RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9365
(98 letters)
>gnl|CDD|144978 pfam01585, G-patch, G-patch domain. This domain is found in a
number of RNA binding proteins, and is also found in
proteins that contain RNA binding domains. This
suggests that this domain may have an RNA binding
function. This domain has seven highly conserved
glycines.
Length = 45
Score = 56.4 bits (137), Expect = 1e-12
Identities = 22/42 (52%), Positives = 31/42 (73%)
Query: 40 GGMGMHLLQKMGWQPGEGLGKNKEGTVQPLSLDIKFDRRGLV 81
+G LLQKMGW+PG+GLGKN++G +P+ I+ DR+GL
Sbjct: 2 SNIGFKLLQKMGWKPGQGLGKNEQGITEPIEAKIRPDRKGLG 43
>gnl|CDD|197727 smart00443, G_patch, glycine rich nucleic binding domain. A
predicted glycine rich nucleic binding domain found in
the splicing factor 45, SON DNA binding protein and
D-type Retrovirus- polyproteins.
Length = 47
Score = 53.7 bits (130), Expect = 2e-11
Identities = 23/44 (52%), Positives = 34/44 (77%)
Query: 37 PVSGGMGMHLLQKMGWQPGEGLGKNKEGTVQPLSLDIKFDRRGL 80
+ +G LL+KMGW+ G+GLGKN++G V+P+S +IK DR+GL
Sbjct: 1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGL 44
>gnl|CDD|221692 pfam12656, G-patch_2, DExH-box splicing factor binding site.
Yeast Spp2, a G-patch protein and spliceosome
component, interacts with the ATP-dependent DExH-box
splicing factor Prp2. As this interaction involves the
G-patch sequence in Spp2 and is required for the
recruitment of Prp2 to the spliceosome before the first
catalytic step of splicing, it is proposed that Spp2
might be an accessory factor that confers spliceosome
specificity on Prp2.
Length = 79
Score = 41.6 bits (98), Expect = 2e-06
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 5/45 (11%)
Query: 34 EAAPVSGGMGMHLLQKMGWQPGEGLGKNKEGTVQPLSLDIKFDRR 78
EA PV G LL+ MGW+ G+G+GKN +G V+P + RR
Sbjct: 26 EAVPVEE-FGAALLRGMGWKEGQGIGKNNKGDVKP----KEPKRR 65
>gnl|CDD|234610 PRK00070, acpS, 4'-phosphopantetheinyl transferase; Provisional.
Length = 126
Score = 29.3 bits (67), Expect = 0.17
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 16/52 (30%)
Query: 12 RILTPQELA--------AGSQA--WARKEQFVEAAPVSGGMGMHLLQKMGWQ 53
R+LTP+E A A A +A KE F +A + G+G + ++
Sbjct: 29 RVLTPKERAKFKSGKRPAEFLAGRFAAKEAFSKA--LGTGIGKG----VSFR 74
>gnl|CDD|173855 cd08490, PBP2_NikA_DppA_OppA_like_3, 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 = 470
Score = 28.0 bits (63), Expect = 0.71
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 46 LLQKMGWQPGEGLGKNKEGTVQPLSLDIK-FDRRGLVSKEELPP 88
LL + GW G+G G K+G +PL L + + R ELPP
Sbjct: 300 LLAEAGWTDGDGDGIEKDG--EPLELTLLTYTSR-----PELPP 336
>gnl|CDD|173883 cd08518, PBP2_NikA_DppA_OppA_like_19, 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 = 464
Score = 26.0 bits (58), Expect = 3.7
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 45 HLLQKMGWQPGEGLGKNKEGTVQPLSLDI 73
+L++ GW+ G+ G+ K+G Q +
Sbjct: 304 KILEEAGWKDGDDGGREKDG--QKAEFTL 330
>gnl|CDD|237018 PRK11905, PRK11905, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1208
Score = 25.6 bits (57), Expect = 6.0
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 5 FTGSTEVRILTPQELAA 21
FTGSTEV L + LA
Sbjct: 761 FTGSTEVARLIQRTLAK 777
>gnl|CDD|233149 TIGR00845, caca, sodium/calcium exchanger 1. The Ca2+:Cation
Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA
family are found ubiquitously, having been identified in
animals, plants, yeast, archaea and widely divergent
bacteria.All of the characterized animal proteins
catalyze Ca2+:Na+ exchange although some also transport
K+. The NCX1 plasma membrane protein exchanges 3 Na+ for
1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+
antiport but may also catalyze Na+:H+ antiport. All
remaining well-characterized members of the family
catalyze Ca2+:H+ exchange.This model is specific for the
eukaryotic sodium ion/calcium ion exchangers of the Caca
family [Transport and binding proteins, Other].
Length = 928
Score = 25.1 bits (55), Expect = 6.7
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 19 LAAGSQAWARKEQFVEAAPVSGG 41
L G+ +W +EQF+EA VS G
Sbjct: 692 LVVGTHSW--REQFIEAITVSAG 712
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 0.133 0.398
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,112,642
Number of extensions: 415837
Number of successful extensions: 213
Number of sequences better than 10.0: 1
Number of HSP's gapped: 213
Number of HSP's successfully gapped: 15
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.0 bits)