RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy547
(282 letters)
>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 = 109 bits (275), Expect = 6e-31
Identities = 46/75 (61%), Positives = 59/75 (78%)
Query: 29 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
V+ATKV G VKWF+V++GYGFI + EDVFVH IK NNPRK +++ +GETVEFD+
Sbjct: 4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63
Query: 89 MQGDKGHEAINVTGP 103
++G+KG EA NVTGP
Sbjct: 64 VEGEKGAEAANVTGP 78
Score = 97.4 bits (243), Expect = 3e-26
Identities = 39/68 (57%), Positives = 53/68 (77%)
Query: 196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
V+ATKV G VKWF+V++GYGFI + EDVFVH IK NNPRK +++ +GETVEFD+
Sbjct: 4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63
Query: 256 MQGDKGNQ 263
++G+KG +
Sbjct: 64 VEGEKGAE 71
>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 = 101 bits (254), Expect = 9e-28
Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 31 ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 83
+ G KWF+V+ G+GFI+ S DVFVH ++ +++L EGE
Sbjct: 6 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEP 61
Query: 84 VEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
VEF + KG E++ VTGP G G++
Sbjct: 62 VEFTFKKSSKGFESLRVTGPGGNPCLGNE 90
Score = 76.4 bits (188), Expect = 4e-18
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 250
+ G KWF+V+ G+GFI+ S DVFVH ++ +++L EGE
Sbjct: 6 VLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEP 61
Query: 251 VEFDIMQGDKGNQ 263
VEF + KG +
Sbjct: 62 VEFTFKKSSKGFE 74
>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 = 97.0 bits (241), Expect = 3e-25
Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 11/94 (11%)
Query: 31 ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 83
G+ KWF+V+ G+GF++ + DVFVH ++ +++L EGE
Sbjct: 7 LLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEA 62
Query: 84 VEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANK 117
VEF + KG E+I VTGP G GS+
Sbjct: 63 VEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKG 96
Score = 73.5 bits (180), Expect = 2e-16
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 11/73 (15%)
Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSN-------EDVFVHSKRIKYNNPRKLYKTLAEGET 250
G+ KWF+V+ G+GF++ + DVFVH ++ +++L EGE
Sbjct: 7 LLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEA 62
Query: 251 VEFDIMQGDKGNQ 263
VEF + KG +
Sbjct: 63 VEFTFKKSAKGLE 75
>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 = 82.7 bits (205), Expect = 1e-20
Identities = 19/72 (26%), Positives = 25/72 (34%), Gaps = 4/72 (5%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G V + YGFI E F+H + L +G V FD KG
Sbjct: 3 GKVVSYLAAKKYGFI-QGDDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPKGL 58
Query: 96 EAINVTGPDGRH 107
A ++ P H
Sbjct: 59 AAKAISLPLEHH 70
Score = 73.9 bits (182), Expect = 2e-17
Identities = 16/61 (26%), Positives = 20/61 (32%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G V + YGFI E F+H + L +G V FD KG
Sbjct: 3 GKVVSYLAAKKYGFI-QGDDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPKGL 58
Query: 263 Q 263
Sbjct: 59 A 59
>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 = 80.0 bits (198), Expect = 1e-19
Identities = 34/70 (48%), Positives = 44/70 (62%), Gaps = 4/70 (5%)
Query: 32 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 91
+K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 4 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59
Query: 92 DKGHEAINVT 101
KG A NVT
Sbjct: 60 AKGPSAANVT 69
Score = 75.0 bits (185), Expect = 7e-18
Identities = 30/65 (46%), Positives = 40/65 (61%), Gaps = 4/65 (6%)
Query: 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258
+K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 4 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59
Query: 259 DKGNQ 263
KG
Sbjct: 60 AKGPS 64
>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 = 79.2 bits (196), Expect = 2e-19
Identities = 32/66 (48%), Positives = 39/66 (59%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF K GYGFI T DVFVH I+ +KTL EG+ VEF+I +G KG
Sbjct: 3 GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57
Query: 96 EAINVT 101
+A +V
Sbjct: 58 QAAHVK 63
Score = 74.2 bits (183), Expect = 2e-17
Identities = 31/61 (50%), Positives = 36/61 (59%), Gaps = 5/61 (8%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF K GYGFI T DVFVH I+ +KTL EG+ VEF+I +G KG
Sbjct: 3 GKVKWFDSKKGYGFI-TKDEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKGP 57
Query: 263 Q 263
Q
Sbjct: 58 Q 58
>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 = 78.4 bits (194), Expect = 3e-19
Identities = 30/66 (45%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFI-EVEGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NV
Sbjct: 59 QAANVV 64
Score = 73.4 bits (181), Expect = 2e-17
Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 5/61 (8%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFI-EVEGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 Q 263
Q
Sbjct: 59 Q 59
>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 = 78.0 bits (193), Expect = 5e-19
Identities = 27/66 (40%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G+VKWF+ G+GFI ED+F H I +KTL EG+ V FD+ G KG
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 96 EAINVT 101
+A N+
Sbjct: 60 QAANIQ 65
Score = 74.2 bits (183), Expect = 1e-17
Identities = 26/61 (42%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G+VKWF+ G+GFI ED+F H I +KTL EG+ V FD+ G KG
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 263 Q 263
Q
Sbjct: 60 Q 60
>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F fold,
RNA binding protein, DNA binding protein; NMR
{Rickettsia rickettsii}
Length = 70
Score = 76.5 bits (189), Expect = 2e-18
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
+AT + G VKW++ +GFI + +DVFVH + +L EG+ V FD+
Sbjct: 1 MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLE 56
Query: 90 QGDKGHEAINVT 101
+ A+N+
Sbjct: 57 EKQGKAYAVNLR 68
Score = 71.1 bits (175), Expect = 2e-16
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
+AT + G VKW++ +GFI + +DVFVH + +L EG+ V FD+
Sbjct: 1 MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLE 56
Query: 257 QGDKGNQ 263
+
Sbjct: 57 EKQGKAY 63
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB
fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 72.4 bits (178), Expect = 7e-17
Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 7/66 (10%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G + + G+GFI + ++ + H ++ + + V F+ +KG
Sbjct: 5 GTITTWFKDKGFGFI-KDENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNNKGL 57
Query: 96 EAINVT 101
A V
Sbjct: 58 SAYAVK 63
Score = 66.6 bits (163), Expect = 1e-14
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G + + G+GFI + ++ + H ++ + + V F+ +KG
Sbjct: 5 GTITTWFKDKGFGFI-KDENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNNKGL 57
Query: 263 Q 263
Sbjct: 58 S 58
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural
genomics, NPPSFA; 1.65A {Thermus thermophilus}
Length = 73
Score = 72.4 bits (178), Expect = 7e-17
Identities = 30/68 (44%), Positives = 39/68 (57%), Gaps = 7/68 (10%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DK 93
G VKWF+ + GYGFI + DVFVH I ++TL EG+ V FD+ G K
Sbjct: 4 GRVKWFNAEKGYGFI-EREGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58
Query: 94 GHEAINVT 101
G +A+NVT
Sbjct: 59 GPQAVNVT 66
Score = 67.3 bits (165), Expect = 6e-15
Identities = 27/63 (42%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DK 260
G VKWF+ + GYGFI + DVFVH I ++TL EG+ V FD+ G K
Sbjct: 4 GRVKWFNAEKGYGFI-EREGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58
Query: 261 GNQ 263
G Q
Sbjct: 59 GPQ 61
>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 = 64.9 bits (158), Expect = 8e-14
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
GVV K +GFI +++F H K + +TL G+ VEF I +
Sbjct: 21 GVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKE 73
Query: 96 EAINVT 101
A +V
Sbjct: 74 VATDVR 79
Score = 58.7 bits (142), Expect = 2e-11
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 7/61 (11%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
GVV K +GFI +++F H K + +TL G+ VEF I +
Sbjct: 21 GVVCAM--KEAFGFIERGDVVKEIFFHYSEFKGD-----LETLQPGDDVEFTIKDRNGKE 73
Query: 263 Q 263
Sbjct: 74 V 74
>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 = 65.0 bits (158), Expect = 3e-13
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 13/79 (16%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG---D 92
GV K F G+GFI D+F+H ++ EG+ V + + +
Sbjct: 65 GVCKCFCRSKGHGFITPADGGPDIFLHISDVEG------EYVPVEGDEVTYKMCSIPPKN 118
Query: 93 KGHEAINVT----GPDGRH 107
+ +A+ V P +H
Sbjct: 119 EKLQAVEVVITHLAPGTKH 137
Score = 60.4 bits (146), Expect = 1e-11
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
GV K F G+GFI D+F+H ++ EG+ V + + N
Sbjct: 65 GVCKCFCRSKGHGFITPADGGPDIFLHISDVEG------EYVPVEGDEVTYKMCSIPPKN 118
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 61.3 bits (149), Expect = 2e-12
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 31 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 90
+ K+ G+VKWF+ G+GFI ++DVFVH +G+ VE I
Sbjct: 14 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAV--RGNPQQGDRVEGKIKS 71
Query: 91 GDKGHEAINV-TGPDG 105
I + G DG
Sbjct: 72 ITDFGIFIGLDGGIDG 87
Score = 57.5 bits (139), Expect = 5e-11
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 198 ATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQ 257
+ K+ G+VKWF+ G+GFI ++DVFVH +G+ VE I
Sbjct: 14 SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAV--RGNPQQGDRVEGKIKS 71
Query: 258 GDKGNQF 264
F
Sbjct: 72 ITDFGIF 78
>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 = 54.8 bits (132), Expect = 3e-10
Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 8/71 (11%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG-DKG 94
G V K +GFI T + ++++F H + +L G+ VE+ + +G
Sbjct: 21 GYVATL--KDNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNK 73
Query: 95 HEAINVTGPDG 105
A V G
Sbjct: 74 VSAEKVNKTSG 84
Score = 51.0 bits (122), Expect = 7e-09
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261
G V K +GFI T + ++++F H + +L G+ VE+ + +G
Sbjct: 21 GYVATL--KDNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGN 72
>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 = 47.2 bits (112), Expect = 2e-07
Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 7/79 (8%)
Query: 185 SASESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKT 244
S S A + GV++ + + YGFI +F H + N +
Sbjct: 3 SGSSGGYPNGTSAALRETGVIE--KLLTSYGFIQCSERQARLFFHCSQYNGN-----LQD 55
Query: 245 LAEGETVEFDIMQGDKGNQ 263
L G+ VEF++ + +
Sbjct: 56 LKVGDDVEFEVSSDRRTGK 74
Score = 46.9 bits (111), Expect = 2e-07
Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 9/86 (10%)
Query: 18 SANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKT 77
S + A + GV++ + + YGFI +F H + N +
Sbjct: 3 SGSSGGYPNGTSAALRETGVIE--KLLTSYGFIQCSERQARLFFHCSQYNGN-----LQD 55
Query: 78 LAEGETVEFDIMQGDKGHE--AINVT 101
L G+ VEF++ + + A+ +
Sbjct: 56 LKVGDDVEFEVSSDRRTGKPIAVKLV 81
>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 = 42.6 bits (100), Expect = 9e-06
Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
GV+ +++ G+GFI + +F H I N L + VEF ++
Sbjct: 11 GVIA--AMRDGFGFIKCVDRDVRMFFHFSEILDGN------QLHIADEVEFTVVPDMLSA 62
Query: 263 Q 263
Q
Sbjct: 63 Q 63
Score = 41.4 bits (97), Expect = 2e-05
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 11/69 (15%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
GV+ +++ G+GFI + +F H I N L + VEF ++
Sbjct: 11 GVIA--AMRDGFGFIKCVDRDVRMFFHFSEILDGN------QLHIADEVEFTVVPDMLSA 62
Query: 96 E---AINVT 101
+ AI +
Sbjct: 63 QRNHAIRIK 71
>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 = 39.5 bits (91), Expect = 0.001
Identities = 37/270 (13%), Positives = 83/270 (30%), Gaps = 78/270 (28%)
Query: 29 VLATKVCGVVKWF---SVKSGYGFIAT--------PSSNEDVFVHSKR----------IK 67
L +K +V+ F ++ Y F+ + PS +++ +R K
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYI-EQRDRLYNDNQVFAK 128
Query: 68 YNNPR-KLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQG-SQFAANKPKYNRRKA 125
YN R + Y L + + + + + + G G G + A +
Sbjct: 129 YNVSRLQPYLKLRQA-------LLELRPAKNVLIDGVLG---SGKTWVALD--------- 169
Query: 126 KANKRKRKSRRNNRLF----GVKYQLEIPMEFSSKTMPFFMILFCCLQM-CDSGTKAEAT 180
K + + + ++F E +E M+ Q+ + ++++ +
Sbjct: 170 VCLSYKVQCKMDFKIFWLNLKNCNSPETVLE---------MLQKLLYQIDPNWTSRSDHS 220
Query: 181 PSNPSASESPKKEP-------------VVLATKVC--GVVKWFSVKSGYGFIATPSSNED 225
+ S + E +VL V F++ + T + +
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLL-NVQNAKAWNAFNLSC--KILLT-TRFKQ 276
Query: 226 V--FVHSKRIKYNNPRKLYKTLAEGETVEF 253
V F+ + + + TL E
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSL 306
>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 = 37.3 bits (86), Expect = 0.006
Identities = 31/168 (18%), Positives = 55/168 (32%), Gaps = 49/168 (29%)
Query: 42 SVKSGYGFIATPS--------SNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDK 93
S+++ G PS + E V + N L G+ VE ++ G K
Sbjct: 327 SLENNEG---VPSPMLSISNLTQEQVQ---DYVNKTN-----SHLPAGKQVEISLVNGAK 375
Query: 94 GHEAINVTGP----DG--RHVQGSQFAANKPKYNRRKAKANKRKRKSRRNNRLFGVKYQL 147
+ V+GP G ++ A ++ + ++RK K F ++ L
Sbjct: 376 ---NLVVSGPPQSLYGLNLTLRK---AKAPSGLDQSRIPFSERKLK-------FSNRF-L 421
Query: 148 EIPMEFSSKTMPFFMILFCCLQMCDSGTKAEATPSNPSASESPKKEPV 195
+ PF L L + +N S + + PV
Sbjct: 422 PV-------ASPFHSHL---LVPASDLINKDLVKNNVSFNAKDIQIPV 459
Score = 28.5 bits (63), Expect = 3.7
Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 15/84 (17%)
Query: 37 VVK--W----FSVKSGYGF-IAT-----PSSNEDVF--VHSKRIKYNNPRKLYKTLAEGE 82
+ W K YGF I P + F KRI+ N +++T+ +G+
Sbjct: 1641 AAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGK 1700
Query: 83 TVEFDIMQG-DKGHEAINVTGPDG 105
I + ++ + G
Sbjct: 1701 LKTEKIFKEINEHSTSYTFRSEKG 1724
Score = 28.1 bits (62), Expect = 4.0
Identities = 21/142 (14%), Positives = 37/142 (26%), Gaps = 29/142 (20%)
Query: 2 QMCDSGTKAEATPSNPSANESPKKEPVVLATKVCGVVKWFSVKSGYGFIATPSSNEDVFV 61
Q+ + K P+ A + P L K F G++++ V
Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPAELVGK-------FL-----GYVSSLVEPSKV-- 77
Query: 62 HSKRIKYNNPRKLYKTLAEGETVEF--DIMQGDKGHEAINVTGPDGRHVQGSQFAANKPK 119
+ + EF ++G+ H + K
Sbjct: 78 -----------GQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNY 126
Query: 120 YNRRKAKANKRKRKSRRNNRLF 141
R KR + N+ LF
Sbjct: 127 ITARIMA--KRPFDKKSNSALF 146
>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 = 34.1 bits (78), Expect = 0.007
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 209 SVKSGYGFIATP-SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGNQFC 265
VK +GFI ++ +F H K ++ L G+ VEF ++ + +
Sbjct: 15 CVKDQFGFINYEVGDSKKLFFHVKEVQDGI------ELQAGDEVEFSVILNQRTGKCS 66
Score = 33.4 bits (76), Expect = 0.010
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 9/63 (14%)
Query: 42 SVKSGYGFIATP-SSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHE--AI 98
VK +GFI ++ +F H K ++ L G+ VEF ++ + + A
Sbjct: 15 CVKDQFGFINYEVGDSKKLFFHVKEVQDGI------ELQAGDEVEFSVILNQRTGKCSAC 68
Query: 99 NVT 101
NV
Sbjct: 69 NVW 71
>1o7f_A CAMP-dependent RAP1 guanine-nucleotide exchange factor; EPAC2,
CAMP-GEF2, campb binding doamin, regulation; 2.5A {Mus
musculus} SCOP: a.4.5.31 b.82.3.2 b.82.3.2
Length = 469
Score = 29.1 bits (64), Expect = 1.7
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 242 YKTLAEGETVEFDIMQGDKGNQFCFVLK 269
Y+ L +G T+ QGD G + VL
Sbjct: 67 YENLEKGITL---FRQGDIGTNWYAVLA 91
>3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; nucleotide
binding protein, structural genomics; HET: MSE CMP;
1.79A {Methylobacillus flagellatus KT}
Length = 187
Score = 27.8 bits (62), Expect = 3.4
Identities = 4/27 (14%), Positives = 9/27 (33%), Gaps = 3/27 (11%)
Query: 243 KTLAEGETVEFDIMQGDKGNQFCFVLK 269
+ + +GD G+ +L
Sbjct: 65 YAAPRDCQL---LTEGDPGDYLLLILT 88
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 28.3 bits (63), Expect = 4.2
Identities = 14/86 (16%), Positives = 21/86 (24%), Gaps = 38/86 (44%)
Query: 59 VFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQFAANKP 118
+ VH P LY + E ++
Sbjct: 1455 IVVH--------PDYLYGAITE------------------------------DRYNEYVA 1476
Query: 119 KYNRRKAKANKRKRKSRRNNRLFGVK 144
K + R+ A K N+LF K
Sbjct: 1477 KVSAREKSAYKFFHNGMIYNKLFVSK 1502
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 5.6
Identities = 5/22 (22%), Positives = 10/22 (45%)
Query: 120 YNRRKAKANKRKRKSRRNNRLF 141
R+ + K K +R ++ F
Sbjct: 124 NQRQSEQVEKNKINNRIADKAF 145
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
0.316 0.132 0.391
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: 4,053,448
Number of extensions: 225863
Number of successful extensions: 547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 495
Number of HSP's successfully gapped: 47
Length of query: 282
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 190
Effective length of database: 4,133,061
Effective search space: 785281590
Effective search space used: 785281590
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: 41 (21.6 bits)
S2: 57 (25.9 bits)