RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3660
(144 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 = 74.3 bits (182), Expect = 5e-18
Identities = 39/107 (36%), Positives = 47/107 (43%), Gaps = 20/107 (18%)
Query: 4 SPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKE 63
P P ++ +E +PSP+ TRRTRT S
Sbjct: 8 PPQPPTHQASVGLLDTPRSRERSPSPLRGNVVPSPLPTRRTRTFSA-------------- 53
Query: 64 QPNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
+ RA Q PV G K FCRSKGHGFITP G P +F+HISD
Sbjct: 54 ------TVRASQGPVYKGVCKCFCRSKGHGFITPADGGPDIFLHISD 94
>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F fold,
RNA binding protein, DNA binding protein; NMR
{Rickettsia rickettsii}
Length = 70
Score = 50.7 bits (122), Expect = 9e-10
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
GK+K + +K GFI D+G VFVH S
Sbjct: 6 VGKVKWYNSTKNFGFIEQDNGGKDVFVHKS 35
>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 = 46.8 bits (112), Expect = 2e-08
Identities = 16/31 (51%), Positives = 19/31 (61%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
TG +K F +KG GFITPD G +F H S
Sbjct: 2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFS 32
>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 = 46.9 bits (112), Expect = 3e-08
Identities = 17/30 (56%), Positives = 19/30 (63%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
G +K F SKG GFITP+ G VFVH S
Sbjct: 7 KGNVKWFNESKGFGFITPEDGSKDVFVHFS 36
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB
fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 46.9 bits (112), Expect = 3e-08
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHISD 110
G I + + KG GFI ++G+ + H+
Sbjct: 4 NGTITTWFKDKGFGFIKDENGDN-RYFHVIK 33
>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 = 44.7 bits (106), Expect = 2e-07
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
G +K F G+GFI + + VFVH +
Sbjct: 9 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQT 39
>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 = 43.4 bits (103), Expect = 7e-07
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
GK+ + +K +GFI D GE F+H S
Sbjct: 2 KGKVVSYLAAKKYGFIQGDDGES-YFLHFS 30
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 44.0 bits (104), Expect = 8e-07
Identities = 18/30 (60%), Positives = 19/30 (63%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
TG +K F KG GFITPD G VFVH S
Sbjct: 18 TGIVKWFNADKGFGFITPDDGSKDVFVHFS 47
>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 = 43.0 bits (102), Expect = 8e-07
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
+ GK+K F KG+GFI + G VFVH +
Sbjct: 2 QRGKVKWFNNEKGYGFIEVEGG-SDVFVHFT 31
>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 = 43.0 bits (102), Expect = 9e-07
Identities = 17/30 (56%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
GK+K F KG+GFIT D G VFVH S
Sbjct: 2 RGKVKWFDSKKGYGFITKDEG-GDVFVHWS 30
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural
genomics, NPPSFA; 1.65A {Thermus thermophilus}
Length = 73
Score = 42.3 bits (100), Expect = 2e-06
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHIS 109
+ G++K F KG+GFI + VFVH +
Sbjct: 2 QKGRVKWFNAEKGYGFIEREGD-TDVFVHYT 31
>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 = 36.3 bits (84), Expect = 4e-04
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 65 PNFLISNRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
+ + R + G + GFI + + +F H S++
Sbjct: 5 SSGRLLGRNSNSKRLLGYVATL--KDNFGFIETANHDKEIFFHYSEF 49
>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 = 35.9 bits (83), Expect = 5e-04
Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 7/38 (18%)
Query: 79 ETGKIKEFCRSKGHGFIT-------PDSGEPAVFVHIS 109
+G K F G GFI+ P VFVH S
Sbjct: 9 GSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQS 46
>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 = 36.0 bits (83), Expect = 7e-04
Identities = 7/33 (21%), Positives = 12/33 (36%), Gaps = 2/33 (6%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
G + + GFI +F H S++
Sbjct: 19 CQGVVCAM--KEAFGFIERGDVVKEIFFHYSEF 49
>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 = 37.0 bits (85), Expect = 0.001
Identities = 29/163 (17%), Positives = 45/163 (27%), Gaps = 73/163 (44%)
Query: 17 SPMLS--------------------PQEPHLHSNNTLSLP-SP---IIT----------- 41
SPMLS P + +SL +++
Sbjct: 336 SPMLSISNLTQEQVQDYVNKTNSHLPAGKQVE----ISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 42 --RRTRTES-MDFKATAQ-RSKGSKEQPNFLISNRALQNPVE-----------TGKIKEF 86
R+ + S +D Q R S+ + F SNR L PV + I +
Sbjct: 392 TLRKAKAPSGLD-----QSRIPFSERKLKF--SNRFL--PVASPFHSHLLVPASDLINKD 442
Query: 87 CRSKGHGFITPDSGEPAVFVHISD--------YVIMPKLISQI 121
F D P V+ D I +++ I
Sbjct: 443 LVKNNVSFNAKDIQIP-VY-DTFDGSDLRVLSGSISERIVDCI 483
Score = 32.3 bits (73), Expect = 0.050
Identities = 18/82 (21%), Positives = 27/82 (32%), Gaps = 29/82 (35%)
Query: 7 PFENKKPALSS---PMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKE 63
PF +K S+ P+ SP HS L P A+ +K +
Sbjct: 408 PFSERKLKFSNRFLPVASP----FHS----HLLVP--------------ASDLINKDLVK 445
Query: 64 QPNFLISNRALQNPV---ETGK 82
N + + +Q PV G
Sbjct: 446 N-NVSFNAKDIQIPVYDTFDGS 466
>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 = 35.8 bits (82), Expect = 0.001
Identities = 11/37 (29%), Positives = 14/37 (37%), Gaps = 7/37 (18%)
Query: 80 TGKIKEFCRSKGHGFITPDSGEPA-------VFVHIS 109
G K F G GF++ + VFVH S
Sbjct: 11 AGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQS 47
>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 = 33.3 bits (77), Expect = 0.017
Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 17/69 (24%)
Query: 63 EQPNFLISNR----ALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYVIMPKLI 118
Q N L++ Q P G +K KG GF+ D+ + Y I P
Sbjct: 2 FQDNPLLAQLKQQLHSQTPRAEGVVK--ATEKGFGFLEVDAQK--------SYFIPPP-- 49
Query: 119 SQINKALQG 127
Q+ K + G
Sbjct: 50 -QMKKVMHG 57
>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 = 31.5 bits (71), Expect = 0.024
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 71 NRALQNPVETGKIKEFCRSKGHGFITPDSGEPAVFVHISDY 111
N ETG I++ +GFI + +F H S Y
Sbjct: 11 NGTSAALRETGVIEKL--LTSYGFIQCSERQARLFFHCSQY 49
>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 = 32.9 bits (74), Expect = 0.032
Identities = 25/144 (17%), Positives = 56/144 (38%), Gaps = 27/144 (18%)
Query: 4 SPLPFENKKPALSSPMLSPQEPHLHSNNTLSLPSPIITRRTRTESMDFKATAQRSKGSKE 63
SP+ E ++P++ + M Q L+++N + + +R + R +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV----SRLQ----PYLKLRQALLEL 147
Query: 64 QPNFLISNRALQNPVETGK---IKEFCRSKGHGFITPDSGEPAVF------VHISDYVIM 114
+P + + + +GK + C S + + +F + + V+
Sbjct: 148 RPAKNV---LIDGVLGSGKTWVALDVCLS--YKVQCKMDFK--IFWLNLKNCNSPETVLE 200
Query: 115 P--KLISQINKALQGSKTCNSCNI 136
KL+ QI+ S++ +S NI
Sbjct: 201 MLQKLLYQIDPNWT-SRSDHSSNI 223
>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 = 30.3 bits (68), Expect = 0.079
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 79 ETGKIKEFCRSKGHGFITPDSGEPAVFVHISDYV 112
E G I G GFI + +F H S+ +
Sbjct: 9 EMGVIAAM--RDGFGFIKCVDRDVRMFFHFSEIL 40
>3p2m_A Possible hydrolase; alpha/beta hydrolase superfamily; 2.80A
{Mycobacterium tuberculosis}
Length = 330
Score = 28.6 bits (64), Expect = 0.71
Identities = 14/89 (15%), Positives = 25/89 (28%), Gaps = 11/89 (12%)
Query: 25 PHLHSNNTLSLPSPIITRRTRTESMDFKATAQR---SKGSKEQPNFLISNRALQNPVETG 81
H H +++ +P R + SM R F + + G
Sbjct: 5 HHHHHHSSGLVP-----RGSHMASMTGGQQMGRVLSDDELTGLDEFALLAENAEQAGVNG 59
Query: 82 KIKEFCRSKG---HGFITPDSGEPAVFVH 107
+ E R + S +F+H
Sbjct: 60 PLPEVERVQAGAISALRWGGSAPRVIFLH 88
>3bcw_A Uncharacterized protein; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; 1.60A {Bordetella bronchiseptica RB50}
Length = 123
Score = 28.0 bits (62), Expect = 0.75
Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 6/43 (13%)
Query: 77 PVETGKIKEFCR-SKGHGFITPDSGEPAVFVHIS--DYVIMPK 116
T E+C +G + G + D IMP+
Sbjct: 62 QSNTTGYIEYCHIIEGEARLVDPDGTV---HAVKAGDAFIMPE 101
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 27.7 bits (62), Expect = 1.2
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 81 GKIKE--FCRSKGHGFI---TPDSGEPAVFVHISDYVIMPKLISQINKALQGSK 129
G+ E R +G GFI + E A + ++ + + +I A G+
Sbjct: 47 GEPSEVFINRDRGFGFIRLESRTLAEIAK-AELDGTILKSRPL-RIRFATHGAA 98
>3myx_A Uncharacterized protein pspto_0244; protein of unknown function
(DUF861), cupin_3 (PF05899), STR genomics; HET: MSE;
1.30A {Pseudomonas syringae PV}
Length = 238
Score = 25.9 bits (56), Expect = 5.4
Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 6/42 (14%)
Query: 78 VETGKIKEFCR-SKGHGFITPDSGEPAVFVHIS--DYVIMPK 116
KI E +G ++ ++G + ++ D V + +
Sbjct: 181 SRPHKIHELMNLIEGRVVLSLENGSS---LTVNTGDTVFVAQ 219
>3mgk_A Intracellular protease/amidase related enzyme (THIJ family);
amidotranferase-like, structural genomics, PSI; 2.00A
{Clostridium acetobutylicum}
Length = 211
Score = 25.6 bits (57), Expect = 6.6
Identities = 3/12 (25%), Positives = 4/12 (33%)
Query: 17 SPMLSPQEPHLH 28
S + H H
Sbjct: 199 SKIYGEGHHHHH 210
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
0.312 0.128 0.367
Gapped
Lambda K H
0.267 0.0653 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,987,622
Number of extensions: 103415
Number of successful extensions: 247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 245
Number of HSP's successfully gapped: 31
Length of query: 144
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,328,508
Effective search space: 255381972
Effective search space used: 255381972
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 (21.9 bits)
S2: 52 (24.0 bits)