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= psy547
(282 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 = 103 bits (258), Expect = 8e-23, Method: Compositional matrix adjust.
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 = 90.9 bits (224), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 40/72 (55%), Positives = 54/72 (75%)
Query: 196 VLATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
V+ATKV G VKWF+V++GYGFI + EDVFVH IK NNPRK +++ +GETVEFD+
Sbjct: 4 VIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV 63
Query: 256 MQGDKGNQFCFV 267
++G+KG + V
Sbjct: 64 VEGEKGAEAANV 75
>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 = 64.3 bits (155), Expect = 7e-11, Method: Compositional matrix adjust.
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 = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 40/63 (63%), Gaps = 4/63 (6%)
Query: 199 TKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG 258
+K+ G VKWF+ G+GFI ++DVFVH I+ N +KTLAEG+ VEF+I G
Sbjct: 4 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNG 59
Query: 259 DKG 261
KG
Sbjct: 60 AKG 62
>pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using
Combined Nmr And Cs-Rosetta Method
Length = 70
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/72 (43%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
++ K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I
Sbjct: 1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56
Query: 90 QGDKGHEAINVT 101
G KG A NVT
Sbjct: 57 SGAKGPAAGNVT 68
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 256
++ K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I
Sbjct: 1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIE 56
Query: 257 QGDKG 261
G KG
Sbjct: 57 SGAKG 61
>pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein Of
Escherichia Coli
Length = 69
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 31/69 (44%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92
K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 93 KGHEAINVT 101
KG A NVT
Sbjct: 59 KGPAAGNVT 67
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259
K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 260 KG 261
KG
Sbjct: 59 KG 60
>pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution
Nmr Structure
Length = 69
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 31/69 (44%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 92
K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 93 KGHEAINVT 101
KG A NVT
Sbjct: 59 KGPAAGNVT 67
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGD 259
K+ G+VKWF+ G+GFI ++DVFVH I+ + YK+L EG+ V F I G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGA 58
Query: 260 KG 261
KG
Sbjct: 59 KG 60
>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 = 57.8 bits (138), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 13/94 (13%)
Query: 26 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 78
EP +L G+ KWF+V+ G+GF++ + DVFVH ++ +++L
Sbjct: 4 EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 57
Query: 79 AEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
EGE VEF + KG E+I VTGP G GS+
Sbjct: 58 KEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSE 91
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 13/76 (17%)
Query: 193 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 245
EP +L G+ KWF+V+ G+GF++ + DVFVH ++ +++L
Sbjct: 4 EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 57
Query: 246 AEGETVEFDIMQGDKG 261
EGE VEF + KG
Sbjct: 58 KEGEAVEFTFKKSAKG 73
>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 = 57.8 bits (138), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 13/94 (13%)
Query: 26 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 78
EP +L G+ KWF+V+ G+GF++ + DVFVH ++ +++L
Sbjct: 2 EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 55
Query: 79 AEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
EGE VEF + KG E+I VTGP G GS+
Sbjct: 56 KEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSE 89
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 13/76 (17%)
Query: 193 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 245
EP +L G+ KWF+V+ G+GF++ + DVFVH ++ +++L
Sbjct: 2 EPQLLHGA--GICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEG----FRSL 55
Query: 246 AEGETVEFDIMQGDKG 261
EGE VEF + KG
Sbjct: 56 KEGEAVEFTFKKSAKG 71
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/66 (46%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NVT
Sbjct: 59 QAANVT 64
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
Q V K
Sbjct: 59 QAANVTK 65
>pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From The
Hyperthermophilic Bacterium Thermotoga Maritima
Length = 66
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/65 (49%), Positives = 39/65 (60%), Gaps = 5/65 (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 EAINV 100
+A +V
Sbjct: 58 QAAHV 62
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/65 (49%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
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 QFCFV 267
Q V
Sbjct: 58 QAAHV 62
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 13/94 (13%)
Query: 26 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 78
+P VL + G KWF+V+ G+GFI+ S DVFVH ++ +++L
Sbjct: 3 DPQVL--RGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSL 56
Query: 79 AEGETVEFDIMQGDKGHEAINVTGPDGRHVQGSQ 112
EGE VEF + KG E++ VTGP G G++
Sbjct: 57 KEGEPVEFTFKKSSKGFESLRVTGPGGNPCLGNE 90
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 13/76 (17%)
Query: 193 EPVVLATKVCGVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTL 245
+P VL + G KWF+V+ G+GFI+ S DVFVH ++ +++L
Sbjct: 3 DPQVL--RGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEG----FRSL 56
Query: 246 AEGETVEFDIMQGDKG 261
EGE VEF + KG
Sbjct: 57 KEGEPVEFTFKKSSKG 72
>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 = 55.5 bits (132), Expect = 3e-08, Method: Composition-based stats.
Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G+VKWF+ G+GFI ED+F H I +KTL EG+ V FD+ G KG
Sbjct: 4 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 96 EAINV 100
+A N+
Sbjct: 60 QAANI 64
Score = 52.8 bits (125), Expect = 2e-07, Method: Composition-based stats.
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 GIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEG----FKTLKEGQRVSFDVTTGPKGK 59
Query: 263 Q 263
Q
Sbjct: 60 Q 60
>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 = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + G+GFI + DVFVH I+ +KTL EG+ V F+I++G++G
Sbjct: 4 GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 96 EAINVT 101
+A NVT
Sbjct: 59 QAANVT 64
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + G+GFI + DVFVH I+ +KTL EG+ V F+I++G++G
Sbjct: 4 GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 263 QFCFVLK 269
Q V K
Sbjct: 59 QAANVTK 65
>pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock Protein
Cspb Variant A46k S48r
Length = 67
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + G+GFI + DVFVH I+ +KTL EG+ V F+I++G++G
Sbjct: 4 GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQKVRFEIVEGNRGP 58
Query: 96 EAINVT 101
+A NVT
Sbjct: 59 QAANVT 64
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + G+GFI + DVFVH I+ +KTL EG+ V F+I++G++G
Sbjct: 4 GKVKWFNSEKGFGFIEVEGQD-DVFVHFSAIQGEG----FKTLEEGQKVRFEIVEGNRGP 58
Query: 263 QFCFVLK 269
Q V K
Sbjct: 59 QAANVTK 65
>pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock Protein
Variant Bs-Cspb M1rE3KK65I
Length = 67
Score = 55.1 bits (131), Expect = 4e-08, Method: Composition-based stats.
Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + G+GFI +DVFVH I+ +KTL EG+ V F+I++G++G
Sbjct: 4 GKVKWFNSEKGFGFIEV-EGQDDVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 96 EAINVT 101
+A NVT
Sbjct: 59 QAANVT 64
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 5/61 (8%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + G+GFI +DVFVH I+ +KTL EG+ V F+I++G++G
Sbjct: 4 GKVKWFNSEKGFGFIEV-EGQDDVFVHFSAIQGEG----FKTLEEGQAVSFEIVEGNRGP 58
Query: 263 Q 263
Q
Sbjct: 59 Q 59
>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 = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NV
Sbjct: 59 QAANVV 64
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
Q V+K
Sbjct: 59 QAANVVK 65
>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 = 55.1 bits (131), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NV
Sbjct: 59 QAANVV 64
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQAVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
Q V+K
Sbjct: 59 QAANVVK 65
>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 = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/84 (38%), Positives = 45/84 (53%), Gaps = 11/84 (13%)
Query: 36 GVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 88
G KWF+V+ G+GFI+ + DVFVH ++ +++L EGE VEF
Sbjct: 11 GHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKEGEPVEFTF 66
Query: 89 MQGDKGHEAINVTGPDGRHVQGSQ 112
+ KG E+I VTGP G GS+
Sbjct: 67 KKSSKGLESIRVTGPGGSPCLGSE 90
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 11/66 (16%)
Query: 203 GVVKWFSVKSGYGFIATPSSNE-------DVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
G KWF+V+ G+GFI+ + DVFVH ++ +++L EGE VEF
Sbjct: 11 GHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEG----FRSLKEGEPVEFTF 66
Query: 256 MQGDKG 261
+ KG
Sbjct: 67 KKSSKG 72
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NV
Sbjct: 59 QAANVV 64
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
Q V+K
Sbjct: 59 QAANVVK 65
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NV
Sbjct: 59 QAANVV 64
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
Q V+K
Sbjct: 59 QAANVVK 65
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/66 (45%), Positives = 41/66 (62%), Gaps = 5/66 (7%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGH 95
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 96 EAINVT 101
+A NV
Sbjct: 59 QAANVV 64
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKGN 262
G VKWF+ + GYGFI + DVFVH I+ +KTL EG+ V F+I+QG++G
Sbjct: 4 GKVKWFNNEKGYGFIEVEGGS-DVFVHFTAIQGEG----FKTLEEGQEVSFEIVQGNRGP 58
Query: 263 QFCFVLK 269
Q V+K
Sbjct: 59 QAANVVK 65
>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 = 51.6 bits (122), Expect = 5e-07, Method: Composition-based stats.
Identities = 31/68 (45%), Positives = 40/68 (58%), Gaps = 7/68 (10%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQG--DK 93
G VKWF+ + GYGFI + DVFVH I K ++TL EG+ V FD+ G K
Sbjct: 4 GRVKWFNAEKGYGFIER-EGDTDVFVHYTAIN----AKGFRTLNEGDIVTFDVEPGRNGK 58
Query: 94 GHEAINVT 101
G +A+NVT
Sbjct: 59 GPQAVNVT 66
Score = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/59 (44%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIMQGDKG 261
G VKWF+ + GYGFI + DVFVH I K ++TL EG+ V FD+ G G
Sbjct: 4 GRVKWFNAEKGYGFIER-EGDTDVFVHYTAIN----AKGFRTLNEGDIVTFDVEPGRNG 57
>pdb|2LSS|A Chain A, Solution Structure Of The R. Rickettsii Cold Shock-like
Protein
Length = 70
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 30 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDIM 89
+AT + G VKW++ +GFI + +DVFVH + +L EG+ V FD+
Sbjct: 1 MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDLE 56
Query: 90 QGDKGHEAINV 100
+ A+N+
Sbjct: 57 EKQGKAYAVNL 67
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 197 LATKVCGVVKWFSVKSGYGFIATPSSNEDVFVHSKRIKYNNPRKLYKTLAEGETVEFDI 255
+AT + G VKW++ +GFI + +DVFVH + +L EG+ V FD+
Sbjct: 1 MATNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAG----LHSLEEGQDVIFDL 55
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 33 KVCGVVKWFSVKSGYGFIATPSSNEDVFVH 62
K+ G+VKWF+ G+GFI ++DVFVH
Sbjct: 16 KMTGIVKWFNADKGFGFITPDDGSKDVFVH 45
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 200 KVCGVVKWFSVKSGYGFIATPSSNEDVFVH 229
K+ G+VKWF+ G+GFI ++DVFVH
Sbjct: 16 KMTGIVKWFNADKGFGFITPDDGSKDVFVH 45
>pdb|2Q3A|A Chain A, Crystal Structure Of Rhesus Macaque Cd8 Alpha-Alpha
Homodimer
pdb|2Q3A|B Chain B, Crystal Structure Of Rhesus Macaque Cd8 Alpha-Alpha
Homodimer
Length = 120
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 254 DIMQGDKGNQFCFVLKNIVLYFS-FVP 279
D Q ++G FC L N ++YFS FVP
Sbjct: 83 DFRQENEGYYFCSALSNSIMYFSHFVP 109
>pdb|1G8S|A Chain A, Methanococcus Jannaschii Fibrillarin Pre-Rrna Processing
Protein
Length = 230
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 39 KWFSVKSGYGFIATPSSNEDVFVHSKRI 66
KWF K GYG IA + + DV K I
Sbjct: 165 KWFLKKGGYGMIAIKARSIDVTKDPKEI 192
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 206 KWFSVKSGYGFIATPSSNEDVFVHSKRI 233
KWF K GYG IA + + DV K I
Sbjct: 165 KWFLKKGGYGMIAIKARSIDVTKDPKEI 192
>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 = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 36 GVVKWFSVKSGYGFIATPSSNEDVFVH 62
GV K F G+GFI D+F+H
Sbjct: 65 GVCKCFCRSKGHGFITPADGGPDIFLH 91
Score = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 203 GVVKWFSVKSGYGFIATPSSNEDVFVH 229
GV K F G+GFI D+F+H
Sbjct: 65 GVCKCFCRSKGHGFITPADGGPDIFLH 91
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
0.317 0.133 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,972,508
Number of Sequences: 62578
Number of extensions: 303988
Number of successful extensions: 778
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 685
Number of HSP's gapped (non-prelim): 58
length of query: 282
length of database: 14,973,337
effective HSP length: 98
effective length of query: 184
effective length of database: 8,840,693
effective search space: 1626687512
effective search space used: 1626687512
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)