RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2164
(68 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 = 56.4 bits (137), Expect = 2e-11
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 3 EKHPMTKYWLPLTWATNIINRARREATITSDHMVQTILNEMSDIRWRLGSLIGYDNVNLP 62
+ Y L + WA ++ +ARRE I D + + E++++R LG D +P
Sbjct: 150 LQSSNPPYALLIVWAASL-AKARREGRI-DDIQLVQLDEELNELRDALGGCERIDWTPIP 207
Query: 63 LVYTQ 67
L YTQ
Sbjct: 208 LAYTQ 212
>gnl|CDD|226757 COG4307, COG4307, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 349
Score = 29.1 bits (65), Expect = 0.11
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 9 KYWLPLTWATNIINRA 24
WLPL+WA N INR+
Sbjct: 292 DRWLPLSWALNSINRS 307
>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 = 29.1 bits (66), Expect = 0.12
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 7 MTKYWLPLTWATNIINRA 24
+ W+PLT A N +NR+
Sbjct: 297 LVNAWVPLTLALNSLNRS 314
>gnl|CDD|119275 pfam10755, DUF2585, Protein of unknown function (DUF2585). This
family is conserved in Proteobacteria. The function is
not known.
Length = 165
Score = 26.5 bits (59), Expect = 0.92
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 20 IINRARREATITSDHMVQTILNEMSDIRW 48
II+R R ATI+ D+ ++LN +SD
Sbjct: 83 IIDR-YRAATISLDYYGDSVLNSVSDTLA 110
>gnl|CDD|240102 cd04754, Commd6, COMM_Domain containing protein 6. The COMM
Domain is found at the C-terminus of a variety of
proteins; presumably all COMM_Domain containing
proteins are located in the nucleus and the COMM domain
plays a role in protein-protein interactions. Several
family members have been shown to bind and inhibit
NF-kappaB.
Length = 86
Score = 25.7 bits (56), Expect = 1.5
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 41 NEMSDIRWRLGSLIGYD---NVNLPLV 64
++ D +W+LG + D ++N P V
Sbjct: 20 GQLVDFKWKLGMAVSSDTCRSLNSPYV 46
>gnl|CDD|222213 pfam13546, DDE_5, DDE superfamily endonuclease. This family of
proteins are related to pfam00665 and are probably
endonucleases of the DDE superfamily. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction.
Length = 272
Score = 25.8 bits (57), Expect = 1.7
Identities = 7/40 (17%), Positives = 12/40 (30%)
Query: 10 YWLPLTWATNIINRARREATITSDHMVQTILNEMSDIRWR 49
+ P R R+ V I +E+ + W
Sbjct: 222 WLPPPQVTGRKRGRPRKYGRKILPLTVDEIADELKAVPWT 261
>gnl|CDD|165586 PHA03342, PHA03342, US22 family homolog; Provisional.
Length = 511
Score = 25.3 bits (55), Expect = 2.7
Identities = 16/64 (25%), Positives = 21/64 (32%), Gaps = 15/64 (23%)
Query: 2 DEKHPMTKYWLPLTWATNIINRARREATITSDHMVQTILNEMSDIRWRLGSLIGYDNVNL 61
D PM +Y L A I + A T+ +D R G G +
Sbjct: 413 DNGDPMKEYEDNLELA---IAHVKLAAAATA-----------ADRE-RGGGRAGEGLARV 457
Query: 62 PLVY 65
P VY
Sbjct: 458 PCVY 461
>gnl|CDD|225851 COG3314, COG3314, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 427
Score = 25.0 bits (55), Expect = 2.8
Identities = 2/19 (10%), Positives = 5/19 (26%)
Query: 3 EKHPMTKYWLPLTWATNII 21
+ P + I+
Sbjct: 213 ATLLLMPLLKPYFGSPVIV 231
>gnl|CDD|236250 PRK08373, PRK08373, aspartate kinase; Validated.
Length = 341
Score = 25.0 bits (55), Expect = 3.4
Identities = 5/17 (29%), Positives = 13/17 (76%)
Query: 48 WRLGSLIGYDNVNLPLV 64
WR+G+L+ ++ +P++
Sbjct: 271 WRMGTLVSNESSGMPIL 287
>gnl|CDD|234871 PRK00944, PRK00944, hypothetical protein; Provisional.
Length = 195
Score = 24.6 bits (54), Expect = 3.7
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 20 IINRARREATITSDHMVQTILNEMSDI 46
II R R ATI+ D+ +ILN + D
Sbjct: 112 IIER-YRAATISLDYYGDSILNSVMDT 137
>gnl|CDD|198369 cd07798, FGGY_AI-2K_like, Autoinducer-2 kinase-like proteins;
belongs to the FGGY family of carbohydrate kinases.
This subgroup consists of uncharacterized hypothetical
bacterial proteins with similarity to bacterial
autoinducer-2 (AI-2) kinases, which catalyzes the
phosphorylation of intracellular AI-2 to phospho-AI-2,
leading to the inactivation of lsrR, the repressor of
the lsr operon. Members of this subgroup belong to the
FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 437
Score = 24.9 bits (54), Expect = 3.8
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 2 DEKHPMTKYWLPLTWATNIINRARREATITSDHMVQTI 39
D+ +P +Y+ P ++ A+ + + V I
Sbjct: 36 DKLYPDARYFSPEELWKQLLGGAKELLKESPEIPVIGI 73
>gnl|CDD|216771 pfam01896, DNA_primase_S, Eukaryotic and archaeal DNA primase small
subunit. DNA primase synthesises the RNA primers for
the Okazaki fragments in lagging strand DNA synthesis.
DNA primase is a heterodimer of large and small
subunits. This family also includes baculovirus late
expression factor 1 or LEF-1 proteins. Baculovirus LEF-1
is a DNA primase enzyme. Bacterial DNA primase adopts a
different fold to archaeal and eukaryotic primases.
Length = 133
Score = 24.8 bits (54), Expect = 3.8
Identities = 10/44 (22%), Positives = 18/44 (40%)
Query: 11 WLPLTWATNIINRARREATITSDHMVQTILNEMSDIRWRLGSLI 54
W+P A ++ + RRE + +T+L E D +
Sbjct: 59 WVPFKEARSLGDARRREIADYAKAFAETLLEEQDDFPTATKPRL 102
>gnl|CDD|198029 smart00961, RuBisCO_small, Ribulose bisphosphate carboxylase,
small chain. RuBisCO (ribulose-1,5-bisphosphate
carboxylase/oxygenase) is a bifunctional enzyme that
catalyses both the carboxylation and oxygenation of
ribulose-1,5-bisphosphate (RuBP), thus fixing carbon
dioxide as the first step of the Calvin cycle. RuBisCO
is the major protein in the stroma of chloroplasts, and
in higher plants exists as a complex of 8 large and 8
small subunits. The function of the small subunit is
unknown. While the large subunit is coded for by a
single gene, the small subunit is coded for by several
different genes, which are distributed in a tissue
specific manner. They are transcriptionally regulated
by light receptor phytochrome. which results in RuBisCO
being more abundant during the day when it is required.
Length = 96
Score = 24.0 bits (53), Expect = 4.9
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 18/62 (29%)
Query: 2 DEKHPMTKYW--LPLTWATNIINRARREATITSDHMVQTILNEMSD--IRWRLGSLIGYD 57
D + T W LP+ A A + ++ ++ L E +R LIG D
Sbjct: 36 DPRRFRTSSWQKLPMF-------GATDAAEVLAE--LEACLAEHPGEYVR-----LIGID 81
Query: 58 NV 59
Sbjct: 82 PK 83
>gnl|CDD|233811 TIGR02289, M3_not_pepF, oligoendopeptidase, M3 family. This
family consists of probable oligoendopeptidases in the
M3 family, related to lactococcal PepF and group B
streptococcal PepB (TIGR00181) but in a distinct clade
with considerable sequence differences. The likely
substrate is small peptides and not whole proteins, as
with PepF, but members are not characterized and the
activity profile may differ. Several bacteria have both
a member of this family and a member of the PepF
family.
Length = 549
Score = 24.3 bits (53), Expect = 6.4
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 27 EATITSDHMVQTILNEMSDIRWRLGSLIG 55
E I S + +NE++D+R + +I
Sbjct: 13 EKFINSKEEQENWINEINDVRDDIEEMIT 41
>gnl|CDD|233357 TIGR01322, scrB_fam, sucrose-6-phosphate hydrolase. [Energy
metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 445
Score = 23.9 bits (52), Expect = 9.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 26 REATITSDHMVQTILNEMSDIR 47
RE T+ +VQT L E+ +R
Sbjct: 310 RELTLKDGKLVQTPLRELKALR 331
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
0.320 0.133 0.420
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,427,981
Number of extensions: 235635
Number of successful extensions: 230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 17
Length of query: 68
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 29
Effective length of database: 9,207,796
Effective search space: 267026084
Effective search space used: 267026084
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: 53 (24.0 bits)