RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2163
(188 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 = 88.7 bits (221), Expect = 1e-21
Identities = 35/101 (34%), Positives = 49/101 (48%), Gaps = 18/101 (17%)
Query: 1 WRGSVYKLVWRELVVYLVIYYIINFTYRFALIESHQRLFERLQKYCAKKTEV----IPMS 56
WRGS+ K +W EL+V+L++ ++ Y FE L KYC + +S
Sbjct: 16 WRGSILKSIWPELLVFLLLSALVTAIYI----------FELLAKYCLPIAPFTLIGLALS 65
Query: 57 FVLGFYVSLVVKRWWEQYRL----LPWPDTLALFVSAAIPG 93
F LGF + RWWE +L + W +LA VS IPG
Sbjct: 66 FFLGFRNNAAYDRWWEARKLWGALVNWSRSLARQVSTLIPG 106
Score = 59.5 bits (145), Expect = 6e-11
Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 4/78 (5%)
Query: 97 VVFLIFPLLQNYEKKTVLIGLDHITYLQAHYLSSPMSFVLGFYVSLVVKRWWEQYRL--- 153
+VFL+ L L+ + + +SF LGF + RWWE +L
Sbjct: 29 LVFLLLSALVTAIYIFELLAKYCLPIAPFTLIGLALSFFLGFRNNAAYDRWWEARKLWGA 88
Query: 154 -LPWPDTLALFVSAAIPG 170
+ W +LA VS IPG
Sbjct: 89 LVNWSRSLARQVSTLIPG 106
>gnl|CDD|227765 COG5478, COG5478, Predicted small integral membrane protein
[Function unknown].
Length = 141
Score = 28.9 bits (65), Expect = 0.87
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 116 GLDHITYLQAHYLSSPMSFVLGFYVSLVVKRWWEQYRLLPWPDTLALFVSAAIPGVVSV- 174
D A +L P +FV+ V+++V W L + DT L ++ ++ + +
Sbjct: 5 WFDRFANRVADFLGRPPAFVV-ALVAILV--WAGSGPLFGFSDTWQLVINTSVAIITFLM 61
Query: 175 VFLI 178
V LI
Sbjct: 62 VVLI 65
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 28.5 bits (64), Expect = 2.2
Identities = 23/98 (23%), Positives = 34/98 (34%), Gaps = 22/98 (22%)
Query: 85 LFVS-AAIPGVVSVVFLIFPLLQNYEKKTVLIGLDHITYLQAHYLSSPMSFVLGFYVSLV 143
LFVS + G V ++ IFP++ E + + L VSL+
Sbjct: 332 LFVSWVGLRGAVPIILAIFPMMAGLENARLFFNVAFFVVL----------------VSLL 375
Query: 144 VKRWWEQYRLLPWPDTLALFVSAAIPGVVSVVFLIFPP 181
++ LPW + G VS V L P
Sbjct: 376 IQGS-----TLPWAAKKLKVIVPPRGGPVSKVGLDIHP 408
>gnl|CDD|183857 PRK13057, PRK13057, putative lipid kinase; Reviewed.
Length = 287
Score = 26.8 bits (60), Expect = 6.2
Identities = 14/36 (38%), Positives = 14/36 (38%), Gaps = 10/36 (27%)
Query: 59 LGFYVSLVVKRWWEQYRLLP---------WPDTLAL 85
L Y SL V WW LLP WPD A
Sbjct: 209 LDLY-SLEVAHWWRLLALLPALRRGRHGEWPDVRAF 243
Score = 26.8 bits (60), Expect = 6.2
Identities = 14/36 (38%), Positives = 14/36 (38%), Gaps = 10/36 (27%)
Query: 136 LGFYVSLVVKRWWEQYRLLP---------WPDTLAL 162
L Y SL V WW LLP WPD A
Sbjct: 209 LDLY-SLEVAHWWRLLALLPALRRGRHGEWPDVRAF 243
>gnl|CDD|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional.
Length = 457
Score = 26.7 bits (59), Expect = 8.9
Identities = 10/34 (29%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 81 DTLALFVSAAIPGVVSVVFLIFPLL--QNYEKKT 112
D+LA ++SA +P V+ + +F + ++Y ++T
Sbjct: 6 DSLAKWLSALLPVVIVGLVGLFSVTVIRDYGRET 39
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
0.331 0.144 0.473
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,124,527
Number of extensions: 985560
Number of successful extensions: 1613
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1592
Number of HSP's successfully gapped: 82
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
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: 56 (25.3 bits)