RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2634
(749 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 = 300 bits (772), Expect = 1e-96
Identities = 109/340 (32%), Positives = 159/340 (46%), Gaps = 67/340 (19%)
Query: 1 MTVTYTAEVASCTGFGCFLKLLARWRGSIYKLVWPDLMAYLTLYYALNLTYRYQLNPEQK 60
M V F +LL RWRGSI K +WP+L+ +L L + Y
Sbjct: 1 MIVRPR---------PNFFRLLFRWRGSILKSIWPELLVFLLLSALVTAIYI-------- 43
Query: 61 KTFESIVEYCDTYSNL----IPLSFVLGFYISIIMTRWWDQYNN----IPWPDAMAVYVS 112
FE + +YC + + LSF LGF + RWW+ + W ++A VS
Sbjct: 44 --FELLAKYCLPIAPFTLIGLALSFFLGFRNNAAYDRWWEARKLWGALVNWSRSLARQVS 101
Query: 113 SQVHGQDERGRMMRRTIMRYVCVCITMVLANISPRVKKRFPSLDHFVEVGLLLENEKNII 172
+ + G DER R++RRTI Y + L ISP V L+H LL E E+ +
Sbjct: 102 TLIPGDDERRRLLRRTIA-YAHALRAL-LRGISPAVD-----LEH-----LLSEEEEEKL 149
Query: 173 SAINDKFPGPPKHWMPIVWAASVVTRARKEGRVRDDFSVKSIIDELNRIRGQCGKLLSYD 232
++ P + + IVWAAS+ +AR+EGR+ DD + + +ELN +R G D
Sbjct: 150 LQSSN-----PPYALLIVWAASL-AKARREGRI-DDIQLVQLDEELNELRDALGGCERID 202
Query: 233 TVSVPLVYTQVVTLAVYSFLITTIMGRQWLDVPAESDTSHPLRIHNNYIDLYFPIFTILQ 292
+PL YTQ+V AVY + + G Q + + P+FT+L
Sbjct: 203 WTPIPLAYTQLVHRAVYLYCLLLPFGLQD------------------TLGWFTPLFTVLI 244
Query: 293 FFFYMGWLKVAEVLINPFGDDDEDFEVNWM---IDRNIQV 329
F+F+ G KV E L NPFG+DD D +N + I+RN+
Sbjct: 245 FYFFFGLDKVGEELENPFGEDDNDLPLNALCRTIERNLLE 284
>gnl|CDD|216155 pfam00856, SET, SET domain. SET domains are protein lysine
methyltransferase enzymes. SET domains appear to be
protein-protein interaction domains. It has been
demonstrated that SET domains mediate interactions with
a family of proteins that display similarity with
dual-specificity phosphatases (dsPTPases). A subset of
SET domains have been called PR domains. These domains
are divergent in sequence from other SET domains, but
also appear to mediate protein-protein interaction. The
SET domain consists of two regions known as SET-N and
SET-C. SET-C forms an unusual and conserved knot-like
structure of probably functional importance.
Additionally to SET-N and SET-C, an insert region
(SET-I) and flanking regions of high structural
variability form part of the overall structure.
Length = 113
Score = 50.6 bits (121), Expect = 1e-07
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 695 NHSCVPNAEIKF--PYSNFVLNMVATRDIASGDEICISY 731
NHSC PN E++F + + A RDI G+E+ I Y
Sbjct: 74 NHSCEPNCEVRFVFVNGGDRIVVRALRDIKPGEELTIDY 112
>gnl|CDD|214614 smart00317, SET, SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)
domain. Putative methyl transferase, based on outlier
plant homologues.
Length = 124
Score = 46.2 bits (110), Expect = 4e-06
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 695 NHSCVPNAEIKFPYSNFVLNMV--ATRDIASGDEICISY 731
NHSC PN E+ F N +V A RDI G+E+ I Y
Sbjct: 79 NHSCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDY 117
>gnl|CDD|225491 COG2940, COG2940, Proteins containing SET domain [General function
prediction only].
Length = 480
Score = 41.3 bits (97), Expect = 0.001
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 694 SNHSCVPNAEIKFPYSN--FVLNMVATRDIASGDEICISY 731
NHSC PN E N F +++ A RDI +G+E+ Y
Sbjct: 409 INHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDY 448
>gnl|CDD|198371 cd07803, FGGY_D-XK, D-xylulose kinases; a subgroup of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial D-xylulose kinases
(XK, also known as xylulokinase; EC 2.7.1.17), which
catalyze the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. Some uncharacterized
sequences are also included in this subfamily. The
prototypical member of this subfamily is Escherichia
coli xylulokinase (EcXK), which exists as a dimer. Each
monomer consists of two large domains separated by an
open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. XKs do not have any known allosteric
regulators, and they may have weak but significant
activity in the absence of substrate. The presence of
Mg2+ or Mn2+ is required for catalytic activity. Members
of this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 482
Score = 35.8 bits (83), Expect = 0.082
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 90 IMTRWWDQYNNIPWPDAMAVYVSSQVHGQ---DERGRMMRRTIM 130
+ DQ + D A+ V+ Q+HG D++GR++R I+
Sbjct: 55 ALEALLDQAGDSAE-DIAAIGVTGQMHGAVLLDQQGRVLRPAIL 97
>gnl|CDD|226206 COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and
metabolism].
Length = 433
Score = 35.7 bits (82), Expect = 0.095
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 439 CDSTSSM--NTLGM---GSIANSLNKISGGSMQTLRKIFSGSNDNKLTCANDGVAMKPAS 493
+ SSM N GM G+ + KIS G+ + + +D +T N+G+
Sbjct: 346 SMAISSMIGNLSGMICDGAKNSCAMKISSGASAAWKAVLMALDDTAVT-GNEGIVGHDVE 404
Query: 494 QSSDNLAKSAGTSMRITDQVIEEL 517
+S NL A SM+ TD+ I E+
Sbjct: 405 ESIANLGALASHSMKQTDRQIIEI 428
>gnl|CDD|226304 COG3781, COG3781, Predicted membrane protein [Function unknown].
Length = 306
Score = 31.3 bits (71), Expect = 1.6
Identities = 29/143 (20%), Positives = 54/143 (37%), Gaps = 28/143 (19%)
Query: 191 WAASVVTRARKEGRVRDDFSVKSIIDELNRIR---GQCGKLLSYDTVSVPLVYTQVVTLA 247
W + + R+ G++ D S+ LN I G C ++ +P YT +
Sbjct: 165 WMGEWLQQQRRNGQL-DAIQFTSLDRRLNSISAVLGGCERIAY---TPIPFAYTLHLHRT 220
Query: 248 VYSFLITTIMGRQWLDVPAESDTSHPLRIHNNYIDLYFPIFTILQFFFYMGWLKVAEVLI 307
VY F P + + P F++L + + G +AE +
Sbjct: 221 VYLFCFLL-----------------PFGLVET-LGWATPFFSVLIAYTFFGLEAIAEEIE 262
Query: 308 NPFGDDDEDFEVNWM---IDRNI 327
+PFG + D ++ + I+ N+
Sbjct: 263 DPFGTEANDLPLDAICNTIEINL 285
>gnl|CDD|236512 PRK09430, djlA, Dna-J like membrane chaperone protein; Provisional.
Length = 267
Score = 31.3 bits (72), Expect = 1.8
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 10/47 (21%)
Query: 499 LAKSAGTSMRITDQVI---EELDEQMTITASGRLEPRRAAQDIFSEG 542
LAK+ G R+T+ I +L ++M + E RRAAQ F EG
Sbjct: 65 LAKAKG---RVTEADIRIASQLMDRMNLHG----EARRAAQQAFREG 104
>gnl|CDD|185201 PRK15301, PRK15301, hypothetical protein; Provisional.
Length = 186
Score = 30.6 bits (69), Expect = 1.8
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 15/73 (20%)
Query: 380 AVDACQVEYTNPTSVKVEGSNNPNYALLQEDSQSENDRNFIIGSVSSKLPRREREKSISC 439
A D CQ+ + P NY ++ D + +N+ +K+P RE S+SC
Sbjct: 22 ADDDCQLTLSRP---------EVNYGQMRRDDIVGSQQNW------NKMPEREVNVSVSC 66
Query: 440 DSTSSMNTLGMGS 452
M G+
Sbjct: 67 PEPQQMALFVQGA 79
>gnl|CDD|233595 TIGR01845, outer_NodT, efflux transporter, outer membrane factor
(OMF) lipoprotein, NodT family. Members of This model
comprise a subfamily of the Outer Membrane Factor (TCDB
1.B.17) porins. OMF proteins operate in conjunction with
a primary transporter of the RND, MFS, ABC, or PET
systems, and a MFP (membrane fusion protein) to tranport
substrates across membranes. The complex thus formed
allows transport (export) of various solutes (heavy
metal cations; drugs, oligosaccharides, proteins, etc.)
across the two envelopes of the Gram-negative bacterial
cell envelope in a single energy-coupled step. Current
data suggest that the OMF (and not the MFP) is largely
responsible for the formation of both the trans-outer
membrane and trans-periplasmic channels. The roles
played by the MFP have yet to be determined [Cellular
processes, Detoxification, Transport and binding
proteins, Porins].
Length = 454
Score = 31.2 bits (71), Expect = 2.3
Identities = 21/93 (22%), Positives = 33/93 (35%), Gaps = 9/93 (9%)
Query: 492 ASQSSDNLAKSAGTSMRITDQVIEE---LDEQMTITASGRLEPRRAAQDIFSEGNIPSSL 548
A+ S A++A S ++ G+ R A + L
Sbjct: 205 AAASDVRQAEAAVASAEAELPSLDVQIAQARNALAALLGKGPSRGLAIA---RPLLLDQL 261
Query: 549 PIDVPTNPNSDYPRNRPD---SSARSSGTYAEI 578
P D+P + SD R RPD + R + A+I
Sbjct: 262 PPDLPLSLPSDLLRRRPDIRAAERRLAAANAQI 294
>gnl|CDD|143585 cd07316, terB_like_DjlA, N-terminal tellurium resistance protein
terB-like domain of heat shock DnaJ-like proteins.
Tellurium resistance terB-like domain of the DnaJ-like
DjlA proteins. This family represents the terB-like
domain of DjlA-like proteins, a subgroup of heat shock
DnaJ-like proteins. Escherichia coli DjlA is a type III
membrane protein with a small N-terminal transmembrane
region and DnaJ-like domain on the extreme C-terminus.
Overproduction has been shown to activate the RcsC
pathway, which regulates the production of the capsular
exopolysaccharide colanic acid. The specific function
of this domain is unknown.
Length = 106
Score = 29.0 bits (66), Expect = 2.9
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 499 LAKSAGTSMRITDQVIEELDEQMTITASGRLEPRRAAQDIFSEG 542
LAK+ G R+++ I+ M E RR A +F+EG
Sbjct: 9 LAKADG---RVSEAEIQAARALMDQMG-LDAEARREAIRLFNEG 48
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 29.4 bits (67), Expect = 4.0
Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 23/100 (23%)
Query: 91 MTRW-WDQYNNIPWPDAMAVYVSSQVHGQDERG-----RMMRRT--IMRYVCVCITMVLA 142
+T + ++ I + + S +D + + R + R+V T +L+
Sbjct: 12 LTLIESELFSAIDPRE----LLDSAWGKKDSKLSPNIEAFISRFNQLSRWV---ATEILS 64
Query: 143 NISPRVKKRFPSLDHFVEVGLLLENEKN------IISAIN 176
+KKR + F+++ N IIS +N
Sbjct: 65 --EEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLN 102
>gnl|CDD|205223 pfam13042, DUF3902, Protein of unknown function (DUF3902). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are approximately 170 amino acids in
length. There is a conserved LGI sequence motif.
Length = 161
Score = 29.4 bits (66), Expect = 4.7
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 37 LMAYLTLYYALNLTYRYQLNPEQKKTFESIVEYCDTYSNLIPLSF-VLGFYISIIM 91
LMAYL+LY ++L K T++ +++I SF VLG II
Sbjct: 40 LMAYLSLYILIDLY--------CKNTYDKKFPKVLIKTSVISFSFAVLGIIFGIIH 87
>gnl|CDD|176454 cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V. umuC
subunit of Pol V. Pol V is a bacterial translesion
synthesis (TLS) polymerase that consists of the
heterotrimer of one umuC and two umuD subunits.
Translesion synthesis is a process that allows the
bypass of a variety of DNA lesions. TLS polymerases
lack proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. Pol V, RecA,
single stranded DNA-binding protein, beta sliding clamp,
and gamma clamp loading complex are responsible for
inducing the SOS response in bacteria to repair
UV-induced DNA damage.
Length = 344
Score = 29.8 bits (68), Expect = 5.5
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 109 VYVSSQVHGQD--ERGRMMRRTIMR----YVCVCI--TMVLANISPRVKKRFPSLDHFV 159
+ ++ + D E R +RR I++ V V I T LA ++ + K+ V
Sbjct: 103 LDLTGSLRFGDLEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVV 161
>gnl|CDD|180446 PRK06180, PRK06180, short chain dehydrogenase; Provisional.
Length = 277
Score = 29.5 bits (67), Expect = 5.6
Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 11/57 (19%)
Query: 503 AGTSMRITDQVIEELDE------QMTITASGRL--EPRRAAQ---DIFSEGNIPSSL 548
AG SM T + I + D Q SG+ +P +AAQ P L
Sbjct: 188 AGRSMVRTPRSIADYDALFGPIRQAREAKSGKQPGDPAKAAQAILAAVESDEPPLHL 244
>gnl|CDD|148372 pfam06729, NRIF3, Nuclear receptor co-activator NRIF3. This family
consists of mammalian nuclear receptor co-activator
NRIF3 proteins. NRIF3 exhibits a distinct receptor
specificity in interacting with and potentiating the
activity of only TRs and RXRs but not other examined
nuclear receptors. NRIF3 as a coregulator that possesses
both transactivation and transrepression domains and/or
functions. Collectively, the NRIF3 family of
coregulators may play dual roles in mediating both
positive and negative regulatory effects on gene
expression.
Length = 131
Score = 28.6 bits (63), Expect = 5.7
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 11/77 (14%)
Query: 582 APTTPNEENFDLGAFDNDLMSSDGSSTVHSSRRNSSTFKDSDAKAAFESLKRSRQQEKMS 641
+P + E+ G D +S+ R T +D DA A S K+
Sbjct: 6 SPASHKAEDHRNGLSHEDEKNSELRLPR---RGQEQTAEDRDAFAELLS--------KIE 54
Query: 642 VKLVRSISAAPSHTSEQ 658
+ L + + A + +S Q
Sbjct: 55 ISLEKILEAMENLSSIQ 71
>gnl|CDD|221446 pfam12158, DUF3592, Protein of unknown function (DUF3592). This
family of proteins is functionally uncharacterized.This
family of proteins is found in bacteria, archaea,
eukaryotes and viruses. Proteins in this family are
typically between 150 and 242 amino acids in length.
Length = 134
Score = 28.6 bits (64), Expect = 6.9
Identities = 10/56 (17%), Positives = 20/56 (35%), Gaps = 1/56 (1%)
Query: 79 LSFVLGFYISIIMTRWWDQYNNI-PWPDAMAVYVSSQVHGQDERGRMMRRTIMRYV 133
L ++G + ++ R Q WP+ V S+ D R ++ +
Sbjct: 10 LFLLIGLVLLVVGVRLLLQAQRSRTWPETPGTVVDSESRDSDGRRATTYYPVVEFR 65
>gnl|CDD|215570 PLN03091, PLN03091, hypothetical protein; Provisional.
Length = 459
Score = 29.2 bits (65), Expect = 8.3
Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 539 FSEGNIPSSLPIDVPTNPNSDYPRNRPDSSARSSGTYAEIFTGAPTTPNEENFDLGAFDN 598
FS PS LP V ++ +P S S + T N++ GAF N
Sbjct: 279 FSSSMTPSILPPSVTSSFLPTPMSYKPSISLPSDNPS----IPSFTVNGVRNWEAGAFSN 334
Query: 599 DLMSSDGSSTVHSSRRNSSTFKDS 622
+ SS+GSS+ + NSS F++S
Sbjct: 335 NSNSSNGSSSSIELQSNSSFFENS 358
>gnl|CDD|177952 PLN02318, PLN02318, phosphoribulokinase/uridine kinase.
Length = 656
Score = 29.4 bits (66), Expect = 8.8
Identities = 34/164 (20%), Positives = 56/164 (34%), Gaps = 16/164 (9%)
Query: 428 LPRREREK-SISCDSTSSMNTLGMGSIANSLNKISGGSMQTLRKIFSGSNDNKLTCANDG 486
LP + K S+ D SS + A+ NK + N +KLT
Sbjct: 420 LPEDLKTKLSLDDDLVSSPKEALSRASADRRNKNLKSGLSHSYSTQRDKNLSKLTGLAVT 479
Query: 487 VAMKPASQSSDNLAKSAGTSMRITDQV-------------IEELDEQMTITASGRLEPRR 533
S A + G ++++Q+ IEEL+ +++I + +
Sbjct: 480 NRRFDERNSESPAALNQGAITQLSEQISSLNERMDEFTSRIEELNSKLSIKKNSPSQQNL 539
Query: 534 AAQDIFSEGNIPSSLPIDVPTNPNSDYPRNRPDSSARSSGTYAE 577
A Q G+ P+S + N + SS SS E
Sbjct: 540 ALQAEACNGSAPTSYFVSGLGNGSLTGSILPLSSS--SSQLAKE 581
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
0.317 0.132 0.393
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 37,809,973
Number of extensions: 3676991
Number of successful extensions: 3172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3159
Number of HSP's successfully gapped: 25
Length of query: 749
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 645
Effective length of database: 6,324,786
Effective search space: 4079486970
Effective search space used: 4079486970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.1 bits)