254780913

254780913

cold shock protein

GeneID in NCBI database:8209933Locus tag:CLIBASIA_04060
Protein GI in NCBI database:254780913Protein Accession:YP_003065326.1
Gene range:-(890554, 890790)Protein Length:78aa
Gene description:cold shock protein
COG prediction:[K] Cold shock proteins
KEGG prediction:cold shock protein; K03704 cold shock protein (beta-ribbon, CspA family)
SEED prediction:Cold shock protein CspE
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Cold shock, CspA family of proteins
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------
MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN
cccccEEEEEEccccEEEEEcccccccccEEEEEEEEEccccccccccccEEEEEEEEccccccccEEEEEEEEcccc
cccccEEEEEccccccEEEcccccccccccEEEEHHHHHHccccccccccEEEEEEEEccccccccHHHcEEcccccc
mvhrgsikwynpdkgygfitpegstesgddvFLHRSAVAsaglfnltegqlVTYDYvqndangkysaenlklvpkssn
mvhrgsikwynpdkgYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDAngkysaenlklvpkssn
MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN
**HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTY*****************LVP****
MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN
***RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDA*****************
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MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN
MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN
MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
31512240874 cold shock protein [Candidatus Liberibacter solanacearu 1 1e-17
2737923868 cold shock protein [Bradyrhizobium japonicum USDA 110] 1 1e-13
158424300117 cold shock DNA-binding domain-containing protein [Azorh 1 5e-13
2738237067 cold shock protein [Bradyrhizobium japonicum USDA 110] 1 5e-13
9211885766 cold-shock DNA-binding domain-containing protein [Nitro 1 1e-12
8674960767 cold-shock DNA-binding domain-containing protein [Rhodo 1 1e-12
29913209166 cold-shock DNA-binding domain protein [Afipia sp. 1NLS2 1 1e-12
7567723466 cold-shock protein, DNA-binding [Nitrobacter winogradsk 1 1e-12
20988420366 hypothetical protein OCAR_5060 [Oligotropha carboxidovo 1 1e-12
14825525169 cold-shock DNA-binding protein family protein [Bradyrhi 1 2e-12
>gi|315122408|ref|YP_004062897.1| cold shock protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 74 Back     alignment and organism information
 Score = 92.8 bits (229), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/70 (64%), Positives = 55/70 (78%), Gaps = 2/70 (2%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
          RGSIKWY+ +KGYGFIT   + E   DVFLHRSAV SAGL ++ EGQ V YD+V+N+  G
Sbjct: 7  RGSIKWYDANKGYGFITSASAGEK--DVFLHRSAVMSAGLPDVREGQEVIYDFVENETTG 64

Query: 64 KYSAENLKLV 73
          K+SAEN+KLV
Sbjct: 65 KFSAENIKLV 74


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|27379238|ref|NP_770767.1| cold shock protein [Bradyrhizobium japonicum USDA 110] Length = 68 Back     alignment and organism information
>gi|158424300|ref|YP_001525592.1| cold shock DNA-binding domain-containing protein [Azorhizobium caulinodans ORS 571] Length = 117 Back     alignment and organism information
>gi|27382370|ref|NP_773899.1| cold shock protein [Bradyrhizobium japonicum USDA 110] Length = 67 Back     alignment and organism information
>gi|92118857|ref|YP_578586.1| cold-shock DNA-binding domain-containing protein [Nitrobacter hamburgensis X14] Length = 66 Back     alignment and organism information
>gi|86749607|ref|YP_486103.1| cold-shock DNA-binding domain-containing protein [Rhodopseudomonas palustris HaA2] Length = 67 Back     alignment and organism information
>gi|299132091|ref|ZP_07025286.1| cold-shock DNA-binding domain protein [Afipia sp. 1NLS2] Length = 66 Back     alignment and organism information
>gi|75677234|ref|YP_319655.1| cold-shock protein, DNA-binding [Nitrobacter winogradskyi Nb-255] Length = 66 Back     alignment and organism information
>gi|209884203|ref|YP_002288060.1| hypothetical protein OCAR_5060 [Oligotropha carboxidovorans OM5] Length = 66 Back     alignment and organism information
>gi|148255251|ref|YP_001239836.1| cold-shock DNA-binding protein family protein [Bradyrhizobium sp. BTAi1] Length = 69 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
cd0445865 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an 7e-14
pfam0031366 pfam00313, CSD, 'Cold-shock' DNA-binding domain 8e-13
smart0035764 smart00357, CSP, Cold shock protein domain 2e-12
TIGR0238168 TIGR02381, cspD, cold shock domain protein CspD 1e-09
PRK0950769 PRK09507, cspE, cold shock protein CspE; Reviewed 2e-09
PRK1035470 PRK10354, PRK10354, RNA chaperone/anti-terminator; Prov 3e-08
PRK1499873 PRK14998, PRK14998, cold shock-like protein CspD; Provi 8e-08
PRK0993774 PRK09937, PRK09937, stationary phase/starvation inducib 9e-08
PRK1094369 PRK10943, PRK10943, cold shock-like protein CspC; Provi 9e-08
PRK0989070 PRK09890, PRK09890, cold shock protein CspG; Provisiona 1e-06
KOG3070 235 KOG3070, KOG3070, KOG3070, Predicted RNA-binding protei 1e-05
COG127867 COG1278, CspC, Cold shock proteins [Transcription] 2e-14
>gnl|CDD|88424 cd04458, CSP_CDS, Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea Back     alignment and domain information
>gnl|CDD|144050 pfam00313, CSD, 'Cold-shock' DNA-binding domain Back     alignment and domain information
>gnl|CDD|128651 smart00357, CSP, Cold shock protein domain Back     alignment and domain information
>gnl|CDD|131434 TIGR02381, cspD, cold shock domain protein CspD Back     alignment and domain information
>gnl|CDD|169931 PRK09507, cspE, cold shock protein CspE; Reviewed Back     alignment and domain information
>gnl|CDD|182402 PRK10354, PRK10354, RNA chaperone/anti-terminator; Provisional Back     alignment and domain information
>gnl|CDD|184960 PRK14998, PRK14998, cold shock-like protein CspD; Provisional Back     alignment and domain information
>gnl|CDD|77494 PRK09937, PRK09937, stationary phase/starvation inducible regulatory protein CspD; Provisional Back     alignment and domain information
>gnl|CDD|170841 PRK10943, PRK10943, cold shock-like protein CspC; Provisional Back     alignment and domain information
>gnl|CDD|77467 PRK09890, PRK09890, cold shock protein CspG; Provisional Back     alignment and domain information
>gnl|CDD|38280 KOG3070, KOG3070, KOG3070, Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|31469 COG1278, CspC, Cold shock proteins [Transcription] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 78 cold shock protein [Candidatus Liberibacter asiaticus s
PRK0993774 stationary phase/starvation inducible regulatory protei 99.93
COG127867 CspC Cold shock proteins [Transcription] 99.91
PRK1035470 major cold shock protein; Provisional 99.9
PRK1094369 cold shock-like protein CspC; Provisional 99.9
PRK0989070 cold shock protein CspG; Provisional 99.9
PRK0950769 cspE cold shock protein CspE; Reviewed 99.9
LOAD_cold67 consensus 99.89
pfam0031366 CSD 'Cold-shock' DNA-binding domain. 99.88
smart0035764 CSP Cold shock protein domain. RNA-binding domain that 99.83
cd0445865 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like co 99.82
TIGR0238168 cspD cold shock domain protein CspD; InterPro: IPR01275 99.67
KOG3070 235 consensus 99.49
pfam0820658 OB_RNB Ribonuclease B OB domain. This family includes t 97.75
PRK11642 813 exoribonuclease R; Provisional 97.71
PRK05054 644 exoribonuclease II; Provisional 96.93
TIGR02063 755 RNase_R ribonuclease R; InterPro: IPR011805 This family 96.31
pfam0749778 Rho_RNA_bind Rho termination factor, RNA-binding domain 95.97
cd0445968 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). R 95.71
PRK09376 416 rho transcription termination factor Rho; Provisional 94.71
PRK08059119 general stress protein 13; Validated 94.34
TIGR02062 664 RNase_B exoribonuclease II; InterPro: IPR011804 This fa 92.85
TIGR00717 534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 92.26
PRK12608 379 transcription termination factor Rho; Provisional 92.22
PRK07400314 30S ribosomal protein S1; Reviewed 91.05
COG1158 422 Rho Transcription termination factor [Transcription] 90.18
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPa 90.03
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional Back     alignment and domain information
>COG1278 CspC Cold shock proteins [Transcription] Back     alignment and domain information
>PRK10354 major cold shock protein; Provisional Back     alignment and domain information
>PRK10943 cold shock-like protein CspC; Provisional Back     alignment and domain information
>PRK09890 cold shock protein CspG; Provisional Back     alignment and domain information
>PRK09507 cspE cold shock protein CspE; Reviewed Back     alignment and domain information
>LOAD_cold consensus Back     alignment and domain information
>pfam00313 CSD 'Cold-shock' DNA-binding domain Back     alignment and domain information
>smart00357 CSP Cold shock protein domain Back     alignment and domain information
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea Back     alignment and domain information
>TIGR02381 cspD cold shock domain protein CspD; InterPro: IPR012751 This entry represents what appears to be a phylogenetically distinct clade, containing Escherichia coli CspD (P24245 from SWISSPROT) and related proteobacterial proteins within the larger family of cold shock domain proteins Back     alignment and domain information
>KOG3070 consensus Back     alignment and domain information
>pfam08206 OB_RNB Ribonuclease B OB domain Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB Back     alignment and domain information
>pfam07497 Rho_RNA_bind Rho termination factor, RNA-binding domain Back     alignment and domain information
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD) Back     alignment and domain information
>PRK09376 rho transcription termination factor Rho; Provisional Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804 This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK12608 transcription termination factor Rho; Provisional Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>COG1158 Rho Transcription termination factor [Transcription] Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
3a0j_A73 Crystal Structure Of Cold Shock Protein 1 From Ther 2e-18
1hz9_A66 Bacillus Caldolyticus Cold-Shock Protein Mutants To 2e-16
1hza_A67 Bacillus Caldolyticus Cold-Shock Protein Mutants To 2e-16
1c9o_A66 Crystal Structure Analysis Of The Bacillus Caldolyt 2e-16
3cam_A67 Crystal Structure Of The Cold Shock Domain Protein 3e-16
1i5f_A66 Bacillus Caldolyticus Cold-Shock Protein Mutants To 4e-16
3i2z_B71 Structure Of Cold Shock Protein E From Salmonella T 4e-16
2es2_A67 Crystal Structure Analysis Of The Bacillus Subtilis 8e-16
2i5l_X67 Crystal Structure Of Bacillus Subtilis Cold Shock P 9e-16
1hzb_A66 Bacillus Caldolyticus Cold-Shock Protein Mutants To 9e-16
1mjc_A69 Crystal Structure Of Cspa, The Major Cold Shock Pro 9e-16
2l15_A70 Solution Structure Of Cold Shock Protein Cspa Using 1e-15
3mef_A69 Major Cold-Shock Protein From Escherichia Coli Solu 1e-15
2i5m_X67 Crystal Structure Of Bacillus Subtilis Cold Shock P 1e-15
1hzc_A66 Bacillus Caldolyticus Cold-Shock Protein Mutants To 1e-15
1g6p_A66 Solution Nmr Structure Of The Cold Shock Protein Fr 2e-14
1h95_A79 Solution Structure Of The Single-Stranded Dna-Bindi 4e-09
3aqq_A147 Crystal Structure Of Human Crhsp-24 Length = 147 3e-07
2bh8_A101 Combinatorial Protein 1b11 Length = 101 2e-06
2ytx_A97 Solution Structure Of The Second Cold-Shock Domain 6e-04
gi|291463422|pdb|3A0J|A Chain A, Crystal Structure Of Cold Shock Protein 1 From Thermus Thermophilus Hb8 Length = 73 Back     alignment and structure
 Score = 95.5 bits (237), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 2  VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDA 61
          + +G +KW+N +KGYGFI  E       DVF+H +A+ + G   L EG +VT+D      
Sbjct: 1  MQKGRVKWFNAEKGYGFIERE----GDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRN 56

Query: 62 NGKYSAENLKLVPKS 76
               A N+ +V  +
Sbjct: 57 GKGPQAVNVTVVEPA 71


>gi|16974801|pdb|1HZ9|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66 Back     alignment and structure
>gi|16974803|pdb|1HZA|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 67 Back     alignment and structure
gi|7546262|pdb|1C9O|A Chain A, Crystal Structure Analysis Of The Bacillus Caldolyticus Cold Shock Protein Bc-Csp Length = 66 Back     alignment and structure
>gi|170785227|pdb|3CAM|A Chain A, Crystal Structure Of The Cold Shock Domain Protein From Neisseria Meningitidis Length = 67 Back     alignment and structure
>gi|16974809|pdb|1I5F|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66 Back     alignment and structure
>gi|281500776|pdb|3I2Z|B Chain B, Structure Of Cold Shock Protein E From Salmonella Typhimurium Length = 71 Back     alignment and structure
gi|114793771|pdb|2ES2|A Chain A, Crystal Structure Analysis Of The Bacillus Subtilis Cold Shock Protein Bs-Cspb In Complex With Hexathymidine Length = 67 Back     alignment and structure
>gi|149242120|pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock Protein Variant Bs-Cspb M1rE3KK65I Length = 67 Back     alignment and structure
>gi|16974805|pdb|1HZB|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66 Back     alignment and structure
>gi|157831974|pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein Of Escherichia Coli Length = 69 Back     alignment and structure
gi|306991504|pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using Combined Nmr And Cs-Rosetta Method Length = 70 Back     alignment and structure
>gi|3891780|pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution Nmr Structure Length = 69 Back     alignment and structure
>gi|149242121|pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock Protein Cspb Variant A46k S48r Length = 67 Back     alignment and structure
>gi|16974807|pdb|1HZC|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To Study Determinants Of Protein Stability Length = 66 Back     alignment and structure
gi|16974798|pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From The Hyperthermophilic Bacterium Thermotoga Maritima Length = 66 Back     alignment and structure
>gi|159162382|pdb|1H95|A Chain A, Solution Structure Of The Single-Stranded Dna-Binding Cold Shock Domain (Csd) Of Human Y-Box Protein 1 (Yb1) Determined By Nmr (10 Lowest Energy Structures) Length = 79 Back     alignment and structure
gi|315364426|pdb|3AQQ|A Chain A, Crystal Structure Of Human Crhsp-24 Length = 147 Back     alignment and structure
>gi|61680881|pdb|2BH8|A Chain A, Combinatorial Protein 1b11 Length = 101 Back     alignment and structure
>gi|178847413|pdb|2YTX|A Chain A, Solution Structure Of The Second Cold-Shock Domain Of The Human Kiaa0885 Protein (Unr Protein) Length = 97 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
3a0j_A73 Cold shock protein; OB-fold, cytoplasm, transcription, 4e-18
1g6p_A66 Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fo 8e-16
3i2z_B71 RNA chaperone, negative regulator of CSPA transcription 1e-14
2kcm_A74 Cold shock domain family protein; nucleic acid binding 3e-14
1c9o_A66 CSPB, cold-shock protein; beta barrel, homodimer; 1.17A 1e-13
3cam_A67 Cold-shock domain family protein; cold shock protein, c 5e-13
2k5n_A74 Putative cold-shock protein; GFT protein structure, PSI 9e-13
1h95_A79 CSD, Y-box binding protein; translation factor, transcr 2e-12
1x65_A89 UNR protein; cell-free protein synthesis, beta-barrel, 2e-10
2yty_A88 Cold shock domain-containing protein E1; cell-free prot 3e-10
2ytv_A79 Cold shock domain-containing protein E1; cell-free prot 1e-09
1wfq_A89 UNR protein; beta-barrel, translational regulation, RNA 3e-09
2ytx_A97 Cold shock domain-containing protein E1; cell-free prot 6e-08
2bh8_A101 1B11; transcription, molecular evolution, unique archit 5e-06
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus} Length = 73 Back     alignment and structure
 Score = 84.7 bits (210), Expect = 4e-18
 Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
          +G +KW+N +KGYGFI  EG      DVF+H +A+ + G   L EG +VT+D        
Sbjct: 3  KGRVKWFNAEKGYGFIEREG----DTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGK 58

Query: 64 KYSAENLKLV 73
             A N+ +V
Sbjct: 59 GPQAVNVTVV 68


>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5 Length = 66 Back     alignment and structure
>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 1mjc_A 3mef_A Length = 71 Back     alignment and structure
>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Shewanella oneidensis mr-1} Length = 74 Back     alignment and structure
>1c9o_A CSPB, cold-shock protein; beta barrel, homodimer; 1.17A {Bacillus caldolyticus} SCOP: b.40.4.5 PDB: 2hax_A 1hz9_A 1hzb_A 1i5f_A 1hza_A 1hzc_A 2es2_A 1csq_A 1nmf_A 1nmg_A 1csp_A 2f52_A 2i5m_X 2i5l_X Length = 66 Back     alignment and structure
>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP, structural genomics, oxford protein production facility, OPPF; 2.60A {Neisseria meningitidis MC58} Length = 67 Back     alignment and structure
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Length = 74 Back     alignment and structure
>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5 Length = 79 Back     alignment and structure
>1x65_A UNR protein; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek- KEY topology; NMR {Homo sapiens} Length = 89 Back     alignment and structure
>2yty_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} Length = 88 Back     alignment and structure
>2ytv_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} Length = 79 Back     alignment and structure
>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek-KEY topology, structural genomics; NMR {Homo sapiens} SCOP: b.40.4.5 Length = 89 Back     alignment and structure
>2ytx_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} Length = 97 Back     alignment and structure
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, activator, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Length = 101 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
3a0j_A73 Cold shock protein; OB-fold, cytoplasm, transcription, 99.9
3cam_A67 Cold-shock domain family protein; cold shock protein, c 99.88
3i2z_B71 RNA chaperone, negative regulator of CSPA transcription 99.87
1c9o_A66 CSPB, cold-shock protein; beta barrel, homodimer, trans 99.87
1h95_A79 CSD, Y-box binding protein; translation factor, transcr 99.86
2k5n_A74 Putative cold-shock protein; GFT protein structure, PSI 99.85
1g6p_A66 Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fo 99.84
2kcm_A74 Cold shock domain family protein; nucleic acid binding 99.8
1wfq_A89 UNR protein; beta-barrel, translational regulation, RNA 99.76
2ytx_A97 Cold shock domain-containing protein E1; cell-free prot 99.74
2bh8_A101 1B11; transcription, molecular evolution, unique archit 99.72
2yty_A88 Cold shock domain-containing protein E1; cell-free prot 99.72
1x65_A89 UNR protein; cell-free protein synthesis, beta-barrel, 99.69
2ytv_A79 Cold shock domain-containing protein E1; cell-free prot 99.68
2id0_A 644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA 96.91
1a62_A130 RHO; transcription termination, termination, RNA bindin 94.11
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zinc, zi 93.18
3ice_A 422 Transcription termination factor RHO; transcription, AT 93.1
3l0o_A 427 Transcription termination factor RHO; helicase, RHO fac 92.95
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural genomics, NPPSFA; 1.65A {Thermus thermophilus} Back     alignment and structure
Probab=99.90  E-value=4.8e-24  Score=153.93  Aligned_cols=72  Identities=36%  Similarity=0.714  Sum_probs=63.3

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCC
Q ss_conf             8776277514688746588548877883799995000235884468998899999986999711105999635788
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSS   77 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~   77 (78)
                      |++|+|||||++||||||++|    +++|||||+|+|+..+++.|.+||+|+|++.+++.+..++|.+|++|.++.
T Consensus         1 M~~G~Vkwf~~~kGfGFI~~d----~g~dvFvH~s~i~~~g~~~l~~G~~V~f~~~~~~~~kg~~A~~V~~v~~a~   72 (73)
T 3a0j_A            1 MQKGRVKWFNAEKGYGFIERE----GDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGPQAVNVTVVEPAR   72 (73)
T ss_dssp             CEEEEEEEEETTTTEEEEECT----TSCCEEEEGGGBCSSSCSSCCTTCEEEEEEECCSCCSSSEEEEEEEEECCC
T ss_pred             CCCEEEEEEECCCCEEEECCC----CCCEEEEEEHHHCCCCCCCCCCCCEEEEEEEECCCCCCCEEEEEEECCCCC
T ss_conf             998399989299984783158----997099984775523698789999999999989999887588888615789



>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP, structural genomics, oxford protein production facility, OPPF; 2.60A {Neisseria meningitidis MC58} Back     alignment and structure
>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 1mjc_A 3mef_A Back     alignment and structure
>1c9o_A CSPB, cold-shock protein; beta barrel, homodimer, transcription; 1.17A {Bacillus caldolyticus} SCOP: b.40.4.5 PDB: 2hax_A 1hz9_A 1hzb_A 1i5f_A 1hza_A 1hzc_A 2es2_A 1csq_A 1nmf_A 1nmg_A 1csp_A 2f52_A 2i5m_X 2i5l_X Back     alignment and structure
>1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Back     alignment and structure
>1g6p_A Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} SCOP: b.40.4.5 Back     alignment and structure
>2kcm_A Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Shewanella oneidensis mr-1} Back     alignment and structure
>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek-KEY topology, structural genomics; NMR {Homo sapiens} SCOP: b.40.4.5 Back     alignment and structure
>2ytx_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens} Back     alignment and structure
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, activator, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>2yty_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens} Back     alignment and structure
>1x65_A UNR protein; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek- KEY topology; NMR {Homo sapiens} Back     alignment and structure
>2ytv_A Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational REGU RNA chaperone, RNA/DNA binding, QB fold; NMR {Homo sapiens} Back     alignment and structure
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Back     alignment and structure
>1a62_A RHO; transcription termination, termination, RNA binding domain, transcription regulation, OB fold, F1-ATPase; 1.55A {Escherichia coli BL21} SCOP: a.140.3.1 b.40.4.5 PDB: 1a63_A 2a8v_A 1a8v_A Back     alignment and structure
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold, motor, ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A Back     alignment and structure
>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima} Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 78 cold shock protein [Candidatus Liberibacter asiaticus s
d1g6pa_66 b.40.4.5 (A:) Major cold shock protein {Thermotoga mari 3e-14
d1mjca_69 b.40.4.5 (A:) Major cold shock protein {Escherichia col 3e-14
d1c9oa_66 b.40.4.5 (A:) Major cold shock protein {Bacillus caldol 5e-14
d1h95a_79 b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CS 3e-13
d1wfqa_89 b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human 4e-10
>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]} Length = 66 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Thermotoga maritima [TaxId: 2336]
 Score = 70.9 bits (174), Expect = 3e-14
 Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
          RG +KW++  KGYGFIT +     G DVF+H SA+   G   L EGQ+V ++  +     
Sbjct: 2  RGKVKWFDSKKGYGFITKDE----GGDVFVHWSAIEMEGFKTLKEGQVVEFEIQEGK--K 55

Query: 64 KYSAENLKLV 73
             A ++K+V
Sbjct: 56 GPQAAHVKVV 65


>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]} Length = 69 Back     information, alignment and structure
>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]} Length = 66 Back     information, alignment and structure
>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]} Length = 79 Back     information, alignment and structure
>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]} Length = 89 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
d1mjca_69 Major cold shock protein {Escherichia coli [TaxId: 562] 99.87
d1c9oa_66 Major cold shock protein {Bacillus caldolyticus [TaxId: 99.87
d1h95a_79 Y-box protein 1 cold shock domain (YB1-CSD) {Human (Hom 99.85
d1g6pa_66 Major cold shock protein {Thermotoga maritima [TaxId: 2 99.85
d1wfqa_89 Cold shock domain protein E1 (UNR) {Human (Homo sapiens 99.73
d2ix0a279 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 97.52
d1a62a278 Rho termination factor, RNA-binding domain {Escherichia 96.09
d2ix0a190 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 94.16
>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Major cold shock protein
species: Escherichia coli [TaxId: 562]
Probab=99.87  E-value=6e-23  Score=146.50  Aligned_cols=67  Identities=39%  Similarity=0.720  Sum_probs=60.2

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      ..+|+|||||.+||||||+||   ++++|||||+|+|+..+++.|.+||+|+|++.+++++  ++|.||+.|
T Consensus         3 r~~G~Vk~f~~~kGfGFI~~d---~g~~diFvH~s~l~~~~~~~L~~G~~V~f~~~~~~~G--~~A~~V~~l   69 (69)
T d1mjca_           3 KMTGIVKWFNADKGFGFITPD---DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG--PAAGNVTSL   69 (69)
T ss_dssp             CEEEEEEEEETTTTEEEEEET---TSCCCEEEEGGGBCCTTTCCCCTTCEEEEEEECCSSS--CEEEEEEEC
T ss_pred             CEEEEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC
T ss_conf             788999999399997999976---8983299995890522798689999999999959899--677879949



>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus caldolyticus [TaxId: 1394]} Back     information, alignment and structure
>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1a62a2 b.40.4.5 (A:48-125) Rho termination factor, RNA-binding domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ix0a1 b.40.4.5 (A:83-172) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 78 cold shock protein [Candidatus Liberibacter asiati
2kcm_A_74 (A:) Cold shock domain family protein; nucleic aci 5e-15
1g6p_A_66 (A:) Cold shock protein TMCSP; greek-KEY, beta bar 4e-14
3i2z_B_71 (B:) RNA chaperone, negative regulator of CSPA tra 8e-14
1c9o_A_66 (A:) CSPB, cold-shock protein; beta barrel, homodi 3e-13
1x65_A_89 (A:) UNR protein; cell-free protein synthesis, bet 4e-13
2yty_A_88 (A:) Cold shock domain-containing protein E1; cell 4e-13
2ytv_A_79 (A:) Cold shock domain-containing protein E1; cell 5e-13
1h95_A_79 (A:) CSD, Y-box binding protein; translation facto 2e-12
2bh8_A_1-7171 (A:1-71) 1B11; transcription, molecular evolution, 2e-12
1wfq_A_89 (A:) UNR protein; beta-barrel, translational regul 2e-12
2ytx_A_97 (A:) Cold shock domain-containing protein E1; cell 4e-12
2k5n_A_74 (A:) Putative cold-shock protein; GFT protein stru 5e-12
3cam_A_1-3939 (A:1-39) Cold-shock domain family protein; cold sh 9e-09
>2kcm_A (A:) Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Shewanella oneidensis mr-1}Length = 74 Back     alignment and structure
 Score = 74.4 bits (183), Expect = 5e-15
 Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 5/74 (6%)

Query: 4  RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
          +G +  Y   K YGFI  +               +       L +G +V +D        
Sbjct: 2  KGKVVSYLAAKKYGFIQGDD---GESYFLHFSELLDKKDEGKLVKGSMVHFDPTPTP--K 56

Query: 64 KYSAENLKLVPKSS 77
            +A+ + L  +  
Sbjct: 57 GLAAKAISLPLEHH 70


>1g6p_A (A:) Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima}Length = 66 Back     alignment and structure
>3i2z_B (B:) RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 1mjc_A 3mef_ALength = 71 Back     alignment and structure
>1c9o_A (A:) CSPB, cold-shock protein; beta barrel, homodimer; 1.17A {Bacillus caldolyticus}Length = 66 Back     alignment and structure
>1x65_A (A:) UNR protein; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek- KEY topology; NMR {Homo sapiens}Length = 89 Back     alignment and structure
>2yty_A (A:) Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens}Length = 88 Back     alignment and structure
>2ytv_A (A:) Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens}Length = 79 Back     alignment and structure
>1h95_A (A:) CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens}Length = 79 Back     alignment and structure
>2bh8_A (A:1-71) 1B11; transcription, molecular evolution, unique architecture, activator, transcription regulation, phosphorylation; 1.9A {Escherichia coli}Length = 71 Back     alignment and structure
>1wfq_A (A:) UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek-KEY topology, structural genomics; NMR {Homo sapiens}Length = 89 Back     alignment and structure
>2ytx_A (A:) Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens}Length = 97 Back     alignment and structure
>2k5n_A (A:) Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum}Length = 74 Back     alignment and structure
>3cam_A (A:1-39) Cold-shock domain family protein; cold shock protein, chain SWAP, structural genomics, oxford protein production facility, OPPF; 2.60A {Neisseria meningitidis MC58}Length = 39 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target78 cold shock protein [Candidatus Liberibacter asiaticus s
3i2z_B_71 RNA chaperone, negative regulator of CSPA transcri 99.86
1h95_A_79 CSD, Y-box binding protein; translation factor, tr 99.86
2kcm_A_74 Cold shock domain family protein; nucleic acid bin 99.84
1c9o_A_66 CSPB, cold-shock protein; beta barrel, homodimer; 99.83
2k5n_A_74 Putative cold-shock protein; GFT protein structure 99.82
2bh8_A_1-7171 1B11; transcription, molecular evolution, unique a 99.79
2ytv_A_79 Cold shock domain-containing protein E1; cell-free 99.79
1wfq_A_89 UNR protein; beta-barrel, translational regulation 99.78
1g6p_A_66 Cold shock protein TMCSP; greek-KEY, beta barrel, 99.77
2ytx_A_97 Cold shock domain-containing protein E1; cell-free 99.75
2yty_A_88 Cold shock domain-containing protein E1; cell-free 99.75
1x65_A_89 UNR protein; cell-free protein synthesis, beta-bar 99.71
2id0_A_20-8364 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 97.52
1a62_A_130 RHO; transcription termination, termination, RNA b 95.34
3ice_A_1-141141 Transcription termination factor RHO; transcriptio 95.25
3go5_A_65-13571 Multidomain protein with S1 RNA-binding domains; s 93.04
2id0_A_84-17895 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 90.7
3cam_A_1-3939 Cold-shock domain family protein; cold shock prote 99.48
3cam_A_40-6728 Cold-shock domain family protein; cold shock prote 97.49
>3i2z_B (B:) RNA chaperone, negative regulator of CSPA transcription; beta barrel, DNA binding protein/transcription, cytoplasm, gene regulation; 1.10A {Salmonella typhimurium} PDB: 1mjc_A 3mef_A Back     alignment and structure
Probab=99.86  E-value=5.4e-22  Score=143.36  Aligned_cols=68  Identities=40%  Similarity=0.750  Sum_probs=62.5

Q ss_pred             CCCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             9877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         1 mm~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      .|.+|+|||||.+||||||++|   ++++|||+|+|+|...+++.|.+|++|+|++++++++  ++|.+|++|
T Consensus         4 ~~~~G~Vk~f~~~kGyGFI~~~---~g~~dif~h~s~l~~~~~~~l~~G~~V~f~~~~~~kG--~~A~~V~~i   71 (71)
T 3i2z_B            4 SKIKGNVKWFNESKGFGFITPE---DGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG--PSAANVTAL   71 (71)
T ss_dssp             -CEEEEEEEEETTTTEEEEEET---TCCCCEEEEGGGBCCSSCCCCCTTCEEEEEEEEETTE--EEEEEEEEC
T ss_pred             CCCEEEEEEECCCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC
T ss_conf             5004799999099984899868---9981299991880613798589999999999969999--786888959



>1h95_A (A:) CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} Back     alignment and structure
>2kcm_A (A:) Cold shock domain family protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Shewanella oneidensis mr-1} Back     alignment and structure
>1c9o_A (A:) CSPB, cold-shock protein; beta barrel, homodimer; 1.17A {Bacillus caldolyticus} Back     alignment and structure
>2k5n_A (A:) Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Back     alignment and structure
>2bh8_A (A:1-71) 1B11; transcription, molecular evolution, unique architecture, activator, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>2ytv_A (A:) Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} Back     alignment and structure
>1wfq_A (A:) UNR protein; beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek-KEY topology, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>1g6p_A (A:) Cold shock protein TMCSP; greek-KEY, beta barrel, OB-fold, structural genomics; NMR {Thermotoga maritima} Back     alignment and structure
>2ytx_A (A:) Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} Back     alignment and structure
>2yty_A (A:) Cold shock domain-containing protein E1; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding; NMR {Homo sapiens} Back     alignment and structure
>1x65_A (A:) UNR protein; cell-free protein synthesis, beta-barrel, translational regulation, RNA chaperone, RNA/DNA binding, QB fold, greek- KEY topology; NMR {Homo sapiens} Back     alignment and structure
>2id0_A (A:20-83) Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} Back     alignment and structure
>1a62_A (A:) RHO; transcription termination, termination, RNA binding domain, transcription regulation, OB fold, F1-ATPase; 1.55A {Escherichia coli} Back     alignment and structure
>3ice_A (A:1-141) Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold, motor, ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A Back     alignment and structure
>3go5_A (A:65-135) Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} Back     alignment and structure
>2id0_A (A:84-178) Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} Back     alignment and structure
>3cam_A (A:1-39) Cold-shock domain family protein; cold shock protein, chain SWAP, structural genomics, oxford protein production facility, OPPF; 2.60A {Neisseria meningitidis MC58} Back     alignment and structure
>3cam_A (A:40-67) Cold-shock domain family protein; cold shock protein, chain SWAP, structural genomics, oxford protein production facility, OPPF; 2.60A {Neisseria meningitidis MC58} Back     alignment and structure