RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5544
(96 letters)
>gnl|CDD|239370 cd03072, PDI_b'_ERp44, PDIb' family, ERp44 subfamily, second
redox inactive TRX-like domain b'; ERp44 is an
endoplasmic reticulum (ER)-resident protein, induced
during stress, involved in thiol-mediated ER retention.
It contains an N-terminal TRX domain with a CXFS motif
followed by two redox inactive TRX-like domains,
homologous to the b and b' domains of PDI. Through the
formation of reversible mixed disulfides, ERp44
mediates the ER localization of Ero1alpha, a protein
that oxidizes protein disulfide isomerases into their
active form. ERp44 also prevents the secretion of
unassembled cargo protein with unpaired cysteines.
ERp44 also modulates the activity of inositol
1,4,5-triphosphate type I receptor (IP3R1), an
intracellular channel protein that mediates calcium
release from the ER to the cytosol. Similar to PDI, the
b' domain of ERp44 is likely involved in substrate
recognition and may be the primary binding site.
Length = 111
Score = 77.8 bits (192), Expect = 2e-20
Identities = 33/47 (70%), Positives = 38/47 (80%)
Query: 47 VREITFENAEELTEEGLPFLILFYAPGDTETIKLFKSIVSEQLLGEK 93
VREITFENAEELTEEGLPFLILF+ D E++K FK V+ QL+ EK
Sbjct: 1 VREITFENAEELTEEGLPFLILFHDKDDLESLKEFKQAVARQLISEK 47
>gnl|CDD|222416 pfam13848, Thioredoxin_6, Thioredoxin-like domain.
Length = 183
Score = 62.7 bits (153), Expect = 8e-14
Identities = 30/94 (31%), Positives = 42/94 (44%), Gaps = 7/94 (7%)
Query: 1 MHPPGEPIIVFRPDVTTPLEEHETYRGNLSA-YDETKVWTADKCVPLVREITFENAEELT 59
I++FR E+ TY G +D+ K + +PLV E T ENAEEL
Sbjct: 37 YGIKEPTILLFRKF----DEKQVTYPGEDKTTFDDLKKFIQKNSLPLVGEFTPENAEELF 92
Query: 60 EEGLPFLILFYAPGDTETIKLFKSIVSEQLLGEK 93
E G P +L + D+E + K+ V E K
Sbjct: 93 ESGKP--LLLFIKKDSEETEKLKNRVEEVAKKFK 124
>gnl|CDD|239368 cd03070, PDI_b_ERp44, PDIb family, ERp44 subfamily, first redox
inactive TRX-like domain b; ERp44 is an endoplasmic
reticulum (ER)-resident protein, induced during stress,
involved in thiol-mediated ER retention. It contains an
N-terminal TRX domain with a CXFS motif followed by two
redox inactive TRX-like domains, homologous to the b
and b' domains of PDI. Through the formation of
reversible mixed disulfides, ERp44 mediates the ER
localization of Ero1alpha, a protein that oxidizes
protein disulfide isomerases into their active form.
ERp44 also prevents the secretion of unassembled cargo
protein with unpaired cysteines. ERp44 also modulates
the activity of inositol 1,4,5-triphosphate type I
receptor (IP3R1), an intracellular channel protein that
mediates calcium release from the ER to the cytosol.
Similar to PDI, the b domain of ERp44 is likely
involved in binding to substrates.
Length = 91
Score = 35.0 bits (81), Expect = 7e-04
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 1 MHPPGEPIIVFRPDVTTPLEEHETYRGNLSAYDETK 36
PPG+ II F P Y G+L+ +D K
Sbjct: 59 ERPPGDNIIYFPPGHN---APDMVYLGSLTNFDLLK 91
>gnl|CDD|239384 cd03110, Fer4_NifH_child, This protein family's function is unkown.
It contains nucleotide binding site. It uses NTP as
energy source to transfer electron or ion.
Length = 179
Score = 32.6 bits (75), Expect = 0.012
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 9 IVFRPDVTTPLEEHETYRGNLSAY-DETKVWTADKCVPLVREITFENAEELTEEGLPFLI 67
+ +P++ EE + G A D + C LV E+ E EG +I
Sbjct: 41 LFLKPEI---EEEEDFIVGGKKAVIDPELCISCGLCGKLVTEVRKHAKEIAKAEGAELII 97
Query: 68 LFYAPG 73
+ PG
Sbjct: 98 IDGPPG 103
>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 = 27.6 bits (62), Expect = 0.48
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 49 EITFENAEELTEEGLPFLILFYAP 72
E+T +N +EL ++ L+ FYAP
Sbjct: 2 ELTDDNFDELVKDSKDVLVEFYAP 25
>gnl|CDD|239280 cd02982, PDI_b'_family, Protein Disulfide Isomerase (PDIb')
family, redox inactive TRX-like domain b'; 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, calsequestrin and other PDI-related
proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and
PDIR. PDI, ERp57, ERp72, P5 and PDIR 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 contain multiple copies of a redox active TRX
(a) domain containing a CXXC motif, and one or more
redox inactive TRX-like (b) domains. The molecular
structure of PDI is abb'a'. Also included in this
family is the PDI-related protein ERp27, which contains
only redox-inactive TRX-like (b and b') domains. The
redox inactive domains are implicated in substrate
recognition with the b' domain serving as the primary
substrate binding site. Only the b' domain is necessary
for the binding of small peptide substrates. In
addition to the b' domain, other domains are required
for the binding of larger polypeptide substrates. The
b' domain is also implicated in chaperone activity.
Length = 103
Score = 25.7 bits (57), Expect = 2.3
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 48 REITFENAEELTEEGLPFLILFYAPGDTETIKLFKSIVSE 87
TF N EE G P L+LFY D+E+ + + E
Sbjct: 1 NAETFFNYEES---GKPLLVLFYNKDDSES-EELRERFKE 36
>gnl|CDD|153084 cd01675, RNR_III, Class III ribonucleotide reductase.
Ribonucleotide reductase (RNR) catalyzes the reductive
synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in strict or facultative anaerobic bacteria,
bacteriophage, and archaea, use an FeS cluster and
S-adenosylmethionine to generate a glycyl radical. Many
organisms have more than one class of RNR present in
their genomes. All three RNRs have a ten-stranded
alpha-beta barrel domain that is structurally similar to
the domain of PFL (pyruvate formate lyase). The class
III enzyme from phage T4 consists of two subunits, this
model covers the larger subunit which contains the
active and allosteric sites.
Length = 555
Score = 26.5 bits (59), Expect = 2.6
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 7/63 (11%)
Query: 29 LSAYDETKVWTA-DKCVPLVR---EITFENAEELTEEGLPFLILFYAPGDTETIKL---F 81
+ DE K + D+ + L + EI + +E GLP L G L
Sbjct: 303 EARGDEEKFFELLDEYLELAKDALEIRRKRLKEALARGLPPLYQEGLGGGKLLFILKRHT 362
Query: 82 KSI 84
+I
Sbjct: 363 LTI 365
>gnl|CDD|233070 TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ.
All proteins in this family are 5'-3' single-strand DNA
exonucleases. These proteins are used in some aspects of
mismatch repair, recombination, and recombinational
repair [DNA metabolism, DNA replication, recombination,
and repair].
Length = 539
Score = 25.7 bits (57), Expect = 4.6
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 41 DKCVPLVREITFENAEELTEEGLPFLILFYAPGDTETIKLFK--SIVSEQLLGEKHIK 96
D + EIT E E++ E+ PF G+ E + L K + +LLGE H+K
Sbjct: 435 DAELK-AEEITRELIEQI-EKLEPF-----GQGNPEPLFLLKNLRVEDIKLLGENHLK 485
>gnl|CDD|214823 smart00799, DENN, Domain found in a variety of signalling proteins,
always encircled by uDENN and dDENN. The DENN domain is
found in a variety of signalling proteins involved in
Rab-mediated processes or regulation of MAPKs signalling
pathways. The DENN domain is always encircled on both
sides by more divergent domains, called uDENN (for
upstream DENN) and dDENN (for downstream DENN). The
function of the DENN domain remains to date unclear,
although it appears to represent a good candidate for a
GTP/GDP exchange activity.
Length = 183
Score = 24.8 bits (55), Expect = 7.5
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 48 REITFENAEELTEEGLPFLILFYAPGDTETIKLFKSIVSEQ 88
E+ L LF G ++LF +++ E+
Sbjct: 65 IELQRPLDSSLPLIDFSLHELFECLGVENILQLFAALLLER 105
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 24.8 bits (55), Expect = 7.6
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 31/77 (40%)
Query: 8 IIVFRPDVTTPLEEHETYRGNLSAYDETKVW------TADKCVPLV-----------REI 50
++V+ D+T + +++ K W AD+ VP+V R +
Sbjct: 76 LLVY--DIT-----------SRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQRVV 122
Query: 51 TFENAEELTEE-GLPFL 66
+ E E L +E GLPF+
Sbjct: 123 STEEGEALAKELGLPFM 139
>gnl|CDD|185205 PRK15305, PRK15305, putative fimbrial protein StkG; Provisional.
Length = 353
Score = 25.0 bits (54), Expect = 7.7
Identities = 10/30 (33%), Positives = 12/30 (40%)
Query: 1 MHPPGEPIIVFRPDVTTPLEEHETYRGNLS 30
M P +PII F P V T L+
Sbjct: 36 MSPGVQPIITFHPSVQTATLLASGITMELT 65
>gnl|CDD|226899 COG4512, AgrB, Membrane protein putatively involved in
post-translational modification of the autoinducing
quorum-sensing peptide [Posttranslational modification,
protein turnover, chaperones / Signal transduction
mechanisms / Transcription].
Length = 198
Score = 24.8 bits (54), Expect = 9.3
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 9/31 (29%)
Query: 66 LILFYAPGDTETIKLFKSIVSEQLLGEKHIK 96
LI YAP DTE + L+G +H K
Sbjct: 119 LIFKYAPADTE---------AHPLVGTEHRK 140
>gnl|CDD|216898 pfam02141, DENN, DENN (AEX-3) domain. DENN (after differentially
expressed in neoplastic vs normal cells) is a domain
which occurs in several proteins involved in Rab-
mediated processes or regulation of MAPK signalling
pathways.
Length = 185
Score = 24.4 bits (54), Expect = 10.0
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 48 REITFENAEELTEEGLPFLILFYAPGDTETIKLFKSIVSEQ 88
+ + EL G+ +LF G ++LF++ ++E+
Sbjct: 68 ILLQRPSDSELPLSGVDLHLLFRCLGPENVLQLFEAALTER 108
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 24.5 bits (54), Expect = 10.0
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 76 ETIKLFKSIVSEQLLGEKHI 95
E++ LF+ I + I
Sbjct: 219 ESLNLFEEICNSPWFKNTPI 238
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
0.316 0.138 0.410
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,052,321
Number of extensions: 412730
Number of successful extensions: 433
Number of sequences better than 10.0: 1
Number of HSP's gapped: 431
Number of HSP's successfully gapped: 25
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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 (21.6 bits)
S2: 53 (24.1 bits)