RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10678
(136 letters)
>gnl|CDD|218697 pfam05694, SBP56, 56kDa selenium binding protein (SBP56). This
family consists of several eukaryotic selenium binding
proteins as well as three sequences from archaea. The
exact function of this protein is unknown although it is
thought that SBP56 participates in late stages of
intra-Golgi protein transport. The Lotus japonicus
homologue of SBP56, LjSBP is thought to have more than
one physiological role and can be implicated in
controlling the oxidation/reduction status of target
proteins, in vesicular Golgi transport.
Length = 461
Score = 97.0 bits (242), Expect = 1e-24
Identities = 31/51 (60%), Positives = 38/51 (74%)
Query: 71 AMVTDILISLDDRYLYTSNWMHGDIRQYDIRDTAHPVLVGQIFLGGKIQSD 121
+VTDIL+SLDDR+LY S W HGD+RQYDI D +P L GQ+ LGG I+
Sbjct: 312 PLVTDILLSLDDRFLYVSCWGHGDLRQYDISDPFNPKLTGQVRLGGIIRRA 362
Score = 80.4 bits (199), Expect = 1e-18
Identities = 30/52 (57%), Positives = 36/52 (69%), Gaps = 3/52 (5%)
Query: 13 GPGYRTPVDAMRYGPRETLLYVICIQPNGQ--HPDYLAVIDVDPQSKTYQQV 62
GPGY +P+DAM+ PRE L YV + P PDYLAV+DVDP+S TY QV
Sbjct: 4 GPGYASPLDAMK-APREKLAYVAALYPGTGIEKPDYLAVVDVDPESPTYGQV 54
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 31.8 bits (73), Expect = 0.089
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 90 WMHGDIRQYDIRDTAHPVLVGQIFL 114
W H D+R Y + D +G +L
Sbjct: 351 W-HEDVRLYSVWDADTGEFLGYFYL 374
>gnl|CDD|107155 PHA02241, PHA02241, hypothetical protein.
Length = 182
Score = 30.5 bits (68), Expect = 0.19
Identities = 10/70 (14%), Positives = 27/70 (38%)
Query: 34 VICIQPNGQHPDYLAVIDVDPQSKTYQQVRNTLRAGLAMVTDILISLDDRYLYTSNWMHG 93
I + ++ D I++ ++ + + + DI+ + +L ++
Sbjct: 102 DFSINKDDKNFDSPFSINMFSHNRNSIGIEFIMFSEYDDKEDIIEKEKNSFLMKLKYLLK 161
Query: 94 DIRQYDIRDT 103
++ DIR T
Sbjct: 162 HSKEADIRST 171
>gnl|CDD|240135 cd04865, LigD_Pol_like_2, LigD_Pol_like_2: Polymerase (Pol) domain
of bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain
belongs to the archaeal/eukaryal primase (AEP)
superfamily. In prokaryotes, LigD along with Ku is
required for non-homologous end joining (NHEJ)-mediated
repair of DNA double-strand breaks (DSB). NHEJ-mediated
DNA DSB repair is error-prone. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The Pol domains of PaeLigD and Mycobacterium
tuberculosis (Mt)LigD are stimulated by manganese, are
error-prone, and prefer adding rNTPs to dNTPs in vitro;
however PaeLigD and MtLigD belong to other subgroups,
proteins in this subgroup await functional
characterization.
Length = 228
Score = 30.7 bits (70), Expect = 0.20
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 13/46 (28%)
Query: 29 ETLLYVI---CI--------QPNGQHPDYLAVIDVDPQSKT-YQQV 62
LL++ CI + HPD L VID+DPQ T ++ V
Sbjct: 73 AALLWLANLGCIELHPWPSRAGDLDHPDEL-VIDLDPQPGTSFEDV 117
>gnl|CDD|220674 pfam10282, Lactonase, Lactonase, 7-bladed beta-propeller. This
entry contains bacterial 6-phosphogluconolactonases
(6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse
6-phosphogluconolactone to 6-phosphogluconate. The entry
also contains the fungal muconate lactonising enzyme
carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and
muconate cycloisomerase (EC:5.5.1.1), which convert
cis,cis-muconates to muconolactones and vice versa as
part of the microbial beta-ketoadipate pathway.
Structures of proteins in this family have revealed a
7-bladed beta-propeller fold.
Length = 344
Score = 29.5 bits (67), Expect = 0.44
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 75 DILISLDDRYLYTSNWMHGDIRQYDI-RDTAHPVLVGQIFLGGK 117
I IS D R+LY SN H I + + LV ++ G
Sbjct: 248 AIRISPDGRFLYVSNRGHDSIAVFAVDEAGGTLTLVERVSTEGD 291
Score = 27.9 bits (63), Expect = 1.4
Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 6/88 (6%)
Query: 27 PRETLLYVIC-IQPNGQHPDYLAVIDVDPQSKTYQQVRNTLRAGLAMVTDILISLDDRYL 85
P LY + +G ++ +DP + + N + G A + + D R+L
Sbjct: 46 PDGKTLYAVNETGEDG----GVSAFRIDPDTGKLTLL-NQVPTGGASPCHLSVDPDGRFL 100
Query: 86 YTSNWMHGDIRQYDIRDTAHPVLVGQIF 113
+ +N+ G + Y + Q+
Sbjct: 101 FVANYGGGSVSVYPLDADGSLGEASQVV 128
>gnl|CDD|225333 COG2706, COG2706, 3-carboxymuconate cyclase [Carbohydrate transport
and metabolism].
Length = 346
Score = 28.5 bits (64), Expect = 1.0
Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 4/89 (4%)
Query: 27 PRETLLYVICIQPNGQHPDYLAVIDVDPQSKTYQQVRNTLRAGLAMVTDILISLDDRYLY 86
P + LYV+ +P + +A +DP + G + + + D R+++
Sbjct: 49 PDQRHLYVV-NEPGEE--GGVAAYRIDPDDGRLTFLNRQTLPG-SPPCYVSVDEDGRFVF 104
Query: 87 TSNWMHGDIRQYDIRDTAHPVLVGQIFLG 115
+N+ G + Y ++ V Q+
Sbjct: 105 VANYHSGSVSVYPLQADGSLQPVVQVVKH 133
Score = 25.8 bits (57), Expect = 9.1
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 75 DILISLDDRYLYTSNWMHGDIRQYDI-RDTAHPVLVGQIFLGG 116
I IS D R+LY SN H I + + D LVG G
Sbjct: 248 AIHISPDGRFLYASNRGHDSIAVFSVDPDGGKLELVGITPTEG 290
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 28.2 bits (63), Expect = 1.4
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 10/67 (14%)
Query: 66 LRAGLAMVTDILISLDDRYLYTSNWMHGDIRQYDIRDTAHPVLVGQIFLGGKIQSDSGVT 125
L+ GLA I+ + D +Y +N + I+++ R G+ LGG I +G +
Sbjct: 137 LQKGLADDVYIVTTCDPMAIYAANNICKGIKRFAKR--------GKSALGGIIY--NGRS 186
Query: 126 VIDDPEL 132
VID P++
Sbjct: 187 VIDAPDI 193
>gnl|CDD|217362 pfam03090, Replicase, Replicase family. This is a family of
bacterial plasmid DNA replication initiator proteins.
Pfam: PF01051 is a similar family. These RepA proteins
exist as monomers and dimers in equilibrium: monomers
bind directly to repeated DNA sequences and thus
activate replication; dimers repress repA transcription
by binding an inversely repeated DNA operator. Dimer
dissociation can occur spontaneously or be mediated by
Hsp70 chaperones.
Length = 137
Score = 27.3 bits (61), Expect = 1.9
Identities = 8/33 (24%), Positives = 11/33 (33%)
Query: 21 DAMRYGPRETLLYVICIQPNGQHPDYLAVIDVD 53
+ R L IQ N V+D+D
Sbjct: 1 PGLYRRSRAAALRCRYIQANPPQLVSWLVVDID 33
>gnl|CDD|143298 cd05890, Ig2_Nectin-1_like, Second immunoglobulin (Ig) domain of
nectin-1 (also known as poliovirus receptor related
protein 1, or as CD111) and similar proteins.
Ig2_Nectin-1_like: domain similar to the second
immunoglobulin (Ig) domain of nectin-1 (also known as
poliovirus receptor related protein 1, or as CD111).
Nectin-1 belongs to the nectin family comprised of four
transmembrane glycoproteins (nectins-1 through 4).
Nectins are synaptic cell adhesion molecules (CAMs)
which facilitate adhesion and signaling at various
intracellular junctions. Nectins form homophilic
cis-dimers, followed by homophilic and heterophilic
trans-dimers involved in cell-cell adhesion. Nectins
also heterophilically trans-interact with other CAMs
such as nectin-like molecules (necls); nectin-1 for
example, has been shown to trans-interact with necl-1.
Nectins also interact with various other proteins,
including the actin filament (F-actin)-binding protein,
afadin. Mutation in the human nectin-1 gene is
associated with cleft lip/palate ectodermal dysplasia
syndrome (CLPED1). Nectin-1 is a major receptor for
herpes simplex virus through interaction with the viral
envelope glycoprotein D.
Length = 98
Score = 25.3 bits (55), Expect = 6.4
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 18 TPVDAMRYGPRETLLYVICIQPNGQHPDYLAVIDVDPQSK---TYQQVRN 64
TP + G + +L C+ NG+ P +V+ D + K +Q++RN
Sbjct: 9 TPTLVAKRGQKRKMLVATCVSANGKPP---SVVRWDTRLKGEAEFQEIRN 55
>gnl|CDD|213021 cd10916, CE4_PuuE_HpPgdA_like, Catalytic domain of bacterial PuuE
allantoinases, Helicobacter pylori peptidoglycan
deacetylase (HpPgdA), and similar proteins. This family
is a member of the very large and functionally diverse
carbohydrate esterase 4 (CE4) superfamily. It contains
bacterial PuuE (purine utilization E) allantoinases, a
peptidoglycan deacetylase from Helicobacter pylori
(HpPgdA), Escherichia coli ArnD, and many
uncharacterized homologs from all three kingdoms of
life. PuuE allantoinase appears to be metal-independent
and specifically catalyzes the hydrolysis of
(S)-allantoin into allantoic acid. Different from PuuE
allantoinase, HpPgdA has the ability to bind a metal ion
at the active site and is responsible for a
peptidoglycan modification that counteracts the host
immune response. Both PuuE allantoinase and HpPgdA
function as a homotetramer. The monomer is composed of a
7-stranded barrel with detectable sequence similarity to
the 6-stranded barrel NodB homology domain of
polysaccharide deacetylase (DCA)-like proteins in the
CE4 superfamily, which removes N-linked or O-linked
acetyl groups from cell wall polysaccharides. However,
in contrast with the typical DCAs, PuuE allantoinase and
HpPgdA might not exhibit a solvent-accessible
polysaccharide binding groove and only recognize a small
substrate molecule. ArnD catalyzes the deformylation of
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to
4-amino-4-deoxy-L-arabinose-phosphoundecaprenol.
Length = 247
Score = 26.1 bits (58), Expect = 6.6
Identities = 6/26 (23%), Positives = 10/26 (38%)
Query: 84 YLYTSNWMHGDIRQYDIRDTAHPVLV 109
YLY + D+ Y T ++
Sbjct: 138 YLYDGDTYDDDLPYYWRDATGGGPIL 163
>gnl|CDD|218058 pfam04390, LptE, Lipopolysaccharide-assembly. LptE (formerly
known as RplB) is involved in
lipopolysaccharide-assembly on the outer membrane of
Gram-negative organisms. The lipopolysaccharide
component of the outer bacterial membrane is
transported from its source of origin to the outer
membrane by a set of proteins constituting a transport
machinery that is made up of LptA, LptB, LptC, LptD,
LptE. LptD appears to be anchored in the outer
membrane, and LptE forms a complex with it. This part
of the machinery complex is involved in the assembly of
lipopolysaccharide in the outer leaflet of the outer
membrane.
Length = 142
Score = 25.4 bits (56), Expect = 9.8
Identities = 10/45 (22%), Positives = 19/45 (42%)
Query: 38 QPNGQHPDYLAVIDVDPQSKTYQQVRNTLRAGLAMVTDILISLDD 82
G+ P L + V+P+ + ++R LR L L+ +
Sbjct: 7 GGGGKVPVSLKTLIVNPEPRNGSELRRALRDRLRRSGVKLLVDAN 51
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
0.320 0.139 0.429
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,270,404
Number of extensions: 651624
Number of successful extensions: 514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 512
Number of HSP's successfully gapped: 21
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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 (21.8 bits)
S2: 54 (24.5 bits)