RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6806
(89 letters)
>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 = 159 bits (403), Expect = 8e-53
Identities = 67/87 (77%), Positives = 79/87 (90%)
Query: 2 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVD 61
+TSQKH+NFVSEPMG+KPVT LAG+G+VLG RLE KGFDKAYVVLGQFLLLK++EELF +
Sbjct: 3 TTSQKHRNFVSEPMGDKPVTALAGIGEVLGGRLEDKGFDKAYVVLGQFLLLKKDEELFKE 62
Query: 62 WMKETCQANAKQSGDCYNCLKDWCGEF 88
W+K+TC ANAKQ+ DCYNCLK+WC F
Sbjct: 63 WLKDTCGANAKQARDCYNCLKEWCSCF 89
>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 = 157 bits (399), Expect = 3e-52
Identities = 66/87 (75%), Positives = 79/87 (90%)
Query: 2 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVD 61
+TSQKH+NFV EPMGEKPVT LAG+G+VLG RLE+KGFDKAYVVLGQFLLLK++EELF +
Sbjct: 1 TTSQKHRNFVGEPMGEKPVTALAGIGEVLGGRLETKGFDKAYVVLGQFLLLKKDEELFKE 60
Query: 62 WMKETCQANAKQSGDCYNCLKDWCGEF 88
W+K+TC ANAKQ+ DCYNCL++WC F
Sbjct: 61 WLKDTCGANAKQARDCYNCLREWCDSF 87
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 32.5 bits (75), Expect = 0.013
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 13 EPMGEKPVTELAGVGDVLGKRLESKGFD 40
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 = 0.032
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 11 VSEPMGEKPVTELAGVGDVLGKRLESKG 38
V E + P++++ G+G ++LE+ G
Sbjct: 4 VPEFLWPLPISKIPGIGRKTAEKLEALG 31
>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 = 31.2 bits (71), Expect = 0.037
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 11 VSEPMGEKPVTELAGVGDVLGKRLESKG 38
+ + + P+T+L G+G V KRLE+ G
Sbjct: 166 LPGFLSKLPLTDLPGIGAVTAKRLEAVG 193
>gnl|CDD|179473 PRK02794, PRK02794, DNA polymerase IV; Provisional.
Length = 419
Score = 29.5 bits (67), Expect = 0.17
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 15 MGEKPVTELAGVGDVLGKRLESKGF 39
+ KPV + GVG RL G
Sbjct: 206 LAPKPVGIIWGVGPATAARLARDGI 230
>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 = 29.2 bits (66), Expect = 0.20
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 18/70 (25%)
Query: 10 FVSEPMGEKPVTELAGVGDVLGKRLESKG--------------FDKAYVVLGQFL--LLK 53
++ P + VGD L + LE G ++++Y + + LLK
Sbjct: 86 YLPTPDPGGAEYNVVKVGDRLAQELEKYGIGVIHDKTVHDLPDYNQSYKRSRETVKKLLK 145
Query: 54 QNE--ELFVD 61
+N + +D
Sbjct: 146 ENPDIKAVID 155
>gnl|CDD|190724 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal
domain.
Length = 74
Score = 27.8 bits (63), Expect = 0.26
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 18 KPVTELAGVGDVLGKRLESK 37
+ V ELAG+ DVL K L S+
Sbjct: 28 RAVLELAGIKDVLAKSLGSR 47
>gnl|CDD|182835 PRK10916, PRK10916, ADP-heptose:LPS heptosyltransferase II;
Provisional.
Length = 348
Score = 28.1 bits (63), Expect = 0.52
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 30 LGKRLESKGFDKAYVVLGQF 49
LG L K +D+AYV+ F
Sbjct: 72 LGHSLREKRYDRAYVLPNSF 91
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 27.5 bits (62), Expect = 0.73
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 18 KPVTELAGVGDVLGKRLESK 37
+ V ELAG+ DVL K L S+
Sbjct: 126 RAVLELAGIKDVLAKSLGSR 145
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 27.4 bits (62), Expect = 0.85
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 14 PMGEKPVTELAGVGDVLGKRLES 36
+ + V ELAGV DVL K L S
Sbjct: 112 AV--RAVLELAGVKDVLAKSLGS 132
>gnl|CDD|173935 cd08176, LPO, Lactadehyde:propanediol oxidoreductase (LPO)
catalyzes the interconversion between L-lactaldehyde
and L-1,2-propanediol in Escherichia coli and other
enterobacteria. Lactadehyde:propanediol oxidoreductase
(LPO) is a member of the group III iron-activated
dehydrogenases which catalyze the interconversion
between L-lactaldehyde and L-1,2-propanediol in
Escherichia coli and other enterobacteria. L-Fucose and
L-rhamnose is used by Escherichia coli through an
inducible pathway mediated by the fucose regulon
comprising four linked oeprons fucO, fucA, fucPIK, and
fucR. The fucA-encoded aldolase catalyzes the formation
of dihydroxyacetone phosphate and L-lactaldehyde. Under
anaerobic conditions, with NADH as a cofactor,
lactaldehyde is converted by a fucO-encoded
Lactadehyde:propanediol oxidoreductase (LPO) to
L-1,2-propanediol, which is excreted as a fermentation
product. In mutant strains, E. coli adapted to grow on
L-1,2-propanediol, FucO catalyzes the oxidation of the
polyol to L-lactaldehyde. FucO is induced regardless of
the respiratory conditions of the culture, remains
fully active in the absence of oxygen. In the presence
of oxygen, this enzyme becomes oxidatively inactivated
by a metal-catalyzed oxidation mechanism. FucO is an
iron-dependent metalloenzyme that is inactivated by
other metals, such as zinc, copper, or cadmium. This
enzyme can also reduces glycol aldehyde with similar
efficiency. Beside L-1,2-propanediol, the enzyme is
also able to oxidize methanol as alternative
substrates.
Length = 377
Score = 27.6 bits (62), Expect = 0.90
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 19 PVTELAGVG--DVLGKRLESKGFDKAYVVLGQFL 50
P T L G G +G L++ GF KA +V + L
Sbjct: 6 PPTNLFGAGAIKEIGDELKNLGFKKALIVTDKGL 39
>gnl|CDD|234040 TIGR02867, spore_II_P, stage II sporulation protein P. Stage II
sporulation protein P is a protein of the endospore
formation program in a number of lineages in the
Firmicutes (low-GC Gram-positive bacteria). It is
expressed in the mother cell compartment, under control
of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is
one of three major proteins involved in engulfment of
the forespore by the mother cell. This protein family
is named for the single member in Bacillus subtilis,
although most sporulating bacteria have two members
[Cellular processes, Sporulation and germination].
Length = 196
Score = 27.3 bits (61), Expect = 1.0
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 18/54 (33%)
Query: 26 VGDVLGKRLESKG--------------FDKAYVVLGQFL--LLKQNEEL--FVD 61
VGD L K LE KG ++++Y + + LK+N++L +D
Sbjct: 35 VGDRLAKELEEKGIGVIHDKTVHDGLNYEQSYDRSRETVKKALKENKDLKYIID 88
>gnl|CDD|179564 PRK03352, PRK03352, DNA polymerase IV; Validated.
Length = 346
Score = 27.3 bits (61), Expect = 1.1
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 15 MGEKPVTELAGVGDVLGKRL 34
MG++P L GVG KRL
Sbjct: 174 MGDRPTDALWGVGPKTAKRL 193
>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 = 1.3
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 18 KPVTELAGVGDVLGKRLES 36
+ + ELAGV D+L K L S
Sbjct: 103 RAILELAGVKDILAKSLGS 121
>gnl|CDD|177296 PHA00728, PHA00728, hypothetical protein.
Length = 151
Score = 26.4 bits (58), Expect = 1.9
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 16 GEKPVTELAGVGDVLGKRLESKG 38
GE+PVTELA L L SKG
Sbjct: 88 GEEPVTELAEFAHKLKHYLVSKG 110
>gnl|CDD|235022 PRK02271, PRK02271, methylenetetrahydromethanopterin reductase;
Provisional.
Length = 325
Score = 26.1 bits (58), Expect = 2.5
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 17 EKPVTELAGVGDVLGKRLESKGFDKAYV 44
PV ++A L K E GFD A++
Sbjct: 10 NHPVKKIAY----LAKLAEDNGFDYAWI 33
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 25.7 bits (57), Expect = 3.7
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 17 EKPVTELAGVGDVLGKRLESKGF 39
+ PV E GVG V ++L G
Sbjct: 175 QLPVLEFWGVGKVTAEKLRRLGI 197
>gnl|CDD|200503 cd11242, Sema_6, The Sema domain, a protein interacting module,
of class 6 semaphorins (Sema6). Class 6 semaphorins
(Sema6s) are membrane associated semaphorins. There are
6 subfamilies named 6A to 6D. Sema6s bind to plexin As
in a neuropilin independent fashion. Sema6-plexin A
signaling plays important roles in lamina-specific axon
projections. Interactions between plexin A2, plexin A4,
and Sema6A control lamina-restricted projection of
hippocampal mossy fibers. Interactions between Sema6C,
Sema6D and plexin A1 shape the stereotypic trajectories
of sensory axons in the spinal cord. In addition to
axon targeting, Sema6D-plexin A1 interactions influence
a wide range of other biological processes. During
cardiac development, Sema6D attracts or repels
endothelial cells in the cardiac tube depending on the
expression patterns of specific coreceptors in addition
to plexin A1. Furthermore, Sema6D binds a receptor
complex comprising of plexin A1, Trem2 (triggering
receptor expressed on myeloid cells 2), and DAP12 on
dendritic cells and osteoclasts to mediate T-cell-DC
interactions and to control bone development,
respectively. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 465
Score = 25.2 bits (55), Expect = 5.0
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 65 ETCQANAKQSGDCYNCLK 82
E C+ K +C+N +K
Sbjct: 58 ENCRMKGKHKDECHNFIK 75
>gnl|CDD|179607 PRK03609, umuC, DNA polymerase V subunit UmuC; Reviewed.
Length = 422
Score = 25.1 bits (55), Expect = 6.1
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 15 MGEKPVTELAGVGDVLGKRLESKGFDKA 42
+ +PV E+ GVG + K+L + G A
Sbjct: 176 LSLQPVEEVWGVGRRISKKLNAMGIKTA 203
>gnl|CDD|183150 PRK11468, PRK11468, dihydroxyacetone kinase subunit DhaK;
Provisional.
Length = 356
Score = 24.6 bits (54), Expect = 7.7
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 15 MGEKPVTELAGVGDVLGKRLESKGF 39
+G P++EL GV + L R E G
Sbjct: 285 LGATPLSELYGVYNRLATRCEQAGL 309
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
0.318 0.135 0.418
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: 4,236,987
Number of extensions: 334526
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 311
Number of HSP's successfully gapped: 22
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
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 (21.7 bits)
S2: 53 (24.2 bits)