RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9900
(191 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 = 82.0 bits (203), Expect = 3e-21
Identities = 36/70 (51%), Positives = 53/70 (75%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++ G+K
Sbjct: 9 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 68
Query: 69 DIEAINVTGP 78
EA NVTGP
Sbjct: 69 GAEAANVTGP 78
Score = 82.0 bits (203), Expect = 3e-21
Identities = 36/70 (51%), Positives = 53/70 (75%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+F++ G+K
Sbjct: 9 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEK 68
Query: 170 DIEAINVTGP 179
EA NVTGP
Sbjct: 69 GAEAANVTGP 78
>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 = 80.1 bits (197), Expect = 1e-19
Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 11/94 (11%)
Query: 105 PAVHTVRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLG 157
P + GI K+++ + GFGF++ LD D+FVH+S + F+SL G
Sbjct: 5 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEG 60
Query: 158 EIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKVP 191
E V+F K +E+I VTGP G+ G+ + P
Sbjct: 61 EAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRP 94
Score = 78.9 bits (194), Expect = 3e-19
Identities = 30/89 (33%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 9 VRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 61
GI K+++ + GFGF++ LD D+FVH+S + F+SL GE V+F
Sbjct: 10 GAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEF 65
Query: 62 NIGVGKKDIEAINVTGPNGIPVQGAPKSS 90
K +E+I VTGP G+ G+ +
Sbjct: 66 TFKKSAKGLESIRVTGPGGVFCIGSERRP 94
>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 = 75.2 bits (185), Expect = 2e-18
Identities = 32/90 (35%), Positives = 45/90 (50%), Gaps = 11/90 (12%)
Query: 105 PAVHTVRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLG 157
P V G K+++ + GFGFI+ L+N D+FVH+S + F+SL G
Sbjct: 4 PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEG 59
Query: 158 EIVDFNIGVGKKDIEAINVTGPNGIPVQGA 187
E V+F K E++ VTGP G P G
Sbjct: 60 EPVEFTFKKSSKGFESLRVTGPGGNPCLGN 89
Score = 75.2 bits (185), Expect = 2e-18
Identities = 30/85 (35%), Positives = 43/85 (50%), Gaps = 11/85 (12%)
Query: 9 VRGIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDF 61
G K+++ + GFGFI+ L+N D+FVH+S + F+SL GE V+F
Sbjct: 9 GSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEPVEF 64
Query: 62 NIGVGKKDIEAINVTGPNGIPVQGA 86
K E++ VTGP G P G
Sbjct: 65 TFKKSSKGFESLRVTGPGGNPCLGN 89
>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 = 62.3 bits (152), Expect = 1e-13
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
++G V Y + + +GFI D+ E F+H S ++ L G +V F+ K
Sbjct: 1 MKGKVVSYLAAKKYGFIQG-DDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPK 56
Query: 69 DIEAINVTGP 78
+ A ++ P
Sbjct: 57 GLAAKAISLP 66
Score = 62.3 bits (152), Expect = 1e-13
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
++G V Y + + +GFI D+ E F+H S ++ L G +V F+ K
Sbjct: 1 MKGKVVSYLAAKKYGFIQG-DDGESYFLHFSELLDKKD---EGKLVKGSMVHFDPTPTPK 56
Query: 170 DIEAINVTGP 179
+ A ++ P
Sbjct: 57 GLAAKAISLP 66
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc,
OB fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 57.7 bits (140), Expect = 7e-12
Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 7/69 (10%)
Query: 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67
+ G + + +GFGFI +N ++ + H + + V F
Sbjct: 2 AMNGTITTWFKDKGFGFIKD-ENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNN 54
Query: 68 KDIEAINVT 76
K + A V
Sbjct: 55 KGLSAYAVK 63
Score = 57.7 bits (140), Expect = 7e-12
Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 7/69 (10%)
Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168
+ G + + +GFGFI +N ++ + H + + V F
Sbjct: 2 AMNGTITTWFKDKGFGFIKD-ENGDNRYFHVIKVAN------PDLIKKDAAVTFEPTTNN 54
Query: 169 KDIEAINVT 177
K + A V
Sbjct: 55 KGLSAYAVK 63
>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 = 56.1 bits (136), Expect = 2e-11
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G
Sbjct: 5 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGA 60
Query: 68 KDIEAINVT 76
K A NVT
Sbjct: 61 KGPSAANVT 69
Score = 56.1 bits (136), Expect = 2e-11
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G
Sbjct: 5 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGA 60
Query: 169 KDIEAINVT 177
K A NVT
Sbjct: 61 KGPSAANVT 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 = 54.1 bits (131), Expect = 1e-10
Identities = 30/68 (44%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+RG VK++DSK+G+GFIT+ D D+FVH S+I F++L G++V+F I GKK
Sbjct: 1 MRGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKK 55
Query: 69 DIEAINVT 76
+A +V
Sbjct: 56 GPQAAHVK 63
Score = 54.1 bits (131), Expect = 1e-10
Identities = 30/68 (44%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
+RG VK++DSK+G+GFIT+ D D+FVH S+I F++L G++V+F I GKK
Sbjct: 1 MRGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKK 55
Query: 170 DIEAINVT 177
+A +V
Sbjct: 56 GPQAAHVK 63
>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 = 54.1 bits (131), Expect = 1e-10
Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
GIVK+++ +GFGFIT + ED+F H S+I F++L G+ V F++ G K
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 71 EAINVT 76
+A N+
Sbjct: 60 QAANIQ 65
Score = 54.1 bits (131), Expect = 1e-10
Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
GIVK+++ +GFGFIT + ED+F H S+I F++L G+ V F++ G K
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINMEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 172 EAINVT 177
+A N+
Sbjct: 60 QAANIQ 65
>2lss_A Cold shock-like protein; CSD, CSP, oligonucleotide binding F
fold, RNA binding protein, DNA binding protein; NMR
{Rickettsia rickettsii}
Length = 70
Score = 53.8 bits (130), Expect = 2e-10
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 67
+ G VK+Y+S + FGFI + + +D+FVHKS++ SL G+ V F++ +
Sbjct: 4 NIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLEEKQ 59
Query: 68 KDIEAINVT 76
A+N+
Sbjct: 60 GKAYAVNLR 68
Score = 53.8 bits (130), Expect = 2e-10
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK 168
+ G VK+Y+S + FGFI + + +D+FVHKS++ SL G+ V F++ +
Sbjct: 4 NIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLEEKQ 59
Query: 169 KDIEAINVT 177
A+N+
Sbjct: 60 GKAYAVNLR 68
>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 = 52.2 bits (126), Expect = 5e-10
Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 5/66 (7%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
G VK++++++G+GFI + D+FVH ++I F++L G+ V F I G +
Sbjct: 4 GKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 71 EAINVT 76
+A NV
Sbjct: 59 QAANVV 64
Score = 52.2 bits (126), Expect = 5e-10
Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 5/66 (7%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
G VK++++++G+GFI + D+FVH ++I F++L G+ V F I G +
Sbjct: 4 GKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 172 EAINVT 177
+A NV
Sbjct: 59 QAANVV 64
>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 = 52.9 bits (127), Expect = 7e-10
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
+G+V K FGFI R D ++IF H S K ++L G+ V+F I
Sbjct: 20 QGVVCAM--KEAFGFIERGDVVKEIFFHYSEF-----KGDLETLQPGDDVEFTIKDRNGK 72
Query: 70 IEAINVT 76
A +V
Sbjct: 73 EVATDVR 79
Score = 52.9 bits (127), Expect = 7e-10
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
+G+V K FGFI R D ++IF H S K ++L G+ V+F I
Sbjct: 20 QGVVCAM--KEAFGFIERGDVVKEIFFHYSEF-----KGDLETLQPGDDVEFTIKDRNGK 72
Query: 171 IEAINVT 177
A +V
Sbjct: 73 EVATDVR 79
>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 = 53.5 bits (128), Expect = 1e-09
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 9/89 (10%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 67
+G+ K + +G GFIT D DIF+H S + + G+ V + +
Sbjct: 64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDV------EGEYVPVEGDEVTYKMCSIPPK 117
Query: 68 -KDIEAINVTGPNGIPVQGAPKSSSETVS 95
+ ++A+ V + P S +S
Sbjct: 118 NEKLQAVEVVITHLAPGTKHETWSGHVIS 146
Score = 50.8 bits (121), Expect = 1e-08
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 168
+G+ K + +G GFIT D DIF+H S + + G+ V + +
Sbjct: 64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDV------EGEYVPVEGDEVTYKMCSIPPK 117
Query: 169 -KDIEAINVTGPNGIP 183
+ ++A+ V + P
Sbjct: 118 NEKLQAVEVVITHLAP 133
>3a0j_A Cold shock protein; OB-fold, cytoplasm, transcription, structural
genomics, NPPSFA; 1.65A {Thermus thermophilus}
Length = 73
Score = 49.2 bits (118), Expect = 9e-09
Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 7/68 (10%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGKK 68
G VK++++++G+GFI R + D+FVH ++I F++L G+IV F++ G K
Sbjct: 4 GRVKWFNAEKGYGFIER-EGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58
Query: 69 DIEAINVT 76
+A+NVT
Sbjct: 59 GPQAVNVT 66
Score = 49.2 bits (118), Expect = 9e-09
Identities = 25/68 (36%), Positives = 43/68 (63%), Gaps = 7/68 (10%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI--GVGKK 169
G VK++++++G+GFI R + D+FVH ++I F++L G+IV F++ G K
Sbjct: 4 GRVKWFNAEKGYGFIER-EGDTDVFVHYTAINAKG----FRTLNEGDIVTFDVEPGRNGK 58
Query: 170 DIEAINVT 177
+A+NVT
Sbjct: 59 GPQAVNVT 66
>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 = 4e-08
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTG 77
K FGFI ++ ++IF H S SL LG++V++++ GK + A V
Sbjct: 27 KDNFGFIETANHDKEIFFHYSEF-----SGDVDSLELGDMVEYSLSKGKGNKVSAEKVNK 81
Query: 78 PNGIPVQG 85
+G P G
Sbjct: 82 TSG-PSSG 88
Score = 47.9 bits (114), Expect = 4e-08
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-KDIEAINVTG 178
K FGFI ++ ++IF H S SL LG++V++++ GK + A V
Sbjct: 27 KDNFGFIETANHDKEIFFHYSEF-----SGDVDSLELGDMVEYSLSKGKGNKVSAEKVNK 81
Query: 179 PNGIPVQG 186
+G P G
Sbjct: 82 TSG-PSSG 88
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 47.8 bits (114), Expect = 5e-08
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 94 VSGTYRNDSFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQS 153
+ G++ + + GIVK++++ +GFGFIT D +D+FVH S+ + +
Sbjct: 1 MRGSHHHHGSRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAG--SSGAAVRGN 58
Query: 154 LGLGEIVDFNIGVGKKDIEAINVTG 178
G+ V+ I I + G
Sbjct: 59 PQQGDRVEGKIKSITDFGIFIGLDG 83
Score = 47.5 bits (113), Expect = 9e-08
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+ GIVK++++ +GFGFIT D +D+FVH S+ + + G+ V+ I
Sbjct: 17 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAG--SSGAAVRGNPQQGDRVEGKIKSITD 74
Query: 69 DIEAINVTG 77
I + G
Sbjct: 75 FGIFIGLDG 83
>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 = 39.5 bits (92), Expect = 5e-05
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 7/60 (11%)
Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVT 76
+GFI + + +F H S Q L +G+ V+F + ++ A+ +
Sbjct: 27 LTSYGFIQCSERQARLFFHCSQY-----NGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLV 81
Score = 39.5 bits (92), Expect = 5e-05
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 7/60 (11%)
Query: 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK--DIEAINVT 177
+GFI + + +F H S Q L +G+ V+F + ++ A+ +
Sbjct: 27 LTSYGFIQCSERQARLFFHCSQY-----NGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLV 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 = 36.8 bits (85), Expect = 4e-04
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 13/80 (16%)
Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDIEAINVTGP 78
+ GFGFI +D +F H S I+ L + + V+F + +
Sbjct: 17 RDGFGFIKCVDRDVRMFFHFSEILD------GNQLHIADEVEFTVVPDML-----SAQRN 65
Query: 79 NGIPVQGAPKSS--SETVSG 96
+ I ++ PK + + SG
Sbjct: 66 HAIRIKKLPKGTVSFHSHSG 85
Score = 34.5 bits (79), Expect = 0.003
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINV 176
+ GFGFI +D +F H S I+ L + + V+F + AI +
Sbjct: 17 RDGFGFIKCVDRDVRMFFHFSEILD------GNQLHIADEVEFTVVPDMLSAQRNHAIRI 70
Query: 177 T 177
Sbjct: 71 K 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 = 34.1 bits (77), Expect = 0.028
Identities = 27/166 (16%), Positives = 55/166 (33%), Gaps = 45/166 (27%)
Query: 3 KFEIHTVRGIVKFYDSKRGFGFITRLDNKED--IFV----HKSSIVKMNPKKFFQSLGLG 56
++ +H R IV Y+ + F + D + H +I F+ + L
Sbjct: 442 EYALH--RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL- 498
Query: 57 EIVDFNIGVGKKDIEAINVTGPNGIPVQGAPKSSSETVS--GTYR-----NDSFFPAVHT 109
DF + +K I A S T+ Y+ ND + +
Sbjct: 499 ---DFRF-LEQK----IRHDSTA----WNASGSILNTLQQLKFYKPYICDNDPKYERL-- 544
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHK-SSIVK---MNPKKFF 151
V I+ F+ +++ E++ K + +++ M +
Sbjct: 545 VNAILD---------FLPKIE--ENLICSKYTDLLRIALMAEDEAI 579
Score = 33.7 bits (76), Expect = 0.036
Identities = 38/193 (19%), Positives = 64/193 (33%), Gaps = 50/193 (25%)
Query: 24 FITRLDNKEDIFVHK------SSIVKMNP---KKFFQSLGLGEI--VDFNI--------- 63
+ DN + + K SS+ + P +K F L + +I
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS---VFPPSAHIPTILLSLIW 396
Query: 64 -GVGKKDIEAINVTGPNGIPVQGAPKSSSETVSGTY-------RNDSFFPAVHTVRGIVK 115
V K D+ + V+ PK S+ ++ Y N+ A+H R IV
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE---YALH--RSIVD 451
Query: 116 FYDSKRGFGFITRLDNKED--IFV----HKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
Y+ + F + D + H +I F+ + L DF + +K
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL----DFRF-LEQK 506
Query: 170 ---DIEAINVTGP 179
D A N +G
Sbjct: 507 IRHDSTAWNASGS 519
Score = 32.9 bits (74), Expect = 0.064
Identities = 18/186 (9%), Positives = 51/186 (27%), Gaps = 61/186 (32%)
Query: 37 HKSSIVKMNPKKFFQSLGLGEIVDFNIGV-GKKDIEAINVTGPNGI-------------- 81
I+ + F + ++ D + K++I+ I + + +
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI-IMSKDAVSGTLRLFWTLLSKQ 75
Query: 82 ---------------------PVQGAPKSSS-------ETVSGTYRNDSFFPAVHTVRGI 113
P++ + S E Y ++ F + R +
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR-L 134
Query: 114 VKFYDSKRGFGFITRLDNKEDIFVH------KSSIVKMNPKKFFQSLGLGEIVDFNI--- 164
+ ++ + L +++ + K+ + S + +DF I
Sbjct: 135 QPYLKLRQA---LLELRPAKNVLIDGVLGSGKTWVALD----VCLSYKVQCKMDFKIFWL 187
Query: 165 GVGKKD 170
+ +
Sbjct: 188 NLKNCN 193
>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 = 29.2 bits (65), Expect = 1.1
Identities = 22/124 (17%), Positives = 40/124 (32%), Gaps = 40/124 (32%)
Query: 4 FE--IHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGL------ 55
E + V RG + ++++ ++ +NP + S
Sbjct: 1779 IESLVEVVF--------YRGM-TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYV 1829
Query: 56 --------G---EIVDFNI-G---V--G-KKDIEA----INVTGPNGIPVQGAPKS-SSE 92
G EIV++N+ V G + ++ +N I + KS S E
Sbjct: 1830 VERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLE 1889
Query: 93 TVSG 96
V G
Sbjct: 1890 EVEG 1893
Score = 27.7 bits (61), Expect = 2.7
Identities = 28/133 (21%), Positives = 41/133 (30%), Gaps = 40/133 (30%)
Query: 68 KDIEAINVTGP----------NGIP----VQGAPKSSSETVSGTYRNDSFFPAVHTVRGI 113
+ N P NG V G P+ S ++ T R + R
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNG-AKNLVVSGPPQ-SLYGLNLTLRKAKAPSGLDQSR-- 406
Query: 114 VKFYDSKRGFGFITRLDNKEDIFV--HKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
+ F S+R F R + H S + + P L ++V N+ KDI
Sbjct: 407 IPF--SERKLKFSNRFLP---VASPFH-SHL--LVPA---SDLINKDLVKNNVSFNAKDI 455
Query: 172 EAINVTGPNGIPV 184
IPV
Sbjct: 456 ---------QIPV 459
Score = 26.6 bits (58), Expect = 7.0
Identities = 17/98 (17%), Positives = 32/98 (32%), Gaps = 34/98 (34%)
Query: 102 SFFPAVHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGL----- 156
S V V RG + ++++ ++ +NP + S
Sbjct: 1778 SIESLVEVVF--------YRGM-TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQY 1828
Query: 157 ---------G---EIVDFNI-G---V--GKKDIEAINV 176
G EIV++N+ V G D+ A++
Sbjct: 1829 VVERVGKRTGWLVEIVNYNVENQQYVAAG--DLRALDT 1864
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 26.4 bits (58), Expect = 8.3
Identities = 4/57 (7%), Positives = 16/57 (28%), Gaps = 14/57 (24%)
Query: 8 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSI----VKMNPKKFFQSLGLGEIVD 60
V I +++ + V+ ++ + ++ +G+
Sbjct: 912 RVERFWHN-------DIICTTNSEVECVVNAQRHAGAQLRRPANEIYE---IGKTYP 958
Score = 26.4 bits (58), Expect = 8.3
Identities = 4/57 (7%), Positives = 16/57 (28%), Gaps = 14/57 (24%)
Query: 109 TVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSI----VKMNPKKFFQSLGLGEIVD 161
V I +++ + V+ ++ + ++ +G+
Sbjct: 912 RVERFWHN-------DIICTTNSEVECVVNAQRHAGAQLRRPANEIYE---IGKTYP 958
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
0.320 0.141 0.411
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: 2,972,981
Number of extensions: 175892
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 537
Number of HSP's successfully gapped: 55
Length of query: 191
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 103
Effective length of database: 4,244,745
Effective search space: 437208735
Effective search space used: 437208735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.7 bits)