RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780913|ref|YP_003065326.1| cold shock protein [Candidatus
Liberibacter asiaticus str. psy62]
(78 letters)
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural
genomics, NPPSFA; 1.65A {Thermus thermophilus}
Length = 73
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
Score = 77.1 bits (190), Expect = 8e-16
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
>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
Score = 73.6 bits (181), Expect = 1e-14
Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
+G++KW+N KG+GFITPE + DVF+H SA+ + G L EGQ V ++
Sbjct: 7 KGNVKWFNESKGFGFITPE---DGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA--K 61
Query: 64 KYSAENLKLV 73
SA N+ +
Sbjct: 62 GPSAANVTAL 71
>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
Score = 72.1 bits (177), Expect = 3e-14
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFN-LTEGQLVTYDYVQNDAN 62
+G + Y K YGFI + G+ FLH S + L +G +V +D
Sbjct: 2 KGKVVSYLAAKKYGFIQGDD----GESYFLHFSELLDKKDEGKLVKGSMVHFDPTPTP-- 55
Query: 63 GKYSAENLKL 72
+A+ + L
Sbjct: 56 KGLAAKAISL 65
>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
Score = 70.2 bits (172), Expect = 1e-13
Identities = 30/69 (43%), Positives = 42/69 (60%), Gaps = 5/69 (7%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
RG +KW+N +KGYGFI EG DVF+H +A+ G L EGQ V+++ VQ + G
Sbjct: 3 RGKVKWFNNEKGYGFIEVEGG----SDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGN-RG 57
Query: 64 KYSAENLKL 72
+A +KL
Sbjct: 58 PQAANVVKL 66
>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
Score = 67.9 bits (166), Expect = 5e-13
Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 5/67 (7%)
Query: 5 GSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK 64
G +KW+N KG+GFITP+ E G+D+F H SA+ G L EGQ V++D
Sbjct: 4 GIVKWFNDAKGFGFITPD---EGGEDLFAHFSAINMEGFKTLKEGQRVSFDVTTGP--KG 58
Query: 65 YSAENLK 71
A N++
Sbjct: 59 KQAANIQ 65
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc,
OB fold, structural genomics, protein structure
initiative; NMR {Pectobacterium atrosepticum}
Length = 74
Score = 67.2 bits (164), Expect = 9e-13
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQND 60
M G+I + DKG+GFI E+GD+ + H V A + + VT++ N+
Sbjct: 1 MAMNGTITTWFKDKGFGFIKD----ENGDNRYFHVIKV--ANPDLIKKDAAVTFEPTTNN 54
Query: 61 ANGKYSAENLKLVP 74
SA +K+VP
Sbjct: 55 --KGLSAYAVKVVP 66
>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
Score = 65.7 bits (160), Expect = 2e-12
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 5 GSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLF----NLTEGQLVTYDYVQND 60
G++KW+N GYGFI ++ +DVF+H++A+ ++ +G+ V +D V+ +
Sbjct: 11 GTVKWFNVRNGYGFINRN---DTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGE 67
Query: 61 ANGKYSAENLKLV 73
A N+
Sbjct: 68 --KGAEAANVTGP 78
>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
Score = 59.5 bits (144), Expect = 2e-10
Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 8/75 (10%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQND-AN 62
G I G+GFI + +F H S + L V + V + +
Sbjct: 10 MGVIAAMR--DGFGFIKCV---DRDVRMFFHFSEIL--DGNQLHIADEVEFTVVPDMLSA 62
Query: 63 GKYSAENLKLVPKSS 77
+ A +K +PK +
Sbjct: 63 QRNHAIRIKKLPKGT 77
>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
Score = 58.7 bits (142), Expect = 3e-10
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 7/70 (10%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
G + +GFI ++F H S S + +L G +V Y +
Sbjct: 20 LGYVATLK--DNFGFIETA---NHDKEIFFHYSEF-SGDVDSLELGDMVEYSLSKGK-GN 72
Query: 64 KYSAENLKLV 73
K SAE +
Sbjct: 73 KVSAEKVNKT 82
>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
Score = 57.1 bits (138), Expect = 1e-09
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 6/72 (8%)
Query: 2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDA 61
+ R +++ +GFI E +F H V L G V + + N
Sbjct: 8 LRRATVECVK--DQFGFINYEV--GDSKKLFFHVKEVQ--DGIELQAGDEVEFSVILNQR 61
Query: 62 NGKYSAENLKLV 73
GK SA N+ V
Sbjct: 62 TGKCSACNVWRV 73
>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
Score = 55.7 bits (134), Expect = 3e-09
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 6/71 (8%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG 63
G I+ YGFI E +F H S L +L G V ++ + G
Sbjct: 20 TGVIEKLL--TSYGFIQCS---ERQARLFFHCSQYNG-NLQDLKVGDDVEFEVSSDRRTG 73
Query: 64 KYSAENLKLVP 74
K A L +
Sbjct: 74 KPIAVKLVKIS 84
>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
Score = 51.1 bits (122), Expect = 6e-08
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQND 60
+G + + +GFI + ++F H S L L G V + +
Sbjct: 17 ARCQGVVCAMK--EAFGFIERG---DVVKEIFFHYSEF-KGDLETLQPGDDVEFTIKDRN 70
Query: 61 ANGKYSAENLKLVPKSS 77
GK A +++L+P+ +
Sbjct: 71 --GKEVATDVRLLPQGT 85
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
activator, transcription regulation, phosphorylation;
1.9A {Escherichia coli}
Length = 101
Score = 44.6 bits (105), Expect = 5e-06
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAV--ASAGLFNLTEGQLVTYDYVQNDA 61
G +KW+N DKG+GFITP+ + DVF+H SA +A N +G V
Sbjct: 18 TGIVKWFNADKGFGFITPD---DGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITD 74
Query: 62 NGKYSAEN 69
G + +
Sbjct: 75 FGIFIGLD 82
>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
Length = 644
Score = 31.1 bits (69), Expect = 0.059
Identities = 5/29 (17%), Positives = 11/29 (37%), Gaps = 4/29 (13%)
Query: 13 DKGYGFITPEGSTESGDDVFLHRSAVASA 41
+KG+GF+ + F+ +
Sbjct: 30 EKGFGFLEVDA----QKSYFIPPPQMKKV 54
>3d8m_A BPP, baseplate protein, receptor binding protein; lactococcal phage
P2, lactococcal phage TP901-1, virus/viral protein
complex; 3.35A {Lactococcus phage tp901-1}
Length = 165
Score = 24.4 bits (53), Expect = 6.4
Identities = 6/21 (28%), Positives = 8/21 (38%)
Query: 3 HRGSIKWYNPDKGYGFITPEG 23
GSI W+ + I G
Sbjct: 138 PNGSITWWGANIDKTPIATRG 158
>3da0_A Cleaved chimeric receptor binding protein from bacteriophages
TP901-1 and P2; lactococcal phage P2; 1.65A {Lactococcus
phage tp901-1}
Length = 136
Score = 24.1 bits (52), Expect = 8.5
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 3 HRGSIKWYNPDKGYGFITPEGS 24
GSI W+ + I G+
Sbjct: 106 PNGSITWWGANIDKTPIATRGN 127
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.312 0.131 0.386
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 649,994
Number of extensions: 22090
Number of successful extensions: 69
Number of sequences better than 10.0: 1
Number of HSP's gapped: 52
Number of HSP's successfully gapped: 20
Length of query: 78
Length of database: 5,693,230
Length adjustment: 47
Effective length of query: 31
Effective length of database: 4,553,762
Effective search space: 141166622
Effective search space used: 141166622
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 (21.8 bits)
S2: 50 (23.1 bits)