RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2033
(124 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 = 70.4 bits (173), Expect = 5e-16
Identities = 32/77 (41%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 24 LSGVVPAMHYGYVEGWFSKVAQASLGWLLLMGVLYIIGGLIYALRVPERYFPGKCDIWFQ 83
G++P H G L L+L GVLY +G + YALR P G DIW
Sbjct: 142 WLGIIPIKHLILALGG------GGLVLLVLGGVLYTLGAIFYALRFP-----GPFDIWGH 190
Query: 84 SHQIFHVLVVSAAFVHY 100
SHQIFH+ VV A HY
Sbjct: 191 SHQIFHLFVVLGALCHY 207
>gnl|CDD|224191 COG1272, COG1272, Predicted membrane protein, hemolysin III homolog
[General function prediction only].
Length = 226
Score = 55.3 bits (134), Expect = 3e-10
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 40 FSKVAQASLGWLLLMGVLYIIGGLIYALRVPERYFPGKCDIWFQSHQIFHVLVVSAAFVH 99
+K+ L L L GVLY +G + Y LR+ D SH I+H+ VV A H
Sbjct: 165 IAKLGLIGLVLLALGGVLYSVGAIFYVLRI---------DRIPYSHAIWHLFVVGGAACH 215
Query: 100 YHGI 103
+ I
Sbjct: 216 FIAI 219
>gnl|CDD|233258 TIGR01065, hlyIII, channel protein, hemolysin III family. This
family includes proteins from pathogenic and
non-pathogenic bacteria, Homo sapiens and Drosophila. In
Bacillus cereus, a pathogen, it has been show to
function as a channel-forming cytolysin. The human
protein is expressed preferentially in mature
macrophages, consistent with a role cytolytic role.
Length = 204
Score = 39.6 bits (93), Expect = 9e-05
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 9/55 (16%)
Query: 46 ASLGWLLLMGVLYIIGGLIYALRVPERYFPGKCDIWFQSHQIFHVLVVSAAFVHY 100
A L G+LY +G + YAL+ P I F H I+H+ V+ A+ H+
Sbjct: 152 AGFSLLAAGGLLYTVGAIFYALKWP---------IPFTYHAIWHLFVLGASACHF 197
>gnl|CDD|217194 pfam02706, Wzz, Chain length determinant protein. This family
includes proteins involved in lipopolysaccharide (lps)
biosynthesis. This family comprises the whole length of
chain length determinant protein (or wzz protein) that
confers a modal distribution of chain length on the
O-antigen component of lps. This region is also found
as part of bacterial tyrosine kinases.
Length = 139
Score = 27.3 bits (61), Expect = 1.8
Identities = 6/24 (25%), Positives = 13/24 (54%)
Query: 50 WLLLMGVLYIIGGLIYALRVPERY 73
++L+ +L+ + YA P +Y
Sbjct: 18 LIILVTLLFALLAAAYAFLAPPKY 41
>gnl|CDD|171510 PRK12452, PRK12452, cardiolipin synthetase; Reviewed.
Length = 509
Score = 27.2 bits (60), Expect = 2.3
Identities = 10/34 (29%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 41 SKVAQASLGWLLLMGVLYIIGGLIYAL--RVPER 72
++ Q++L W L++ +L ++G L+Y++ R R
Sbjct: 52 NRSPQSTLAWFLVLALLPVVGVLLYSIFGRSRWR 85
>gnl|CDD|225105 COG2194, COG2194, Predicted membrane-associated, metal-dependent
hydrolase [General function prediction only].
Length = 555
Score = 26.6 bits (59), Expect = 4.1
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 50 WLLLMGVLYIIGGLIYALRVPERYFPGKCDIWFQSHQIFHVLVVSAAFV 98
WL+L+G+L + ++ +R + S I L+V AF
Sbjct: 122 WLVLVGLLPALLIVLVIIRYYRVWLRRLW-ARLVS--ILLSLLVILAFA 167
>gnl|CDD|131216 TIGR02161, napC_nirT, periplasmic nitrate (or nitrite) reductase
c-type cytochrome, NapC/NirT family. Nearly every
member of this subfamily is NapC, a predicted
membrane-anchored four-heme c-type cytochrome that
forms one component of the periplasmic nitrate
reductase along with NapA, NapB, NapD, NapE, and NapF
subunits. A single known exception at this time is
NirT, which is instead a component of a nitrite
reductase. This family excludes TorC subunits of
trimethylamine N-oxide (TMAO) reductases.
Length = 185
Score = 26.3 bits (58), Expect = 4.3
Identities = 9/27 (33%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 39 WFSKVAQASLGWLLLMGVLYIIGGLIY 65
W + ++ +LG LLL G +GG+++
Sbjct: 8 WLRRPSRLALGTLLLGG---FVGGIVF 31
>gnl|CDD|183181 PRK11534, PRK11534, DNA-binding transcriptional regulator CsiR;
Provisional.
Length = 224
Score = 26.0 bits (57), Expect = 5.9
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 79 DIWFQSHQIFHVLVVSAAFVHY 100
D W HQ FH +V+ HY
Sbjct: 129 DEWDLRHQAFHTAIVAGCGSHY 150
>gnl|CDD|131740 TIGR02693, arsenite_ox_L, arsenite oxidase, large subunit. This
model represents the large subunit of an arsenite
oxidase complex. The small subunit is a Rieske protein.
Homologs to both large and small subunits that score in
the gray zone between the set trusted and noise bit
score cutoffs for the respective models are found in
Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7.
This enzyme acts in energy metabolim by arsenite
oxidation, rather than detoxification by reduction of
arsenate to arsenite prior to export [Energy
metabolism, Electron transport].
Length = 806
Score = 26.0 bits (57), Expect = 6.9
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 2/32 (6%)
Query: 3 EKGTIPSH--LGAGQTEQQPPESLSGVVPAMH 32
E G P G + QPP + P MH
Sbjct: 35 EGGVKPEQNAFGLDLSTPQPPLAGQSYTPTMH 66
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Many, not all,
members of this family are dimeric.
Length = 308
Score = 25.9 bits (58), Expect = 7.0
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 5/37 (13%)
Query: 20 PPESLSGVVPAMHYGYV-----EGWFSKVAQASLGWL 51
P L V+ H GYV EG++ + + WL
Sbjct: 270 PLRGLPNVLLTPHIGYVTEEAYEGFYGQAVENIAAWL 306
>gnl|CDD|217699 pfam03729, DUF308, Short repeat of unknown function (DUF308).
Family of short repeats that occurs in a limited number
of membrane proteins. It may divide further in short
repeats of around 7-10 residues of the pattern
G-#-X(2)-#(2)-X (#=hydrophobic).
Length = 72
Score = 24.7 bits (55), Expect = 7.1
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 36 VEGWFSKVAQASLGWLLLMGVLYIIGGLI 64
+ + + WLLL G+L +I GL+
Sbjct: 41 IAAFQRRKGGGGRWWLLLSGILSLIAGLL 69
>gnl|CDD|179518 PRK02975, PRK02975, putative common antigen polymerase;
Provisional.
Length = 450
Score = 25.7 bits (57), Expect = 7.5
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 9/40 (22%)
Query: 34 GYVEGWFSKVAQASLGWLLLMGVLYIIGGLIYALRVPERY 73
G + GW S L L GVL I+G AL+ RY
Sbjct: 218 GIIRGWIS------LWMLAAAGVLGIVGMFWLALK---RY 248
>gnl|CDD|143349 cd07844, STKc_PCTAIRE_like, Catalytic domain of PCTAIRE-like
Serine/Threonine Kinases. Serine/Threonine Kinases
(STKs), PCTAIRE-like subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The PCTAIRE-like subfamily is part of a
larger superfamily that includes the catalytic domains
of other protein STKs, protein tyrosine kinases, RIO
kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. Members of this
subfamily share sequence similarity with
Cyclin-Dependent Kinases (CDKs), which belong to a large
family of STKs that are regulated by their cognate
cyclins. Together, CDKs and cyclins are involved in the
control of cell-cycle progression, transcription, and
neuronal function. The association of PCTAIRE-like
proteins with cyclins has not been widely studied,
although PFTAIRE-1 has been shown to function as a CDK
which is regulated by cyclin D3 as well as the
membrane-associated cyclin Y. PCTAIRE-like proteins show
unusual expression patterns with high levels in
post-mitotic tissues, suggesting that they may be
involved in regulating post-mitotic cellular events.
Length = 291
Score = 25.8 bits (57), Expect = 7.6
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 74 FPGKCDIWFQSHQIFHVLVVSAAFVHYHGITEMAMYRLSSGGCEAPQP 121
FPG D+ Q H+IF VL G++ ++ S P+P
Sbjct: 204 FPGSTDVEDQLHKIFRVLGTPTEETW-PGVSSNPEFKPYSFPFYPPRP 250
>gnl|CDD|239216 cd02865, Heme_Cu_Oxidase_III_2, Heme-copper oxidase subunit III
subfamily. Heme-copper oxidases are transmembrane
protein complexes in the respiratory chains of
prokaryotes and mitochondria which couple the reduction
of molecular oxygen to water to, proton pumping across
the membrane. The heme-copper oxidase superfamily is
diverse in terms of electron donors, subunit
composition, and heme types. This superfamily includes
cytochrome c and ubiquinol oxidases. Bacterial oxidases
typically contain 3 or 4 subunits in contrast to the 13
subunit bovine cytochrome c oxidase (CcO). Subunits I,
II, and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Subunits I, II and
III of ubiquinol oxidase are homologous to the
corresponding subunits in CcO. Although not required
for catalytic activity, subunit III is believed to play
a role in assembly of the multimer complex. Rhodobacter
CcO subunit III stabilizes the integrity of the
binuclear center in subunit I. It has been proposed
that Archaea acquired heme-copper oxidases through gene
transfer from Gram-positive bacteria.
Length = 184
Score = 25.4 bits (56), Expect = 7.7
Identities = 10/41 (24%), Positives = 15/41 (36%)
Query: 29 PAMHYGYVEGWFSKVAQASLGWLLLMGVLYIIGGLIYALRV 69
G S A + L + L++IGGL+ V
Sbjct: 103 WHALNDAGYGPTSNPAGSFFYLLTGLHGLHVIGGLVALAIV 143
>gnl|CDD|152201 pfam11765, Hyphal_reg_CWP, Hyphally regulated cell wall protein
N-terminal. The proteins in this family are all fungal
and largely annotated as being hyphally regulated cell
wall proteins, and several are listed as the enzyme
EC:3.2.1.18. This enzyme is acetylneuraminyl hydrolase
or exo-alpha-sialidase, that hydrolyses glycosidic
linkages of terminal sialic acid residues in
oligosaccharides, glycoproteins, glycolipids, colominic
acid and synthetic substrates.
Length = 332
Score = 25.5 bits (56), Expect = 8.1
Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 34 GYVEGWFSKVAQASLGWLLLMGVLYIIGGLIYALRVPERYFPGKC 78
GY FS V G L V I+G + Y+ VP R P C
Sbjct: 283 GYNPSLFSIVTDNGAG---LPSV--ILGAVSYSGPVPNRKLPASC 322
>gnl|CDD|220692 pfam10324, 7TM_GPCR_Srw, Serpentine type 7TM GPCR chemoreceptor
Srw. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srw is a solo family
amongst the superfamilies of chemoreceptors.
Chemoperception is one of the central senses of soil
nematodes like C. elegans which are otherwise 'blind'
and 'deaf'. The genes encoding Srw do not appear to be
under as strong an adaptive evolutionary pressure as
those of Srz.
Length = 317
Score = 25.6 bits (57), Expect = 8.4
Identities = 13/75 (17%), Positives = 27/75 (36%), Gaps = 9/75 (12%)
Query: 38 GWFSKVAQASLGWLLLMGVLYIIGGL--IYALR-----VPERYFPGKCDIWFQSH--QIF 88
K+++ G ++++ V + Y R + P F + +
Sbjct: 113 NKIQKLSKPKFGLIIIIIVFILSLPFSIFYYFRYEIVEEGGIWKPPPNCAGFPPNYTEPR 172
Query: 89 HVLVVSAAFVHYHGI 103
+VLV+S F G+
Sbjct: 173 YVLVLSELFTDNDGL 187
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
0.324 0.140 0.450
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,494,929
Number of extensions: 566221
Number of successful extensions: 741
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 66
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)