RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2167
(79 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 = 57.5 bits (140), Expect = 1e-11
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 4 ERSPMAKYWMPLVWATNIINRARKEALISSDHVVQTLLYELSEHRRKLGSIISYDTVCVP 63
+S Y + +VWA ++ +AR+E I D + L EL+E R LG D +P
Sbjct: 150 LQSSNPPYALLIVWAASL-AKARREGRID-DIQLVQLDEELNELRDALGGCERIDWTPIP 207
Query: 64 LVYTQ 68
L YTQ
Sbjct: 208 LAYTQ 212
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 27.9 bits (62), Expect = 0.42
Identities = 8/44 (18%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 11 YWMPLVWATNIINRARKEALISSDHVVQTLLYELSEHRRKLGSI 54
W+ + +NII + I HV + + + + L ++
Sbjct: 509 TWIKPLEESNIIPENARRNFIK--HVFANINEIYAVNSKLLKAL 550
>gnl|CDD|215235 PLN02426, PLN02426, cytochrome P450, family 94, subfamily C
protein.
Length = 502
Score = 27.3 bits (61), Expect = 0.76
Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 9/51 (17%)
Query: 13 MPLVWAT----NI-INRARKEALISSDHVVQTLLYELSEHRRKLGSIISYD 58
PL+W NI R KEA+ +V L E+ RRKLG S D
Sbjct: 233 SPLLWKIKRLLNIGSERKLKEAI----KLVDELAAEVIRQRRKLGFSASKD 279
>gnl|CDD|226757 COG4307, COG4307, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 349
Score = 26.0 bits (57), Expect = 2.0
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 10 KYWMPLVWATNIINRA 25
W+PL WA N INR+
Sbjct: 292 DRWLPLSWALNSINRS 307
>gnl|CDD|236933 PRK11573, PRK11573, hypothetical protein; Provisional.
Length = 413
Score = 25.9 bits (57), Expect = 2.0
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 6 SPMAKYWMPLVWATNIINR 24
+P+ MPLVW N I R
Sbjct: 118 APLQILMMPLVWLLNTITR 136
>gnl|CDD|214552 smart00197, SAA, Serum amyloid A proteins. Serum amyloid A
proteins are induced during the acute-phase response.
Secondary amyloidosis is characterised by the
extracellular accumulation in tissues of SAA proteins.
SAA proteins are apolipoproteins.
Length = 103
Score = 25.2 bits (55), Expect = 2.9
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 16 VWATNIINRARK--EALISSDHVVQTL 40
VWA +I+ AR+ + LIS + +
Sbjct: 50 VWAAKVISDAREYFQGLISGRGLEDSK 76
>gnl|CDD|220517 pfam10005, DUF2248, Uncharacterized protein conserved in bacteria
(DUF2248). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 340
Score = 25.7 bits (57), Expect = 3.1
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 8 MAKYWMPLVWATNIINRA 25
+ W+PL A N +NR+
Sbjct: 297 LVNAWVPLTLALNSLNRS 314
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 24.9 bits (55), Expect = 3.9
Identities = 9/45 (20%), Positives = 15/45 (33%)
Query: 31 ISSDHVVQTLLYELSEHRRKLGSIISYDTVCVPLVYTQQNFLDAP 75
I + + + R+ G I V + NF+D P
Sbjct: 26 IDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPKRRINFIDTP 70
>gnl|CDD|182601 PRK10632, PRK10632, transcriptional regulator; Provisional.
Length = 309
Score = 24.7 bits (54), Expect = 6.7
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 12 WMPLVWATNIINRARKEALISSDHVVQTLLYELSEHRRKL 51
++PL+W + INR E L +Y L + KL
Sbjct: 238 YVPLMWVIDEINRGELEILFPRYQSDPRPVYALYTEKDKL 277
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 24.3 bits (53), Expect = 8.5
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 25 ARK------EALISSDHVVQTLLYELSEHR 48
ARK L+ +HVV+ L L + R
Sbjct: 7 ARKWRPKSFSELVGQEHVVRALTNALEQQR 36
>gnl|CDD|173843 cd01154, AidB, Proteins involved in DNA damage response, similar to
the AidB gene product. AidB is one of several genes
involved in the SOS adaptive response to DNA alkylation
damage, whose expression is activated by the Ada
protein. Its function has not been entirely elucidated;
however, it is similar in sequence and function to
acyl-CoA dehydrogenases. It has been proposed that aidB
directly destroys DNA alkylating agents such as
nitrosoguanidines (nitrosated amides) or their reaction
intermediates.
Length = 418
Score = 24.3 bits (53), Expect = 9.5
Identities = 12/58 (20%), Positives = 16/58 (27%), Gaps = 3/58 (5%)
Query: 22 INRARKEALISSDHVVQTLLYELSEHRRKLGSIISYDTVCVPLVYTQQNFLDAPTKHY 79
IN A HV Y LS+ L ++ V + K Y
Sbjct: 80 INIEDGPAGEGRRHVHFAAGYLLSDAAAGLLCPLTMTDAAVYALRKY---GPEELKQY 134
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 0.133 0.408
Gapped
Lambda K H
0.267 0.0632 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,937,523
Number of extensions: 291895
Number of successful extensions: 225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 11
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
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 (22.0 bits)
S2: 53 (24.4 bits)