RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10865
(667 letters)
>gnl|CDD|217523 pfam03381, CDC50, LEM3 (ligand-effect modulator 3) family / CDC50
family. Members of this family have been predicted to
contain transmembrane helices. The family member LEM3 is
a ligand-effect modulator, mutation of which increases
glucocorticoid receptor activity in response to
dexamethasone and also confers increased activity on
other intracellular receptors including the
progesterone, oestrogen and mineralocorticoid receptors.
LEM3 is thought to affect a downstream step in the
glucocorticoid receptor pathway. Factors that modulate
ligand responsiveness are likely to contribute to the
context-specific actions of the glucocorticoid receptor
in mammalian cells. The products of genes YNR048w,
YNL323w and YCR094w (CDC50) show redundancy of function
and are involved in regulation of transcription via
CDC39. CDC39 (also known as NOT1) is normally a negative
regulator of transcription either by affecting the
general RNA polymerase II machinery or by altering
chromatin structure. One function of CDC39 is to block
activation of the mating response pathway in the absence
of pheromone, and mutation causes arrest in G1 by
activation of the pathway. It may be that the
cold-sensitive arrest in G1 noticed in CDC50 mutants may
be due to inactivation of CDC39. The effects of LEM3 on
glucocorticoid receptor activity may also be due to
effects on transcription via CDC39.
Length = 275
Score = 222 bits (567), Expect = 1e-67
Identities = 90/215 (41%), Positives = 118/215 (54%), Gaps = 21/215 (9%)
Query: 443 LVYFADNVKELSLDYTHCLSVEQPDKTCAQIINNSRQMNCTCELQFALSEEIEGNVYIYY 502
L+ ++NV+E+ + Y C +I + ++ TC + F + E+++G VY YY
Sbjct: 1 LLVASNNVQEIEIRYDDC------CTAAPEIGESFAEIPSTCTITFTIPEDMKGPVYFYY 54
Query: 503 GLTNFYQNHRRYVKSRDDLQL---TATHSFNLLQPCTLAMYLS--VAPCGAIANSLFSDS 557
LTNFYQNHRRYVKSR D QL + N +P Y +APCG IANS+F+D+
Sbjct: 55 QLTNFYQNHRRYVKSRSDDQLRGKAVSGDDNNCEPLRSNDYNGKPIAPCGLIANSMFNDT 114
Query: 558 FKIFNDKN--KEVPVLRTGIAWPSDKAVKFHNPPGPDLKEAFKNFAKPTDWKKNIWELDP 615
F + N V + + GIAW SDK KF N P +WK N +E D
Sbjct: 115 FSLPLANNGTTNVTLDKKGIAWSSDKEKKFKNTKYNP-----SGTVPPPNWKPN-YEDDH 168
Query: 616 ENPDNNGFQNEDFIVWMRTAALPNFRKLYRRVNHE 650
PDN NEDFIVWMRTAALP FRKLYRR++
Sbjct: 169 TIPDNQT--NEDFIVWMRTAALPTFRKLYRRIDAT 201
>gnl|CDD|227368 COG5035, CDC50, Cell cycle control protein [Cell division and
chromosome partitioning / Transcription / Signal
transduction mechanisms].
Length = 372
Score = 182 bits (463), Expect = 2e-51
Identities = 101/291 (34%), Positives = 145/291 (49%), Gaps = 37/291 (12%)
Query: 385 NHDEPDIVLNSNQKQNYKPKESAFNQQKLPAWQPILTAGTVMPAFFTFGLFFIPIGVGLV 444
D+ IV + ++ +P +AF QQ+L AWQPIL+ TV+P F G+ F P+G GL+
Sbjct: 5 RKDKKAIVSKPSLLKSRRPPNTAFRQQRLKAWQPILSPRTVLPLLFLIGIVFAPLGGGLL 64
Query: 445 YFADNVKELSLDYTHCLSV----------EQPDKTCAQIINNSRQM---------NCTCE 485
+ +V+EL++DYT C+++ E + +N Q C+
Sbjct: 65 VASSSVQELTIDYTDCMTLASDEFSDIPSEYIQFHFKKKVNVLPQWRFSTDEEDDFQKCQ 124
Query: 486 LQFALSEEIEGNVYIYYGLTNFYQNHRRYVKSRDDLQL--TATHSFNLLQPCTLAMYLS- 542
++F + +++ V+IYY LTNFYQNHRRYVKS D+ QL A S +L C Y
Sbjct: 125 IRFTVPSDMKKPVFIYYRLTNFYQNHRRYVKSFDEDQLRGEALKSDDLKSNCKPLSYNED 184
Query: 543 --VAPCGAIANSLFSDSFKIF--NDKNKEVPVLRT-GIAWPSDKAVKFHNPPGPDLKEAF 597
+ PCG IANS+F+D+F ++ L T GIAW SD+ + K
Sbjct: 185 KIIYPCGLIANSMFNDTFSSLLTGIEDTSNYNLTTKGIAWESDR--HRYKKT----KYNA 238
Query: 598 KNFAKPTDWKKNI--WELDPENPDNNGFQNEDFIVWMRTAALPNFRKLYRR 646
+ P +W K D PD + E+F WMRTAA P F KL R
Sbjct: 239 SDIVPPPNWAKMYPDGYTDDNIPDLS--TWEEFQNWMRTAAFPKFSKLAMR 287
>gnl|CDD|216157 pfam00858, ASC, Amiloride-sensitive sodium channel.
Length = 442
Score = 159 bits (403), Expect = 2e-42
Identities = 64/199 (32%), Positives = 95/199 (47%), Gaps = 17/199 (8%)
Query: 151 NAPVDSIPWRPWGAGRHLGLTVVLDANIEEYF-CSSEASYGFKLLLQNPVETPKLAAFGE 209
+S P R G GL++VLD +EY +S GFK+L+ +P E P + + G
Sbjct: 182 GQTGNSYPLRSSRPGPGNGLSLVLDIQQDEYLYSPGTSSAGFKVLIHSPNEYPFVDSLGF 241
Query: 210 LISPGRESLIVIKPIINKSNPSIATSDPELRQCLFNKERALRFYRHYTQRNCILECEANF 269
+ PG E+ I ++P ++P + P R C F+ ER L +++ Y+Q NC+LEC AN+
Sbjct: 242 TVPPGTETFISVRPQETSTSPELRRLPPPYRNCTFSDERNLYYFKIYSQSNCLLECRANY 301
Query: 270 TLSFCQCVMYFMPKDRFTRICGKKDT-DCADKAKLAMEMRLSQNLSNISKIFNDTTQKPN 328
L C CV YFMP++ +C +D +C D A F+
Sbjct: 302 LLKLCGCVPYFMPRNNNAPVCTPRDLRECLDDAL---------------DEFSTEEDSLG 346
Query: 329 CGCLPGCFSLGYSKTQSSS 347
C CLP C Y SS+
Sbjct: 347 CDCLPPCNETEYDVELSSA 365
Score = 41.6 bits (98), Expect = 0.001
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 42 NAPVDSIPWRPWGAGRHLGLTVVLDANIEEYF-CSSEASYGFKSIV 86
+S P R G GL++VLD +EY +S GFK ++
Sbjct: 182 GQTGNSYPLRSSRPGPGNGLSLVLDIQQDEYLYSPGTSSAGFKVLI 227
>gnl|CDD|233154 TIGR00859, ENaC, sodium channel transporter. The Epithelial Na+
Channel (ENaC) Family (TC 1.A.06)The ENaC family
consists of sodium channels from animals and has no
recognizable homologues in other eukaryotes or bacteria.
The vertebrate ENaC proteins from epithelial cells
cluster tightly together on the phylogenetic tree:
voltage-insensitive ENaC homologues are also found in
the brain. Eleven sequenced C. elegans proteins,
including the degenerins, are distantly related to the
vertebrate proteins as well as to each other. At least
some ofthese proteins form part of a mechano-transducing
complex for touch sensitivity. Other members of the ENaC
family, the acid-sensing ion channels, ASIC1-3,are homo-
or hetero-oligomeric neuronal H+-gated channels that
mediate pain sensation in response to tissue acidosis.
The homologous Helix aspersa(FMRF-amide)-activated Na+
channel is the first peptide neurotransmitter-gated
ionotropic receptor to be sequenced.Mammalian ENaC is
important for the maintenance of Na+ balance and the
regulation of blood pressure. Three homologous ENaC
subunits, a, b and g, havebeen shown to assemble to form
the highly Na+-selective channel.This model is designed
from the vertebrate members of the ENaC family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 595
Score = 43.2 bits (102), Expect = 4e-04
Identities = 30/122 (24%), Positives = 53/122 (43%), Gaps = 19/122 (15%)
Query: 169 GLTVVLDANIEEY--FCSSEASYGFKLLLQNPVETPKLAAFGELISPGRESLIVIK--PI 224
GL +VLD +EY S+EA G ++++ + E P + G + PG E+ I ++ +
Sbjct: 274 GLKLVLDIEQDEYLPLLSTEA--GARVMVHSQDEPPFIDDLGFGVRPGTETSISMQEDEL 331
Query: 225 INKSNP----SIATSDPELRQCLFNKERALRFYRHYTQRNCILECEANFTLSFCQCVMYF 280
P + SD + + L+N Y+ + C+ C + + C C Y
Sbjct: 332 QRLGGPYGDCTENGSDVPV-ENLYNSS--------YSIQACLRSCFQRYMVENCGCAYYH 382
Query: 281 MP 282
P
Sbjct: 383 YP 384
>gnl|CDD|233159 TIGR00867, deg-1, degenerin. The Epithelial Na+ Channel (ENaC)
Family (TC 1.A.06)The ENaC family consists of sodium
channels from animals and has no recognizable homologues
in other eukaryotes or bacteria. The vertebrate ENaC
proteins from epithelial cells cluster tightly together
on the phylogenetic tree: voltage-insensitive ENaC
homologues are also found in the brain. Eleven sequenced
C. elegans proteins, including the degenerins, are
distantly related to the vertebrate proteins as well as
to each other. At least some ofthese proteins form part
of a mechano-transducing complex for touch sensitivity.
Other members of the ENaC family, the acid-sensing ion
channels, ASIC1-3,are homo- or hetero-oligomeric
neuronal H+-gated channels that mediate pain sensation
in response to tissue acidosis. The homologous Helix
aspersa(FMRF-amide)-activated Na+ channel is the first
peptide neurotransmitter-gated ionotropic receptor to be
sequenced.Mammalian ENaC is important for the
maintenance of Na+ balance and the regulation of blood
pressure. Three homologous ENaC subunits, a, b and g,
havebeen shown to assemble to form the highly
Na+-selective channel.This model is designed from the
invertebrate members of the ENaC family [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 600
Score = 34.8 bits (80), Expect = 0.15
Identities = 39/189 (20%), Positives = 66/189 (34%), Gaps = 26/189 (13%)
Query: 164 AGRHLGLTVVLDANIEEYFCSSEASYGFKLLLQNPVETPKLAAFGELISPGRESLIVIKP 223
AG GL ++L N +Y ++EA+ G +L + + E P FG G S ++
Sbjct: 352 AGPMYGLRLLLFVNQSDYLPTTEAA-GVRLTIHDKDEFPFPDTFGYSAPTGYISSFGVRL 410
Query: 224 IINKSNPSIATSDPELRQCLFNKERALRFYR--HYTQRNCILECEANFTLSFCQCVMYFM 281
P C+ + + Y+ Y+ C C ++ C C
Sbjct: 411 KQMSRLP------APYGNCVDTGKDSSYIYKGYIYSPEGCHRSCFQRLIIAKCGCADPRF 464
Query: 282 PKDRFTRIC---GKKDTDCADKAKLAMEMRLSQNLSNISKIFNDTTQKPNCGCLPGCFSL 338
P TR C K D +C L ++ ++ + C C C
Sbjct: 465 PVPEGTRHCQAFNKTDREC-----------LETLTGDLGELHH---SIFKCRCQQPCQES 510
Query: 339 GYSKTQSSS 347
Y+ T S++
Sbjct: 511 IYTTTYSAA 519
>gnl|CDD|234272 TIGR03592, yidC_oxa1_cterm, membrane protein insertase, YidC/Oxa1
family, C-terminal domain. This model describes
full-length from some species, and the C-terminal region
only from other species, of the YidC/Oxa1 family of
proteins. This domain appears to be univeral among
bacteria (although absent from Archaea). The
well-characterized YidC protein from Escherichia coli
and its close homologs contain a large N-terminal
periplasmic domain in addition to the region modeled
here [Protein fate, Protein and peptide secretion and
trafficking].
Length = 181
Score = 32.8 bits (76), Expect = 0.31
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 9/55 (16%)
Query: 396 NQKQNYKPKESAFNQQKLPAWQPILTAGTVMPAFFTFGLFFIPIGVGLVYFADNV 450
QK + QQK+ + +MP F F P G+ L + N+
Sbjct: 125 QQKLSPSGPPD-PAQQKIMMY--------IMPVMFLFFFLSFPAGLVLYWVVSNL 170
>gnl|CDD|233130 TIGR00797, matE, putative efflux protein, MATE family. The Multi
Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The
MATE family consists of probable efflux proteins
including a functionally characterized multi drug efflux
system from Vibrio parahaemolyticus, a putative
ethionine resistance protein of Saccharomyces
cerevisiae, and the functionally uncharacterized DNA
damage-inducible protein F (DinF) of E. coli. These
proteins have 12 probable TMS [Transport and binding
proteins, Other].
Length = 342
Score = 33.0 bits (76), Expect = 0.49
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 409 NQQKLP--AWQPILTAGTVMPAFFTFGLFFIPIGVGLVYFADNVKELSLDYTHCLS 462
N Q+L A Q +L A + G FFI + L+ V EL+ DY L
Sbjct: 64 NYQRLGRQAQQSLLLALLLGLPVLLVGYFFIDPLLSLMGADGEVAELAQDYLRILI 119
>gnl|CDD|179580 PRK03449, PRK03449, putative inner membrane protein translocase
component YidC; Provisional.
Length = 304
Score = 31.2 bits (71), Expect = 1.6
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 19/74 (25%)
Query: 382 AVANHDEPDIVLNSNQKQNYKPKESAFNQQ-----KLPAWQPILTAGTVMPAFFTFGLFF 436
VA H NS + E+A N Q KL W V P G F
Sbjct: 198 GVATH------FNSRASVARQSAEAAANPQTAMMNKLALW--------VFPLGVLVGGPF 243
Query: 437 IPIGVGLVYFADNV 450
+P+ + L + ++N+
Sbjct: 244 LPLAILLYWVSNNI 257
>gnl|CDD|223047 PHA03332, PHA03332, membrane glycoprotein; Provisional.
Length = 1328
Score = 31.1 bits (70), Expect = 2.7
Identities = 23/111 (20%), Positives = 37/111 (33%), Gaps = 9/111 (8%)
Query: 419 ILTAGTVMPAFFTFGLFFIPIGVGLVY-----FADNVKELSLDYTHCLSVEQPD-KTCAQ 472
L G G +F+ GV D V+ + +D T C++ +C
Sbjct: 725 YLINGRFTGFVIDAGTYFL--GVSAYIKIISDNTDVVEYIPVDQT-CMNYSNSSIPSCLA 781
Query: 473 IINNSRQMNCTCELQFALSEEIEGNVYIYYGLTNFYQNHRRYVKSRDDLQL 523
+ CT S ++ V I L F ++ RY + L L
Sbjct: 782 TVCAGNVTECTPRATLVCSMDVSVRVSIAGLLLEFEYSNERYKNTLSVLDL 832
>gnl|CDD|202768 pfam03788, LrgA, LrgA family. This family is uncharacterized. It
contains the protein LrgA that has been hypothesised to
export murein hydrolases.
Length = 96
Score = 28.1 bits (64), Expect = 4.9
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 433 GLFFIPIGVGLV 444
L F+P GVG++
Sbjct: 52 ALLFVPAGVGVM 63
>gnl|CDD|216872 pfam02096, 60KD_IMP, 60Kd inner membrane protein.
Length = 193
Score = 29.0 bits (66), Expect = 6.0
Identities = 11/51 (21%), Positives = 15/51 (29%), Gaps = 8/51 (15%)
Query: 400 NYKPKESAFNQQKLPAWQPILTAGTVMPAFFTFGLFFIPIGVGLVYFADNV 450
P Q K +MP F F P G+ L + N+
Sbjct: 137 QDPPDLQQSAQMK--------IMMYIMPLIFLFFFLNFPAGLVLYWIVSNL 179
>gnl|CDD|223778 COG0706, YidC, Preprotein translocase subunit YidC [Intracellular
trafficking and secretion].
Length = 314
Score = 29.3 bits (66), Expect = 6.9
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 423 GTVMPAFFTFGLFFIPIGVGLVYFADNV 450
+MP FTF F P G+ L + N+
Sbjct: 257 MYIMPIIFTFFFFNFPAGLVLYWIVSNL 284
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 0.135 0.423
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,974,261
Number of extensions: 3284545
Number of successful extensions: 2336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2321
Number of HSP's successfully gapped: 17
Length of query: 667
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 564
Effective length of database: 6,369,140
Effective search space: 3592194960
Effective search space used: 3592194960
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: 62 (27.6 bits)