RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2165
(145 letters)
>gnl|CDD|216274 pfam01062, Bestrophin, Bestrophin, RFP-TM, chloride channel.
Bestrophin is a 68-kDa basolateral plasma membrane
protein expressed in retinal pigment epithelial cells
(RPE). It is encoded by the VMD2 gene, which is mutated
in Best macular dystrophy, a disease characterized by a
depressed light peak in the electrooculogram. VMD2
encodes a 585-amino acid protein with an approximate
mass of 68 kDa which has been designated bestrophin.
Bestrophin shares homology with the Caenorhabditis
elegans RFP gene family, named for the presence of a
conserved arginine (R), phenylalanine (F), proline (P),
amino acid sequence motif. Bestrophin is a plasma
membrane protein, localised to the basolateral surface
of RPE cells consistent with a role for bestrophin in
the generation or regulation of the EOG light peak.
Bestrophin and other RFP family members represent a new
class of chloride channels, indicating a direct role for
bestrophin in generating the light peak. The VMD2 gene
underlying Best disease was shown to represent the first
human member of the RFP-TM protein family. More than 97%
of the disease-causing mutations are located in the
N-terminal RFP-TM domain implying important functional
properties. The bestrophins are four-pass transmembrane
chloride-channel proteins, and the RFP-TM or bestrophin
domain extends from the N-terminus through approximately
350 amino acids and contains all of the TM domains as
well as nearly all reported disease causing mutations.
Interestingly, the RFP motif is not conserved
evolutionarily back beyond Metazoa, neither is it in
plant members.
Length = 284
Score = 79.5 bits (197), Expect = 9e-19
Identities = 24/51 (47%), Positives = 33/51 (64%), Gaps = 3/51 (5%)
Query: 1 MDVYIPIFTVLQFCFYLGWLKVAEVLIGPFGEDDDDIELNWL---IDRHIK 48
+ + P+FTVL F F+ G KV E L PFGEDD+D+ LN L I+R++
Sbjct: 233 LGWFTPLFTVLIFYFFFGLDKVGEELENPFGEDDNDLPLNALCRTIERNLL 283
>gnl|CDD|200584 cd10962, CE4_GT2-like, Catalytic NodB homology domain of
uncharacterized bacterial glycosyl transferase, group
2-like family proteins. This family includes many
uncharacterized bacterial proteins containing an
N-terminal GH18 (glycosyl hydrolase, family 18) domain,
a middle NodB-like homology domain, and a C-terminal
GT2-like (glycosyl transferase group 2) domain.
Although their biological function is unknown, members
in this family contain a middle NodB homology domain
that is similar to the catalytic domain of
Streptococcus pneumoniae polysaccharide deacetylase
PgdA (SpPgdA), an extracellular metal-dependent
polysaccharide deacetylase with de-N-acetylase activity
toward a hexamer of chitooligosaccharide
N-acetylglucosamine, but not shorter
chitooligosaccharides or a synthetic peptidoglycan
tetrasaccharide. Like SpPgdA, this family is a member
of the carbohydrate esterase 4 (CE4) superfamily. The
presence of three domains suggests that members of this
family may be multifunctional.
Length = 196
Score = 30.3 bits (69), Expect = 0.28
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 39 LNWLIDRHIKAAYMIVDEMHEEHPELLKDQYWDE 72
L+ L + I A + ++ E +PEL+K + DE
Sbjct: 20 LDILKEYQIPATFFVIGENAVNNPELVK-RIIDE 52
>gnl|CDD|216110 pfam00771, FHIPEP, FHIPEP family.
Length = 658
Score = 27.4 bits (62), Expect = 3.0
Identities = 10/31 (32%), Positives = 19/31 (61%), Gaps = 5/31 (16%)
Query: 52 MIVDEMHEEHPELLKDQYWDEVVPKDLPYTL 82
++D + +E+P+L+ +E+VPK LP
Sbjct: 481 KLLDRLEKEYPKLV-----EELVPKLLPLGR 506
>gnl|CDD|113931 pfam05179, CDC73, RNA pol II accessory factor, Cdc73 family.
Length = 273
Score = 26.7 bits (59), Expect = 4.6
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 28 GPFGEDDDDIELNWLIDRHIKAAYMIVDEMHEEHPELLKDQYWDEVV 74
G + I+ + + + Y +VD PE LK WD VV
Sbjct: 154 GCQKPELIAIQRKFSRSKFVTVRYRVVDN-----PEKLKPDDWDRVV 195
>gnl|CDD|235672 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
Length = 697
Score = 26.6 bits (60), Expect = 5.5
Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 53 IVDEMHEEHPELLKDQYWDEVVPKDLPYTL 82
++D + +E+P+L+ +E+VPK L
Sbjct: 512 LLDRLAKEYPKLV-----EELVPKVLSLGT 536
>gnl|CDD|216622 pfam01643, Acyl-ACP_TE, Acyl-ACP thioesterase. This family
consists of various acyl-acyl carrier protein (ACP)
thioesterases (TE) these terminate fatty acyl group
extension via hydrolysing an acyl group on a fatty acid.
Length = 249
Score = 25.7 bits (57), Expect = 10.0
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 86 CYRRSEPKGSAEFYKVKEADSLYA--NITSRRKSVAPDDVYADYEIEWNIFREFQGEAYH 143
CYR + A S++ N +RR S PD+V A+Y E ++ + +
Sbjct: 89 CYRDWLVYDCETGEILIRATSVWVMMNQETRRLSKIPDEVRAEYGQEESVKKLPKLPKDE 148
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
0.322 0.141 0.443
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,822,890
Number of extensions: 713163
Number of successful extensions: 590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 23
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (21.8 bits)
S2: 54 (24.5 bits)