RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11070
(148 letters)
>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 = 0.048
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 58 SCPIKNCNKRFTTLSNLKMHMVRH 81
CP C K F+ SNLK H+ H
Sbjct: 1 KCPD--CGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.0 bits (65), Expect = 0.12
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 57 WSCPIKNCNKRFTTLSNLKMHMVRH 81
+ CP C K F + S L+ HM H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.5 bits (68), Expect = 0.27
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 10/77 (12%)
Query: 15 KELNKEIDDEEDAITEALQSLGINKEYFISSTGGKN---------SKKQQLWSCPIKNCN 65
KE+ I E L + ++ G +N K + + CP++ CN
Sbjct: 299 KEIRGGISTGEMIDVRKLPCTNSSSNGKLAHGGERNIDTPSRMLKVKDGKPYKCPVEGCN 358
Query: 66 KRFTTLSNLKMHMVRHG 82
K++ + LK HM HG
Sbjct: 359 KKYKNQNGLKYHM-LHG 374
>gnl|CDD|218670 pfam05639, Pup, Pup-like protein. This family consists of
several short bacterial proteins formely known as
(DUF797). It was recently shown that Mycobacterium
tuberculosis contains a small protein, Pup (Rv2111c),
that is covalently conjugated to the e-NH2 groups of
lysines on several target proteins (pupylation) such as
the malonyl CoA acyl carrier protein (FabD). Pupylation
of FabD was shown to result in its recruitment to the
mycobacterial proteasome and subsequent degradation
analogous to eukaryotic ubiquitin-conjugated proteins.
Searches recovered Pup orthologs in all major
actinobacteria lineages including the basal
bifidobacteria and also sporadically in certain other
bacterial lineages. The Pup proteins were all between
50-90 residues in length and a multiple alignment shows
that they all contain a conserved motif with a G [EQ]
signature at the C-terminus. Thus, all of them are
suitable for conjugation via the terminal glutamate or
the deamidated glutamine (as shown in the case of the
Mycobacterium Pup). The conserved globular core of Pup
is predicted to form a bihelical unit with the extreme
C-terminal 6-7 residues forming a tail in the extended
conformation. Thus, Pup is structurally unrelated to
the ubiquitin fold and has convergently evolved the
function of protein modifier.
Length = 66
Score = 27.8 bits (62), Expect = 0.55
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 3 VATASSDSEGKTKELNKEIDDEEDAITEALQSLGINKEYFISS 45
A A++D + ++L +++DD D I + L+ N E F+ S
Sbjct: 20 TAEATADGAERREKLTEDVDDLLDEIDDVLEE---NAEEFVRS 59
>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 = 0.57
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 57 WSCPIKNCNKRFTTLSNLKMHMVRH 81
+ CP+ C K F++ LK H+ +H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 28.8 bits (65), Expect = 0.93
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 4 ATASSDSEGKTKELNKEIDDEEDAITEALQ 33
A A + +EG+ EL +E+D E+ AL
Sbjct: 108 AGAGAAAEGRAGELAQELDSEKQVSARALA 137
>gnl|CDD|235716 PRK06149, PRK06149, hypothetical protein; Provisional.
Length = 972
Score = 28.8 bits (65), Expect = 1.1
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 4/22 (18%)
Query: 27 AITEALQSLGINKEYFISSTGG 48
I EAL++ G YF SSTGG
Sbjct: 830 EIAEALEAEG----YFFSSTGG 847
>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 = 29.0 bits (65), Expect = 1.2
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 43 ISSTGGKNSKKQQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMK 102
+ + GG ++ + N K +S + P + C C +F +M
Sbjct: 30 VDNDGGIKTQPTSDSIAAVANATKPAAVISPPQSKKATPINPSSYVCNV--CMAEFSSMD 87
Query: 103 QYSTHLK-EHSNVSA 116
Q + H + HS ++
Sbjct: 88 QLAEHQRTTHSIGAS 102
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 27.7 bits (61), Expect = 2.3
Identities = 14/70 (20%), Positives = 21/70 (30%), Gaps = 4/70 (5%)
Query: 57 WSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTM----KQYSTHLKEHS 112
+SCP C K F+ LK H++ H + L KF + S +
Sbjct: 322 FSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDL 381
Query: 113 NVSAPYMCDY 122
Sbjct: 382 KNDKKSETLS 391
>gnl|CDD|220550 pfam10070, DUF2309, Uncharacterized protein conserved in bacteria
(DUF2309). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 783
Score = 28.0 bits (63), Expect = 2.5
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 22 DDEEDAITEALQSLGINKEYF 42
DD E+AI AL+ LGI + +
Sbjct: 180 DDPEEAIARALERLGIPEAAW 200
>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 = 24.4 bits (54), Expect = 3.9
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 57 WSCPIKNCNKRFTTLSNLKMHM 78
+ C + CN FT+ S LK H+
Sbjct: 1 FYCEL--CNVTFTSESQLKSHL 20
>gnl|CDD|176256 cd08296, CAD_like, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADHs), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 333
Score = 26.8 bits (60), Expect = 4.8
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 2 PVATAS-SDSEGKTKELNKE--IDDEEDAITEALQSLG 36
VA + SD ++L ID ++ + EALQ LG
Sbjct: 190 TVAISRGSDKADLARKLGAHHYIDTSKEDVAEALQELG 227
>gnl|CDD|200552 cd10926, CE4_u2, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 253
Score = 26.5 bits (59), Expect = 5.2
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 11/60 (18%)
Query: 29 TEALQSLGINKEYFISSTG---------GKNSKKQQLWSCPIKNCNKRFTTLSNLKMHMV 79
T L+ G+ Y+ +TG GK +LW+ P+ K + T K V
Sbjct: 134 TRWLEQHGVVAYYYTGNTGSGPTRTYLNGK-LVSPKLWAFPVTPFGK-YATFEEAKRGHV 191
>gnl|CDD|216497 pfam01429, MBD, Methyl-CpG binding domain. The Methyl-CpG binding
domain (MBD) binds to DNA that contains one or more
symmetrically methylated CpGs. DNA methylation in
animals is associated with alterations in chromatin
structure and silencing of gene expression. MBD has
negligible non-specific affinity for DNA. In vitro
foot-printing with MeCP2 showed the MBD can protect a 12
nucleotide region surrounding a methyl CpG pair. MBDs
are found in several Methyl-CpG binding proteins and
also DNA demethylase.
Length = 75
Score = 25.4 bits (56), Expect = 5.8
Identities = 6/38 (15%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 94 CGRKFQTMKQYSTHLKEHSNVSA-PYMCDYKGVCMSLT 130
G+KF++ + +L+++ + S D+
Sbjct: 38 TGKKFRSKSELIRYLEKNGDTSLKLEDFDFTVRSEVGR 75
>gnl|CDD|240017 cd04659, Piwi_piwi-like_ProArk, Piwi_piwi-like_ProArk: PIWI domain,
Piwi-like subfamily found in Archaea and Bacteria. RNA
silencing refers to a group of related gene-silencing
mechanisms mediated by short RNA molecules, including
siRNAs, miRNAs, and heterochromatin-related guide RNAs.
The central component of the RNA-induced silencing
complex (RISC) and related complexes is Argonaute. The
PIWI domain is the C-terminal portion of Argonaute and
consists of two subdomains, one of which provides the 5'
anchoring of the guide RNA and the other, the catalytic
site for slicing. This domain is also found in closely
related proteins, including the Piwi subfamily, where it
is believed to perform a crucial role in germline cells,
via a similar mechanism.
Length = 404
Score = 26.6 bits (59), Expect = 6.4
Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 22 DDEEDAITEALQSLGINKEYFIS 44
D+E + + EAL+ LGI + +
Sbjct: 273 DEEIEGLKEALEELGIKVD-LVE 294
>gnl|CDD|219964 pfam08670, MEKHLA, MEKHLA domain. The MEKHLA domain shares
similarity with the PAS domain and is found in the 3'
end of plant HD-ZIP III homeobox genes, and bacterial
proteins.
Length = 148
Score = 26.0 bits (58), Expect = 6.5
Identities = 5/11 (45%), Positives = 7/11 (63%)
Query: 118 YMCDYKGVCMS 128
+ C Y GV +S
Sbjct: 102 FACLYSGVRIS 112
>gnl|CDD|181749 PRK09276, PRK09276, LL-diaminopimelate aminotransferase;
Provisional.
Length = 385
Score = 26.4 bits (59), Expect = 6.6
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 5 TASSDSEGKTKELNKEIDDEEDAITEALQSLGIN 38
A + + +EL K + D + E L+ LG+
Sbjct: 282 AALNGPQEVVEELRKIYQERRDILVEGLRKLGLE 315
>gnl|CDD|234774 PRK00464, nrdR, transcriptional regulator NrdR; Validated.
Length = 154
Score = 25.9 bits (58), Expect = 7.5
Identities = 7/12 (58%), Positives = 7/12 (58%), Gaps = 2/12 (16%)
Query: 59 CPIKNCNKRFTT 70
C C KRFTT
Sbjct: 31 CL--ACGKRFTT 40
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 25.9 bits (57), Expect = 9.0
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 8 SDSEGKTKELNKEIDDEEDAITEALQSLGINKEYFISSTGGKNSKKQQL 56
S+ + + EL +E++D E+ I E L KE S +++L
Sbjct: 82 SELKQQLSELQEELEDLEERIAELESELEDLKEDLQLLRELLKSLEERL 130
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N
terminal domain). Members of this family are involved
in modifying bases in RNA molecules. They carry out the
conversion of uracil bases to pseudouridine. This
family includes TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in
most tRNAs. This family also includes Cbf5p that
modifies rRNA.
Length = 149
Score = 25.5 bits (57), Expect = 9.6
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 3 VATASSDSEGKTKELNKEIDDEEDAITEALQSL 35
VAT + D+EG+ E E+ I E L S
Sbjct: 52 VATDTLDAEGEIVEEPPVDHITEEKIEEVLASF 84
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
0.314 0.127 0.376
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,862,431
Number of extensions: 563949
Number of successful extensions: 713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 711
Number of HSP's successfully gapped: 40
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.7 bits)