RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10080
(101 letters)
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 27.2 bits (61), Expect = 0.80
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 74 CLFCSYKCKHKTDIMHHMRLKH 95
CLFC++ + + HM H
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSH 23
Score = 26.1 bits (58), Expect = 2.0
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 73 MCLFCSYKCKHKTDIMHHMRLK 94
CL+C + K + HMR K
Sbjct: 52 ECLYCGKQFKSLEALRQHMRDK 73
>gnl|CDD|162372 TIGR01458, HAD-SF-IIA-hyp3, HAD-superfamily subfamily IIA
hydrolase, TIGR01458. This hypothetical equivalog is a
member of the IIA subfamily (TIGR01460) of the haloacid
dehalogenase superfamily of aspartate-nucleophile
hydrolases. One sequence (GP|10716807) has been
annotated as a "phospholysine phosphohistidine inorganic
pyrophosphatase," probably in reference to studies on
similarly described (but unsequenced) enzymes from
bovine and rat tissues. However, the supporting
information for this annotation has never been published
[Unknown function, Enzymes of unknown specificity].
Length = 257
Score = 27.5 bits (61), Expect = 1.1
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 1 MVGDKSTDDVFGEQDTGAQNSQ--------DDDEKMLVP 31
M+GD DDV G QD G + Q D+EK+ VP
Sbjct: 201 MIGDDCRDDVGGAQDCGMRGIQVRTGKYRPSDEEKINVP 239
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 25.9 bits (57), Expect = 1.3
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 6/39 (15%)
Query: 34 VDKEGKKTTWA-CPMCRKIYAFKY-----NLMRHLRVEC 66
+ ++ A C C K + NL RHLR +
Sbjct: 9 ILEKDNGKQRAKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47
>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 = 25.0 bits (55), Expect = 1.8
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 45 CPMCRKIYAFKYNLMRHLRV 64
CP C K ++ K NL RHLR
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|222292 pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp. Many of the members of this family carry
only the N-terminal region of Rpb11.
Length = 77
Score = 24.8 bits (55), Expect = 4.3
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 10/48 (20%)
Query: 52 YAFKYNLMRHLRVECGKEPSQMCLFCSYKCKHKTDIMHHMRLKHKEFK 99
+ L++ VE F Y H + ++R++ K K
Sbjct: 16 NLLREELLKDPDVE----------FAGYSVPHPLEDKINLRIQTKSGK 53
>gnl|CDD|223987 COG1059, COG1059, Thermostable 8-oxoguanine DNA glycosylase [DNA
replication, recombination, and repair].
Length = 210
Score = 25.8 bits (57), Expect = 4.5
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 27 KMLVPYNVDKEGKKTTWACPMCRKIYAFKYNLMRHLRVECGKEPSQMCLFCSYK 80
+ LV Y + E KT + RK+Y ++R + E G ++ L+ YK
Sbjct: 155 RWLVRYGLIDENPKT-----LTRKLYLEIEEILRSIAEEVGISLGELDLYIWYK 203
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 24.2 bits (52), Expect = 5.6
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 43 WACPMCRKIYAFKYNLMRHLR 63
+ CP+C +IY + +++ HLR
Sbjct: 6 YECPICGEIYIKRKSMITHLR 26
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and
recognises the first three GAG bases of the consensus
in a manner similar to that seen in other classical
zinc finger-DNA complexes. The second basic region
forms a helix that interacts in the major groove
recognising the last G of the consensus, while the
first basic region wraps around the DNA in the minor
groove and recognises the A in the fourth position of
the consensus sequence.
Length = 54
Score = 23.8 bits (51), Expect = 8.4
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 45 CPMCRKIYAFKYNLMRHLRVECGKEP 70
CP+C+ + NL RHL + K+P
Sbjct: 27 CPICQAVIRQSRNLRRHLELRHFKKP 52
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 25.0 bits (55), Expect = 9.6
Identities = 8/33 (24%), Positives = 9/33 (27%)
Query: 53 AFKYNLMRHLRVECGKEPSQMCLFCSYKCKHKT 85
YNL L GK Y+ H
Sbjct: 8 QLAYNLWWSLDTTAGKLFRDADPEDWYEALHNP 40
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 0.135 0.432
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,706,846
Number of extensions: 352061
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 276
Number of HSP's successfully gapped: 28
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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)