RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2647
(72 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 32.0 bits (73), Expect = 0.002
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 26 NLITHSRKHTGFKPFACDLCGRAF 49
NL H R HTG KP+ C +CG++F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSF 24
Score = 27.7 bits (62), Expect = 0.093
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 7 HGEKPHKCQVCGKAFSQ 23
GEKP+KC VCGK+FS
Sbjct: 10 TGEKPYKCPVCGKSFSS 26
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 33.9 bits (77), Expect = 0.003
Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 10 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQHTEMRP 68
+P C C +FS+ +L H R HTG KP C G R + ++H
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFS---RPLELSRHLRTHH 87
Score = 30.4 bits (68), Expect = 0.049
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 10 KPHKCQVCGKAFSQSSNLITHSRK--HTG--FKPFACD--LCGRAFQRKVDLRRHKETQH 63
P K + C +FS+SS L H R H+G KPF+C LCG+ F R L+RH
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347
Score = 28.1 bits (62), Expect = 0.30
Identities = 14/43 (32%), Positives = 17/43 (39%), Gaps = 2/43 (4%)
Query: 7 HGEKPHKC--QVCGKAFSQSSNLITHSRKHTGFKPFACDLCGR 47
KP C +CGK FS++ L H HT P L
Sbjct: 317 ESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNS 359
Score = 26.6 bits (58), Expect = 1.1
Identities = 14/59 (23%), Positives = 24/59 (40%)
Query: 2 ISNIWHGEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKE 60
I+++ K C K+F++ NLI H + HT P C + + K+
Sbjct: 409 ITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDLSNHGKD 467
>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 = 30.0 bits (68), Expect = 0.011
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 13 KCQVCGKAFSQSSNLITHSRKH 34
KC CGK+FS+ SNL H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 22.7 bits (49), Expect = 6.7
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 42 CDLCGRAFQRKVDLRRHKET 61
C CG++F RK +L+RH T
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 31.6 bits (71), Expect = 0.015
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 21/77 (27%)
Query: 8 GEKPHKCQV--CGKAFSQSSNLITHSR---------------KHTGF----KPFACDLCG 46
KP+KC V C K + + L H K F KP+ C++C
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 47 RAFQRKVDLRRHKETQH 63
+ ++ L+ H++ H
Sbjct: 406 KRYKNLNGLKYHRKHSH 422
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 27.6 bits (62), Expect = 0.080
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 12 HKCQVCGKAFSQSSNLITHSRKH 34
H C VCGK FS L H + H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.4 bits (61), Expect = 0.10
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 12 HKCQVCGKAFSQSSNLITHSRKH 34
++C CGK F S L H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 22.4 bits (48), Expect = 8.5
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 40 FACDLCGRAFQRKVDLRRHKET 61
+ C CG+ F+ K LR H T
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.1 bits (62), Expect = 0.12
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 12 HKCQVCGKAFSQSSNLITHSRKH 34
++C +CG+ + + ++ITH RKH
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH 28
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 27.9 bits (62), Expect = 0.30
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCGRAFQRKVDLRRHKETQH 63
P+ C +C FS S +L H R K C +CG+ F+ H +H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDHVCKKH 123
Score = 26.4 bits (58), Expect = 1.1
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 1 MISNIWHGEKPHKCQVCGKAFSQSSNLITH-SRKH 34
+ +I + E C VCGK F + + + H +KH
Sbjct: 89 LKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
>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 = 0.66
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 40 FACDLCGRAFQRKVDLRRHKETQH 63
F C LCG++F K L+RH H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 23.0 bits (49), Expect = 5.6
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 12 HKCQVCGKAFSQSSNLITHSRKH 34
KC +CGK+FS L H RKH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of
the virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA
plus-strand. lambda1 is an Orthoreovirus core protein,
VP3 is the homologous core protein in Aquareoviruses.
Length = 1166
Score = 27.0 bits (60), Expect = 0.68
Identities = 8/21 (38%), Positives = 9/21 (42%)
Query: 12 HKCQVCGKAFSQSSNLITHSR 32
+ C VC FS L H R
Sbjct: 74 YVCNVCMAEFSSMDQLAEHQR 94
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 25.5 bits (56), Expect = 2.2
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 38 KPFACDLCGRAFQRKVDLRRHKETQHTEMRPVP 70
K + C+ C + +RK L+RH + +++ P
Sbjct: 197 KLYFCEFCLKFMKRKEQLQRHMKK--CDLKHPP 227
>gnl|CDD|218738 pfam05766, NinG, Bacteriophage Lambda NinG protein. NinG or Rap
is involved in recombination. Rap (recombination adept
with plasmid) increases lambda-by-plasmid recombination
catalyzed by Escherichia coli's RecBCD pathway.
Length = 188
Score = 25.0 bits (55), Expect = 3.1
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 10 KPHKCQVCGKAF 21
KP KC+VCG F
Sbjct: 5 KPKKCKVCGVYF 16
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 25.1 bits (56), Expect = 3.3
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 6/38 (15%)
Query: 8 GEKPHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLC 45
+K C CGK+ + LI G + CD C
Sbjct: 6 SKKLLYCSFCGKSQHEVRKLI------AGPGVYICDEC 37
>gnl|CDD|220438 pfam09845, DUF2072, Zn-ribbon containing protein (DUF2072). This
archaeal protein has no known function.
Length = 121
Score = 24.7 bits (54), Expect = 3.5
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 11 PHKCQVCGKAFSQSSNLI 28
PH+C CGK F S I
Sbjct: 1 PHRCTKCGKIFEDGSTEI 18
>gnl|CDD|234736 PRK00359, rpmB, 50S ribosomal protein L28; Reviewed.
Length = 76
Score = 24.4 bits (54), Expect = 3.9
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 13 KCQVCGKAFSQSSNLITHSRKHT 35
C++ GK N ++HS T
Sbjct: 4 VCEITGKG-PMVGNNVSHSNNKT 25
>gnl|CDD|225899 COG3364, COG3364, Zn-ribbon containing protein [General function
prediction only].
Length = 112
Score = 24.5 bits (53), Expect = 5.2
Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 11 PHKCQVCGKAFSQSSNLITHSRKHTGFKPFACDLCG-RAFQRKVDLRRHKETQHTE 65
PH+C CG+ F S I C CG F + +R + +
Sbjct: 2 PHQCTRCGEVFDDGSEEILS----------GCPKCGCNKFLYVPEEKRPAVAEAAD 47
>gnl|CDD|217739 pfam03802, CitX, Apo-citrate lyase phosphoribosyl-dephospho-CoA
transferase.
Length = 171
Score = 24.5 bits (54), Expect = 5.7
Identities = 12/28 (42%), Positives = 13/28 (46%)
Query: 31 SRKHTGFKPFACDLCGRAFQRKVDLRRH 58
SR G P C LCGR + RRH
Sbjct: 124 SRTDLGLPPRRCLLCGRPAKACARSRRH 151
>gnl|CDD|199985 TIGR00009, L28, ribosomal protein L28. This model describes
bacterial and chloroplast forms of the 50S ribosomal
protein L28, a polypeptide about 60 amino acids in
length. Mitochondrial homologs differ substantially in
architecture and are not included [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 56
Score = 23.4 bits (51), Expect = 6.4
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 13 KCQVCGKAFSQSSNLITHSRKHTG--FKP 39
KCQ+ GK S N ++HS + T FKP
Sbjct: 4 KCQLTGKG-PLSGNNVSHSHRKTKRRFKP 31
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 24.2 bits (52), Expect = 7.8
Identities = 9/24 (37%), Positives = 9/24 (37%)
Query: 37 FKPFACDLCGRAFQRKVDLRRHKE 60
F C CGR F R H E
Sbjct: 236 FPKVYCVKCGREFSRSKVFEYHLE 259
>gnl|CDD|223305 COG0227, RpmB, Ribosomal protein L28 [Translation, ribosomal
structure and biogenesis].
Length = 77
Score = 23.4 bits (51), Expect = 8.8
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 13 KCQVCGKAFSQSSNLITHSRKHTG--FKP 39
+CQ+ GK S N ++HS T F P
Sbjct: 4 RCQLTGK-GPMSGNNVSHSHNKTKRRFLP 31
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
0.324 0.134 0.445
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: 3,325,614
Number of extensions: 215361
Number of successful extensions: 329
Number of sequences better than 10.0: 1
Number of HSP's gapped: 327
Number of HSP's successfully gapped: 46
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)