RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8387
(176 letters)
>gnl|CDD|197736 smart00456, WW, Domain with 2 conserved Trp (W) residues. Also
known as the WWP or rsp5 domain. Binds proline-rich
polypeptides.
Length = 33
Score = 55.7 bits (135), Expect = 2e-11
Identities = 16/32 (50%), Positives = 20/32 (62%)
Query: 126 LPPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157
LPPGWE R+ GR YY +H + TQ+ PR
Sbjct: 2 LPPGWEERKDPDGRPYYYNHETKETQWEKPRE 33
Score = 43.4 bits (103), Expect = 8e-07
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 79 DLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRI 111
LP G+E R G+ Y+Y+ T + W PR
Sbjct: 1 PLPPGWEERKDPDGRPYYYNHETKETQWEKPRE 33
>gnl|CDD|238122 cd00201, WW, Two conserved tryptophans domain; also known as the
WWP or rsp5 domain; around 40 amino acids; functions as
an interaction module in a diverse set of signalling
proteins; binds specific proline-rich sequences but at
low affinities compared to other peptide recognition
proteins such as antibodies and receptors; WW domains
have a single groove formed by a conserved Trp and Tyr
which recognizes a pair of residues of the sequence
X-Pro; variable loops and neighboring domains confer
specificity in this domain; there are five distinct
groups based on binding: 1) PPXY motifs 2) the PPLP
motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR
motifs.
Length = 31
Score = 54.5 bits (132), Expect = 5e-11
Identities = 17/31 (54%), Positives = 20/31 (64%)
Query: 127 PPGWEVRQTASGRYYYVDHNNRTTQFTDPRL 157
PPGWE R GR YY +HN + TQ+ DPR
Sbjct: 1 PPGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
Score = 42.9 bits (102), Expect = 1e-06
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 81 PHGYEIRTTQQGQVYFYHLPTGVSTWHDPRI 111
P G+E R G+VY+Y+ T + W DPR
Sbjct: 1 PPGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
>gnl|CDD|215899 pfam00397, WW, WW domain. The WW domain is a protein module with
two highly conserved tryptophans that binds proline-rich
peptide motifs in vitro.
Length = 30
Score = 50.6 bits (122), Expect = 1e-09
Identities = 16/30 (53%), Positives = 18/30 (60%)
Query: 126 LPPGWEVRQTASGRYYYVDHNNRTTQFTDP 155
LPPGWE R GR YY +HN TQ+ P
Sbjct: 1 LPPGWEERTDTDGRPYYYNHNTGETQWERP 30
Score = 39.9 bits (94), Expect = 2e-05
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 80 LPHGYEIRTTQQGQVYFYHLPTGVSTWHDP 109
LP G+E RT G+ Y+Y+ TG + W P
Sbjct: 1 LPPGWEERTDTDGRPYYYNHNTGETQWERP 30
>gnl|CDD|227435 COG5104, PRP40, Splicing factor [RNA processing and modification].
Length = 590
Score = 40.8 bits (95), Expect = 2e-04
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 84 YEIRTTQQGQVYFYHLPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYV 143
+E G++Y+Y+ TG S+W PKEL +L P W+ +TA G+ YY
Sbjct: 17 WEELKAPDGRIYYYNKRTGKSSWEK---PKELLKGSEEDLDVDP--WKECRTADGKVYYY 71
Query: 144 DHNNRTTQFTDP 155
+ R +++ P
Sbjct: 72 NSITRESRWKIP 83
>gnl|CDD|227354 COG5021, HUL4, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 872
Score = 39.8 bits (93), Expect = 4e-04
Identities = 38/164 (23%), Positives = 57/164 (34%), Gaps = 21/164 (12%)
Query: 16 YNNSNLILN--NSHVNNNNTSSPALPLRSRTEDQQHNHRLLVQQPRKRGASKKCSGGNSL 73
+ + V NN+ SS Q ++ L P K S G +
Sbjct: 328 PLLEETLGESTSFLVVNNDDSS----SIKDLPHQVGSNPFLEAHPEFSELLKNQSRGTTR 383
Query: 74 LQQPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKELR-------------PEQA 120
+ + P G+ GQ F T ST+ D R + R ++A
Sbjct: 384 DFR--NKPTGWSSSIEDLGQFLFSDFLTSSSTYEDLRREQLGRESDESFYVASNVQQQRA 441
Query: 121 TELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAIIQN 164
+ G L GW+ R R+Y+V+H +T D RL I N
Sbjct: 442 SREGPLLSGWKTRLNNLYRFYFVEHRKKTLTKNDSRLGSFISLN 485
Score = 33.2 bits (76), Expect = 0.054
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 121 TELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDP 155
L L + R + GR YY+DH+ TQ++ P
Sbjct: 294 DSLLRLNSLFSTRADSFGRTYYLDHDRILTQYSRP 328
>gnl|CDD|173879 cd08514, PBP2_AppA_like, The substrate-binding component of the
oligopeptide-binding protein, AppA, from Bacillus
subtilis contains the type 2 periplasmic-binding fold.
This family represents the substrate-binding domain of
the oligopeptide-binding protein, AppA, from Bacillus
subtilis and its closest homologs from other bacteria
and archaea. Bacillus subtilis has three ABC-type
peptide transport systems, a dipeptide-binding protein
(DppA) and two oligopeptide-binding proteins (OppA and
AppA) with overlapping specificity. The dipeptide (DppA)
and oligopeptide (OppA) binding proteins differ in
several ways. The DppA binds dipeptides and some
tripeptides and also is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which precludes
any involvement in chemotaxis. Most of other periplasmic
binding proteins are comprised of only two globular
subdomains corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 483
Score = 29.9 bits (68), Expect = 0.66
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 114 ELRPEQATELGNLP---PGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAI 161
EL P Q + + S Y Y+ N + F D R+ AI
Sbjct: 218 ELPPPQYDRQTEDKAFDKKINIYEYPSFSYTYLGWNLKRPLFQDKRVRQAI 268
>gnl|CDD|173880 cd08515, PBP2_NikA_DppA_OppA_like_10, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 460
Score = 29.9 bits (68), Expect = 0.68
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 6/58 (10%)
Query: 117 PEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAII-----QNLVKTL 169
P+QA L + PG V + R ++ + D R+ A+ Q +VK L
Sbjct: 221 PDQAERLKS-SPGLTVVGGPTMRIGFITFDAAGPPLKDVRVRQALNHAIDRQAIVKAL 277
>gnl|CDD|224294 COG1376, ErfK, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 232
Score = 29.5 bits (66), Expect = 0.72
Identities = 9/44 (20%), Positives = 15/44 (34%)
Query: 110 RIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFT 153
I ++ P+ PG V T Y VD + ++
Sbjct: 73 PIAPKVIPQVVLYPTGEIPGTIVVDTGLRLLYLVDDSGTAQRYP 116
>gnl|CDD|221313 pfam11917, DUF3435, Protein of unknown function (DUF3435). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 435 to 791 amino acids in
length. This family is related to pfam00589 suggesting
it may be an integrase enzyme.
Length = 418
Score = 29.3 bits (66), Expect = 1.1
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 2/63 (3%)
Query: 99 LPTGVSTWHDPRIPKELRPEQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLT 158
T +S DPR P++L EQ + P E+ + + + T
Sbjct: 260 AATRMSRTRDPRRPRDLTDEQKASVEEDPELQELIRKRDHLKKEIIALYGQVA--KAKGT 317
Query: 159 PAI 161
P
Sbjct: 318 PLY 320
>gnl|CDD|182848 PRK10931, PRK10931, adenosine-3'(2'),5'-bisphosphate nucleotidase;
Provisional.
Length = 246
Score = 28.5 bits (64), Expect = 1.5
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 127 PPGWEVRQTASGRYYYVDHNNRTTQF 152
PP WEVRQ RY+ VD + T +F
Sbjct: 67 PPAWEVRQHWQ-RYWLVDPLDGTKEF 91
>gnl|CDD|217988 pfam04252, RNA_Me_trans, Predicted SAM-dependent RNA
methyltransferase. This family of proteins are
predicted to be alpha/beta-knot SAM-dependent RNA
methyltransferases.
Length = 196
Score = 27.9 bits (62), Expect = 2.1
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 9/30 (30%)
Query: 108 DPRIPKELRPEQATE---------LGNLPP 128
D R +L+PE AT+ LG+ PP
Sbjct: 69 DLRATIDLQPEDATKFDYIVVGGILGDHPP 98
>gnl|CDD|227682 COG5394, COG5394, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 193
Score = 27.5 bits (61), Expect = 2.9
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 1/71 (1%)
Query: 56 QQPRKRGASKKCSGGNSLLQQPPDLPHGYEIRTTQQGQVYFYHLPTGVSTWHDPRIPKEL 115
QQ R R KK GGN L +E + + ++ F S + PKE
Sbjct: 110 QQSRLREQMKKAFGGNPLGPNMATPLQMWEEQIRRNMEM-FQQAMQMFSPFAKAPAPKEA 168
Query: 116 RPEQATELGNL 126
+ +L L
Sbjct: 169 PKPMSDDLDEL 179
>gnl|CDD|225284 COG2428, COG2428, Uncharacterized conserved protein [Function
unknown].
Length = 196
Score = 27.5 bits (61), Expect = 3.0
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 26/67 (38%)
Query: 108 DPRIPKELRPEQATE---------LGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLT 158
D + +EL+PE A+E LG+ PP RT + ++
Sbjct: 70 DLQAEEELKPEDASEDTYIVVGGILGDHPP-----------------RGRTKELITSKME 112
Query: 159 PAIIQNL 165
+++L
Sbjct: 113 GVKVRHL 119
>gnl|CDD|173860 cd08495, PBP2_NikA_DppA_OppA_like_8, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 27.7 bits (62), Expect = 3.6
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 83 GYEIRTTQQGQVYFYHLPTGVSTWHDPRI 111
G+++ T V+ Y L DPR+
Sbjct: 240 GFQLVTNPSPHVWIYQLNMAEGPLSDPRV 268
>gnl|CDD|237395 PRK13482, PRK13482, DNA integrity scanning protein DisA;
Provisional.
Length = 352
Score = 27.4 bits (62), Expect = 3.7
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 155 PRLTPAIIQNLVKTLNVLSK 174
PRL A+I+NLV+ L
Sbjct: 293 PRLPSAVIENLVEHFGSLQG 312
>gnl|CDD|215424 PLN02790, PLN02790, transketolase.
Length = 654
Score = 26.9 bits (60), Expect = 6.3
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 5/24 (20%)
Query: 113 KELRPEQATEL-----GNLPPGWE 131
K+ PE+A EL G LP GWE
Sbjct: 308 KKKYPEEAAELKSLISGELPSGWE 331
>gnl|CDD|173866 cd08501, PBP2_Lpqw, The substrate-binding domain of mycobacterial
lipoprotein Lpqw contains type 2 periplasmic binding
fold. LpqW is one of key players in synthesis and
transport of the unique components of the mycobacterial
cell wall which is a complex structure rich in two
related lipoglycans, the phosphatidylinositol mannosides
(PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly
conserved lipoprotein that transport intermediates from
a pathway for mature PIMs production into a pathway for
LAMs biosynthesis, thus controlling the relative
abundance of these two essential components of cell
wall. LpqW is thought to have been adapted by the
cell-wall biosynthesis machinery of mycobacteria and
other closely related pathogens, evolving to play an
important role in PIMs/LAMs biosynthesis. Most of
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the LpqW protein. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 486
Score = 26.5 bits (59), Expect = 7.8
Identities = 13/44 (29%), Positives = 18/44 (40%)
Query: 118 EQATELGNLPPGWEVRQTASGRYYYVDHNNRTTQFTDPRLTPAI 161
E E L PG EVR RY ++ N ++ D + A
Sbjct: 229 EDTLEALGLLPGVEVRTGDGPRYLHLTLNTKSPALADVAVRKAF 272
>gnl|CDD|152713 pfam12278, SDP_N, Sex determination protein N terminal. This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 168 and 410 amino
acids in length. This family is the N terminal end of
the sex determination protein of many different
animals. It plays a role in the gender determination of
around 20% of all animals.
Length = 168
Score = 26.2 bits (57), Expect = 9.3
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 3/25 (12%)
Query: 40 LRSRTEDQQHNHR---LLVQQPRKR 61
LRSRTED++ HR +QQ R+R
Sbjct: 27 LRSRTEDERLQHRREEWFIQQERER 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
0.315 0.131 0.398
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,772,003
Number of extensions: 769570
Number of successful extensions: 483
Number of sequences better than 10.0: 1
Number of HSP's gapped: 481
Number of HSP's successfully gapped: 25
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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: 56 (25.3 bits)