RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12844
(121 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 = 58.1 bits (140), Expect = 5e-12
Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 17/78 (21%)
Query: 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLL----VIFDIG 70
GV + F + +G GFI DG D F H S+++G Y + V + +
Sbjct: 64 KGVCKCFCRSKGHGFITP--ADGGPDIFLHISDVEGE---------YVPVEGDEVTYKMC 112
Query: 71 VTPGGRR--EAVHIKIFD 86
P +AV + I
Sbjct: 113 SIPPKNEKLQAVEVVITH 130
>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 = 54.7 bits (132), Expect = 2e-11
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG-GTDNILRAIKYSLLVIFDIGVT 72
V G +++FN G+GFINR +D ++D F H + I+ LR++ V FD+
Sbjct: 9 VLGTVKWFNVRNGYGFINR--NDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEG 66
Query: 73 PGG 75
G
Sbjct: 67 EKG 69
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc,
OB fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 53.9 bits (130), Expect = 3e-11
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73
++G I + K++GFGFI ++G + +FH ++ IK V F+
Sbjct: 3 MNGTITTWFKDKGFGFIK--DENG-DNRYFHVIKVANP-----DLIKKDAAVTFEPTTNN 54
Query: 74 GGRREAVHIKI 84
G A +K+
Sbjct: 55 KGLS-AYAVKV 64
>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 = 2e-10
Identities = 18/37 (48%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
+ G +++FN+ +GFGFI +DG KD F HFS IQ
Sbjct: 6 IKGNVKWFNESKGFGFITP--EDGSKDVFVHFSAIQT 40
>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 = 51.5 bits (124), Expect = 3e-10
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73
+ G + + + +GFI DDG + YF HFSE+ D + +V FD TP
Sbjct: 1 MKGKVVSYLAAKKYGFIQG--DDG-ESYFLHFSELLDKKD--EGKLVKGSMVHFDPTPTP 55
Query: 74 GGRREAVHIKI 84
G A I +
Sbjct: 56 KGLA-AKAISL 65
>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 = 49.9 bits (120), Expect = 9e-10
Identities = 16/36 (44%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 15 SGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
+G++++FN +GFGFI D+G +D F HFS I
Sbjct: 3 TGIVKWFNDAKGFGFITP--DEGGEDLFAHFSAINM 36
>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F
fold, RNA binding protein, DNA binding protein; NMR
{Rickettsia rickettsii}
Length = 70
Score = 49.2 bits (118), Expect = 2e-09
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP 73
+ G ++++N + FGFI + D+G KD F H S + L +++ VIFD+
Sbjct: 5 IVGKVKWYNSTKNFGFIEQ--DNGGKDVFVHKSAVDA---AGLHSLEEGQDVIFDLEEKQ 59
Query: 74 GGRREAVHIKI 84
G AV+++I
Sbjct: 60 GK-AYAVNLRI 69
>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 = 47.6 bits (114), Expect = 7e-09
Identities = 13/37 (35%), Positives = 25/37 (67%), Gaps = 3/37 (8%)
Query: 14 VSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
+ G +++F+ ++G+GFI + D+G D F H+S I+
Sbjct: 1 MRGKVKWFDSKKGYGFITK--DEG-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 = 48.3 bits (115), Expect = 9e-09
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
GV+ + FGFI R D K+ FFH+SE +G L ++ V F I G
Sbjct: 21 GVVCAMKE--AFGFIER--GDVVKEIFFHYSEFKGD----LETLQPGDDVEFTIKDRNGK 72
Query: 76 RREAVHIK 83
A ++
Sbjct: 73 EV-ATDVR 79
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural
genomics, NPPSFA; 1.65A {Thermus thermophilus}
Length = 73
Score = 46.9 bits (112), Expect = 1e-08
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI R +G D F H++ I
Sbjct: 4 GRVKWFNAEKGYGFIER---EGDTDVFVHYTAINA 35
>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 = 47.5 bits (113), Expect = 2e-08
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 14 VSGVIQFFNKERGFGFINRIG-----DDGRKDYFFHFSEIQG 50
SG ++FN GFGFI+ + D F H S++
Sbjct: 9 GSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYM 50
>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 = 46.4 bits (111), Expect = 2e-08
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 3/35 (8%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQG 50
G +++FN E+G+GFI +G D F HF+ IQG
Sbjct: 4 GKVKWFNNEKGYGFIEV---EGGSDVFVHFTAIQG 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 = 46.0 bits (109), Expect = 5e-08
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 8/68 (11%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGG 75
G + FGFI + K+ FFH+SE G + +++ +V + + G
Sbjct: 21 GYVATLKD--NFGFIET--ANHDKEIFFHYSEFSGD----VDSLELGDMVEYSLSKGKGN 72
Query: 76 RREAVHIK 83
+ A +
Sbjct: 73 KVSAEKVN 80
>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 = 46.9 bits (111), Expect = 7e-08
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 14 VSGVIQFFNKERGFGFINR-----IGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFD 68
+G+ ++FN GFGF++ + D D F H S++ R++K V F
Sbjct: 10 GAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHM---EGFRSLKEGEAVEFT 66
Query: 69 IGVTPGGRREAVHI 82
+ G E++ +
Sbjct: 67 FKKSAKG-LESIRV 79
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 44.8 bits (106), Expect = 2e-07
Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 4 HLGKIIEEVYVSGVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTD 53
H G ++ ++G++++FN ++GFGFI DDG KD F HFS G
Sbjct: 7 HHGSRLQSGKMTGIVKWFNADKGFGFITP--DDGSKDVFVHFSAGSSGAA 54
>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 = 38.7 bits (90), Expect = 4e-05
Identities = 23/70 (32%), Positives = 27/70 (38%), Gaps = 11/70 (15%)
Query: 16 GVIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP-- 73
GVI GFGFI D FFHFSEI G + + V F +
Sbjct: 11 GVIAAMRD--GFGFIKC--VDRDVRMFFHFSEILDGNQ-----LHIADEVEFTVVPDMLS 61
Query: 74 GGRREAVHIK 83
R A+ IK
Sbjct: 62 AQRNHAIRIK 71
>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 = 38.0 bits (88), Expect = 7e-05
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 26 GFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTP-GGRREAVHIK 83
+GFI + + FFH S+ G L+ +K V F++ G+ AV +
Sbjct: 29 SYGFIQC--SERQARLFFHCSQYNGN----LQDLKVGDDVEFEVSSDRRTGKPIAVKLV 81
>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 = 36.1 bits (83), Expect = 3e-04
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 24 ERGFGFINRIGDDGRKDYFFHFSEIQGGTD 53
+ FGFIN D K FFH E+Q G +
Sbjct: 17 KDQFGFINYEVGDS-KKLFFHVKEVQDGIE 45
>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 = 0.018
Identities = 15/114 (13%), Positives = 32/114 (28%), Gaps = 36/114 (31%)
Query: 17 VIQFFNKERGFGFINRIGDDGRKDYFFHFSEIQGGTDNILRAIKYSLLVIFDIGVTPGGR 76
++ +N + F + + YF+ I + L
Sbjct: 449 IVDHYNIPKTF-DSDDLIPPYLDQYFYSH-------------IGHHL------------- 481
Query: 77 REAVHIKIFD--TRLYLED------LRTCSVDCPCRDSKLNVKTS-RTYRKMVC 121
+ H + ++L+ +R S S LN + Y+ +C
Sbjct: 482 KNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC 535
>3d1c_A Flavin-containing putative monooxygenase; NP_373108.1, struc
genomics, joint center for structural genomics, JCSG;
HET: FAD UNL; 2.40A {Staphylococcus aureus}
Length = 369
Score = 26.7 bits (59), Expect = 2.2
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 89 LYLEDLRTCSVDCPC 103
+YL+D C V C C
Sbjct: 355 MYLDDYSCCEVSCTC 369
>3n9k_A Glucan 1,3-beta-glucosidase; aromatic entranceway/clamp,
exoglucanase, glycoside hydrolas protein-carbohydrate
interaction; HET: BGC; 1.70A {Candida albicans} PDB:
2pc8_A* 2pb1_A* 2pbo_A 3o6a_A 2pf0_A 1cz1_A 1eqc_A*
1eqp_A
Length = 399
Score = 25.6 bits (55), Expect = 5.8
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 48 IQGGTDNILRAI----KYSLLVIFDIGVTPGGRREAVHI 82
+QG + +A+ K ++ V D+ PG + +
Sbjct: 108 VQGQVQYLEKALGWARKNNIRVWIDLHGAPGSQNGFDNS 146
>1mc0_A 3',5'-cyclic nucleotide phosphodiesterase 2A; GAF domain, 3',5'
guanosine monophosphate, hydrolase; HET: PCG; 2.86A {Mus
musculus} SCOP: d.110.2.1 d.110.2.1
Length = 368
Score = 25.0 bits (54), Expect = 7.9
Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 6/29 (20%)
Query: 1 MKAHLGKIIEEVYVSGVIQFFNKERGFGF 29
+K ++I GV + NK G F
Sbjct: 294 IKNENQEVI------GVAELVNKINGPWF 316
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
0.328 0.146 0.445
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: 2,000,491
Number of extensions: 115105
Number of successful extensions: 389
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 30
Length of query: 121
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 39
Effective length of database: 4,412,271
Effective search space: 172078569
Effective search space used: 172078569
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: 51 (23.6 bits)