RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6628
(132 letters)
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 35.5 bits (81), Expect = 0.004
Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 12/89 (13%)
Query: 39 EERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSFFSKYDHKIHSRVH 98
+ +P +KC G C++ + +N L H+ H +Q S I S
Sbjct: 346 DGKP-YKCPVEG-CNKKYKNQNGLKYHMLHGH-------QNQKLHENPSPEKMNIFS--- 393
Query: 99 TGEKPYACEFCPLTFRHSSHLFRHRRSLH 127
+KPY CE C +++ + L HR+ H
Sbjct: 394 AKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422
Score = 28.5 bits (63), Expect = 1.1
Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 24/91 (26%)
Query: 11 VFTCQV--CSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKR 68
+ C V C+K + +NGLK H+ + H + + N +
Sbjct: 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQK-----------------LHENPSPEKMNI 391
Query: 69 DHQKEKPYQCSQCSKSFFS----KYDHKIHS 95
K+KPY+C C K + + KY H+ HS
Sbjct: 392 FSAKDKPYRCEVCDKRYKNLNGLKY-HRKHS 421
Score = 27.0 bits (59), Expect = 3.4
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 12 FTCQVCSKIFSYENGLKAHVRNKH 35
+ C+VC K + NGLK H ++ H
Sbjct: 399 YRCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 32.6 bits (75), Expect = 0.029
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 13 TCQVCSKIFSYENGLKAHVRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQK 72
+ K+F GL+ + G + + + + +G+ D + T L ++R K
Sbjct: 61 IYEELKKLFKI-LGLRVALL--TGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLK 117
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 28.5 bits (64), Expect = 0.13
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 92 KIHSRVHTGEKPYACEFCPLTFRH 115
+ H R HTGEKPY C C +F
Sbjct: 3 RRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 26.2 bits (58), Expect = 0.94
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 61 MLNIHIKRDHQKEKPYQCSQCSKSF 85
L H+ R H EKPY+C C KSF
Sbjct: 1 NLRRHM-RTHTGEKPYKCPVCGKSF 24
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 29.7 bits (66), Expect = 0.38
Identities = 17/61 (27%), Positives = 20/61 (32%)
Query: 72 KEKPYQCSQCSKSFFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSLHQMYE 131
+P C C+ SF H R HTGEKP C + S L R
Sbjct: 30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89
Query: 132 Q 132
Sbjct: 90 P 90
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 29.6 bits (66), Expect = 0.40
Identities = 24/96 (25%), Positives = 33/96 (34%), Gaps = 11/96 (11%)
Query: 43 RFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQCSQCSKSF------FSKYDHKIHSR 96
FKC + +C R + L H K H +C K F F + H
Sbjct: 151 SFKCP-KSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKN 209
Query: 97 VHTGEKPYA----CEFCPLTFRHSSHLFRHRRSLHQ 128
E+ + C FC + F L RH R H+
Sbjct: 210 GGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE 245
>gnl|CDD|184851 PRK14849, PRK14849, putative lipoprotein/autotransporter
domain-containing protein; Provisional.
Length = 1806
Score = 29.7 bits (66), Expect = 0.45
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 31 VRNKHGSSEERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEKPYQ 77
V++ + ++ R + EG G + LN H +RD K++ +Q
Sbjct: 1686 VKDSDHTRKDGTRIETEGDGNVQTRLGVKTYLNSHHQRDDGKQREFQ 1732
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 27.4 bits (62), Expect = 2.4
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 9 RVVFTCQVCSKIFSYENGLKAHV 31
+ + + F YENGLK ++
Sbjct: 205 TITLNDERERQTFHYENGLKDYL 227
>gnl|CDD|234440 TIGR04013, B12_SAM_MJ_1487, B12-binding domain/radical SAM domain
protein, MJ_1487 family. Members of this family have
both a B12 binding homology domain (pfam02310) and a
radical SAM domain (pfam04055), and occur only once per
genome. Some species with members of this family have a
related protein with similar domain architecture. This
protein is occurs largely in archaeal methanogens but
also in a few bacteria, including Thermotoga maritima
and Myxococcus xanthus [Unknown function, Enzymes of
unknown specificity].
Length = 382
Score = 26.8 bits (60), Expect = 3.5
Identities = 7/26 (26%), Positives = 10/26 (38%), Gaps = 2/26 (7%)
Query: 103 PYACEFCPLTFRHSSHLFRHRRSLHQ 128
P+ C +C RH RS+
Sbjct: 161 PFGCAYCQTPRIF-GRRMRH-RSIES 184
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 24.5 bits (54), Expect = 4.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 12 FTCQVCSKIFSYENGLKAHVRNK 34
F C C K F EN L+ H+++K
Sbjct: 2 FYCVACDKYFKSENALENHLKSK 24
>gnl|CDD|223056 PHA03362, PHA03362, single-stranded binding protein UL29;
Provisional.
Length = 1189
Score = 26.9 bits (60), Expect = 4.2
Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 4/19 (21%)
Query: 103 PYACEFCPLTFRHSSHLFR 121
PY+ FCP+ S L+R
Sbjct: 657 PYSSGFCPVL----SFLYR 671
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.3 bits (53), Expect = 4.3
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 76 YQCSQCSKSFFSKYDHKIHSRVH 98
Y+C +C K F SK + H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 23.8 bits (52), Expect = 5.5
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 106 CEFCPLTFRHSSHLFRHRRS 125
C C +F S+L RH R+
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|182371 PRK10309, PRK10309, galactitol-1-phosphate dehydrogenase;
Provisional.
Length = 347
Score = 26.3 bits (58), Expect = 5.9
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 76 YQCSQCSKSFFS---KYDHKIHSRVHTGEKPYAC 106
+ C +C + F+S KYD I SR G Y
Sbjct: 90 FTCPECLRGFYSLCAKYDF-IGSRRDGGNAEYIV 122
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 26.4 bits (58), Expect = 6.1
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 85 FFSKYDHKIHSRVHTGEKPYACEFCPLTFRHSSHLFRHRRSL 126
F K KI + G+ E L FR H+++ RRS+
Sbjct: 48 FTDKRTEKIEDMIKKGKNNLEVE---LEFRIGGHVYQIRRSI 86
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 26.2 bits (58), Expect = 7.0
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 5/56 (8%)
Query: 21 FSYENGLKAHVRNKHGSS--EERPRFKCEGRGECDRVFTTRNMLNIHIKRDHQKEK 74
+ K G + EER R D + T +ML+ + R+H
Sbjct: 138 LISDLPGKVTFGRYTGDTPPEERRAII---RNPPDILLTNPDMLHYLLLRNHDAWL 190
>gnl|CDD|203088 pfam04780, DUF629, Protein of unknown function (DUF629). This
family represents a region of several plant proteins of
unknown function. A C2H2 zinc finger is predicted in
this region in some family members, but the spacing
between the cysteine residues is not conserved
throughout the family.
Length = 463
Score = 26.2 bits (58), Expect = 7.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 14 CQVCSKIFSYENGLKAHVRNKH 35
C+ CSK FS K H+ +H
Sbjct: 60 CRTCSKKFSSSEECKNHLEQEH 81
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 25.9 bits (57), Expect = 7.7
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 102 KPYACEFCPLTFRHSSHLFRHRR 124
K Y CEFC + L RH +
Sbjct: 197 KLYFCEFCLKFMKRKEQLQRHMK 219
>gnl|CDD|237546 PRK13889, PRK13889, conjugal transfer relaxase TraA; Provisional.
Length = 988
Score = 25.8 bits (57), Expect = 8.1
Identities = 11/16 (68%), Positives = 13/16 (81%), Gaps = 2/16 (12%)
Query: 47 EGRGECDRVFTTRNML 62
+GRGE DR FTTR M+
Sbjct: 294 DGRGE-DR-FTTRAMI 307
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
0.326 0.135 0.440
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,275,242
Number of extensions: 497374
Number of successful extensions: 666
Number of sequences better than 10.0: 1
Number of HSP's gapped: 659
Number of HSP's successfully gapped: 66
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.2 bits)