RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12201
(116 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 = 100 bits (251), Expect = 9e-29
Identities = 42/92 (45%), Positives = 51/92 (55%), Gaps = 1/92 (1%)
Query: 1 MVSCSTGCDPLSYKGYGCYCGFLGSGYPVDPIDRCCELHDWCYTGSNCPLFLEYFIPYVW 60
M+ C+TG L Y GYGCYCG GSG PVD DRCC++HD CY + YF Y +
Sbjct: 8 MIKCTTGRSALDYNGYGCYCGLGGSGTPVDDTDRCCQVHDCCYDRAEKGGCSPYFTSYSY 67
Query: 61 TCFRGRPLCQRGK-SCSHRLCECDRRFSECLR 91
TC G+ C C+ LCECDR + C
Sbjct: 68 TCSDGQITCSDANDKCARALCECDRAAALCFA 99
>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 = 75.4 bits (186), Expect = 6e-19
Identities = 44/107 (41%), Positives = 57/107 (53%), Gaps = 4/107 (3%)
Query: 1 MVSCSTGCDP-LSYKGYGCYCGFLGSGYPVDPIDRCCELHDWCYTGSNCPLFLEYFIPYV 59
M+ C+TG P LSY YGCYCG+ GSG PVD +DRCC +HD CY + P Y
Sbjct: 8 MIQCATGKRPVLSYADYGCYCGWGGSGTPVDALDRCCFVHDCCYGEAEKPGCNPKLTTYS 67
Query: 60 WTCFRGRPLCQRGKSCSHRLCECDRRFSECLR--PYSCPRYKAVCRS 104
++C G C C +CECDR + C Y+ +Y +C S
Sbjct: 68 YSCSNGDITCGGNDPCERFVCECDRAAAICFARNTYN-KKYWNICTS 113
>gnl|CDD|214508 smart00085, PA2c, Phospholipase A2.
Length = 117
Score = 60.3 bits (147), Expect = 4e-13
Identities = 38/93 (40%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 1 MVSCSTGCDP-LSYKGYGCYCGFLGSGYPVDPIDRCCELHDWCYTGSNCPLFLEYFIPYV 59
M+ C+TG LSY YGCYCG+ GSG PVD DRCC +HD CY + Y
Sbjct: 8 MIQCATGKRAWLSYGDYGCYCGWGGSGTPVDATDRCCFVHDCCYGKAEKEGCNPKTTTYS 67
Query: 60 WTCFRGRPLCQRGK-SCSHRLCECDRRFSECLR 91
++C G C +C +CECDR + C
Sbjct: 68 YSCDNGFITCGGKNTACLVFVCECDRAAAICFA 100
>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 = 58.3 bits (141), Expect = 2e-12
Identities = 34/91 (37%), Positives = 45/91 (49%), Gaps = 1/91 (1%)
Query: 1 MVSCSTGCDPLSYKGYGCYCGFLGSGYPVDPIDRCCELHDWCYT-GSNCPLFLEYFIPYV 59
M+ C TG P ++ YGCYCG G G PVD +DRCC H C S + +
Sbjct: 5 MLKCLTGRCPREFEDYGCYCGQEGEGLPVDELDRCCFQHRCCLEQASEMGCLQDRKLSTE 64
Query: 60 WTCFRGRPLCQRGKSCSHRLCECDRRFSECL 90
TC +P C+ C LC CD+ +EC+
Sbjct: 65 VTCVDHKPKCEGVSVCEKLLCTCDKTAAECM 95
>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 = 56.4 bits (136), Expect = 7e-12
Identities = 30/84 (35%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 14 KGYGCYCGFLGS----GYPVDPIDRCCELHDWCYTGSNCPLFLEYFIPYVWTCFRGRPLC 69
YGCYCG GS G PVD DRCC HD CY + + + Y + G
Sbjct: 1 LPYGCYCGPGGSACPSGQPVDETDRCCRKHDCCYDQISDGGCCDGCLSYSF-SEGGVTCL 59
Query: 70 QRGKSCSHRLCECDRRFSECLRPY 93
C+ C+CDRR + CL
Sbjct: 60 TNSDLCTRSHCDCDRRLAICLARA 83
>gnl|CDD|153095 cd04706, PLA2_plant, PLA2_plant: Plant-specific sub-family of
Phospholipase A2, a super-family of secretory and
cytosolic enzymes; the latter are either Ca dependent
or Ca independent. Enzymatically active PLA2 cleaves
the sn-2 position of the glycerol backbone of
phospholipids; 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 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. This sub-family does not appear to have a
conserved active site and metal-binding loop.
Length = 117
Score = 33.2 bits (76), Expect = 0.009
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 8 CDPLSYKGYGCYCGFLGSG----YPVDPIDRCCELHDWCY 43
C + YG YCG SG P D +D CC HD C
Sbjct: 16 CSGPPFLRYGKYCGPGYSGCPGERPCDDLDACCMTHDACV 55
>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 = 28.6 bits (64), Expect = 0.65
Identities = 15/36 (41%), Positives = 15/36 (41%), Gaps = 4/36 (11%)
Query: 75 CSHRLCE-C-DRRFSECLRPYSCPRYKAVCRSNVFR 108
C H LCE C D F SCP R N FR
Sbjct: 26 CGHTLCESCVDLLFV--RGSGSCPECDTPLRKNNFR 59
>gnl|CDD|223056 PHA03362, PHA03362, single-stranded binding protein UL29;
Provisional.
Length = 1189
Score = 28.1 bits (63), Expect = 1.2
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 79 LCECDRRFSECLRPYS---CPRYKAVCRSNVFRLMQNLILI 116
L E + FS L PYS CP + R V ++Q+L L
Sbjct: 644 LAEANHTFSLSLDPYSSGFCPVLSFLYRRTVLAVVQDLALS 684
>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 = 27.2 bits (61), Expect = 1.9
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 102 CRSNVFRLMQNLI 114
CR F L+++LI
Sbjct: 83 CRITAFTLLKDLI 95
>gnl|CDD|223326 COG0248, GppA, Exopolyphosphatase [Nucleotide transport and
metabolism / Inorganic ion transport and metabolism].
Length = 492
Score = 27.3 bits (61), Expect = 2.1
Identities = 6/25 (24%), Positives = 10/25 (40%)
Query: 77 HRLCECDRRFSECLRPYSCPRYKAV 101
R +RF+E L + + V
Sbjct: 55 ERALSALKRFAELLDGFGAEEVRVV 79
>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 = 26.8 bits (60), Expect = 2.7
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 20 CGFLGSGYPVDP 31
G GSGYP DP
Sbjct: 162 YGDFGSGYPSDP 173
>gnl|CDD|129812 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/archaeal HII
subfamily. This enzyme cleaves RNA from DNA-RNA
hybrids. Archaeal members of this subfamily of RNase H
are designated RNase HII and one has been shown to be
active as a monomer. A member from Homo sapiens was
characterized as RNase HI, large subunit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 206
Score = 26.3 bits (58), Expect = 4.1
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 21 GFLGSGYPVDP 31
G GSGYP DP
Sbjct: 164 GDFGSGYPSDP 174
>gnl|CDD|237752 PRK14551, rnhB, ribonuclease HII; Provisional.
Length = 212
Score = 26.2 bits (58), Expect = 4.2
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 21 GFLGSGYPVDPIDR 34
G +GSGYP DP R
Sbjct: 160 GDVGSGYPSDPTTR 173
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 26.5 bits (59), Expect = 4.4
Identities = 10/20 (50%), Positives = 10/20 (50%)
Query: 17 GCYCGFLGSGYPVDPIDRCC 36
G CG G P P DRCC
Sbjct: 435 GLLCGICGLRRPDTPSDRCC 454
>gnl|CDD|187691 cd06266, RNase_HII, Ribonuclease H (RNase H) type II family
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2/HII). Ribonuclease H (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, 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. The enzyme can be found in
bacteria, archaea, and eukaryotes. Most prokaryotic and
eukaryotic genomes contain multiple RNase H genes, but
no prokaryotic genome contains the combination of only
RNase HI and HIII. 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 = 210
Score = 25.7 bits (57), Expect = 5.5
Identities = 7/9 (77%), Positives = 7/9 (77%)
Query: 23 LGSGYPVDP 31
GSGYP DP
Sbjct: 174 FGSGYPSDP 182
>gnl|CDD|223949 COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases)
family 1 [Energy production and conversion].
Length = 266
Score = 25.7 bits (57), Expect = 6.6
Identities = 6/35 (17%), Positives = 10/35 (28%)
Query: 50 LFLEYFIPYVWTCFRGRPLCQRGKSCSHRLCECDR 84
+ LE F P + P +S +
Sbjct: 225 VHLEGFGPMLKDTAALLPFTTLARSGKEVRVPPGQ 259
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
0.332 0.148 0.559
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,652,110
Number of extensions: 445808
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 410
Number of HSP's successfully gapped: 43
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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: 40 (21.9 bits)
S2: 53 (24.2 bits)