGK+Y + R+E P+ CP+C
Sbjct: 112 CTKCGKEYPRDELQADIDREE---VPR--CPKC 139
>gnl|CDD|239922 cd04476, RPA1_DBD_C, RPA1_DBD_C: A subfamily of OB folds
corresponding to the C-terminal OB fold, the
ssDNA-binding domain (DBD)-C, of human RPA1 (also
called RPA70). RPA1 is the large subunit of Replication
protein A (RPA). RPA is a nuclear ssDNA-binding protein
(SSB) which appears to be involved in all aspects of
DNA metabolism including replication, recombination,
and repair. RPA also mediates specific interactions of
various nuclear proteins. In animals, plants, and
fungi, RPA is a heterotrimer with subunits of 70KDa
(RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to
DBD-C, RPA1 contains three other OB folds: DBD-A,
DBD-B, and RPA1N. The major DNA binding activity of RPA
is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is
involved in DNA binding and trimerization. It contains
two structural insertions not found to date in other
OB-folds: a zinc ribbon and a three-helix bundle. RPA1
DBD-C also contains a Cys4-type zinc-binding motif,
which plays a role in the ssDNA binding function of
this domain. It appears that zinc itself may not be
required for ssDNA binding.
Length = 166
Score = 25.0 bits (55), Expect = 9.0
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 44 TVRQYNSGMFPCEVCGK-----KYKYK 65
V + +G + CE C K +Y+Y
Sbjct: 43 KVVEEGNGTYRCEKCNKSVPNPEYRYI 69
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 24.9 bits (55), Expect = 10.0
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 54 PCEVCGKKYKYKWGLSRHKRDECGQEPKYQCPQC 87
PC CG++ + +W + + E + +Y CP C
Sbjct: 202 PCPHCGEEQELRWERLKWDKGEAPETARYVCPHC 235
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 0.133 0.439
Gapped
Lambda K H
0.267 0.0692 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,675,901
Number of extensions: 347236
Number of successful extensions: 334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 332
Number of HSP's successfully gapped: 37
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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 (21.9 bits)
S2: 53 (24.3 bits)