RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

Searching..................................................done

Query= psy12844
         (121 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 = 6e-12
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73
          V+G +++F+ E+GFGFI    DDG +D F H S ++G      R+++    V F++    
Sbjct: 1  VTGTVKWFDDEKGFGFITP--DDGGEDVFVHISALEGDG---FRSLEEGDRVEFELEEGD 55

Query: 74 GGRREAVHIKI 84
           G + AV++++
Sbjct: 56 KGPQ-AVNVRL 65


>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain. 
          Length = 66

 Score = 54.5 bits (132), Expect = 3e-11
 Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 5/60 (8%)

Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
          G +++FN ++GFGFI    +DG KD F HFS IQG   +  R+++    V FDI     G
Sbjct: 3  GTVKWFNAKKGFGFITP--EDGDKDVFVHFSAIQG---DGFRSLQEGQRVEFDIVEGTKG 57


>gnl|CDD|224197 COG1278, CspC, Cold shock proteins [Transcription].
          Length = 67

 Score = 49.8 bits (120), Expect = 1e-09
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
          G +++FN  +GFGFI    +DG KD F H S IQ       R ++    V F++     G
Sbjct: 4  GTVKWFNATKGFGFITP--EDGGKDVFVHISAIQR---AGFRTLREGQKVEFEVEQGRKG 58


>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional.
          Length = 70

 Score = 46.9 bits (111), Expect = 3e-08
 Identities = 19/36 (52%), Positives = 27/36 (75%), Gaps = 2/36 (5%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQ 49
          ++G++++FN ++GFGFI    DDG KD F HFS IQ
Sbjct: 5  MTGIVKWFNADKGFGFITP--DDGSKDVFVHFSAIQ 38


>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 = 45.3 bits (108), Expect = 8e-08
 Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 9/70 (12%)

Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDI-GVTPG 74
          GV+++FNK  GFGFI    DDG KD F H S+IQGG    L++++    V F +     G
Sbjct: 2  GVVKWFNK--GFGFIRP--DDGGKDVFVHPSQIQGG----LKSLREGDEVEFKVVSPEGG 53

Query: 75 GRREAVHIKI 84
           + EA ++  
Sbjct: 54 EKPEAENVVK 63


>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional.
          Length = 70

 Score = 44.4 bits (104), Expect = 3e-07
 Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 5/56 (8%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDI 69
          ++G++++FN ++GFGFI    DDG KD F HF+ IQ    N  R +  +  V F I
Sbjct: 5  MTGLVKWFNADKGFGFITP--DDGSKDVFVHFTAIQ---SNEFRTLNENQKVEFSI 55


>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 = 43.7 bits (103), Expect = 5e-07
 Identities = 27/69 (39%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPG 74
           G++++FN  +GFGFI   G DG  D F H+S IQ   D   R +K    V F++   P 
Sbjct: 3  IGIVKWFNNAKGFGFICPEGVDG--DIFAHYSTIQ--MDG-YRTLKAGQKVQFEVVQGPK 57

Query: 75 GRREAVHIK 83
          G   A HI 
Sbjct: 58 G-AHATHIV 65


>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional.
          Length = 69

 Score = 43.5 bits (102), Expect = 5e-07
 Identities = 19/37 (51%), Positives = 25/37 (67%), Gaps = 2/37 (5%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
          + G +++FN+ +GFGFI     DG KD F HFS IQG
Sbjct: 4  IKGQVKWFNESKGFGFITP--ADGSKDVFVHFSAIQG 38


>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed.
          Length = 69

 Score = 42.3 bits (99), Expect = 2e-06
 Identities = 18/36 (50%), Positives = 25/36 (69%), Gaps = 2/36 (5%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQ 49
          + G +++FN+ +GFGFI    +DG KD F HFS IQ
Sbjct: 4  IKGNVKWFNESKGFGFITP--EDGSKDVFVHFSAIQ 37


>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional.
          Length = 73

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPG 74
          +G +++FN  +GFGFI   G  G +D F H+S IQ    +  R +K    V FD+   P 
Sbjct: 3  TGTVKWFNNAKGFGFICPEG--GGEDIFAHYSTIQM---DGYRTLKAGQSVRFDVHQGPK 57

Query: 75 GRREAVHIKI 84
          G   +V + I
Sbjct: 58 GNHASVIVPI 67


>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible
          regulatory protein CspD; Provisional.
          Length = 74

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
          G +++FN  +GFGFI   G  G +D F H+S IQ    +  R +K    V FD+   P G
Sbjct: 4  GTVKWFNNAKGFGFICPEG--GGEDIFAHYSTIQM---DGYRTLKAGQSVQFDVHQGPKG 58

Query: 76 RREAVHIKI 84
             +V + +
Sbjct: 59 NHASVIVPV 67


>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
          exoribonucleases.  This model is defined to identify a
          pair of paralogous 3-prime exoribonucleases in E. coli,
          plus the set of proteins apparently orthologous to one
          or the other in other eubacteria. VacB was
          characterized originally as required for the expression
          of virulence genes, but is now recognized as the
          exoribonuclease RNase R (Rnr). Its paralog in E. coli
          and H. influenzae is designated exoribonuclease II
          (Rnb). Both are involved in the degradation of mRNA,
          and consequently have strong pleiotropic effects that
          may be difficult to disentangle. Both these proteins
          share domain-level similarity (RNB, S1) with a
          considerable number of other proteins, and full-length
          similarity scoring below the trusted cutoff to proteins
          associated with various phenotypes but uncertain
          biochemistry; it may be that these latter proteins are
          also 3-prime exoribonucleases [Transcription,
          Degradation of RNA].
          Length = 654

 Score = 30.8 bits (70), Expect = 0.15
 Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 12/77 (15%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDI-GVT 72
          V GV++  NK  GFGF+ R  DD +KDYF    +++              LV        
Sbjct: 17 VKGVVKAHNK--GFGFL-RPDDDDKKDYFIPPPQMKKVMHGD--------LVEACPLSQP 65

Query: 73 PGGRREAVHIKIFDTRL 89
            GR EA   +I +  L
Sbjct: 66 QRGRFEAEVERILEPAL 82


>gnl|CDD|221468 pfam12222, PNGaseA, Peptide N-acetyl-beta-D-glucosaminyl
           asparaginase amidase A.  This family of proteins is
           found in bacteria, archaea and eukaryotes. Proteins in
           this family are typically between 558 and 775 amino
           acids in length. There is a conserved TGG sequence
           motif. PNGase A is a protein which cleaves
           glycopeptides.
          Length = 427

 Score = 29.0 bits (65), Expect = 0.64
 Identities = 18/50 (36%), Positives = 24/50 (48%)

Query: 45  FSEIQGGTDNILRAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYLEDL 94
           F EIQ   D +L  + +   +IF  G+ PG  R  V I  FD R    D+
Sbjct: 220 FREIQLYIDGLLAGVVWPFPIIFTGGIDPGFWRPVVGIDAFDLRQPEIDI 269


>gnl|CDD|185361 PRK15464, PRK15464, cold shock-like protein CspH; Provisional.
          Length = 70

 Score = 27.4 bits (60), Expect = 0.75
 Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 2/33 (6%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFS 46
          ++G+++ F+++ G GFI  I  DGRK+   H S
Sbjct: 5  MTGIVKTFDRKSGKGFI--IPSDGRKEVQVHIS 35


>gnl|CDD|240201 cd05696, S1_Rrp5_repeat_hs4, S1_Rrp5_repeat_hs4: Rrp5 is a
          trans-acting factor important for biogenesis of both
          the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has
          two distinct regions, an N-terminal region containing
          tandemly repeated S1 RNA-binding domains (12 S1 repeats
          in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
          Homo sapiens Rrp5) and a C-terminal region containing
          tetratricopeptide repeat (TPR) motifs thought to be
          involved in protein-protein interactions. Mutational
          studies have shown that each region represents a
          specific functional domain. Deletions within the
          S1-containing region inhibit pre-rRNA processing at
          either site A3 or A2, whereas deletions within the TPR
          region confer an inability to support cleavage of
          A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4).
          Rrp5 is found in eukaryotes but not in prokaryotes or
          archaea.
          Length = 71

 Score = 26.8 bits (60), Expect = 1.0
 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 10/66 (15%)

Query: 6  GKIIEEVYVSGVIQ----FFN---KERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRA 58
          G +++ V V+ V       F       GF  I+ + DD +          + GT +  R 
Sbjct: 1  GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD-KVP--SDTGPFKAGTTHKARI 57

Query: 59 IKYSLL 64
          I YS +
Sbjct: 58 IGYSPM 63


>gnl|CDD|223374 COG0297, GlgA, Glycogen synthase [Carbohydrate transport and
           metabolism].
          Length = 487

 Score = 28.0 bits (63), Expect = 1.1
 Identities = 13/73 (17%), Positives = 22/73 (30%), Gaps = 7/73 (9%)

Query: 1   MKAHLGKIIEEVYVSGVI-----QFFNKERGFGFINRIGDDGRKDYFF--HFSEIQGGTD 53
           ++     +++ V   GV+     Q F  +                  F    S + G  D
Sbjct: 47  VQKEWRDLLKVVGKFGVLKGGRAQLFIVKEYGKDGGVDLYLIDNPALFKRPDSTLYGYYD 106

Query: 54  NILRAIKYSLLVI 66
           N  R   +SL   
Sbjct: 107 NAERFAFFSLAAA 119


>gnl|CDD|185360 PRK15463, PRK15463, cold shock-like protein CspF; Provisional.
          Length = 70

 Score = 26.8 bits (59), Expect = 1.1
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFS 46
          ++G+++ F+ + G G I     DGRKD   H S
Sbjct: 5  MTGIVKTFDGKSGKGLITP--SDGRKDVQVHIS 35


>gnl|CDD|172945 PRK14470, PRK14470, ribosomal RNA large subunit methyltransferase
           N; Provisional.
          Length = 336

 Score = 27.6 bits (61), Expect = 1.7
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 5/58 (8%)

Query: 66  IFDIGVTPGGRREAVHIKIFDTR--LYLEDLRTCSVDCP-CRDSKLNVKTSRTYRKMV 120
           +F++    G R EAV I +FDT   + L     C++ C  C   KL +  S    ++V
Sbjct: 76  LFELPD--GLRVEAVRIPLFDTHHVVCLSSQAGCALGCAFCATGKLGLDRSLRSWEIV 131


>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
          Length = 259

 Score = 26.6 bits (59), Expect = 4.0
 Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)

Query: 49  QGGTDNIL-RAI-KYSLLVIFDIGVTPGGRREA 79
           QG     L R +    LL+I +IG  P  + EA
Sbjct: 151 QGRYKTTLQRGVMAPRLLIIDEIGYLPFSQEEA 183


>gnl|CDD|176995 CHL00054, psaB, photosystem I P700 chlorophyll a apoprotein A2.
          Length = 734

 Score = 25.8 bits (57), Expect = 7.3
 Identities = 10/30 (33%), Positives = 16/30 (53%)

Query: 58  AIKYSLLVIFDIGVTPGGRREAVHIKIFDT 87
            I +S+  I +  + PGGR    H  ++DT
Sbjct: 296 GIGHSMKDILEAHIPPGGRLGRGHKGLYDT 325


>gnl|CDD|227335 COG5002, VicK, Signal transduction histidine kinase [Signal
           transduction mechanisms].
          Length = 459

 Score = 25.9 bits (57), Expect = 7.4
 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 11/40 (27%)

Query: 53  DNIL-RAIKYSLLVIFDIGVTPGGRREAVHIKIFDTRLYL 91
           DNI+  A+KYS          P G R  V +K  +T + +
Sbjct: 348 DNIISNALKYS----------PDGGRITVSVKQRETWVEI 377


  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
   0.328    0.146    0.445 

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: 6,417,443
Number of extensions: 589375
Number of successful extensions: 588
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 35
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)