RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3654
(140 letters)
>3aqq_A Calcium-regulated heat stable protein 1; compact beta-barrel, cold
shock domain, ssDNA binding, DNA B protein; 2.80A {Homo
sapiens}
Length = 147
Score = 125 bits (316), Expect = 3e-38
Identities = 66/135 (48%), Positives = 78/135 (57%), Gaps = 1/135 (0%)
Query: 4 SPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESISNRALQNPVETGKI 63
P P ++ +E +PSP+ TRRTRT S + RA Q PV G
Sbjct: 8 PPQPPTHQASVGLLDTPRSRERSPSPLRGNVVPSPLPTRRTRTFSATVRASQGPVYKGVC 67
Query: 64 KEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVE 123
K FCRSKGHGFITP G P +F+HISD+EG YVP+ GDEV Y++C IPPK EK QAV V
Sbjct: 68 KCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVV 127
Query: 124 IVHLTPEV-HLQWDS 137
I HL P H W
Sbjct: 128 ITHLAPGTKHETWSG 142
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB
fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 62.7 bits (153), Expect = 2e-14
Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 4/73 (5%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQA 119
G I + + KG GFI ++G+ + H+ + + V + A
Sbjct: 4 NGTITTWFKDKGFGFIKDENGDN-RYFHVIKVANPDLIKKDAAVTFEPTTNNKGL---SA 59
Query: 120 VHVEIVHLTPEVH 132
V++V L H
Sbjct: 60 YAVKVVPLEHHHH 72
>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F
fold, RNA binding protein, DNA binding protein; NMR
{Rickettsia rickettsii}
Length = 70
Score = 56.1 bits (136), Expect = 7e-12
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
GK+K + +K GFI D+G VFVH S ++
Sbjct: 6 VGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDA 39
>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP,
STRU genomics, oxford protein production facility,
OPPF, gene RE; 2.60A {Neisseria meningitidis MC58}
Length = 67
Score = 51.8 bits (125), Expect = 3e-10
Identities = 17/35 (48%), Positives = 20/35 (57%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
TG +K F +KG GFITPD G +F H S I
Sbjct: 2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINM 36
>3i2z_B RNA chaperone, negative regulator of CSPA transcription; beta
barrel, DNA binding protein/transcription, cytoplasm,
gene regulation; 1.10A {Salmonella typhimurium} PDB:
2l15_A 1mjc_A 3mef_A
Length = 71
Score = 51.9 bits (125), Expect = 3e-10
Identities = 18/34 (52%), Positives = 21/34 (61%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
G +K F SKG GFITP+ G VFVH S I+
Sbjct: 7 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQT 40
>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 = 48.5 bits (116), Expect = 7e-09
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 11/67 (16%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQ 118
G +K F G+GFI + + VFVH + I+ R +
Sbjct: 9 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKN-----NPRKYLR------SVGDGE 57
Query: 119 AVHVEIV 125
V ++V
Sbjct: 58 TVEFDVV 64
>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 3pf4_A 1csq_A
1nmf_A 1nmg_A 1csp_A 2f52_A 2es2_A 3pf5_A 2i5m_X 2i5l_X
Length = 66
Score = 47.6 bits (114), Expect = 1e-08
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
+ GK+K F KG+GFI + G VFVH + I+G
Sbjct: 2 QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFTAIQG 35
>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}
Length = 88
Score = 47.9 bits (114), Expect = 2e-08
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 51 NRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPL-PGDEVKYRL 107
R + G + GFI + + +F H S+ G L GD V+Y L
Sbjct: 11 GRNSNSKRLLGYVATL--KDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSL 66
>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 = 47.2 bits (113), Expect = 2e-08
Identities = 19/34 (55%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
GK+K F KG+GFIT D G VFVH S IE
Sbjct: 2 RGKVKWFDSKKGYGFITKDEG-GDVFVHWSAIEM 34
>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}
Length = 97
Score = 47.9 bits (114), Expect = 2e-08
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 41 TRRTRTESISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPL-P 99
+ + + + + G + + GFI +F H S+ +G L P
Sbjct: 3 SGSSGNIMLLKK--KQARCQGVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGDLETLQP 58
Query: 100 GDEVKYRL 107
GD+V++ +
Sbjct: 59 GDDVEFTI 66
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 47.8 bits (114), Expect = 3e-08
Identities = 24/68 (35%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 42 RRTRTESISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG---CYVPL 98
R + S Q+ TG +K F KG GFITPD G VFVH S
Sbjct: 2 RGSHHHHGSRL--QSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNP 59
Query: 99 P-GDEVKY 105
GD V+
Sbjct: 60 QQGDRVEG 67
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural
genomics, NPPSFA; 1.65A {Thermus thermophilus}
Length = 73
Score = 46.9 bits (112), Expect = 3e-08
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
+ G++K F KG+GFI + VFVH + I
Sbjct: 2 QKGRVKWFNAEKGYGFIEREGD-TDVFVHYTAINA 35
>2kcm_A Cold shock domain family protein; nucleic acid binding protein,
beta barrel, structural genomi 2, protein structure
initiative; NMR {Shewanella oneidensis}
Length = 74
Score = 45.0 bits (107), Expect = 2e-07
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEG 93
GK+ + +K +GFI D GE F+H S++
Sbjct: 2 KGKVVSYLAAKKYGFIQGDDGES-YFLHFSELLD 34
>1x65_A UNR protein; cell-free protein synthesis, beta-barrel,
translational REGU RNA chaperone, RNA/DNA binding, QB
fold, greek-KEY topology protein; NMR {Homo sapiens}
Length = 89
Score = 44.9 bits (106), Expect = 2e-07
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 2/81 (2%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQ 118
E G I G GFI + +F H S+I DEV++ + P ++N
Sbjct: 9 EMGVIAAM--RDGFGFIKCVDRDVRMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNH 66
Query: 119 AVHVEIVHLTPEVHLQWDSPS 139
A+ ++ + PS
Sbjct: 67 AIRIKKLPKGTVSFHSHSGPS 87
>1wfq_A UNR protein; beta-barrel, translational regulation, RNA chaperone,
RNA/DN binding, QB fold, greek-KEY topology, structur
genomics; NMR {Homo sapiens} SCOP: b.40.4.5
Length = 89
Score = 43.0 bits (101), Expect = 1e-06
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 4/76 (5%)
Query: 51 NRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPL-PGDEVKYRLCP 109
N ETG I++ +GFI + +F H S G L GD+V++ +
Sbjct: 11 NGTSAALRETGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSS 68
Query: 110 IPPKFEKNQAVHVEIV 125
+ K AV + +
Sbjct: 69 D-RRTGKPIAVKLVKI 83
>3ulj_A LIN28B, DNA-binding protein; beta barrel, cold shock domain fold,
nucleic acid binding, D binding protein; 1.06A
{Silurana} PDB: 4a4i_A
Length = 90
Score = 39.8 bits (93), Expect = 2e-05
Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 7/42 (16%)
Query: 59 ETGKIKEFCRSKGHGFIT-------PDSGEPAVFVHISDIEG 93
+G K F G GFI+ P VFVH S +
Sbjct: 9 GSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYM 50
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA
complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A
{Mus musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 38.5 bits (89), Expect = 1e-04
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 7/41 (17%)
Query: 60 TGKIKEFCRSKGHGFITPDSGEPA-------VFVHISDIEG 93
G K F G GF++ + VFVH S +
Sbjct: 11 AGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHM 51
>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}
Length = 79
Score = 32.6 bits (74), Expect = 0.007
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 71 GHGFITPDSGEPA-VFVHISDIEGCYVPLPGDEVKYRLCPIPPKFEKNQAVHVEIV 125
GFI + G+ +F H+ +++ GDEV++ + + K A +V V
Sbjct: 19 QFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVIL-NQRTGKCSACNVWRV 73
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 34.6 bits (79), Expect = 0.008
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 13/64 (20%)
Query: 7 PFENKKPALSS---PMLSPQEPHLHSNNTLSLPSPIITRR--TRTESISNRALQNPV--- 58
PF +K S+ P+ SP HS + L S +I + S + + +Q PV
Sbjct: 408 PFSERKLKFSNRFLPVASP----FHS-HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT 462
Query: 59 ETGK 62
G
Sbjct: 463 FDGS 466
Score = 29.2 bits (65), Expect = 0.52
Identities = 29/170 (17%), Positives = 54/170 (31%), Gaps = 62/170 (36%)
Query: 17 SPMLS----PQ---EPHLHSNNTLSLPSPIITRRTRTESIS--NRALQNPVETG------ 61
SPMLS Q + +++ N+ LP+ + IS N +N V +G
Sbjct: 336 SPMLSISNLTQEQVQDYVNKTNS-HLPA------GKQVEISLVN-GAKNLVVSGPPQSLY 387
Query: 62 -------KIK----------EFCRSK---GHGF--IT-P---DSGEPAVFVHISDIEGCY 95
K K F K + F + P PA + D+
Sbjct: 388 GLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNN 447
Query: 96 VPLPGDEVKYRLCPIPPKFEKN----QAVHVEIVH-LTPEV---HLQWDS 137
V +++ IP + + + I + + ++W++
Sbjct: 448 VSFNAKDIQ-----IPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWET 492
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} 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 = 32.5 bits (75), Expect = 0.029
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 55 QNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDIEGCYVPLPGDEVKYRLCPIPPKF 114
Q P G +K KG GF+ D+ + F+ ++ + GD + I +
Sbjct: 18 QTPRAEGVVK--ATEKGFGFLEVDAQKS-YFIPPPQMKKV---MHGDRIIAV---IHSEK 68
Query: 115 EKNQAVHVEIV 125
E+ A E+V
Sbjct: 69 ERESAEPEELV 79
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 31.7 bits (71), Expect = 0.079
Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 20/84 (23%)
Query: 4 SPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESISN--RALQN--PVE 59
SP+ E ++P++ + M Q L+++N + + +R + +AL P +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV----SRLQPYLKLRQALLELRPAK 151
Query: 60 ---------TGK---IKEFCRSKG 71
+GK + C S
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYK 175
>2z72_A Protein-tyrosine-phosphatase; cold-active enzyme, psychrophIle,
hydrolase; 1.10A {Shewanella SP} PDB: 1v73_A 2zbm_A
Length = 342
Score = 27.8 bits (61), Expect = 1.2
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 42 RRTRTESISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPA--VFVHISDIEGCYVPL 98
R +T SI + P G + E S I PD+ V +SD+ G Y L
Sbjct: 29 NRLKTTSIEKLQVNRPEHCGDLPETKLSSEIKQIMPDTYLGIKKVVA-LSDVHGQYDVL 86
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 25.6 bits (57), Expect = 2.8
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 6/25 (24%)
Query: 59 ETGKIKEFCRSKGHGFITPDSGEPA 83
+TG SKG+ FI S + +
Sbjct: 43 DTG------NSKGYAFINFASFDAS 61
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 25.7 bits (57), Expect = 5.5
Identities = 7/31 (22%), Positives = 9/31 (29%), Gaps = 8/31 (25%)
Query: 61 GKIKEFC--------RSKGHGFITPDSGEPA 83
G +K F SKG+ F
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex;
1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 24.5 bits (54), Expect = 7.7
Identities = 5/16 (31%), Positives = 9/16 (56%)
Query: 68 RSKGHGFITPDSGEPA 83
SKG+GF++ +
Sbjct: 48 VSKGYGFVSFYNDVDV 63
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.315 0.134 0.415
Gapped
Lambda K H
0.267 0.0532 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,165,261
Number of extensions: 118479
Number of successful extensions: 290
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 34
Length of query: 140
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 56
Effective length of database: 4,356,429
Effective search space: 243960024
Effective search space used: 243960024
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: 52 (24.3 bits)