RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9948
(203 letters)
>gnl|CDD|218653 pfam05603, DUF775, Protein of unknown function (DUF775). This
family consists of several eukaryotic proteins of
unknown function.
Length = 193
Score = 181 bits (461), Expect = 3e-58
Identities = 76/213 (35%), Positives = 113/213 (53%), Gaps = 33/213 (15%)
Query: 1 MFAILVSGRLVQTNYELVAENRFLFTIPEADTINHIAVFMTGTTPFPEGTGGMVYFNWPE 60
MF +V GR VQT+ + V +F+F +P A++I+HI VF+ P P GT VYF P
Sbjct: 1 MFGAIVPGRPVQTDAQQVDPTKFVFDLPNAESISHIVVFLLPNVPLPPGTAAAVYFQLPG 60
Query: 61 PDSPSNWKLLGVIANEKPSSIFKISNLKSTENTLVNGCTSVALYNPFGQQPISRNAQIGI 120
P+ +KLLG + N KPS+IFK+SN+ ++ NP P S AQIGI
Sbjct: 61 PE----FKLLGALTNAKPSAIFKVSNIDMLDDG-----------NPATGNPQS-TAQIGI 104
Query: 121 SVEPIEVVNQHLA-------------SKSNESLSNFVQFCQKMVTSFVNYISSFSTTQAS 167
S+EP++ + Q LA + + + Q QK+V + N++SSF+ +
Sbjct: 105 SIEPLDQLAQQLAALKQSQSGSQAAQQNAQVTSVSTKQLAQKIVENLFNFLSSFAGSD-- 162
Query: 168 MVPNPNETYVPISSVQNWYQNFERKLALNPNFW 200
P+E VP+ + W+ F+RKLA +PNF
Sbjct: 163 --SLPSEGVVPLKAFDKWWDKFQRKLANDPNFL 193
>gnl|CDD|219644 pfam07922, Glyco_transf_52, Glycosyltransferase family 52. This
family features glycosyltransferases belonging to
glycosyltransferase family 52, which have alpha-2,3-
sialyltransferase (EC:4.2.99.4) and
alpha-glucosyltransferase (EC 2.4.1.-) activity. For
example, beta-galactoside alpha-2,3- sialyltransferase
expressed by Neisseria meningitidis is a member of this
family and is involved in a step of lipooligosaccharide
biosynthesis requiring sialic acid transfer; these
lipooligosaccharides are thought to be important in the
process of pathogenesis. This family includes several
bacterial lipooligosaccharide sialyltransferases similar
to the Haemophilus ducreyi LST protein. Haemophilus
ducreyi is the cause of the sexually transmitted disease
chancroid and produces a lipooligosaccharide (LOS)
containing a terminal sialyl N-acetyllactosamine
trisaccharide.
Length = 273
Score = 30.0 bits (68), Expect = 0.73
Identities = 15/119 (12%), Positives = 36/119 (30%), Gaps = 16/119 (13%)
Query: 64 PSNWKLLGVIANEKPSSIFKISNLKSTENTLVNGCTSVALYNPFGQQPISRNAQIG---I 120
+ W +I + +F I T+ + V L P + N + I
Sbjct: 142 KNLWDSKNIIEKTEIIDLFSIDKQNITDEK--SAEIVVLLGQPLSESTEEENIHLYEKII 199
Query: 121 SVEPIEVVNQHLASKSNESLSNF-----------VQFCQKMVTSFVNYISSFSTTQASM 168
I+ H + S + ++ + ++ + + FS+ ++
Sbjct: 200 KEYDIDYYKPHPRETYDYSNVTYIDVELIFEDYILELLELLLHKRIEVYTFFSSAALNI 258
>gnl|CDD|223755 COG0683, LivK, ABC-type branched-chain amino acid transport
systems, periplasmic component [Amino acid transport and
metabolism].
Length = 366
Score = 27.8 bits (62), Expect = 4.3
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 115 NAQIGISVEPIEVVNQHLASKSNESLSNFVQFCQKM-VTSFVNYISSFSTTQAS 167
NA GI +E+V + AS + + + + V + V +S AS
Sbjct: 42 NAAGGILGRKVELVVEDDASDPATAAAVARKLITQDGVDAVVGPTTSGVALAAS 95
>gnl|CDD|129629 TIGR00538, hemN, oxygen-independent coproporphyrinogen III oxidase.
This model represents HemN, the oxygen-independent
coproporphyrinogen III oxidase that replaces HemF
function under anaerobic conditions. Several species,
including E. coli, Helicobacter pylori, and Aquifex
aeolicus, have both a member of this family and a member
of another, closely related family for which there is no
evidence of coproporphyrinogen III oxidase activity.
Members of this family have a perfectly conserved motif
PYRT[SC]YP in a region N-terminal to the region of
homology with the related uncharacterized protein
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 455
Score = 27.4 bits (61), Expect = 6.2
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 111 PISRNAQIGISVEPIEV---VNQHLASKSNESLSNFVQFCQKMVTSFVNYISSFSTTQAS 167
P + +A+I I ++P + V L + LS VQ K V VN I
Sbjct: 133 PFNADAEISIEIDPRYITKDVIDALRDEGFNRLSFGVQDFNKEVQQAVNRIQPEEMIFEL 192
Query: 168 M 168
M
Sbjct: 193 M 193
>gnl|CDD|107261 cd04509, PBP1_ABC_transporter_GCPR_C_like, Family C of G-protein
coupled receptors and their close homologs, the type I
periplasmic-binding proteins of ATP-binding cassette
transporter-like systems. This CD includes members of
the family C of G-protein coupled receptors and their
close homologs, the type I periplasmic-binding proteins
of ATP-binding cassette transporter-like systems. The
family C GPCR includes glutamate/glycine-gated ion
channels such as the NMDA receptor, G-protein-coupled
receptors, metabotropic glutamate, GABA-B, calcium
sensing, phermone receptors, and atrial natriuretic
peptide-guanylate cyclase receptors. The glutamate
receptors that form cation-selective ion channels,
iGluR, can be classified into three different subgroups
according to their binding-affinity for the agonists
NMDA (N-methyl-D-asparate), AMPA
(alpha-amino-3-dihydro-5-methyl-3-oxo-4-
isoxazolepropionic acid), and kainate. L-glutamate is a
major neurotransmitter in the brain of vertebrates and
acts through either mGluRs or iGluRs. mGluRs subunits
possess seven transmembrane segments and a large
N-terminal extracellular domain. ABC-type
leucine-isoleucine-valine-binding protein (LIVBP) is a
bacterial periplasmic binding protein that has homology
with the amino-terminal domain of the glutamate-receptor
ion channels (iGluRs). The extracellular regions of
iGluRs are made of two PBP-like domains in tandem, a
LIVBP-like domain that constitutes the N terminus -
which is included in this CD - followed by a domain
related to lysine-arginine-ornithine-binding protein
(LAOBP) that belongs to the type II periplasmic binding
fold protein superfamily. The uncharacterized
periplasmic components of various ABC-type transport
systems are included in this group.
Length = 299
Score = 27.1 bits (60), Expect = 6.8
Identities = 15/89 (16%), Positives = 32/89 (35%), Gaps = 6/89 (6%)
Query: 115 NAQIGISVEPIEVVNQHLASKSNESLSNFVQFCQKMVTSFVNYISSFSTTQASMVPNP-- 172
NA+ GI +E+V S +L+ + CQ+ V+ + ++ ++ P
Sbjct: 31 NAKGGIPGRKLELVIYDDQSDPARALAAARRLCQQEG---VDALVGPVSSGVALAVAPVA 87
Query: 173 NETYVPISSVQNWYQNFERKLALNPNFWQ 201
+P+ S P ++
Sbjct: 88 EALKIPLISP-GATAPGLTDKKGYPYLFR 115
>gnl|CDD|240432 PTZ00477, PTZ00477, rhoptry-associated protein; Provisional.
Length = 524
Score = 27.1 bits (60), Expect = 7.1
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 133 ASKSNESLSNFVQFCQKMVTSFVN 156
K+ + L+ F Q CQ +V SF++
Sbjct: 484 VDKNLDKLNLFAQSCQHVVFSFLS 507
>gnl|CDD|176507 cd08564, GDPD_GsGDE_like, Glycerophosphodiester phosphodiesterase
domain of putative Galdieria sulphuraria
glycerophosphodiester phosphodiesterase and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in putative Galdieria sulphuraria
glycerophosphodiester phosphodiesterase (GsGDE, EC
3.1.4.46) and its uncharacterized eukaryotic homologs.
Members in this family show high sequence similarity to
Escherichia coli GP-GDE, which catalyzes the degradation
of glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 265
Score = 26.7 bits (59), Expect = 8.1
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 49 GTGGMVYFNWPEPDSPSNWKLL 70
G M YF+ P D+ ++K+
Sbjct: 223 GLKVMTYFDEPVNDNEEDYKVY 244
>gnl|CDD|213771 TIGR03076, near_not_gcvH, Chlamydial GcvH-like protein upstream
region protein. The H protein (GcvH) of the glycine
cleavage system shuttles the methylamine group of
glycine from the P protein to the T protein. Most
Chlamydia but lack the P and T proteins, and have a
single homolog of GcvH that appears deeply split from
canonical GcvH in molecular phylogenetic trees. The
protein family modeled here is observed so far only in
the Chlamydiae, always as part of a two-gene operon,
upstream of the homolog of GcvH. Its function is unknown
[Unknown function, General].
Length = 686
Score = 27.2 bits (60), Expect = 8.2
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 174 ETYVPISSVQNWYQNFE 190
E YVP+ V W QN E
Sbjct: 403 EKYVPMVEVYQWQQNPE 419
>gnl|CDD|181738 PRK09265, PRK09265, aminotransferase AlaT; Validated.
Length = 404
Score = 26.7 bits (60), Expect = 8.4
Identities = 10/14 (71%), Positives = 10/14 (71%), Gaps = 4/14 (28%)
Query: 49 GTGGMVYFNWPEPD 62
GTG FNWPEPD
Sbjct: 366 GTG----FNWPEPD 375
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
0.316 0.130 0.390
Gapped
Lambda K H
0.267 0.0825 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,940,420
Number of extensions: 861811
Number of successful extensions: 687
Number of sequences better than 10.0: 1
Number of HSP's gapped: 682
Number of HSP's successfully gapped: 15
Length of query: 203
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 111
Effective length of database: 6,857,034
Effective search space: 761130774
Effective search space used: 761130774
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: 57 (25.6 bits)