BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy9900
(191 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1H95|A Chain A, Solution Structure Of The Single-Stranded Dna-Binding
Cold Shock Domain (Csd) Of Human Y-Box Protein 1 (Yb1)
Determined By Nmr (10 Lowest Energy Structures)
Length = 79
Score = 80.1 bits (196), Expect = 6e-16, Method: Compositional matrix adjust.
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 = 79.7 bits (195), Expect = 9e-16, Method: Compositional matrix adjust.
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
>pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From
The Hyperthermophilic Bacterium Thermotoga Maritima
Length = 66
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 46/67 (68%), Gaps = 5/67 (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-DEGGDVFVHWSAI----EMEGFKTLKEGQVVEFEIQEGKK 55
Query: 69 DIEAINV 75
+A +V
Sbjct: 56 GPQAAHV 62
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 46/67 (68%), Gaps = 5/67 (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-DEGGDVFVHWSAI----EMEGFKTLKEGQVVEFEIQEGKK 55
Query: 170 DIEAINV 176
+A +V
Sbjct: 56 GPQAAHV 62
>pdb|3TRZ|A Chain A, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|B Chain B, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|C Chain C, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|D Chain D, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|E Chain E, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|F Chain F, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TS2|A Chain A, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
pdb|3TS2|B Chain B, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
Length = 148
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 11/87 (12%)
Query: 112 GIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
GI K+++ + GFGF++ LD D+FVH+S + F+SL GE V+F
Sbjct: 12 GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEFTF 67
Query: 165 GVGKKDIEAINVTGPNGIPVQGAPKVP 191
K +E+I VTGP G+ G+ + P
Sbjct: 68 KKSAKGLESIRVTGPGGVFCIGSERRP 94
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 11/78 (14%)
Query: 11 GIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 63
GI K+++ + GFGF++ LD D+FVH+S + F+SL GE V+F
Sbjct: 12 GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEFTF 67
Query: 64 GVGKKDIEAINVTGPNGI 81
K +E+I VTGP G+
Sbjct: 68 KKSAKGLESIRVTGPGGV 85
>pdb|3TS0|A Chain A, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
pdb|3TS0|B Chain B, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
Length = 146
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 11/87 (12%)
Query: 112 GIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
GI K+++ + GFGF++ LD D+FVH+S + F+SL GE V+F
Sbjct: 10 GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEFTF 65
Query: 165 GVGKKDIEAINVTGPNGIPVQGAPKVP 191
K +E+I VTGP G+ G+ + P
Sbjct: 66 KKSAKGLESIRVTGPGGVFCIGSERRP 92
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 11/78 (14%)
Query: 11 GIVKFYDSKRGFGFIT-------RLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 63
GI K+++ + GFGF++ LD D+FVH+S + F+SL GE V+F
Sbjct: 10 GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSLKEGEAVEFTF 65
Query: 64 GVGKKDIEAINVTGPNGI 81
K +E+I VTGP G+
Sbjct: 66 KKSAKGLESIRVTGPGGV 83
>pdb|3ULJ|A Chain A, Crystal Structure Of Apo Lin28b Cold Shock Domain
pdb|3ULJ|B Chain B, Crystal Structure Of Apo Lin28b Cold Shock Domain
pdb|4A75|A Chain A, The Lin28b Cold Shock Domain In Complex With
Hexathymidine.
pdb|4A75|C Chain C, The Lin28b Cold Shock Domain In Complex With
Hexathymidine.
pdb|4A75|E Chain E, The Lin28b Cold Shock Domain In Complex With
Hexathymidine.
pdb|4A75|G Chain G, The Lin28b Cold Shock Domain In Complex With
Hexathymidine.
pdb|4A76|A Chain A, The Lin28b Cold Shock Domain In Complex With
Heptathymidine
pdb|4A76|C Chain C, The Lin28b Cold Shock Domain In Complex With
Heptathymidine
pdb|4A76|E Chain E, The Lin28b Cold Shock Domain In Complex With
Heptathymidine
pdb|4A76|G Chain G, The Lin28b Cold Shock Domain In Complex With
Heptathymidine
pdb|4ALP|A Chain A, The Lin28b Cold Shock Domain In Complex With Hexauridine
pdb|4ALP|B Chain B, The Lin28b Cold Shock Domain In Complex With Hexauridine
pdb|4ALP|C Chain C, The Lin28b Cold Shock Domain In Complex With Hexauridine
pdb|4ALP|D Chain D, The Lin28b Cold Shock Domain In Complex With Hexauridine
Length = 90
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 11/89 (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 EIVDFNIGVGKKDIEAINVTGPNGIPVQG 186
E V+F K E++ VTGP G P G
Sbjct: 60 EPVEFTFKKSSKGFESLRVTGPGGNPCLG 88
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 11/82 (13%)
Query: 11 GIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 63
G K+++ + GFGFI+ L+N D+FVH+S + F+SL GE V+F
Sbjct: 11 GHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSLKEGEPVEFTF 66
Query: 64 GVGKKDIEAINVTGPNGIPVQG 85
K E++ VTGP G P G
Sbjct: 67 KKSSKGFESLRVTGPGGNPCLG 88
>pdb|4A4I|A Chain A, Crystal Structure Of The Human Lin28b Cold Shock Domain
pdb|4A4I|B Chain B, Crystal Structure Of The Human Lin28b Cold Shock Domain
Length = 90
Score = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 47/91 (51%), Gaps = 13/91 (14%)
Query: 5 EIHTVRGI--VKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGL 55
E +RG K+++ + GFGFI+ LD D+FVH+S + F+SL
Sbjct: 3 ESQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKE 58
Query: 56 GEIVDFNIGVGKKDIEAINVTGPNGIPVQGA 86
GE V+F K +E+I VTGP G P G+
Sbjct: 59 GEPVEFTFKKSSKGLESIRVTGPGGSPCLGS 89
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 11/83 (13%)
Query: 112 GIVKFYDSKRGFGFITR-------LDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
G K+++ + GFGFI+ LD D+FVH+S + F+SL GE V+F
Sbjct: 11 GHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKEGEPVEFTF 66
Query: 165 GVGKKDIEAINVTGPNGIPVQGA 187
K +E+I VTGP G P G+
Sbjct: 67 KKSSKGLESIRVTGPGGSPCLGS 89
>pdb|3I2Z|B Chain B, Structure Of Cold Shock Protein E From Salmonella
Typhimurium
pdb|3I2Z|A Chain A, Structure Of Cold Shock Protein E From Salmonella
Typhimurium
Length = 71
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G K
Sbjct: 6 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 61
Query: 69 DIEAINVTG 77
A NVT
Sbjct: 62 GPSAANVTA 70
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
++G VK+++ +GFGFIT D +D+FVH S+I F++L G+ V+F I G K
Sbjct: 6 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAK 61
Query: 170 DIEAINVTG 178
A NVT
Sbjct: 62 GPSAANVTA 70
>pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein
Of Escherichia Coli
Length = 69
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
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 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 69 DIEAINVT 76
A NVT
Sbjct: 60 GPAAGNVT 67
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
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 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 170 DIEAINVT 177
A NVT
Sbjct: 60 GPAAGNVT 67
>pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using
Combined Nmr And Cs-Rosetta Method
Length = 70
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
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: 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 60
Query: 69 DIEAINVT 76
A NVT
Sbjct: 61 GPAAGNVT 68
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
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: 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 60
Query: 170 DIEAINVT 177
A NVT
Sbjct: 61 GPAAGNVT 68
>pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution
Nmr Structure
Length = 69
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
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 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 69 DIEAINVT 76
A NVT
Sbjct: 60 GPAAGNVT 67
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
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 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAI----QNDGYKSLDEGQKVSFTIESGAK 59
Query: 170 DIEAINVT 177
A NVT
Sbjct: 60 GPAAGNVT 67
>pdb|3CAM|A Chain A, Crystal Structure Of The Cold Shock Domain Protein From
Neisseria Meningitidis
pdb|3CAM|B Chain B, Crystal Structure Of The Cold Shock Domain Protein From
Neisseria Meningitidis
Length = 67
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
GIVK+++ +GFGFIT + ED+F H S+I F++L G+ V F++ G K
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 71 EAINV 75
+A N+
Sbjct: 60 QAANI 64
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
GIVK+++ +GFGFIT + ED+F H S+I F++L G+ V F++ G K
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 172 EAINV 176
+A N+
Sbjct: 60 QAANI 64
>pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Variant Bs-Cspb M1rE3KK65I
Length = 67
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
++G VK+++S++GFGFI ++ ++D+FVH S+I + F++L G+ V F I G +
Sbjct: 2 LKGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 69 DIEAINVT 76
+A NVT
Sbjct: 57 GPQAANVT 64
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 45/68 (66%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
++G VK+++S++GFGFI ++ ++D+FVH S+I + F++L G+ V F I G +
Sbjct: 2 LKGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 170 DIEAINVT 177
+A NVT
Sbjct: 57 GPQAANVT 64
>pdb|2ES2|A Chain A, Crystal Structure Analysis Of The Bacillus Subtilis Cold
Shock Protein Bs-Cspb In Complex With Hexathymidine
pdb|2F52|A Chain A, Solution Structure Of Cold Shock Protein Cspb From
Bacillus Subtilis In Complex With Heptathymidine
pdb|1CSP|A Chain A, Crystal Structure Of The Bacillus Subtilis Major Cold
Shock Protein, Cspb: A Universal Nucleic-Acid Binding
Domain
pdb|1CSQ|A Chain A, Crystal Structure Of The Bacillus Subtilis Major Cold
Shock Protein, Cspb: A Universal Nucleic-Acid Binding
Domain
pdb|1NMF|A Chain A, Major Cold-Shock Protein, Nmr, 20 Structures
pdb|1NMG|A Chain A, Major Cold-Shock Protein, Nmr, Minimized Average
Structure
pdb|3PF4|A Chain A, Crystal Structure Of Bs-Cspb In Complex With R(Gucuuua)
pdb|3PF4|B Chain B, Crystal Structure Of Bs-Cspb In Complex With R(Gucuuua)
pdb|3PF5|A Chain A, Crystal Structure Of Bs-Cspb In Complex With Ru6
pdb|3PF5|B Chain B, Crystal Structure Of Bs-Cspb In Complex With Ru6
Length = 67
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+ G VK+++S++GFGFI ++ ++D+FVH S+I + F++L G+ V F I G +
Sbjct: 2 LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 69 DIEAINVT 76
+A NVT
Sbjct: 57 GPQAANVT 64
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
+ G VK+++S++GFGFI ++ ++D+FVH S+I + F++L G+ V F I G +
Sbjct: 2 LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQAVSFEIVEGNR 56
Query: 170 DIEAINVT 177
+A NVT
Sbjct: 57 GPQAANVT 64
>pdb|3A0J|A Chain A, Crystal Structure Of Cold Shock Protein 1 From Thermus
Thermophilus Hb8
pdb|3A0J|B Chain B, Crystal Structure Of Cold Shock Protein 1 From Thermus
Thermophilus Hb8
Length = 73
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 7/69 (10%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 67
+G VK++++++G+GFI R + D+FVH ++I K F++L G+IV F++ G+
Sbjct: 3 KGRVKWFNAEKGYGFIER-EGDTDVFVHYTAI----NAKGFRTLNEGDIVTFDVEPGRNG 57
Query: 68 KDIEAINVT 76
K +A+NVT
Sbjct: 58 KGPQAVNVT 66
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 46/69 (66%), Gaps = 7/69 (10%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGK-- 168
+G VK++++++G+GFI R + D+FVH ++I K F++L G+IV F++ G+
Sbjct: 3 KGRVKWFNAEKGYGFIER-EGDTDVFVHYTAI----NAKGFRTLNEGDIVTFDVEPGRNG 57
Query: 169 KDIEAINVT 177
K +A+NVT
Sbjct: 58 KGPQAVNVT 66
>pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Cspb Variant A46k S48r
Length = 67
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 9 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 68
+ G VK+++S++GFGFI ++ ++D+FVH S+I + F++L G+ V F I G +
Sbjct: 2 LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQKVRFEIVEGNR 56
Query: 69 DIEAINVT 76
+A NVT
Sbjct: 57 GPQAANVT 64
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKK 169
+ G VK+++S++GFGFI ++ ++D+FVH S+I + F++L G+ V F I G +
Sbjct: 2 LEGKVKWFNSEKGFGFI-EVEGQDDVFVHFSAI----QGEGFKTLEEGQKVRFEIVEGNR 56
Query: 170 DIEAINVT 177
+A NVT
Sbjct: 57 GPQAANVT 64
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 2 TKFEIHTVRGIVKFYDSKRGFGFITRLDNKEDIFVHKS-----SIVKMNPKKFFQSLG-L 55
++ + + GIVK++++ +GFGFIT D +D+FVH S + V+ NP++ + G +
Sbjct: 10 SRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKI 69
Query: 56 GEIVDFNIGVG 66
I DF I +G
Sbjct: 70 KSITDFGIFIG 80
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 6/64 (9%)
Query: 110 VRGIVKFYDSKRGFGFITRLDNKEDIFVHKS-----SIVKMNPKKFFQSLG-LGEIVDFN 163
+ GIVK++++ +GFGFIT D +D+FVH S + V+ NP++ + G + I DF
Sbjct: 17 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFG 76
Query: 164 IGVG 167
I +G
Sbjct: 77 IFIG 80
>pdb|1HZA|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZA|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 67
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 5/67 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 70 IEAINVT 76
+A NVT
Sbjct: 58 PQAANVT 64
Score = 40.0 bits (92), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 42/67 (62%), Gaps = 5/67 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 171 IEAINVT 177
+A NVT
Sbjct: 58 PQAANVT 64
>pdb|1HZ9|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZ9|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQAVSFEIVQGNRG 57
Query: 70 IEAINV 75
+A NV
Sbjct: 58 PQAANV 63
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQAVSFEIVQGNRG 57
Query: 171 IEAINV 176
+A NV
Sbjct: 58 PQAANV 63
>pdb|1HZB|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZB|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 70 IEAINV 75
+A NV
Sbjct: 58 PQAANV 63
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 171 IEAINV 176
+A NV
Sbjct: 58 PQAANV 63
>pdb|1C9O|A Chain A, Crystal Structure Analysis Of The Bacillus Caldolyticus
Cold Shock Protein Bc-Csp
pdb|1C9O|B Chain B, Crystal Structure Analysis Of The Bacillus Caldolyticus
Cold Shock Protein Bc-Csp
pdb|2HAX|A Chain A, Crystal Structure Of Bacillus Caldolyticus Cold Shock
Protein In Complex With Hexathymidine
pdb|2HAX|B Chain B, Crystal Structure Of Bacillus Caldolyticus Cold Shock
Protein In Complex With Hexathymidine
Length = 66
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 70 IEAINV 75
+A NV
Sbjct: 58 PQAANV 63
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
RG VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 RGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 171 IEAINV 176
+A NV
Sbjct: 58 PQAANV 63
>pdb|2LSS|A Chain A, Solution Structure Of The R. Rickettsii Cold Shock-like
Protein
Length = 70
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 11 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 70
G VK+Y+S + FGFI + + +D+FVHKS++ SL G+ V F++ +
Sbjct: 7 GKVKWYNSTKNFGFIEQDNGGKDVFVHKSAV----DAAGLHSLEEGQDVIFDLEEKQGKA 62
Query: 71 EAINV 75
A+N+
Sbjct: 63 YAVNL 67
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 112 GIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKDI 171
G VK+Y+S + FGFI + + +D+FVHKS++ SL G+ V F++ +
Sbjct: 7 GKVKWYNSTKNFGFIEQDNGGKDVFVHKSAV----DAAGLHSLEEGQDVIFDLEEKQGKA 62
Query: 172 EAINV 176
A+N+
Sbjct: 63 YAVNL 67
>pdb|1HZC|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1HZC|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
G VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 EGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQAVSFEIVQGNRG 57
Query: 70 IEAINV 75
+A NV
Sbjct: 58 PQAANV 63
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
G VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 EGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQAVSFEIVQGNRG 57
Query: 171 IEAINV 176
+A NV
Sbjct: 58 PQAANV 63
>pdb|1I5F|A Chain A, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
pdb|1I5F|B Chain B, Bacillus Caldolyticus Cold-Shock Protein Mutants To
Study Determinants Of Protein Stability
Length = 66
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 69
G VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 EGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 70 IEAINV 75
+A NV
Sbjct: 58 PQAANV 63
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD 170
G VK++++++G+GFI ++ D+FVH ++I + F++L G+ V F I G +
Sbjct: 3 EGKVKWFNNEKGYGFI-EVEGGSDVFVHFTAI----QGEGFKTLEEGQEVSFEIVQGNRG 57
Query: 171 IEAINV 176
+A NV
Sbjct: 58 PQAANV 63
>pdb|3AQQ|A Chain A, Crystal Structure Of Human Crhsp-24
pdb|3AQQ|C Chain C, Crystal Structure Of Human Crhsp-24
pdb|3AQQ|B Chain B, Crystal Structure Of Human Crhsp-24
pdb|3AQQ|D Chain D, Crystal Structure Of Human Crhsp-24
Length = 147
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 10 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSI 41
+G+ K + +G GFIT D DIF+H S +
Sbjct: 64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDV 95
Score = 32.0 bits (71), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 111 RGIVKFYDSKRGFGFITRLDNKEDIFVHKSSI 142
+G+ K + +G GFIT D DIF+H S +
Sbjct: 64 KGVCKCFCRSKGHGFITPADGGPDIFLHISDV 95
>pdb|3KM3|A Chain A, Crystal Structure Of Eoxycytidine Triphosphate Deaminase
From Anaplasma Phagocytophilum At 2.1a Resolution
pdb|3KM3|B Chain B, Crystal Structure Of Eoxycytidine Triphosphate Deaminase
From Anaplasma Phagocytophilum At 2.1a Resolution
Length = 206
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 22 FGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 63
+G+ RLDNK IF + S+V ++PK F Q + DF I
Sbjct: 60 YGYDARLDNKFKIFANTHSVV-VDPKNFSQDSFVDREGDFCI 100
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 123 FGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNI 164
+G+ RLDNK IF + S+V ++PK F Q + DF I
Sbjct: 60 YGYDARLDNKFKIFANTHSVV-VDPKNFSQDSFVDREGDFCI 100
>pdb|2YTY|A Chain A, Solution Structure Of The Fourth Cold-Shock Domain Of
The Human Kiaa0885 Protein (Unr Protein)
Length = 88
Score = 26.6 bits (57), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 19 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINV 75
K FGFI ++ ++IF H S SL LG++V++++ GK + E +N
Sbjct: 27 KDNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNKVSAEKVNK 81
Query: 76 T-GPN 79
T GP+
Sbjct: 82 TSGPS 86
Score = 26.6 bits (57), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 120 KRGFGFITRLDNKEDIFVHKSSIVKMNPKKFFQSLGLGEIVDFNIGVGKKD---IEAINV 176
K FGFI ++ ++IF H S SL LG++V++++ GK + E +N
Sbjct: 27 KDNFGFIETANHDKEIFFHYSEFSGD-----VDSLELGDMVEYSLSKGKGNKVSAEKVNK 81
Query: 177 T-GPN 180
T GP+
Sbjct: 82 TSGPS 86
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.141 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,904,015
Number of Sequences: 62578
Number of extensions: 247397
Number of successful extensions: 615
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 561
Number of HSP's gapped (non-prelim): 58
length of query: 191
length of database: 14,973,337
effective HSP length: 93
effective length of query: 98
effective length of database: 9,153,583
effective search space: 897051134
effective search space used: 897051134
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)