RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy9900
(191 letters)
>d1h95a_ b.40.4.5 (A:) Y-box protein 1 cold shock domain (YB1-CSD)
{Human (Homo sapiens) [TaxId: 9606]}
Length = 79
Score = 77.9 bits (192), Expect = 4e-20
Identities = 38/78 (48%), Positives = 55/78 (70%)
Query: 1 MTKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVD 60
M K V G VK+++ + G+GFI R D KED+FVH+++I K NP+K+ +S+G GE V+
Sbjct: 1 MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVE 60
Query: 61 FNIGVGKKDIEAINVTGP 78
F++ G+K EA NVTGP
Sbjct: 61 FDVVEGEKGAEAANVTGP 78
Score = 77.6 bits (191), Expect = 6e-20
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
>d1mjca_ b.40.4.5 (A:) Major cold shock protein {Escherichia coli
[TaxId: 562]}
Length = 69
Score = 62.8 bits (153), Expect = 2e-14
Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+ GIVK++++ +GFGFIT D +D+FVH S+I ++SL G+ V F I G K
Sbjct: 4 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAK 59
Query: 69 DIEAINVT 76
A NVT
Sbjct: 60 GPAAGNVT 67
Score = 62.8 bits (153), Expect = 2e-14
Identities = 29/68 (42%), Positives = 41/68 (60%), Gaps = 4/68 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
+ GIVK++++ +GFGFIT D +D+FVH S+I ++SL G+ V F I G K
Sbjct: 4 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAK 59
Query: 170 DIEAINVT 177
A NVT
Sbjct: 60 GPAAGNVT 67
>d1c9oa_ b.40.4.5 (A:) Major cold shock protein {Bacillus
caldolyticus [TaxId: 1394]}
Length = 66
Score = 55.6 bits (134), Expect = 1e-11
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 5/67 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
RG VK++++++G+GFI + D+FVH ++I F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRG 57
Query: 70 IEAINVT 76
+A NV
Sbjct: 58 PQAANVV 64
Score = 55.6 bits (134), Expect = 1e-11
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 5/67 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
RG VK++++++G+GFI + D+FVH ++I F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFIEV-EGGSDVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRG 57
Query: 171 IEAINVT 177
+A NV
Sbjct: 58 PQAANVV 64
>d1g6pa_ b.40.4.5 (A:) Major cold shock protein {Thermotoga
maritima [TaxId: 2336]}
Length = 66
Score = 55.5 bits (134), Expect = 1e-11
Identities = 30/67 (44%), Positives = 44/67 (65%), Gaps = 5/67 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
RG VK++DSK+G+GFIT+ D D+FVH S+I F++L G++V+F I GKK
Sbjct: 2 RGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKG 56
Query: 70 IEAINVT 76
+A +V
Sbjct: 57 PQAAHVK 63
Score = 55.5 bits (134), Expect = 1e-11
Identities = 30/67 (44%), Positives = 44/67 (65%), Gaps = 5/67 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
RG VK++DSK+G+GFIT+ D D+FVH S+I F++L G++V+F I GKK
Sbjct: 2 RGKVKWFDSKKGYGFITK-DEGGDVFVHWSAIEMEG----FKTLKEGQVVEFEIQEGKKG 56
Query: 171 IEAINVT 177
+A +V
Sbjct: 57 PQAAHVK 63
>d1wfqa_ b.40.4.5 (A:) Cold shock domain protein E1 (UNR) {Human
(Homo sapiens) [TaxId: 9606]}
Length = 89
Score = 46.1 bits (109), Expect = 8e-08
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 9/73 (12%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
G+++ +GFI + + +F H S Q L +G+ V+F + ++
Sbjct: 20 TGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRT 72
Query: 70 --IEAINVTGPNG 80
A+ + +G
Sbjct: 73 GKPIAVKLVKISG 85
Score = 46.1 bits (109), Expect = 8e-08
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 9/73 (12%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
G+++ +GFI + + +F H S Q L +G+ V+F + ++
Sbjct: 20 TGVIEKL--LTSYGFIQCSERQARLFFHCSQYNGN-----LQDLKVGDDVEFEVSSDRRT 72
Query: 171 --IEAINVTGPNG 181
A+ + +G
Sbjct: 73 GKPIAVKLVKISG 85
>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia
coli [TaxId: 562]}
Length = 79
Score = 26.6 bits (59), Expect = 0.73
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKS 39
G+VK +++GFGF+ +D ++ F+
Sbjct: 19 AEGVVKA--TEKGFGFL-EVDAQKSYFIPPP 46
Score = 26.6 bits (59), Expect = 0.73
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKS 140
G+VK +++GFGF+ +D ++ F+
Sbjct: 19 AEGVVKA--TEKGFGFL-EVDAQKSYFIPPP 46
>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo
sapiens) [TaxId: 9606]}
Length = 99
Score = 24.9 bits (54), Expect = 3.9
Identities = 6/45 (13%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 5 EIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKF 49
+ +R ++ F G ++ + E+ I ++ + F
Sbjct: 42 KFGQIRKLLLFDRHPDGVASVS-FRDPEE---ADYCIQTLDGRWF 82
Score = 24.1 bits (52), Expect = 5.9
Identities = 6/44 (13%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 107 VHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKF 150
+R ++ F G ++ + E+ I ++ + F
Sbjct: 43 FGQIRKLLLFDRHPDGVASVS-FRDPEE---ADYCIQTLDGRWF 82
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine
synthase D, RluD {Escherichia coli [TaxId: 562]}
Length = 250
Score = 24.5 bits (52), Expect = 7.8
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 68 KDIEAINVTGPNGIPVQGAPKSSSETVSGTYRNDSFFPAVHTVRGIVKFYD 118
+DI IN P + V + TV + A GIV D
Sbjct: 15 EDIIIIN--KPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLD 63
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.320 0.141 0.411
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 730,728
Number of extensions: 33905
Number of successful extensions: 82
Number of sequences better than 10.0: 1
Number of HSP's gapped: 76
Number of HSP's successfully gapped: 19
Length of query: 191
Length of database: 2,407,596
Length adjustment: 80
Effective length of query: 111
Effective length of database: 1,309,196
Effective search space: 145320756
Effective search space used: 145320756
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: 50 (23.1 bits)