RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15882
(149 letters)
>gnl|CDD|217315 pfam03006, HlyIII, Haemolysin-III related. Members of this family
are integral membrane proteins. This family includes a
protein with hemolytic activity from Bacillus cereus. It
has been proposed that YOL002c encodes a Saccharomyces
cerevisiae protein that plays a key role in metabolic
pathways that regulate lipid and phosphate metabolism.
In eukaryotes, members are seven-transmembrane pass
molecules found to encode functional receptors with a
broad range of apparent ligand specificities, including
progestin and adipoQ receptors, and hence have been
named PAQR proteins. The mammalian members include
progesterone binding proteins. Unlike the case with GPCR
receptor proteins, the evolutionary ancestry of the
members of this family can be traced back to the
Archaea.
Length = 207
Score = 52.3 bits (126), Expect = 4e-09
Identities = 25/112 (22%), Positives = 48/112 (42%), Gaps = 12/112 (10%)
Query: 12 WQNFYLATVFAIFIACMILQIPRLNIHPDIKMLVFVCWAAYGVVPTVHWAVIMGGWDNPI 71
L ++ + + ++L++ L ++ ++++ G++P H + +GG
Sbjct: 103 LGWILLIFIWGLALLGILLKLFWLKRFRWLRTVLYLLMGWLGIIPIKHLILALGGGG--- 159
Query: 72 VNMLLPRVMGMYGISGLAFLIYITRFPECFFTGKVDYIGSSHQWWHFFVVLA 123
L ++ + L + Y RFP G D G SHQ +H FVVL
Sbjct: 160 ----LVLLVLGGVLYTLGAIFYALRFP-----GPFDIWGHSHQIFHLFVVLG 202
>gnl|CDD|224191 COG1272, COG1272, Predicted membrane protein, hemolysin III homolog
[General function prediction only].
Length = 226
Score = 29.5 bits (67), Expect = 0.48
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 101 FFTGKVDYIGSSHQWWHFFVVLA 123
F+ ++D I SH WH FVV
Sbjct: 189 FYVLRIDRIPYSHAIWHLFVVGG 211
>gnl|CDD|143450 cd07132, ALDH_F3AB, Aldehyde dehydrogenase family 3 members A1, A2,
and B1 and related proteins. NAD(P)+-dependent,
aldehyde dehydrogenase, family 3 members A1 and B1
(ALDH3A1, ALDH3B1, EC=1.2.1.5) and fatty aldehyde
dehydrogenase, family 3 member A2 (ALDH3A2, EC=1.2.1.3),
and similar sequences are included in this CD. Human
ALDH3A1 is a homodimer with a critical role in cellular
defense against oxidative stress; it catalyzes the
oxidation of various cellular membrane lipid-derived
aldehydes. Corneal crystalline ALDH3A1 protects the
cornea and underlying lens against UV-induced oxidative
stress. Human ALDH3A2, a microsomal homodimer, catalyzes
the oxidation of long-chain aliphatic aldehydes to fatty
acids. Human ALDH3B1 is highly expressed in the kidney
and liver and catalyzes the oxidation of various medium-
and long-chain saturated and unsaturated aliphatic
aldehydes.
Length = 443
Score = 28.0 bits (63), Expect = 2.3
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 45 VFVCWAAYGVVPTVHWAVIMGGWDNPIVNMLLPRV 79
V++ GVV +I+G W+ P+ L+P V
Sbjct: 94 VYIYKEPLGVV------LIIGAWNYPLQLTLVPLV 122
>gnl|CDD|200573 cd10949, CE4_BsPdaB_like, Putative catalytic NodB homology domain
of Bacillus subtilis putative polysaccharide deacetylase
PdaB, and its bacterial homologs. The Bacillus subtilis
genome contains six polysaccharide deacetylase gene
homologs: pdaA, pdaB (previously known as ybaN), yheN,
yjeA, yxkH and ylxY. This family is represented by the
putative polysaccharide deacetylase PdaB encoded by the
pdaB gene on sporulation of Bacillus subtilis. Although
its biochemical properties remain to be determined, the
PdaB (YbaN) protein is essential for maintaining spores
after the late stage of sporulation and is highly
conserved in spore-forming bacteria. The glycans of the
spore cortex may be candidate PdaB substrates. Based on
sequence similarity, the family members are classified
as carbohydrate esterase 4 (CE4) superfamily members.
However, the classical His-His-Asp zinc-binding motif of
CE4 esterases is missing in this family.
Length = 192
Score = 26.6 bits (59), Expect = 4.4
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 57 TVHWAVIMGGWDNPIVNMLLPRVM 80
VHW+V W NP V ++ RVM
Sbjct: 122 VVHWSVNSLDWKNPGVEAIVDRVM 145
>gnl|CDD|219472 pfam07575, Nucleopor_Nup85, Nup85 Nucleoporin. A family of
nucleoporins conserved from yeast to human. THe nuclear
pore complex is a large assembly composed of two
essential complexes: the heptameric Nup84 complex and
the heteromeric Nic96-containing complex. The Nup84
complex is composed of one copy each of Nup84, Nup85,
Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure
of a complex of Nup85 and Seh1 was solved. The
N-terminus of Nup85 is inserted and forms a
three-stranded blade that completes the Seh1 6-bladed
beta-propeller in trans. Following its N-terminal
insertion blade, Nup85 forms a compact cuboid structure
composed of 20 helices, with two distinct modules,
referred to as crown and trunk.
Length = 564
Score = 26.9 bits (60), Expect = 5.1
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 109 IGSSHQWWHFFVVLALYY 126
+ S W+ F V LYY
Sbjct: 254 LEYSSTWYEFLVGFLLYY 271
>gnl|CDD|176963 CHL00020, psbN, photosystem II protein N.
Length = 43
Score = 24.7 bits (54), Expect = 6.1
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 18 ATVFAIFIACMILQI 32
AT+ AIFI+ +++
Sbjct: 4 ATLVAIFISGLLVSF 18
>gnl|CDD|216696 pfam01782, RimM, RimM N-terminal domain. The RimM protein is
essential for efficient processing of 16S rRNA. The RimM
protein was shown to have affinity for free ribosomal
30S subunits but not for 30S subunits in the 70S
ribosomes. This N-terminal domain is found associated
with a PRC-barrel domain.
Length = 84
Score = 25.2 bits (56), Expect = 6.5
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 78 RVMGMYGISGLAFLIYITRFPECFFT-GKVDYIGSSHQWWHFFVV 121
+++G +G+ G + T FPE F G + +W V
Sbjct: 4 KIVGTHGLKGEVKVKSFTDFPEAIFDYGPWFLLKKKGEWKPLTVE 48
>gnl|CDD|145503 pfam02392, Ycf4, Ycf4. This family consists of hypothetical Ycf4
proteins from various chloroplast genomes. It has been
suggested that Ycf4 is involved in the assembly and/or
stability of the photosystem I complex in chloroplasts.
Length = 180
Score = 25.9 bits (58), Expect = 7.5
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 79 VMGMYGISGLAFLIYI 94
VM YGI+GL +Y+
Sbjct: 62 VMCFYGIAGLLLSLYL 77
>gnl|CDD|131920 TIGR02873, spore_ylxY, probable sporulation protein, polysaccharide
deacetylase family. Members of this protein family are
most closely related to TIGR02764, a subset of
polysaccharide deacetylase family proteins found in a
species if and only if the species forms endospores like
those of Bacillus subtilis or Clostridium tetani. This
family is likewise restricted to spore-formers, but is
not universal among them in having sequences with
full-length matches to the model [Energy metabolism,
Biosynthesis and degradation of polysaccharides,
Cellular processes, Sporulation and germination].
Length = 268
Score = 26.0 bits (57), Expect = 7.7
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 57 TVHWAVIMGGWDNPIVNMLLPRVM 80
T+ W V W NP ++++ RV+
Sbjct: 202 TIMWTVDTIDWKNPSPSVMVNRVL 225
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
0.334 0.145 0.522
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,972,221
Number of extensions: 739792
Number of successful extensions: 1316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1314
Number of HSP's successfully gapped: 62
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 54 (24.6 bits)