RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy370
(111 letters)
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing
archaeal-type C2H2 Zn-finger [General function
prediction only].
Length = 65
Score = 28.8 bits (64), Expect = 0.16
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 42 LETHDNEMDYSCEHCDMQFNCKSDMRKHVH-SHLSMEERG 80
+ D E C C M F + D +HV+ +H + RG
Sbjct: 9 VRDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHGWLFGRG 48
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.8 bits (62), Expect = 0.19
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 51 YSCEHCDMQFNCKSDMRKHVHSH 73
Y C C F KS +R+H+ +H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.1 bits (55), Expect = 2.1
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 24 QCPVCKKIYTDQQLFQNHLETH 45
+CP C K++ + + H+ TH
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.1 bits (62), Expect = 0.25
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 24 QCPVCKKIYTDQQLFQNHLETHDNEMDYS 52
+CP+C +IY ++ HL H+ + S
Sbjct: 7 ECPICGEIYIKRKSMITHLRKHNTNLKLS 35
>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 = 27.3 bits (61), Expect = 0.29
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 24 QCPVCKKIYTDQQLFQNHLETH 45
+CP C K ++ + + HL TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>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 = 26.8 bits (59), Expect = 0.38
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 51 YSCEHCDMQFNCKSDMRKHVHSH 73
+ C C F+ K +++H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.1 bits (52), Expect = 4.5
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 24 QCPVCKKIYTDQQLFQNHLETH 45
+CP+C K ++ + + HL H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 26.7 bits (60), Expect = 0.41
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 51 YSCEHCDMQFNCKSDMRKHVHSH 73
+ CE C++ F +S ++ H+
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGK 23
Score = 24.0 bits (53), Expect = 5.0
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 25 CPVCKKIYTDQQLFQNHL 42
C +C +T + ++HL
Sbjct: 3 CELCNVTFTSESQLKSHL 20
>gnl|CDD|235761 PRK06266, PRK06266, transcription initiation factor E subunit
alpha; Validated.
Length = 178
Score = 28.0 bits (63), Expect = 0.76
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 11/52 (21%)
Query: 42 LETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93
LE +N M + C +C ++F M E GF C CG +++E
Sbjct: 109 LEEEENNMFFFCPNCHIRFTFDEAM-----------EYGFRCPQCGEMLEEY 149
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 25.8 bits (57), Expect = 0.95
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 38 FQNHLETHDNEMDYSCEHCDMQFNC 62
+ H+ TH E Y C C F+
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 27.9 bits (62), Expect = 1.2
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 10/51 (19%)
Query: 28 CKKIYTDQQ---LFQNHLETHDNE-------MDYSCEHCDMQFNCKSDMRK 68
K I T +Q F+ +E +D E + S +H D N +
Sbjct: 467 AKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDL 517
>gnl|CDD|128804 smart00531, TFIIE, Transcription initiation factor IIE.
Length = 147
Score = 27.0 bits (60), Expect = 1.6
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 6/52 (11%)
Query: 42 LETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93
LE N Y C +C ++ + L + F C CG ++E
Sbjct: 91 LEDETNNAYYKCPNCQSKYTFLEANQ------LLDMDGTFTCPRCGEELEED 136
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 27.3 bits (60), Expect = 1.7
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 11/64 (17%)
Query: 30 KIYTDQQLFQNHLETHDNEMDYS----CEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEI 85
+++ L ++H E + C C + F ++R+H R C I
Sbjct: 197 RLFRSSTL-RDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRH------CRLRHEACHI 249
Query: 86 CGHV 89
C V
Sbjct: 250 CDMV 253
>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 = 27.3 bits (60), Expect = 1.7
Identities = 6/43 (13%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 7 QMQSEIIPGSYTIFVAS-------QCPVCKKIYTDQQLFQNHL 42
Q+ S+ + + + QCP+C++ ++ + ++
Sbjct: 159 QLSSDPSKRNDADYRSEPPNEGLVQCPICQQRMPEKAVERHLD 201
>gnl|CDD|239265 cd02967, mauD, Methylamine utilization (mau) D family; mauD
protein is the translation product of the mauD gene
found in methylotrophic bacteria, which are able to use
methylamine as a sole carbon source and a nitrogen
source. mauD is an essential accessory protein for the
biosynthesis of methylamine dehydrogenase (MADH), the
enzyme that catalyzes the oxidation of methylamine and
other primary amines. MADH possesses an alpha2beta2
subunit structure; the alpha subunit is also referred
to as the large subunit. Each beta (small) subunit
contains a tryptophan tryptophylquinone (TTQ)
prosthetic group. Accessory proteins are essential for
the proper transport of MADH to the periplasm, TTQ
synthesis and the formation of several structural
disulfide bonds. Bacterial mutants containing an
insertion on the mauD gene were unable to grow on
methylamine as a sole carbon source, were found to lack
the MADH small subunit and had decreased amounts of the
MADH large subunit.
Length = 114
Score = 26.6 bits (59), Expect = 1.9
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 12 IIPGSYTI--FVASQCPVCKKI 31
I PG T+ F++ CPVCKK+
Sbjct: 18 ISPGRPTLLFFLSPTCPVCKKL 39
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 26.9 bits (60), Expect = 1.9
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 13/50 (26%)
Query: 51 YSCEHCDMQFNCKSDMRKHVHSHLSMEERG-FVCEICGHVVDEMPVATQS 99
SC C S + + ERG VC CG V+++ +
Sbjct: 2 MSCP------ECGSTNI--ITDY----ERGEIVCADCGLVLEDSLIDPGP 39
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 26.7 bits (60), Expect = 2.3
Identities = 6/13 (46%), Positives = 7/13 (53%)
Query: 46 DNEMDYSCEHCDM 58
DNE YS D+
Sbjct: 314 DNEWGYSNRVVDL 326
>gnl|CDD|234758 PRK00423, tfb, transcription initiation factor IIB; Reviewed.
Length = 310
Score = 26.9 bits (60), Expect = 2.5
Identities = 9/16 (56%), Positives = 11/16 (68%), Gaps = 1/16 (6%)
Query: 78 ERG-FVCEICGHVVDE 92
ERG VC CG V++E
Sbjct: 27 ERGEIVCADCGLVIEE 42
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding. The transcription
factor TFIIB contains a zinc-binding motif near the
N-terminus. This domain is involved in the interaction
with RNA pol II and TFIIF and plays a crucial role in
selecting the transcription initiation site. The domain
adopts a zinc ribbon like structure.
Length = 40
Score = 24.9 bits (55), Expect = 2.6
Identities = 8/20 (40%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 77 EERG-FVCEICGHVVDEMPV 95
ERG +VC CG V+++ +
Sbjct: 15 YERGEYVCTECGLVLEDNII 34
>gnl|CDD|129469 TIGR00373, TIGR00373, transcription factor E. This family of
proteins is, so far, restricted to archaeal genomes. The
family appears to be distantly related to the N-terminal
region of the eukaryotic transcription initiation factor
IIE alpha chain [Transcription, Transcription factors].
Length = 158
Score = 26.4 bits (58), Expect = 2.6
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 11/52 (21%)
Query: 42 LETHDNEMDYSCEHCDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEM 93
LE N M + C + ++F M E F C CG ++D +
Sbjct: 101 LEFETNNMFFICPNMCVRFTFNEAM-----------ELNFTCPRCGAMLDYL 141
>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 = 3.1
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 25 CPVCKKIYTDQQLFQNHLET 44
C C K + + +NHL++
Sbjct: 4 CVACDKYFKSENALENHLKS 23
>gnl|CDD|218228 pfam04720, DUF506, Protein of unknown function (DUF506). Family of
uncharacterized plant proteins.
Length = 218
Score = 26.3 bits (58), Expect = 3.1
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 62 CKSDMRKHVHSHLSMEERGFVCEIC 86
+S +R+ V S L E G+ IC
Sbjct: 85 NRSCLRRKVMSLL--RELGYDAAIC 107
>gnl|CDD|225995 COG3464, COG3464, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 402
Score = 26.7 bits (59), Expect = 3.3
Identities = 10/66 (15%), Positives = 17/66 (25%), Gaps = 11/66 (16%)
Query: 19 IFVASQCPVCK---KIYTDQQLFQ-NHLET-------HDNEMDYSCEHCDMQFNCKSDMR 67
+ +CP C ++ + L + Y C C +F K D
Sbjct: 35 MPRKHRCPECGQRTIRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRFAEKVDFV 94
Query: 68 KHVHSH 73
Sbjct: 95 DRAQRI 100
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type
zinc fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 24.5 bits (54), Expect = 3.6
Identities = 4/24 (16%), Positives = 11/24 (45%)
Query: 50 DYSCEHCDMQFNCKSDMRKHVHSH 73
+ C+ C++ F + + H+
Sbjct: 3 GFYCKLCNVTFTDEISVEAHLKGK 26
>gnl|CDD|185542 PTZ00293, PTZ00293, thymidine kinase; Provisional.
Length = 211
Score = 26.2 bits (58), Expect = 3.7
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 25 CPVCKKIYTDQQLFQNHLETHD 46
C+K + +QL + LE D
Sbjct: 169 IATCRKCFRTKQLAEKELEKQD 190
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma
subunit. The RNA polymerase gamma subunit, encoded by
the rpoC1 gene, is found in cyanobacteria and
corresponds to the N-terminal region the beta' subunit,
encoded by rpoC, in other bacteria. The equivalent
subunit in plastids and chloroplasts is designated
beta', while the product of the rpoC2 gene is
designated beta''.
Length = 619
Score = 26.1 bits (57), Expect = 4.6
Identities = 14/40 (35%), Positives = 17/40 (42%)
Query: 56 CDMQFNCKSDMRKHVHSHLSMEERGFVCEICGHVVDEMPV 95
C+ F D H + + RG VCE CG V E V
Sbjct: 52 CEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRV 91
>gnl|CDD|216792 pfam01927, DUF82, Protein of unknown function DUF82. This
prokaryotic protein family has no known function. The
protein contains four conserved cysteines that may be
involved in metal binding or disulphide bridges.
Length = 146
Score = 25.3 bits (56), Expect = 5.7
Identities = 6/20 (30%), Positives = 10/20 (50%), Gaps = 2/20 (10%)
Query: 13 IPGSYTIFVASQCPVCKKIY 32
+ Y F +CP C ++Y
Sbjct: 116 VYERYDEF--WRCPKCGRVY 133
>gnl|CDD|222444 pfam13901, DUF4206, Domain of unknown function (DUF4206). This is
a family of cysteine-rich proteins. Many members also
carry a pleckstrin-homology domain, pfam00169.
Length = 202
Score = 25.3 bits (56), Expect = 7.3
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 67 RKHVHSHLSMEERGFVCEICGH 88
+HV S +GF+CE C +
Sbjct: 139 EEHVTSCELCTGKGFICEFCDN 160
>gnl|CDD|189494 pfam00301, Rubredoxin, Rubredoxin.
Length = 47
Score = 23.9 bits (52), Expect = 8.1
Identities = 6/12 (50%), Positives = 10/12 (83%)
Query: 81 FVCEICGHVVDE 92
+VC++CG+V D
Sbjct: 2 YVCKVCGYVYDP 13
>gnl|CDD|129606 TIGR00515, accD, acetyl-CoA carboxylase, carboxyl transferase,
beta subunit. The enzyme acetyl-CoA carboxylase
contains a biotin carboxyl carrier protein or domain, a
biotin carboxylase, and a carboxyl transferase. This
model represents the beta chain of the carboxyl
transferase for cases in which the architecture of the
protein is as in E. coli, in which the
carboxyltransferase portion consists of two
non-identical subnits, alpha and beta [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 285
Score = 25.1 bits (55), Expect = 8.7
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 14/59 (23%)
Query: 11 EIIPGSYTIFVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCEHCDMQFNCKSDMRKH 69
E+ G +T +CP C ++ ++L +N C CD + R
Sbjct: 20 EVPEGVWT-----KCPKCGQVLYTKELERNL---------EVCPKCDHHMRMDARERIE 64
>gnl|CDD|237118 PRK12496, PRK12496, hypothetical protein; Provisional.
Length = 164
Score = 25.0 bits (55), Expect = 8.8
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 82 VCEICGHVVDEMPVATQSSK 101
VCEICG V V + K
Sbjct: 145 VCEICGSPVKRKMVKRRLKK 164
>gnl|CDD|216902 pfam02146, SIR2, Sir2 family. This region is characteristic of
Silent information regulator 2 (Sir2) proteins, or
sirtuins. These are protein deacetylases that depend on
nicotine adenine dinucleotide (NAD). They are found in
many subcellular locations, including the nucleus,
cytoplasm and mitochondria. Eukaryotic forms play in
important role in the regulation of transcriptional
repression. Moreover, they are involved in microtubule
organisation and DNA damage repair processes.
Length = 177
Score = 24.9 bits (55), Expect = 9.3
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 12/52 (23%)
Query: 20 FVASQCPVCKKIYTDQQLFQNHLETHDNEMDYSCE-HCDMQFNCKSDMRKHV 70
F ++C C K YT + L +D + CD C ++ +
Sbjct: 102 FAKARCVSCHKKYTGETLP--------ERIDAAKVPKCD---KCGGLLKPDI 142
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
0.322 0.133 0.421
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,155,547
Number of extensions: 389003
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 60
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (22.0 bits)
S2: 53 (24.1 bits)