RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3660
(144 letters)
>gnl|CDD|239905 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like
cold-shock domain (CSD) that is found in eukaryotes,
prokaryotes, and archaea. CSP's include the major
cold-shock proteins CspA and CspB in bacteria and the
eukaryotic gene regulatory factor Y-box protein. CSP
expression is up-regulated by an abrupt drop in growth
temperature. CSP's are also expressed under normal
condition at lower level. The function of cold-shock
proteins is not fully understood. They preferentially
bind poly-pyrimidine region of single-stranded RNA and
DNA. CSP's are thought to bind mRNA and regulate
ribosomal translation, mRNA degradation, and the rate
of transcription termination. The human Y-box protein,
which contains a CSD, regulates transcription and
translation of genes that contain the Y-box sequence in
their promoters. This specific ssDNA-binding properties
of CSD are required for the binding of Y-box protein to
the promoter's Y-box sequence, thereby regulating
transcription.
Length = 65
Score = 56.0 bits (136), Expect = 1e-11
Identities = 19/31 (61%), Positives = 20/31 (64%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
TG +K F KG GFITPD G VFVHIS
Sbjct: 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISA 32
>gnl|CDD|224197 COG1278, CspC, Cold shock proteins [Transcription].
Length = 67
Score = 49.8 bits (120), Expect = 3e-09
Identities = 18/31 (58%), Positives = 21/31 (67%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
TG +K F +KG GFITP+ G VFVHIS
Sbjct: 2 ATGTVKWFNATKGFGFITPEDGGKDVFVHIS 32
>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain.
Length = 66
Score = 47.2 bits (113), Expect = 3e-08
Identities = 17/33 (51%), Positives = 20/33 (60%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
TG +K F KG GFITP+ G+ VFVH S
Sbjct: 1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAI 33
>gnl|CDD|214633 smart00357, CSP, Cold shock protein domain. RNA-binding domain
that functions as a RNA-chaperone in bacteria and is
involved in regulating translation in eukaryotes.
Contains sub-family of RNA-binding domains in the Rho
transcription termination factor.
Length = 64
Score = 41.4 bits (98), Expect = 4e-06
Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
TG +K F +KG GFI PD G VFVH S
Sbjct: 1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQI 30
>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional.
Length = 70
Score = 39.2 bits (91), Expect = 4e-05
Identities = 18/30 (60%), Positives = 19/30 (63%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
TG +K F KG GFITPD G VFVH S
Sbjct: 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFS 35
>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed.
Length = 69
Score = 38.5 bits (89), Expect = 8e-05
Identities = 17/29 (58%), Positives = 19/29 (65%)
Query: 81 GKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
G +K F SKG GFITP+ G VFVH S
Sbjct: 6 GNVKWFNESKGFGFITPEDGSKDVFVHFS 34
>gnl|CDD|131434 TIGR02381, cspD, cold shock domain protein CspD. This model
represents what appears to be a phylogenetically
distinct clade, containing E. coli CspD (SP|P24245) and
related proteobacterial proteins within the larger
family of cold shock domain proteins described by Pfam
model pfam00313. The gene symbol cspD may have been used
idependently for other subfamilies of cold shock domain
proteins, such as for B. subtilis CspD. These proteins
typically are shorter than 70 amino acids. In E. coli,
CspD is a stress response protein induced in stationary
phase. This homodimer binds single-stranded DNA and
appears to inhibit DNA replication [DNA metabolism, DNA
replication, recombination, and repair, Cellular
processes, Adaptations to atypical conditions].
Length = 68
Score = 38.3 bits (89), Expect = 8e-05
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
+ G +K F +KG GFI P+ + +F H S
Sbjct: 1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYS 32
>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional.
Length = 69
Score = 37.7 bits (87), Expect = 1e-04
Identities = 17/29 (58%), Positives = 19/29 (65%)
Query: 81 GKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
G++K F SKG GFITP G VFVH S
Sbjct: 6 GQVKWFNESKGFGFITPADGSKDVFVHFS 34
>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional.
Length = 70
Score = 37.1 bits (85), Expect = 3e-04
Identities = 17/30 (56%), Positives = 19/30 (63%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
TG +K F KG GFITPD G VFVH +
Sbjct: 6 TGLVKWFNADKGFGFITPDDGSKDVFVHFT 35
>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional.
Length = 73
Score = 35.4 bits (81), Expect = 0.001
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
+ETG +K F +KG GFI P+ G +F H S
Sbjct: 1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYS 32
>gnl|CDD|185361 PRK15464, PRK15464, cold shock-like protein CspH; Provisional.
Length = 70
Score = 34.3 bits (78), Expect = 0.003
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDY------VIMPKL 117
TG +K F R G GFI P G V VHIS + V++P L
Sbjct: 6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGL 49
>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible
regulatory protein CspD; Provisional.
Length = 74
Score = 33.6 bits (76), Expect = 0.006
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 78 VETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
+E G +K F +KG GFI P+ G +F H S
Sbjct: 1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYS 32
>gnl|CDD|185360 PRK15463, PRK15463, cold shock-like protein CspF; Provisional.
Length = 70
Score = 30.6 bits (69), Expect = 0.056
Identities = 15/30 (50%), Positives = 16/30 (53%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
TG +K F G G ITP G V VHIS
Sbjct: 6 TGIVKTFDGKSGKGLITPSDGRKDVQVHIS 35
>gnl|CDD|203875 pfam08206, OB_RNB, Ribonuclease B OB domain. This family includes
the N-terminal OB domain found in ribonuclease B
proteins in one or two copies.
Length = 58
Score = 30.2 bits (69), Expect = 0.074
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 12/47 (25%)
Query: 81 GKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLISQINKALQG 127
G ++ KG GF+ PD E +F+ P Q+ KA+ G
Sbjct: 1 GTVR--GHKKGFGFLIPDDEEDDIFI--------PP--EQMKKAMHG 35
>gnl|CDD|240627 cd05302, FDH, NAD-dependent Formate Dehydrogenase (FDH).
NAD-dependent formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of a formate anion to carbon
dioxide coupled with the reduction of NAD+ to NADH.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxy acid dehydrogenase family have 2
highly similar subdomains of the alpha/beta form, with
NAD binding occurring in the cleft between subdomains.
NAD contacts are primarily to the Rossmann-fold
NAD-binding domain which is inserted within the linear
sequence of the more diverse flavodoxin-like catalytic
subdomain. Some related proteins have similar structural
subdomain but with a tandem arrangement of the catalytic
and NAD-binding subdomains in the linear sequence. FDHs
of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production from C1 compounds such as methanol,
and in the stress responses of plants. NAD-dependent FDH
is useful in cofactor regeneration in asymmetrical
biocatalytic reduction processes, where FDH irreversibly
oxidizes formate to carbon dioxide, while reducing the
oxidized form of the cofactor to the reduced form.
Length = 348
Score = 30.0 bits (68), Expect = 0.42
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 16/67 (23%)
Query: 59 KGSKEQPNFL--ISNRALQNPVETGKIKEFCRSKGHGFITPDS--GEPAVF-VHISDYVI 113
+ + PN L + N E G ++++ S+GH + G + H+ D +
Sbjct: 12 EHGYKPPNLLGCVEN-------ELG-LRKWLESQGHELVVTSDKDGPDSELEKHLPDADV 63
Query: 114 MPKLISQ 120
+IS
Sbjct: 64 ---VIST 67
>gnl|CDD|238768 cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat 1.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the first repeat of Ub-E1.
Length = 286
Score = 29.2 bits (66), Expect = 0.64
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 15/63 (23%)
Query: 82 KIKEFCRSKGHGFITPDS----GEPAVFVHISD-YVIM------PK--LISQINKALQGS 128
KI EFC S G FI+ D+ G +F D + + PK +IS I+K G
Sbjct: 121 KINEFCHSPGIKFISADTRGLFGS--IFCDFGDEFTVYDPNGEEPKSGMISSISKDNPGV 178
Query: 129 KTC 131
TC
Sbjct: 179 VTC 181
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 26.4 bits (59), Expect = 2.0
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 88 RSKGHGFITPDSGEPAV 104
RS+G GF+ +S E A
Sbjct: 39 RSRGFGFVYFESVEDAK 55
>gnl|CDD|220447 pfam09861, DUF2088, Domain of unknown function (DUF2088). This
domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 203
Score = 26.8 bits (60), Expect = 3.8
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 18/60 (30%)
Query: 72 RALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY-------VIMPKLISQINKA 124
AL+NP+ + + E + GE V V +SD +I+P L+ ++N
Sbjct: 36 EALENPIGSKPLDELVK----------PGEKVVIV-VSDITRPTPSDIILPLLLEELNAV 84
>gnl|CDD|192328 pfam09649, CHZ, Histone chaperone domain CHZ. This domain is
highly conserved from yeasts to humans and is part of
the chaperone protein HIRIP3 in vertebrates which
interacts with the H3.3 chaperone HIRA, implicated in
histone replacement during transcription. N- and C-
termini of Chz family members are relatively divergent
but do contain similar acidic stretches rich in Glu/Asp
residues, characteristic of all histone chaperones.
Length = 38
Score = 24.6 bits (54), Expect = 5.4
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 36 PSPIIT--RRTRTESMDFKATAQ 56
S II+ RRTR +++DF A+
Sbjct: 12 TSNIISSGRRTRGKTIDFAKAAE 34
>gnl|CDD|224388 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal
structure and biogenesis].
Length = 241
Score = 26.5 bits (59), Expect = 5.8
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 75 QNPVETGKIKEFCRSKGHGF--ITPDSGEPAVFVHISDYVIM 114
++ G I E + +T + E F I DYV +
Sbjct: 186 RHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFV 227
>gnl|CDD|182972 PRK11113, PRK11113, D-alanyl-D-alanine
carboxypeptidase/endopeptidase; Provisional.
Length = 477
Score = 26.1 bits (58), Expect = 7.9
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 93 GFITPDSGEPAVFVH-ISDY 111
GFIT SG+ FV +S Y
Sbjct: 429 GFITTASGQRMAFVQFLSGY 448
>gnl|CDD|185086 PRK15132, PRK15132, tyrosine transporter TyrP; Provisional.
Length = 403
Score = 25.8 bits (57), Expect = 9.6
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 19 MLSPQEPHLHSNNTLSLP 36
ML+ PH+H N L+LP
Sbjct: 160 MLALMMPHIHKVNLLTLP 177
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
0.312 0.128 0.367
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,902,901
Number of extensions: 581956
Number of successful extensions: 328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 25
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (24.5 bits)