RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy161
(148 letters)
>gnl|CDD|215741 pfam00135, COesterase, Carboxylesterase family.
Length = 510
Score = 130 bits (328), Expect = 2e-36
Identities = 42/63 (66%), Positives = 55/63 (87%)
Query: 82 GFLSFGNAEVPGNLGMKDQVLALQWIQENIEEFGGNPDSVTIFGESAGAASVSYHLVSPL 141
GFLS G++E+PGN G+ DQVLAL+W+++NI FGG+PD+VT+FGESAGAASVS L+SP
Sbjct: 145 GFLSTGDSELPGNAGLLDQVLALRWVKDNIAAFGGDPDNVTLFGESAGAASVSLLLLSPA 204
Query: 142 SKG 144
S+G
Sbjct: 205 SRG 207
Score = 69.7 bits (171), Expect = 8e-15
Identities = 26/59 (44%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 1 LFHRAILQSGTASCSWASTPAWLARDRAHAFATLVGCP-TQPIETVLDCLRQLPTETFV 58
LFHRAIL SG+A WA T R RA A L+GCP +L+CLR+ E +
Sbjct: 208 LFHRAILMSGSALSPWAITSN--PRQRAKRLAKLLGCPGEDSSAELLECLRKKSAEELL 264
>gnl|CDD|238191 cd00312, Esterase_lipase, Esterases and lipases (includes fungal
lipases, cholinesterases, etc.) These enzymes act on
carboxylic esters (EC: 3.1.1.-). The catalytic apparatus
involves three residues (catalytic triad): a serine, a
glutamate or aspartate and a histidine.These catalytic
residues are responsible for the nucleophilic attack on
the carbonyl carbon atom of the ester bond. In contrast
with other alpha/beta hydrolase fold family members,
p-nitrobenzyl esterase and acetylcholine esterase have a
Glu instead of Asp at the active site carboxylate.
Length = 493
Score = 116 bits (293), Expect = 2e-31
Identities = 45/63 (71%), Positives = 53/63 (84%)
Query: 82 GFLSFGNAEVPGNLGMKDQVLALQWIQENIEEFGGNPDSVTIFGESAGAASVSYHLVSPL 141
GFLS G+ E+PGN G+KDQ LAL+W+Q+NI FGG+PDSVTIFGESAG ASVS L+SP
Sbjct: 139 GFLSTGDIELPGNYGLKDQRLALKWVQDNIAAFGGDPDSVTIFGESAGGASVSLLLLSPD 198
Query: 142 SKG 144
SKG
Sbjct: 199 SKG 201
Score = 67.0 bits (164), Expect = 9e-14
Identities = 35/87 (40%), Positives = 40/87 (45%), Gaps = 13/87 (14%)
Query: 1 LFHRAILQSGTASCSWASTPAWLARDRAHAFATLVGCPTQPIETVLDCLRQLPTETFVTT 60
LFHRAI QSG+A WA AR RA A L+GC +LDCLR E +
Sbjct: 202 LFHRAISQSGSALSPWAI--QENARGRAKRLARLLGCNDTSSAELLDCLRSKSAEELLDA 259
Query: 61 LNKFHNILFHYSVVKNSLLFPGFLSFG 87
K +LF YS FL FG
Sbjct: 260 TRKL--LLFSYS---------PFLPFG 275
>gnl|CDD|225181 COG2272, PnbA, Carboxylesterase type B [Lipid metabolism].
Length = 491
Score = 85.2 bits (211), Expect = 3e-20
Identities = 35/67 (52%), Positives = 47/67 (70%), Gaps = 4/67 (5%)
Query: 82 GFL---SFGNAE-VPGNLGMKDQVLALQWIQENIEEFGGNPDSVTIFGESAGAASVSYHL 137
GFL S + NLG+ DQ+LAL+W+++NIE FGG+P +VT+FGESAGAAS+ L
Sbjct: 139 GFLDLSSLDTEDAFASNLGLLDQILALKWVRDNIEAFGGDPQNVTLFGESAGAASILTLL 198
Query: 138 VSPLSKG 144
P +KG
Sbjct: 199 AVPSAKG 205
Score = 52.4 bits (126), Expect = 9e-09
Identities = 27/58 (46%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 1 LFHRAILQSGTASCSWASTPAWLARDRAHAFATLVGCPTQPIETVLDCLRQLPTETFV 58
LFHRAI SG AS T AR++A AFA +G P E LD LR L E V
Sbjct: 206 LFHRAIALSGAASR---VTSREEAREKAAAFARALGIP----EATLDKLRALSAEDLV 256
>gnl|CDD|219611 pfam07859, Abhydrolase_3, alpha/beta hydrolase fold. This
catalytic domain is found in a very wide range of
enzymes.
Length = 207
Score = 39.5 bits (93), Expect = 2e-04
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 103 ALQWIQENIEEFGGNPDSVTIFGESAG---AASVS 134
AL+W+ E+ E G +P + + G+SAG AA+V+
Sbjct: 55 ALRWLAEHAWELGADPSRIAVAGDSAGGNLAAAVA 89
>gnl|CDD|223730 COG0657, Aes, Esterase/lipase [Lipid metabolism].
Length = 312
Score = 39.5 bits (92), Expect = 2e-04
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 103 ALQWIQENIEEFGGNPDSVTIFGESAGA 130
A +W++ N E G +P + + G+SAG
Sbjct: 136 AYRWLRANAAELGIDPSRIAVAGDSAGG 163
>gnl|CDD|215228 PLN02408, PLN02408, phospholipase A1.
Length = 365
Score = 34.4 bits (79), Expect = 0.012
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 82 GFLSFGNAEVPGNLGMKDQVLALQWIQENIEEFGGNPDSVTIFGESAGAA 131
GFLS + +++ V + I ++ +G P S+TI G S GAA
Sbjct: 165 GFLSLYTSGTAMGPSLQEMVR--EEIARLLQSYGDEPLSLTITGHSLGAA 212
>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome
partitioning].
Length = 440
Score = 28.2 bits (63), Expect = 1.9
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 38 PTQPIETVLDCLRQLPTETFVTTLNKFHNILFHYSVVKNSLL 79
+ ++D L QL T T ++ FH+ VV L
Sbjct: 38 ILETRSAIVDFLNQLSTVTRLSNGINFHSSKSTKLVVGTCLW 79
>gnl|CDD|176164 cd08475, PBP2_CrgA_like_6, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 6. The LTTRs are acting as
both auto-repressors and activators of target promoters,
controlling operons involved in a wide variety of
cellular processes such as amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of nitrogen-fixing bacteria,
and synthesis of virulence factors, to name a few. In
contrast to the tetrameric form of other LTTRs, CrgA
from Neisseria meningitides assembles into an octameric
ring, which can bind up to four 63-bp DNA
oligonucleotides. Phylogenetic cluster analysis showed
that the CrgA-like regulators form a subclass of the
LTTRs that function as octamers. The CrgA is an
auto-repressor of its own gene and activates the
expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 199
Score = 27.5 bits (62), Expect = 2.1
Identities = 10/43 (23%), Positives = 13/43 (30%), Gaps = 5/43 (11%)
Query: 5 AILQSGTASCSWASTPAWLARDRAHAFATLV----GCPTQPIE 43
AI + A A P WL D LV + +
Sbjct: 136 AIADAALAGLGIAQLPTWLVADHLQR-GELVEVLPELAPEGLP 177
>gnl|CDD|193522 cd05644, M28_like_3, M28 Zn-Peptidases. Peptidase family M28 (also
called aminopeptidase Y family), uncharacterized
subfamily. The M28 family contains aminopeptidases as
well as carboxypeptidases. They typically have
co-catalytic zinc ions; each zinc ion is tetrahedrally
co-ordinated, with three amino acid ligands plus
activated water; one aspartate residue binds both metal
ions. Proteins in this subfamily conserve some of the
metal-coordinating residues of the typically
co-catalytic M28 family, and appear to bind a single
metal (Zn) ion.
Length = 415
Score = 27.2 bits (61), Expect = 3.3
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 71 YSVVKNSLLFPGFLSFGNAEVPG 93
Y VV +S L G L++G +PG
Sbjct: 136 YEVVIDSTLEDGSLTYGELVIPG 158
>gnl|CDD|130052 TIGR00979, fumC_II, fumarate hydratase, class II. Putative
fumarases from several species (Mycobacterium
tuberculosis, Streptomyces coelicolor, Pseudomonas
aeruginosa) branch deeply, although within the same
branch of a phylogenetic tree rooted by aspartate
ammonia-lyase sequences, and score between the trusted
and noise cutoffs [Energy metabolism, TCA cycle].
Length = 458
Score = 27.0 bits (60), Expect = 3.9
Identities = 12/45 (26%), Positives = 19/45 (42%)
Query: 30 AFATLVGCPTQPIETVLDCLRQLPTETFVTTLNKFHNILFHYSVV 74
A T + E V + + + FVT NKF + H ++V
Sbjct: 228 AVGTGLNTHPGFDEKVAEEIAKETGLPFVTAPNKFEALAAHDAIV 272
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein which
is localized in the photoreceptor outer segment discs.
Mutation/s in its genetic loci is implicated in the
recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 27.3 bits (60), Expect = 4.0
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 42 IETVLDCLRQLPTETFVTTLNKFHNILFHYSVVKNSLLF 80
IET LD +RQ + HNILFH+ V +LF
Sbjct: 994 IETNLDAVRQ------SLGMCPQHNILFHHLTVAEHILF 1026
>gnl|CDD|220483 pfam09940, DUF2172, Domain of unknown function (DUF2172). This
domain, found in various hypothetical prokaryotic
proteins, has no known function. An aminopeptidase
domain is conserved within the family, but its relevance
has not been established yet.
Length = 384
Score = 26.8 bits (60), Expect = 4.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 71 YSVVKNSLLFPGFLSFGNAEVPGNLGMKDQVL 102
Y VV +S L G L++G +PG +++L
Sbjct: 104 YRVVIDSTLADGSLTYGELVIPGET--DEEIL 133
>gnl|CDD|224780 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 26.5 bits (59), Expect = 6.1
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 29 HAFATLVGCPTQPIETVLDCLRQL 52
H A+ +G P+E V++ LR
Sbjct: 323 HRIASKLGLSAPPLEEVVEALRSA 346
>gnl|CDD|215110 PLN00412, PLN00412, NADP-dependent glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 496
Score = 26.3 bits (58), Expect = 7.9
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 4 RAILQSGTASCSWASTPAWLARDRAHAFATLVGCPTQPIETVLDCL 49
+A+ + A +WA TP W + H A ++ PI +CL
Sbjct: 57 KAMESAKAAQKAWAKTPLWKRAELLHKAAAILKEHKAPIA---ECL 99
>gnl|CDD|211974 TIGR04251, SCM_rSAM_ScmF, SynChlorMet cassette radical SAM/SPASM
protein ScmF. A biosynthesis cassette found in
Syntrophobacter fumaroxidans MPOB, Chlorobium limicola
DSM 245, Methanocella paludicola SANAE, and delta
proteobacterium NaphS2 contains two PqqE-like radical
SAM/SPASM domain proteins, a PqqD homolog, and a
conserved hypothetical protein. These components suggest
modification of a ribosomally produced peptide
precursor, but the precursor has not been identified. Of
the two PqqE homologs of the cassette, this family is
the more distant in sequence.
Length = 353
Score = 26.0 bits (57), Expect = 8.3
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 126 ESAGAASVSYHLVSPLSKG 144
ES GA SV ++ V P S+G
Sbjct: 170 ESLGAESVKFNHVQPTSRG 188
>gnl|CDD|200399 TIGR04148, GG_samocin_CFB, radical SAM peptide maturase,
GG-Bacteroidales family. Members of this protein family
are radical SAM enzymes (pfam04055) with the additional
C-terminal region (TIGR04085) that is frequently a
marker of peptide modification. Many members of this
family are found in the vicinity of one or several ORFs
encoding short polypeptides with a Gly-Gly motif (common
for bacteriocin leader peptide cleavage), followed by a
Cys-rich patch and then poorly conserved sequences.
Length = 411
Score = 26.2 bits (58), Expect = 8.9
Identities = 8/34 (23%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 55 ETFVTTLNKFH--NILFHYSVVKNSLLFPGFLSF 86
+ + + K H + FHY++ N++L ++ F
Sbjct: 96 KEIINYIEKLHIDGLNFHYNMTTNAMLLRKYMDF 129
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
0.321 0.135 0.423
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,470,142
Number of extensions: 655709
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 573
Number of HSP's successfully gapped: 23
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.6 bits)