RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6808
(132 letters)
>gnl|CDD|198091 smart01023, BAF, Barrier to autointegration factor.
Barrier-to-autointegration factor (BAF) is an essential
protein that is highly conserved in metazoan evolution,
and which may act as a DNA-bridging protein. BAF binds
directly to double-stranded DNA, to transcription
activators, and to inner nuclear membrane proteins,
including lamin A filament proteins that anchor
nuclear-pore complexes in place, and nuclear LEM-domain
proteins that bind to laminins filaments and chromatin.
New findings suggest that BAF has structural roles in
nuclear assembly and chromatin organization, represses
gene expression and might interlink chromatin
structure, nuclear architecture and gene regulation in
metazoans. BAF can be exploited by retroviruses to act
as a host component of pre-integration complexes, which
promote the integration of the retroviral DNA into the
host chromosome by preventing autointegration of
retroviral DNA. BAF might contribute to the assembly or
activity of retroviral pre-integration complexes
through direct binding to the retroviral proteins p55
Gag and matrix, as well as to DNA.
Length = 87
Score = 81.6 bits (202), Expect = 1e-21
Identities = 32/41 (78%), Positives = 38/41 (92%)
Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
+TSQKH+NFV EPMGEKPVT LAG+G+VLG RLE+KGFDK+
Sbjct: 1 TTSQKHRNFVGEPMGEKPVTALAGIGEVLGGRLETKGFDKA 41
>gnl|CDD|111809 pfam02961, BAF, Barrier to autointegration factor. The BAF
protein has a SAM-domain-like bundle of orthogonally
packed alpha-hairpins - one classic and one pseudo
helix-hairpin-helix motif. The protein is involved in
the prevention of retroviral DNA integration.
Length = 89
Score = 81.3 bits (201), Expect = 2e-21
Identities = 32/41 (78%), Positives = 38/41 (92%)
Query: 29 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69
+TSQKH+NFVSEPMG+KPVT LAG+G+VLG RLE KGFDK+
Sbjct: 3 TTSQKHRNFVSEPMGDKPVTALAGIGEVLGGRLEDKGFDKA 43
>gnl|CDD|176453 cd00424, PolY, Y-family of DNA polymerases. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active
sites of TLS polymerases are large and flexible to allow
the accomodation of distorted bases. Most TLS
polymerases are members of the Y-family, including Pol
eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is
found exclusively in bacteria. In eukaryotes, the
B-family polymerase Pol zeta also functions as a TLS
polymerase. Expression of Y-family polymerases is often
induced by DNA damage and is believed to be highly
regulated. TLS is likely induced by the
monoubiquitination of the replication clamp PCNA, which
provides a scaffold for TLS polymerases to bind in order
to access the lesion. Because of their high error
rates, TLS polymerases are potential targets for cancer
treatment and prevention.
Length = 343
Score = 34.3 bits (79), Expect = 0.012
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 20 SPTQELAKMSTSQKHQN--------FVSEPMGEKPVTELAGVGDVLGKRLESKG 65
+ + LAK++ + + + + P+T+L G+G V KRLE+ G
Sbjct: 140 ASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRLEAVG 193
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 32.9 bits (76), Expect = 0.031
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 40 EPMGEKPVTELAGVGDVLGKRLESKGFD 67
E M EK + +L GVG ++L G+D
Sbjct: 1 EKMKEKDLEDLPGVGPATAEKLREAGYD 28
>gnl|CDD|204747 pfam11798, IMS_HHH, IMS family HHH motif. These proteins are
involved in UV protection, eg.
Length = 32
Score = 29.3 bits (67), Expect = 0.060
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 38 VSEPMGEKPVTELAGVGDVLGKRLESKG 65
V E + P++++ G+G ++LE+ G
Sbjct: 4 VPEFLWPLPISKIPGIGRKTAEKLEALG 31
>gnl|CDD|179473 PRK02794, PRK02794, DNA polymerase IV; Provisional.
Length = 419
Score = 29.9 bits (68), Expect = 0.31
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 42 MGEKPVTELAGVGDVLGKRLESKGF 66
+ KPV + GVG RL G
Sbjct: 206 LAPKPVGIIWGVGPATAARLARDGI 230
>gnl|CDD|190724 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal
domain.
Length = 74
Score = 28.2 bits (64), Expect = 0.45
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 45 KPVTELAGVGDVLGKRLESK 64
+ V ELAG+ DVL K L S+
Sbjct: 28 RAVLELAGIKDVLAKSLGSR 47
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 29.2 bits (66), Expect = 0.50
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 20 SPTQELAKMSTSQKHQN--FVSEP------MGEKPVTELAGVGDVLGKRLESKGF 66
S + LAK+++ + V EP + + PV E GVG V ++L G
Sbjct: 143 SDNKFLAKIASDLNKPDGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLRRLGI 197
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa. Pol IV, also
known as Pol kappa, DinB, and Dpo4, is a translesion
synthesis (TLS) polymerase. Translesion synthesis is a
process that allows the bypass of a variety of DNA
lesions. TLS polymerases lack proofreading activity and
have low fidelity and low processivity. They use
damaged DNA as templates and insert nucleotides opposite
the lesions. Known primarily as Pol IV in prokaryotes
and Pol kappa in eukaryotes, this polymerase has a
propensity for generating frameshift mutations. The
eukaryotic Pol kappa differs from Pol IV and Dpo4 by an
N-terminal extension of ~75 residues known as the
"N-clasp" region. The structure of Pol kappa shows DNA
that is almost totally encircled by Pol kappa, with the
N-clasp region augmenting the interactions between DNA
and the polymerase. Pol kappa is more resistant than Pol
eta and Pol iota to bulky guanine adducts and is
efficient at catalyzing the incorporation of dCTP.
Bacterial pol IV has a higher error rate than other
Y-family polymerases.
Length = 334
Score = 29.0 bits (66), Expect = 0.73
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 20 SPTQELAKMSTSQKHQN--FVSEP------MGEKPVTELAGVGDVLGKRLESKGF 66
+P + LAK+++ N V P + PV ++ GVG V ++L+ G
Sbjct: 138 APNKFLAKIASDLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLKELGI 192
>gnl|CDD|179595 PRK03564, PRK03564, formate dehydrogenase accessory protein FdhE;
Provisional.
Length = 309
Score = 28.5 bits (64), Expect = 1.1
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 56 VLGKRLESKGFDKS-INPQMFPDPDI 80
VL R+E +GF +S INP +FP
Sbjct: 284 VLDARMEQEGFARSSINPFLFPGEGE 309
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 27.8 bits (63), Expect = 1.2
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 41 PMGEKPVTELAGVGDVLGKRLES 63
+ + V ELAGV DVL K L S
Sbjct: 112 AV--RAVLELAGVKDVLAKSLGS 132
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 27.9 bits (63), Expect = 1.3
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 45 KPVTELAGVGDVLGKRLESK 64
+ V ELAG+ DVL K L S+
Sbjct: 126 RAVLELAGIKDVLAKSLGSR 145
>gnl|CDD|227895 COG5608, COG5608, LEA14-like dessication related protein [Defense
mechanisms].
Length = 161
Score = 27.8 bits (62), Expect = 1.4
Identities = 12/45 (26%), Positives = 14/45 (31%), Gaps = 16/45 (35%)
Query: 69 SINPQMFPDPDIE--------------EKVLLFK--NPNSLPIPI 97
S P +E E V K NPN PIP+
Sbjct: 24 SGCMIPVKKPGVESMKAKWGKVTNSETEIVGTLKIYNPNPFPIPV 68
>gnl|CDD|129252 TIGR00148, TIGR00148, UbiD family decarboxylase. The member of
this family in E. coli is UbiD,
3-octaprenyl-4-hydroxybenzoate carboxy-lyase. The family
described by This model, however, is broad enough that
it is likely to contain several different
decarboxylases. Found in bacteria, archaea, and yeast,
with two members in A. fulgidus. No homologs were
detected besides those classified as orthologs. The
member from H. pylori has a C-terminal extension of just
over 100 residues that is shared in part by the Aquifex
aeolicus homolog [Unknown function, General].
Length = 438
Score = 28.1 bits (63), Expect = 1.4
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 59 KRLESKGFDKSINPQMFPDPDIEE----------KVLLFKNPNSLPIPIGVEVLG 103
+ LE +G I ++ PD ++ E LLFKNP P+ + + G
Sbjct: 6 QLLEKEGELLRITEEVDPDLEVAEIARRALRAGGPALLFKNPKGYGFPVLMNLFG 60
>gnl|CDD|151411 pfam10964, DUF2766, Protein of unknown function (DUF2766). This
family of proteins with unknown function appears to be
restricted to Enterobacteriaceae.
Length = 79
Score = 26.5 bits (58), Expect = 2.0
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 20 SPTQELAKMSTSQKHQNFVSEPMGEKPVTELA 51
+P + KMS+ K+ +F + P PVT A
Sbjct: 33 APAEVRDKMSSQLKNIDFGTHPAAADPVTRRA 64
>gnl|CDD|239496 cd03402, Band_7_2, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing
proteins are lipid raft-associated. Individual
proteins of this band 7 domain family may cluster to
form membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units
with their own regulatory functions. Flotillins have
been implicated in signal transduction, vesicle
trafficking, cytoskeleton rearrangement and are known
to interact with a variety of proteins. Stomatin
interacts with and regulates members of the
degenerin/epithelia Na+ channel family in
mechanosensory cells of Caenorhabditis elegans and
vertebrate neurons and participates in trafficking of
Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth
during lambda phage infection. Flotillins have been
implicated in the progression of prion disease, in the
pathogenesis of neurodegenerative diseases such as
Parkinson's and Alzheimer's disease and, in cancer
invasion and metastasis. Mutations in the podicin gene
give rise to autosomal recessive steroid resistant
nephritic syndrome.
Length = 219
Score = 27.3 bits (61), Expect = 2.2
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 9/38 (23%)
Query: 16 WPFTSPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGV 53
PF+S K S + +NF SE + V + G
Sbjct: 32 NPFSS------KKRVSLRVRNFESEKL---KVNDANGN 60
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle
type. This model finds chloroplast ribosomal protein S5
as well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included
in this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 26.9 bits (60), Expect = 2.4
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 45 KPVTELAGVGDVLGKRLES 63
+ + ELAGV D+L K L S
Sbjct: 103 RAILELAGVKDILAKSLGS 121
>gnl|CDD|177296 PHA00728, PHA00728, hypothetical protein.
Length = 151
Score = 26.8 bits (59), Expect = 2.5
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 43 GEKPVTELAGVGDVLGKRLESKG 65
GE+PVTELA L L SKG
Sbjct: 88 GEEPVTELAEFAHKLKHYLVSKG 110
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated.
Length = 346
Score = 26.9 bits (60), Expect = 3.4
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 42 MGEKPVTELAGVGDVLGKRL 61
MG++P L GVG KRL
Sbjct: 174 MGDRPTDALWGVGPKTAKRL 193
>gnl|CDD|219415 pfam07454, SpoIIP, Stage II sporulation protein P (SpoIIP). This
family contains the bacterial stage II sporulation
protein P (SpoIIP) (approximately 350 residues long). It
has been shown that a block in polar cytokinesis in
Bacillus subtilis is mediated partly by transcription of
spoIID, spoIIM and spoIIP. This inhibition of polar
division is involved in the locking in of asymmetry
after the formation of a polar septum during
sporulation. Engulfment in Bacillus subtilis is mediated
by two complementary systems: the first includes the
proteins SpoIID, SpoIIM and SpoIIP (DMP) which carry out
the engulfment, and the second includes the
SpoIIQ-SpoIIIAGH (Q-AH) zipper, that recruits other
proteins to the septum in a second-phase of the
engulfment. The course of events follows as the
incorporation firstly of SpoIIB into the septum during
division to serve directly or indirectly as a landmark
for localising SpoIIM and then SpoIIP and SpoIID to the
septum. SpoIIP and SpoIID interact together to form part
of the DMP complex. SpoIIP itself has been identified as
an autolysin with peptidoglycan hydrolase activity.
Length = 258
Score = 26.9 bits (60), Expect = 3.6
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 37 FVSEPMGEKPVTELAGVGDVLGKRLESKGF 66
++ P + VGD L + LE G
Sbjct: 86 YLPTPDPGGAEYNVVKVGDRLAQELEKYGI 115
>gnl|CDD|233444 TIGR01510, coaD_prev_kdtB, pantetheine-phosphate
adenylyltransferase, bacterial. This model describes
pantetheine-phosphate adenylyltransferase, the
penultimate enzyme of coenzyme A (CoA) biosynthesis in
bacteria. It does not show any strong homology to
eukaryotic enzymes of coenzyme A biosynthesis. This
protein was previously designated KdtB and postulated
(because of cytidyltransferase homology and proximity
to kdtA) to be an enzyme of LPS biosynthesis, a
cytidyltransferase for 3-deoxy-D-manno-2-octulosonic
acid. However, no activity toward that compound was
found with either CTP or ATP. The phylogenetic
distribution of this enzyme is more consistent with
coenzyme A biosynthesis than with LPS biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 155
Score = 26.5 bits (59), Expect = 3.9
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 66 FDK-----SINPQMFPDPDIEEKVLLFKN 89
FD+ + NP P +EE+V L K+
Sbjct: 26 FDEVIVAVAKNPSKKPLFSLEERVELIKD 54
>gnl|CDD|238294 cd00529, RuvC_resolvase, Holliday junction resolvases (HJRs) are
endonucleases that specifically resolve Holliday
junction DNA intermediates during homologous
recombination. HJR's occur in archaea, bacteria, and in
the mitochondria of certain fungi, however this CD
includes only the bacterial and mitochondrial HJR's.
These are referred to as the RuvC family of Holliday
junction resolvases, RuvC being the E.coli HJR. RuvC
and its orthologs are homodimers and are structurely
similar to RNase H and Hsp70.
Length = 154
Score = 26.1 bits (58), Expect = 4.5
Identities = 9/33 (27%), Positives = 11/33 (33%)
Query: 93 LPIPIGVEVLGYTKIKNNKSRYPYLDYGCTEIH 125
L I G GY I+ + YL G
Sbjct: 3 LGIDPGSRNTGYGVIEQEGRKLIYLASGVIRTS 35
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases family. LDH is
homologous to D-2-hydroxyisocaproic acid
dehydrogenase(D-HicDH) and shares the 2 domain structure
of formate dehydrogenase. D-HicDH is a NAD-dependent
member of the hydroxycarboxylate dehydrogenase family,
and shares the Rossmann fold typical of many NAD binding
proteins. HicDH from Lactobacillus casei forms a monomer
and catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 26.3 bits (59), Expect = 5.8
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 49 ELAGVG-DVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPN 91
++AG D E+ F+K + + D ++E L PN
Sbjct: 252 KIAGAALDTYEN--ETGYFNKDWSGKEIEDEVLKE---LIAMPN 290
>gnl|CDD|225420 COG2865, COG2865, Predicted transcriptional regulator containing an
HTH domain and an uncharacterized domain shared with the
mammalian protein Schlafen [Transcription].
Length = 467
Score = 26.1 bits (58), Expect = 6.1
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 66 FDKSINPQMFPDPD-IEEKVLLFKNPNSLPIPIGVEVL--GYTKIKN 109
+ N + D IE NP LP I E L G +K +N
Sbjct: 289 SIRGRNVHIEIYDDRIE-----ITNPGGLPPGITPEDLLKGRSKSRN 330
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
0.315 0.134 0.422
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,613,175
Number of extensions: 572240
Number of successful extensions: 320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 319
Number of HSP's successfully gapped: 27
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.2 bits)