RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12202
(157 letters)
>gnl|CDD|153091 cd00125, PLA2c, PLA2c: Phospholipase A2, a family of secretory and
cytosolic enzymes; the latter are either Ca dependent or
Ca independent. PLA2 cleaves the sn-2 position of the
glycerol backbone of phospholipids (PC or
phosphatidylethanolamine), usually in a metal-dependent
reaction, to generate lysophospholipid (LysoPL) and a
free fatty acid (FA). The resulting products are either
dietary or used in synthetic pathways for leukotrienes
and prostaglandins. Often, arachidonic acid is released
as a free fatty acid and acts as second messenger in
signaling networks. Secreted PLA2s have also been found
to specifically bind to a variety of soluble and
membrane proteins in mammals, including receptors. As a
toxin, PLA2 is a potent presynaptic neurotoxin which
blocks nerve terminals by binding to the nerve membrane
and hydrolyzing stable membrane lipids. The products of
the hydrolysis (LysoPL and FA) cannot form bilayers
leading to a change in membrane conformation and
ultimately to a block in the release of
neurotransmitters. PLA2 may form dimers or oligomers.
Length = 115
Score = 73.8 bits (182), Expect = 8e-18
Identities = 48/145 (33%), Positives = 58/145 (40%), Gaps = 47/145 (32%)
Query: 6 SAVQLYSMVSCSTGCDPLSYKGYGCYCGFLGSGYPVDPIDRTSQLNMARDHD-------- 57
+ +Q M+ C+TG L Y GYGCYCG GSG PVD DR Q+ HD
Sbjct: 1 NLLQFGKMIKCTTGRSALDYNGYGCYCGLGGSGTPVDDTDRCCQV-----HDCCYDRAEK 55
Query: 58 SGHEIYIIFIYSGVVSYTTGAIQGPTVLSFSNISSPTCGPASEDGPYVVSKASKRGKSCS 117
G Y Y SYT S+ TC A+ C+
Sbjct: 56 GGCSPYFT-SY----SYT-----------CSD-GQITCSDAN--------------DKCA 84
Query: 118 HRLCECDRRFSECLR--PYSCPKYK 140
LCECDR + C PY PKY+
Sbjct: 85 RALCECDRAAALCFARAPY-NPKYR 108
>gnl|CDD|200972 pfam00068, Phospholip_A2_1, Phospholipase A2. Phospholipase A2
releases fatty acids from the second carbon group of
glycerol. Perhaps the best known members are secreted
snake venoms, but also found in secreted pancreatic and
membrane-associated forms. Structure is all-alpha, with
two core disulfide-linked helices and a calcium-binding
loop. This alignment represents the major family of
PLA2s. A second minor family, defined by the honeybee
venom PLA2 PDB:1POC and related sequences from Gila
monsters (Heloderma), is not recognised. This minor
family conserves the core helix pair but is
substantially different elsewhere. The PROSITE pattern
PA2_HIS, specific to the first core helix, recognises
both families.
Length = 116
Score = 52.2 bits (126), Expect = 2e-09
Identities = 47/144 (32%), Positives = 58/144 (40%), Gaps = 39/144 (27%)
Query: 8 VQLYSMVSCSTGCDP-LSYKGYGCYCGFLGSGYPVDPIDRTSQLNMARDHDSGH---EIY 63
VQ +M+ C+TG P LSY YGCYCG+ GSG PVD +DR + HD + E
Sbjct: 3 VQFGNMIQCATGKRPVLSYADYGCYCGWGGSGTPVDALDRCCFV-----HDCCYGEAEKP 57
Query: 64 IIFIYSGVVSYTTGAIQGPTVLSFSNISSPTCGPASEDGPYVVSKASKRGKSCSHRLCEC 123
SY S SN TCG C +CEC
Sbjct: 58 GCNPKLTTYSY-----------SCSN-GDITCGG---------------NDPCERFVCEC 90
Query: 124 DRRFSECLR--PYSCPKYKAVCRS 145
DR + C Y+ KY +C S
Sbjct: 91 DRAAAICFARNTYN-KKYWNICTS 113
>gnl|CDD|214508 smart00085, PA2c, Phospholipase A2.
Length = 117
Score = 44.1 bits (105), Expect = 2e-06
Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 8 VQLYSMVSCSTGCDP-LSYKGYGCYCGFLGSGYPVDPIDR 46
Q +M+ C+TG LSY YGCYCG+ GSG PVD DR
Sbjct: 3 WQFGNMIQCATGKRAWLSYGDYGCYCGWGGSGTPVDATDR 42
>gnl|CDD|153096 cd04707, otoconin_90, otoconin_90: Phospholipase A2-like domains
present in otoconin-90 and otoconin-95, mammal proteins
that are principal matrix proteins of calcitic
otoconia. Interactions involving otoconin-90 may
trigger or constitute key events in otoconia formation.
The PLA2-like domains in otoconins may have lost their
metal-binding sites.
Length = 117
Score = 42.1 bits (99), Expect = 1e-05
Identities = 20/38 (52%), Positives = 24/38 (63%)
Query: 9 QLYSMVSCSTGCDPLSYKGYGCYCGFLGSGYPVDPIDR 46
QL M+ C TG P ++ YGCYCG G G PVD +DR
Sbjct: 1 QLGEMLKCLTGRCPREFEDYGCYCGQEGEGLPVDELDR 38
>gnl|CDD|153092 cd00618, PLA2_like, PLA2_like: Phospholipase A2, a super-family of
secretory and cytosolic enzymes; the latter are either
Ca dependent or Ca independent. PLA2 cleaves the sn-2
position of the glycerol backbone of phospholipids (PC
or phosphatidylethanolamine), usually in a
metal-dependent reaction, to generate lysophospholipid
(LysoPL) and a free fatty acid (FA). The resulting
products are either dietary or used in synthetic
pathways for leukotrienes and prostaglandins. Often,
arachidonic acid is released as a free fatty acid and
acts as second messenger in signaling networks. Secreted
PLA2s have also been found to specifically bind to a
variety of soluble and membrane proteins in mammals,
including receptors. As a toxin, PLA2 is a potent
presynaptic neurotoxin which blocks nerve terminals by
binding to the nerve membrane and hydrolyzing stable
membrane lipids. The products of the hydrolysis (LysoPL
and FA) cannot form bilayers leading to a change in
membrane conformation and ultimately to a block in the
release of neurotransmitters. PLA2 may form dimers or
oligomers.
Length = 83
Score = 34.1 bits (78), Expect = 0.005
Identities = 32/114 (28%), Positives = 38/114 (33%), Gaps = 36/114 (31%)
Query: 26 KGYGCYCGFLGS----GYPVDPIDRTSQLNMARDHDSG-HEIYIIFIYSGVVSYTTGAIQ 80
YGCYCG GS G PVD DR R HD +I G +SY
Sbjct: 1 LPYGCYCGPGGSACPSGQPVDETDRC-----CRKHDCCYDQISDGGCCDGCLSY------ 49
Query: 81 GPTVLSFSNISSPTCGPASEDGPYVVSKASKRGKSCSHRLCECDRRFSECLRPY 134
SFS + C+ C+CDRR + CL
Sbjct: 50 -----SFSEGGVTCLTNSD---------------LCTRSHCDCDRRLAICLARA 83
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 309
Score = 29.8 bits (67), Expect = 0.54
Identities = 15/36 (41%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 116 CSHRLCE-C-DRRFSECLRPYSCPKYKAVCRSNVFR 149
C H LCE C D F SCP+ R N FR
Sbjct: 26 CGHTLCESCVDLLFV--RGSGSCPECDTPLRKNNFR 59
>gnl|CDD|131954 TIGR02908, CoxD_Bacillus, cytochrome c oxidase, subunit IVB. This
model represents a small clade of cytochrome oxidase
subunit IV's found in the Bacilli [Energy metabolism,
Electron transport].
Length = 110
Score = 27.9 bits (62), Expect = 1.1
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 57 DSGHEIYIIFIYSGVVSYTTGAIQGPTVLSFSNI 90
D GHE+ FIY GV + VL+F+ I
Sbjct: 80 DKGHEVPAQFIYGGV------FVTMLVVLAFTTI 107
>gnl|CDD|227032 COG4688, COG4688, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 665
Score = 28.5 bits (63), Expect = 1.9
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 15 SCSTGCDPLSYKGYGCYCGFLGSGYPVDPIDRTSQLNMARDHDS 58
T D + YG +C L S + VDP + + N H S
Sbjct: 547 YLKTEADGVHATPYG-HC--LNS-FTVDPCPKHLECNTGCRHLS 586
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.1 bits (62), Expect = 2.1
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 51 NMARDHDSGHEIYIIFIYSGVVSYTTGAIQGPTVLSFSNISSPTCGPA--SEDGPYVVS 107
NM + H+ II + +T+GA+ P+V+ + SS T P+ G V +
Sbjct: 123 NMHQSQHPHHQQNII--QQQLQVHTSGAVPTPSVMGSATASSTTANPSITGAPGLLVDA 179
>gnl|CDD|223056 PHA03362, PHA03362, single-stranded binding protein UL29;
Provisional.
Length = 1189
Score = 28.1 bits (63), Expect = 2.3
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 120 LCECDRRFSECLRPYS---CPKYKAVCRSNVFRLMQNLILI 157
L E + FS L PYS CP + R V ++Q+L L
Sbjct: 644 LAEANHTFSLSLDPYSSGFCPVLSFLYRRTVLAVVQDLALS 684
>gnl|CDD|100113 cd05821, TLP_Transthyretin, Transthyretin (TTR) is a 55 kDa protein
responsible for the transport of thyroid hormones and
retinol in vertebrates. TTR distributes the two thyroid
hormones T3 (3,5,3'-triiodo-L-thyronine) and T4
(Thyroxin, or 3,5,3',5'-tetraiodo-L-thyronine), as well
as retinol (vitamin A) through the formation of a
macromolecular complex that includes each of these as
well as retinol-binding protein. Misfolded forms of TTR
are implicated in the amyloid diseases familial
amyloidotic polyneuropathy and senile systemic
amyloidosis. TTR forms a homotetramer with each subunit
consisting of eight beta-strands arranged in two sheets
and a short alpha-helix. The central channel of the
tetramer contains two independent binding sites, each
located between a pair of subunits, which differ in
their ligand binding affinity. A negative cooperativity
has been observed for the binding of T4 and other TTR
ligands. A fraction of plasma TTR is carried in high
density lipoproteins by binding to apolipoprotein AI
(apoA-I). TTR is able to proteolytically process apoA-I
by cleaving its C-terminus; therefore TTR has protease
activity in addition to its function in protein
transport.
Length = 121
Score = 26.0 bits (57), Expect = 5.3
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 56 HDSGHEIYIIFIYSGVVSYTTGAI 79
+DSGH Y I SY+T A+
Sbjct: 95 NDSGHRHYTIAALLSPYSYSTTAV 118
>gnl|CDD|213072 cd11756, GH94N_ChvB_NdvB_1_like, First GH94N domain of cyclic beta
1-2 glucan synthetase and similar domains. The
glycoside hydrolase family 94 (previously known as
glycosyltransferase family 36) includes cyclic beta 1-2
glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the
chromosomal chvB virulence gene). This first of two
tandemly repeated GH94-N-terminal-like domains has not
been characterized functionally. Some beta 1-2 glucan
synthetases are annotated as NdvB (nodule development B)
gene products, glycosyltransferases required for the
synthesis of cyclic beta-(1,2)-glucans, which play a
role in interactions between bacteria and plants.
Length = 284
Score = 26.7 bits (60), Expect = 5.7
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 92 SPTCGPASEDGPYVV 106
SPT P GPY V
Sbjct: 91 SPTPLPIRGGGPYRV 105
>gnl|CDD|188424 TIGR03909, pyrrolys_PylC, pyrrolysine biosynthesis protein PylC.
This protein is PylC, part of a three-gene cassette that
is sufficient to direct the biosynthesis of pyrrolysine,
the twenty-second amino acid, incorporated in some
species at a UAG canonical stop codon [Amino acid
biosynthesis, Other].
Length = 374
Score = 26.7 bits (59), Expect = 6.5
Identities = 12/51 (23%), Positives = 18/51 (35%)
Query: 87 FSNISSPTCGPASEDGPYVVSKASKRGKSCSHRLCECDRRFSECLRPYSCP 137
F++I PT P G K S S + R +E L+ +
Sbjct: 109 FASIDLPTPKPWPGCGFPYFVKPSCESGSEGVYIINDRRELNELLKLGNLD 159
>gnl|CDD|222565 pfam14133, DUF4300, Domain of unknown function (DUF4300). This
family of lipoproteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 281 and 303 amino
acids in length. There are two conserved sequence
motifs: NCR and PYQ.
Length = 251
Score = 26.4 bits (59), Expect = 6.5
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 143 CRSNVFRLMQNLI 155
CR F L+++LI
Sbjct: 83 CRITAFTLLKDLI 95
>gnl|CDD|187693 cd07180, RNase_HII_Archaea_like, Archaeal ribonuclease HII.
Ribonuclease (RNase) H is classified into two families,
type I (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type II (prokaryotic RNase HII and
HIII, archaeal RNase HII and eukaryotic RNase H2/HII).
RNase H endonucleolytically hydrolyzes an RNA strand
when it is annealed to a complementary DNA strand in the
presence of divalent cations, in DNA replication or
repair. Some archaeal RNase HII show broad divalent
cation specificity. It is proposed that three of the
four acidic residues at the active site are involved in
metal binding and the fourth one involved in the
catalytic process in archaea. Most archaeal genomes
contain multiple RNase H genes. Despite a lack of
evidence for homology from sequence comparisons, type I
and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. It appears that type I and type II RNases H
also have overlapping functions in cells, as
over-expression of Escherichia coli RNase HII can
complement an RNase HI deletion phenotype in E. coli.
Length = 204
Score = 26.0 bits (58), Expect = 7.2
Identities = 11/31 (35%), Positives = 12/31 (38%)
Query: 32 CGFLGSGYPVDPIDRTSQLNMARDHDSGHEI 62
G GSGYP DP R+H I
Sbjct: 162 YGDFGSGYPSDPRTIKFLREYYREHGELPPI 192
>gnl|CDD|180505 PRK06278, PRK06278, cobyrinic acid a,c-diamide synthase; Validated.
Length = 476
Score = 26.2 bits (58), Expect = 9.3
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 58 SGHEIYIIFIYSGVVSYTTGAIQGPTVLSFSNISSPTCGPASEDGPYVVSKASKRG 113
S ++ YII GV+ TGA+ S + I+ P Y+VS SK G
Sbjct: 316 SDYDYYII---EGVMGAFTGALNKKNPYSGAEIAKALGFPV-----YIVSSCSKSG 363
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
0.323 0.137 0.437
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,500,297
Number of extensions: 622330
Number of successful extensions: 427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 425
Number of HSP's successfully gapped: 30
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.9 bits)