RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3654
(140 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 = 74.5 bits (184), Expect = 7e-19
Identities = 29/67 (43%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE--GCYVPLPGDEVKYRLCPIPPKFEKN 117
TG +K F KG GFITPD G VFVHIS +E G GD V++ L
Sbjct: 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGP--- 58
Query: 118 QAVHVEI 124
QAV+V +
Sbjct: 59 QAVNVRL 65
>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 = 57.6 bits (140), Expect = 3e-12
Identities = 28/67 (41%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGC-YVPLPGDEVKYRLCPIPPKFEKNQ 118
TG +K F +KG GFI PD G VFVH S I+G GDEV++++ P EK +
Sbjct: 1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVS-PEGGEKPE 57
Query: 119 AVHVEIV 125
A +V +
Sbjct: 58 AENVVKL 64
>gnl|CDD|224197 COG1278, CspC, Cold shock proteins [Transcription].
Length = 67
Score = 56.0 bits (136), Expect = 1e-11
Identities = 22/51 (43%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE--GCYVPLPGDEVKYRL 107
TG +K F +KG GFITP+ G VFVHIS I+ G G +V++ +
Sbjct: 2 ATGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEV 52
>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain.
Length = 66
Score = 51.1 bits (123), Expect = 1e-09
Identities = 19/35 (54%), Positives = 23/35 (65%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
TG +K F KG GFITP+ G+ VFVH S I+G
Sbjct: 1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQG 35
>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional.
Length = 69
Score = 43.9 bits (103), Expect = 6e-07
Identities = 19/33 (57%), Positives = 22/33 (66%)
Query: 61 GKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
G++K F SKG GFITP G VFVH S I+G
Sbjct: 6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQG 38
>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional.
Length = 70
Score = 43.0 bits (101), Expect = 1e-06
Identities = 19/33 (57%), Positives = 21/33 (63%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE 92
TG +K F KG GFITPD G VFVH S I+
Sbjct: 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQ 38
>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 = 41.8 bits (98), Expect = 3e-06
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE 92
+ G +K F +KG GFI P+ + +F H S I+
Sbjct: 1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQ 35
>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed.
Length = 69
Score = 41.6 bits (97), Expect = 4e-06
Identities = 18/32 (56%), Positives = 21/32 (65%)
Query: 61 GKIKEFCRSKGHGFITPDSGEPAVFVHISDIE 92
G +K F SKG GFITP+ G VFVH S I+
Sbjct: 6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQ 37
>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional.
Length = 70
Score = 40.5 bits (94), Expect = 1e-05
Identities = 18/33 (54%), Positives = 21/33 (63%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE 92
TG +K F KG GFITPD G VFVH + I+
Sbjct: 6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQ 38
>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional.
Length = 73
Score = 37.0 bits (85), Expect = 2e-04
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE 92
+ETG +K F +KG GFI P+ G +F H S I+
Sbjct: 1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible
regulatory protein CspD; Provisional.
Length = 74
Score = 35.1 bits (80), Expect = 0.001
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 58 VETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIE 92
+E G +K F +KG GFI P+ G +F H S I+
Sbjct: 1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 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 = 32.9 bits (76), Expect = 0.006
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 61 GKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRL 107
G ++ KG GF+ PD E +F+ ++ + GD V R+
Sbjct: 1 GTVR--GHKKGFGFLIPDDEEDDIFIPPEQMKKA---MHGDRVLVRI 42
>gnl|CDD|185361 PRK15464, PRK15464, cold shock-like protein CspH; Provisional.
Length = 70
Score = 32.8 bits (74), Expect = 0.010
Identities = 16/30 (53%), Positives = 17/30 (56%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 89
TG +K F R G GFI P G V VHIS
Sbjct: 6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHIS 35
>gnl|CDD|185360 PRK15463, PRK15463, cold shock-like protein CspF; Provisional.
Length = 70
Score = 31.4 bits (71), Expect = 0.028
Identities = 15/30 (50%), Positives = 16/30 (53%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 89
TG +K F G G ITP G V VHIS
Sbjct: 6 TGIVKTFDGKSGKGLITPSDGRKDVQVHIS 35
>gnl|CDD|222962 PHA03036, PHA03036, DNA polymerase; Provisional.
Length = 1004
Score = 30.8 bits (70), Expect = 0.22
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 82 PAVFVH-ISDIEGCYVPLPGDEVKYRL--CPIPPKFEKNQAV 120
P+VF++ +S I CY+ L G E ++ L + + E +AV
Sbjct: 176 PSVFINPVSHISCCYIDLSGKEKRFTLINEDMLSEDEIEEAV 217
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal protein.
This superfamily also contains the Cold Shock Domain
(CSD), which is a homolog of the S1 domain. Both domains
are members of the Oligonucleotide/oligosaccharide
Binding (OB) fold.
Length = 65
Score = 28.1 bits (63), Expect = 0.40
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 9/53 (16%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLP------GDEVKYR 106
TGK+ +K F+ + G VHIS++ +V P GDEV+ +
Sbjct: 2 TGKVVSI--TKFGVFVELEDGVEG-LVHISELSDKFVKDPSEVFKVGDEVEVK 51
>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 = 1.9
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 68 RSKGHGFITPDSGEPAV 84
RS+G GF+ +S E A
Sbjct: 39 RSRGFGFVYFESVEDAK 55
>gnl|CDD|225891 COG3355, COG3355, Predicted transcriptional regulator
[Transcription].
Length = 126
Score = 27.2 bits (61), Expect = 2.0
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 16/60 (26%)
Query: 45 RTESISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVK 104
R+ S R+LQN +E G ++ R K + G ++ Y P+ +E+K
Sbjct: 54 RSRSTVYRSLQNLLEAGLVE---REK----VNLKGGGY---YYL------YKPIDPEEIK 97
>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 = 26.8 bits (60), Expect = 3.7
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 62 KIKEFCRSKGHGFITPDS 79
KI EFC S G FI+ D+
Sbjct: 121 KINEFCHSPGIKFISADT 138
>gnl|CDD|182972 PRK11113, PRK11113, D-alanyl-D-alanine
carboxypeptidase/endopeptidase; Provisional.
Length = 477
Score = 26.8 bits (60), Expect = 4.0
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 7/46 (15%)
Query: 73 GFITPDSGEPAVFVH-ISDIEGCYVPLPGDEVKYRLCPIPPKFEKN 117
GFIT SG+ FV +S Y P D+ + R P+ +FE
Sbjct: 429 GFITTASGQRMAFVQFLSG----YAVPPADQ-RNRRIPL-VRFESR 468
>gnl|CDD|218300 pfam04870, Moulting_cycle, Moulting cycle. This family of proteins
plays a role in the moulting cycle of nematodes, which
involves the synthesis of a new collagen-rich cuticle
underneath the existing cuticle and the subsequent
removal of the old cuticle.
Length = 323
Score = 26.3 bits (58), Expect = 5.9
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 8 FENKKPALSSPMLSPQEPHLHSNNTLSLPSPII 40
F++KK SP P +NNT+ L SP I
Sbjct: 122 FDDKKIRFLSPRFMSILPEEVANNTVGLLSPSI 154
>gnl|CDD|185086 PRK15132, PRK15132, tyrosine transporter TyrP; Provisional.
Length = 403
Score = 26.2 bits (58), Expect = 7.7
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 19 MLSPQEPHLHSNNTLSLP 36
ML+ PH+H N L+LP
Sbjct: 160 MLALMMPHIHKVNLLTLP 177
>gnl|CDD|217067 pfam02495, 7kD_coat, 7kD viral coat protein. This family consists
of a 7kD coat protein from carlavirus and potexvirus.
Length = 59
Score = 24.5 bits (54), Expect = 7.7
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 92 EGCYVPLPGDEVKYRLCPIPPKFEK 116
EGC + + G+ V C P+F +
Sbjct: 25 EGCVIVITGESVTITGCEFTPEFIE 49
>gnl|CDD|185336 PRK15439, PRK15439, autoinducer 2 ABC transporter ATP-binding
protein LsrA; Provisional.
Length = 510
Score = 25.8 bits (57), Expect = 9.5
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 5/49 (10%)
Query: 7 PFENKKPALSSPM---LSPQEPHLHSNNTLSLPSPIITRRTRTESISNR 52
P PA + + L PQEP L N LS+ I+ + ++ +
Sbjct: 74 PCARLTPAKAHQLGIYLVPQEPLLFPN--LSVKENILFGLPKRQASMQK 120
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
0.315 0.134 0.415
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: 7,282,695
Number of extensions: 632676
Number of successful extensions: 390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 389
Number of HSP's successfully gapped: 34
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 42 (22.0 bits)
S2: 54 (24.5 bits)