RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3889
(243 letters)
>gnl|CDD|239305 cd03007, PDI_a_ERp29_N, PDIa family, endoplasmic reticulum
protein 29 (ERp29) subfamily; ERp29 is a ubiquitous
ER-resident protein expressed in high levels in
secretory cells. It forms homodimers and higher
oligomers in vitro and in vivo. It contains a redox
inactive TRX-like domain at the N-terminus, which is
homologous to the redox active TRX (a) domains of PDI,
and a C-terminal helical domain similar to the
C-terminal domain of P5. The expression profile of
ERp29 suggests a role in secretory protein production
distinct from that of PDI. It has also been identified
as a member of the thyroglobulin folding complex. The
Drosophila homolog, Wind, is the product of windbeutel,
an essential gene in the development of dorsal-ventral
patterning. Wind is required for correct targeting of
Pipe, a Golgi-resident type II transmembrane protein
with homology to 2-O-sulfotransferase.
Length = 116
Score = 89.9 bits (223), Expect = 4e-23
Identities = 44/73 (60%), Positives = 52/73 (71%), Gaps = 1/73 (1%)
Query: 21 KGHVSLDTHNFDKILSKFHTTLVKFDIAYPYGAKHEAFLEVAESS-KHQPDFLVAEVGVK 79
KG V LDT F K++ KF +LVKFD AYPYG KHEAF +AESS D LVAEVG+K
Sbjct: 1 KGCVDLDTVTFYKVIPKFKYSLVKFDTAYPYGEKHEAFTRLAESSASATDDLLVAEVGIK 60
Query: 80 DYGERDNEDLAKR 92
DYGE+ N +L +R
Sbjct: 61 DYGEKLNMELGER 73
>gnl|CDD|116524 pfam07912, ERp29_N, ERp29, N-terminal domain. ERp29 is a
ubiquitously expressed endoplasmic reticulum protein,
and is involved in the processes of protein maturation
and protein secretion in this organelle. The protein
exists as a homodimer, with each monomer being composed
of two domains. The N-terminal domain featured in this
family is organised into a thioredoxin-like fold that
resembles the a domain of human protein disulphide
isomerase (PDI). However, this domain lacks the C-X-X-C
motif required for the redox function of PDI; it is
therefore thought that ERp29's function is similar to
the chaperone function of PDI. The N-terminal domain is
exclusively responsible for the homodimerisation of the
protein, without covalent linkages or additional
contacts with other domains.
Length = 126
Score = 89.1 bits (221), Expect = 1e-22
Identities = 42/76 (55%), Positives = 54/76 (71%), Gaps = 1/76 (1%)
Query: 18 VLSKGHVSLDTHNFDKILSKFHTTLVKFDIAYPYGAKHEAFLEVA-ESSKHQPDFLVAEV 76
+ +KG V LDT F K++ KF +LVKFD AYPYG KHEAF +A E+S + LVAEV
Sbjct: 1 LTTKGCVDLDTVTFYKVIPKFKYSLVKFDTAYPYGEKHEAFTRLAKENSASTEELLVAEV 60
Query: 77 GVKDYGERDNEDLAKR 92
G+KDYGE+ N +L +R
Sbjct: 61 GIKDYGEKLNMELGER 76
>gnl|CDD|191840 pfam07749, ERp29, Endoplasmic reticulum protein ERp29, C-terminal
domain. ERp29 is a ubiquitously expressed endoplasmic
reticulum protein found in mammals. ERp29 is comprised
of two domains. This domain, the C-terminal domain, has
an all helical fold. ERp29 is thought to form part of
the thyroglobulin folding complex.
Length = 95
Score = 85.0 bits (211), Expect = 2e-21
Identities = 39/101 (38%), Positives = 63/101 (62%), Gaps = 6/101 (5%)
Query: 131 GCLQDFDRLAKDFIRSASQERKTLLKSAEDLWDEIKTNSARKSAEFYVKTMRKLVEISGE 190
G +++ D LA +F+ ++ ERK LL E+ ++K +SA K A++YVK M K++E
Sbjct: 1 GTIEELDELAAEFVTASDDERKELLSEVEEAVAKLK-DSAAKYAKYYVKVMEKILE---- 55
Query: 191 GSESEFLTREKARLKGLLNQKVSAQKKDELKSRMNILDSFA 231
+++ +E ARL+ LL ++ +K DEL SR+NIL SF
Sbjct: 56 -KGEDYVAKELARLERLLEGSLAPEKADELTSRLNILRSFQ 95
>gnl|CDD|238146 cd00238, ERp29c, ERp29 and ERp38, C-terminal domain; composed of
the protein disulfide isomerase (PDI)-like proteins
ERp29 and ERp38. ERp29 (also called ERp28) is a
ubiquitous endoplasmic reticulum (ER)-resident protein
expressed in high levels in secretory cells. It contains
a redox inactive TRX-like domain at the N-terminus. The
expression profile of ERp29 suggests a role in secretory
protein production, distinct from that of PDI. It has
also been identified as a member of the thyroglobulin
folding complex and is essential in regulating the
secretion of thyroglobulin. The Drosophila homolog,
Wind, is the product of windbeutel, an essential gene in
the development of dorsal-ventral patterning. Wind is
required for correct targeting of Pipe, a Golgi-resident
type II transmembrane protein with homology to
2-O-sulfotransferase. ERp38 is a P5-like protein, first
isolated from alfalfa (the cDNA clone was named G1),
which contains two redox active TRX domains at the
N-terminus, like human P5. However, unlike human P5,
ERp38 also contains a C-terminal domain with homology to
the C-terminal domain of ERp29. It may be a
glucose-regulated protein. The function of the
all-helical C-terminal domain of ERp29 and ERp38 remains
unclear. The C-terminal domain of Wind is thought to
provide a distinct site required for interaction with
its substrate, Pipe.
Length = 93
Score = 71.6 bits (176), Expect = 2e-16
Identities = 35/96 (36%), Positives = 58/96 (60%), Gaps = 7/96 (7%)
Query: 136 FDRLAKDFIRSASQERKTLLKSAEDLWDEIKTNSARKSAEFYVKTMRKLVEISGEGSESE 195
D LAK+F+ ++ +ERK LL+ ++ E + K A++YVK M K++E +
Sbjct: 4 LDELAKEFVDASDEERKELLEKVKEA-VEKLKEAEAKYAKYYVKVMEKILE-----KGED 57
Query: 196 FLTREKARLKGLL-NQKVSAQKKDELKSRMNILDSF 230
++ +E ARL+ LL + ++ +K DEL R+NIL SF
Sbjct: 58 YVEKELARLERLLEKKGLAPEKADELTRRLNILRSF 93
>gnl|CDD|239259 cd02961, PDI_a_family, Protein Disulfide Isomerase (PDIa) family,
redox active TRX domains; composed of eukaryotic
proteins involved in oxidative protein folding in the
endoplasmic reticulum (ER) by acting as catalysts and
folding assistants. Members of this family include PDI
and PDI-related proteins like ERp72, ERp57 (or ERp60),
ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI,
ERp57, ERp72, P5, PDIR and ERp46 are all oxidases,
catalyzing the formation of disulfide bonds of newly
synthesized polypeptides in the ER. They also exhibit
reductase activity in acting as isomerases to correct
any non-native disulfide bonds, as well as chaperone
activity to prevent protein aggregation and facilitate
the folding of newly synthesized proteins. These
proteins usually contain multiple copies of a redox
active TRX (a) domain containing a CXXC motif, and may
also contain one or more redox inactive TRX-like (b)
domains. Only one a domain is required for the oxidase
function but multiple copies are necessary for the
isomerase function. The different types of PDIs may
show different substrate specificities and
tissue-specific expression, or may be induced by
stress. PDIs are in their reduced form at steady state
and are oxidized to the active form by Ero1, which is
localized in the ER through ERp44. Some members of this
family also contain a DnaJ domain in addition to the
redox active a domains; examples are ERdj5 and Pfj2.
Also included in the family is the redox inactive
N-terminal TRX-like domain of ERp29.
Length = 101
Score = 34.5 bits (80), Expect = 0.008
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 24 VSLDTHNFDKILSKFHTTLVKFDIAY--PYGAKHEAFLEVAESSKHQPDFLVAEVGVKDY 81
V L NFD+++ LV+F + A + ++A+ K +VA+V
Sbjct: 1 VELTDDNFDELVKDSKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTAN 60
Query: 82 GE 83
+
Sbjct: 61 ND 62
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.8 bits (73), Expect = 0.34
Identities = 34/127 (26%), Positives = 53/127 (41%), Gaps = 18/127 (14%)
Query: 114 FILIIFFSSIGIWIG-------AVGCLQDFDRLAKDFIRSASQERKTLLKSAE-DLWDEI 165
+L + +G+ IG A L + LAK I A +E +TL K A + +E+
Sbjct: 1 ILLALVALIVGLIIGYLLRKRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEV 60
Query: 166 KTNSARKSAEFYVKTMRKLVEISGEGSESEFLTREK--ARLKGLLNQKVSA--QKKDELK 221
R E +K R E+ E L RE+ R L++K +K+ EL
Sbjct: 61 H--KLRAELERELKERRN--ELQRL--ERRLLQREETLDRKMESLDKKEENLEKKEKELS 114
Query: 222 SRMNILD 228
++ LD
Sbjct: 115 NKEKNLD 121
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.0 bits (66), Expect = 2.5
Identities = 27/121 (22%), Positives = 51/121 (42%), Gaps = 16/121 (13%)
Query: 115 ILIIFFSSIGIWIGAVGCLQDFDRLAKDFIRSASQERKTLLKSAEDLWDEIKTNSARKSA 174
++II + + + +GAV ++A+ I+ A +E K +L+ A + + + +K A
Sbjct: 4 LIIILIALVALVVGAVIGYFVRKKIAEAKIKEAEEEAKRILEEA-----KKEAEAIKKEA 58
Query: 175 EFYVKT--MRKLVEISGEGSESEFLTREK--ARLKGLLNQKVSA--QKKDELKSRMNILD 228
K + E E E R +L+ L QK +K + L+ R L+
Sbjct: 59 LLEAKEEIHKLRNEF-----EKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELE 113
Query: 229 S 229
Sbjct: 114 K 114
>gnl|CDD|235534 PRK05618, PRK05618, 50S ribosomal protein L25/general stress
protein Ctc; Reviewed.
Length = 197
Score = 27.9 bits (63), Expect = 4.4
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 23 HVSLDTHNFDKILSK--FHTTLVKFDIAYPYGAKHEAFL 59
+S+D K L K F +TL+ ++ G K + +
Sbjct: 41 SISVDEKELIKALKKGAFLSTLLDLEVG---GKKQKVLV 76
>gnl|CDD|131099 TIGR02044, CueR, Cu(I)-responsive transcriptional regulator. This
model represents the copper-, silver- and gold- (I)
responsive transcriptional activator of the gamma
proteobacterial copper efflux system. This protein is a
member of the MerR family of transcriptional activators
(pfam00376) and contains a distinctive pattern of
cysteine residues in its metal binding loop, Cys-X7-Cys.
This family also lacks a conserved cysteine at the
N-terminal end of the dimerization helix which is
required for the binding of divalent metals such as
zinc; here it is replaced by a serine residue
[Regulatory functions, DNA interactions].
Length = 127
Score = 26.6 bits (59), Expect = 7.5
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 149 QERKTLLKSAEDLWDEIKTNSARKSAEFYVKTMRKLVEISGEGSESEFLTREKARLKGLL 208
+E K LL LW+ + R SA+ +T+ K+ EI + SE L + +L+ L
Sbjct: 61 EECKELLN----LWN----DPNRTSADVKARTLEKVAEIERKISE---LQSMRDQLEALA 109
Query: 209 N 209
Sbjct: 110 Q 110
>gnl|CDD|180548 PRK06380, PRK06380, metal-dependent hydrolase; Provisional.
Length = 418
Score = 27.5 bits (61), Expect = 7.7
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 78 VKDYGERDNEDLAKRGCLTPQLLWAFCVADSLNK 111
VK GER E L K G L +L+ A CV + ++
Sbjct: 217 VKRTGERPVEHLEKIGFLNSKLIAAHCVWATYHE 250
>gnl|CDD|169983 PRK09579, PRK09579, multidrug efflux protein; Reviewed.
Length = 1017
Score = 27.5 bits (61), Expect = 8.1
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 120 FSSIGIW--IGAVGCLQDFDRLAKDFIRSASQERKTLLKSAED--LWDEIKTNSARKSAE 175
FS I I+ IGA D DRL + + A++ + L + AED L E SA
Sbjct: 88 FSIISIYARIGA-----DSDRLFTELLAKANEVKNQLPQDAEDPVLSKEAADASALMYIS 142
Query: 176 FYVKTM 181
FY + M
Sbjct: 143 FYSEEM 148
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
0.321 0.136 0.395
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,992,140
Number of extensions: 1113218
Number of successful extensions: 1301
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1293
Number of HSP's successfully gapped: 33
Length of query: 243
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 149
Effective length of database: 6,768,326
Effective search space: 1008480574
Effective search space used: 1008480574
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: 58 (26.0 bits)