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= 030905
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/66 (53%), Positives = 48/66 (72%), Gaps = 1/66 (1%)
Query: 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTK 66
++G VKWF+ KGFGFI P++GGEDLF H ++I EGF+TL EGQ V F V G G+ +
Sbjct: 2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEGFKTLKEGQRVSFDVTTGPKGK-Q 60
Query: 67 AVDVEA 72
A +++A
Sbjct: 61 AANIQA 66
>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 = 75.1 bits (183), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 33/66 (50%), Positives = 47/66 (71%)
Query: 2 AEVQRSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGE 61
+ + + G VKWF+ KGFGFI PEDG +D+FVH ++I++ GF+TL+EGQ VEF + G
Sbjct: 1 SHMSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA 60
Query: 62 DGRTKA 67
G + A
Sbjct: 61 KGPSAA 66
>pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using
Combined Nmr And Cs-Rosetta Method
Length = 70
Score = 72.0 bits (175), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 46/58 (79%)
Query: 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
+ +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G G
Sbjct: 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61
>pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution
Nmr Structure
Length = 69
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 46/58 (79%)
Query: 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
+ +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60
>pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein
Of Escherichia Coli
Length = 69
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 46/58 (79%)
Query: 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDG 63
+ +G VKWF+A KGFGFI P+DG +D+FVH ++I+++G+++L EGQ V F+++ G G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60
>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 = 66.2 bits (160), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 34/65 (52%), Positives = 47/65 (72%), Gaps = 2/65 (3%)
Query: 7 SSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGR-T 65
G VKWF+A+KG+GFI E G D+FVH T+I ++GFRTL+EG V F V+ G +G+
Sbjct: 2 QKGRVKWFNAEKGYGFIERE-GDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGP 60
Query: 66 KAVDV 70
+AV+V
Sbjct: 61 QAVNV 65
>pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From
The Hyperthermophilic Bacterium Thermotoga Maritima
Length = 66
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 43/59 (72%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF ++KG+GFI ++GG D+FVH ++I+ EGF+TL EGQ VEF + G+ G A
Sbjct: 3 GKVKWFDSKKGYGFITKDEGG-DVFVHWSAIEMEGFKTLKEGQVVEFEIQEGKKGPQAA 60
>pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Variant Bs-Cspb M1rE3KK65I
Length = 67
Score = 63.2 bits (152), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 35/68 (51%), Positives = 46/68 (67%), Gaps = 2/68 (2%)
Query: 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRT 65
R G VKWF+++KGFGFI E G +D+FVH ++I+ EGF+TL EGQ V F + G G
Sbjct: 1 RLKGKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQ 59
Query: 66 KA-VDVEA 72
A V +EA
Sbjct: 60 AANVTIEA 67
>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 = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+ +KG+GFI E GG D+FVH T+I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEIVQGNRGPQAA 61
>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 = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+ +KG+GFI E GG D+FVH T+I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEIVQGNRGPQAA 61
>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 = 62.0 bits (149), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+ +KG+GFI E GG D+FVH T+I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+ +KG+GFI E GG D+FVH T+I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+ +KG+GFI E GG D+FVH T+I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61
>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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+ +KG+GFI E GG D+FVH T+I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEIVQGNRGPQAA 61
>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 = 61.6 bits (148), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEG----FRTLSEGQTVEFSVDVGEDG 63
GTVKWF+ + G+GFI D ED+FVHQT+IK R++ +G+TVEF V GE G
Sbjct: 11 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKG 69
>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 = 60.5 bits (145), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+++KGFGFI E G +D+FVH ++I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEIVEGNRGPQAA 61
>pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Cspb Variant A46k S48r
Length = 67
Score = 60.1 bits (144), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKA 67
G VKWF+++KGFGFI E G +D+FVH ++I+ EGF+TL EGQ V F + G G A
Sbjct: 4 GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQKVRFEIVEGNRGPQAA 61
>pdb|2LSS|A Chain A, Solution Structure Of The R. Rickettsii Cold Shock-like
Protein
Length = 70
Score = 57.8 bits (138), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 44/62 (70%), Gaps = 1/62 (1%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
G VKW+++ K FGFI ++GG+D+FVH++++ + G +L EGQ V F ++ + G+ AV
Sbjct: 7 GKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLE-EKQGKAYAV 65
Query: 69 DV 70
++
Sbjct: 66 NL 67
>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 = 57.0 bits (136), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 40/69 (57%), Gaps = 7/69 (10%)
Query: 2 AEVQRSSGTVKWFSAQKGFGFIA-------PEDGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
+V R SG KWF+ + GFGFI+ P + D+FVHQ+ + EGFR+L EG+ VE
Sbjct: 4 PQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVE 63
Query: 55 FSVDVGEDG 63
F+ G
Sbjct: 64 FTFKKSSKG 72
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/62 (45%), Positives = 40/62 (64%), Gaps = 7/62 (11%)
Query: 2 AEVQRSSGTVKWFSAQKGFGFIA-------PEDGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
++V R +G KWF+ + GFGFI+ P D D+FVHQ+ + EGFR+L EG+ VE
Sbjct: 4 SQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 63
Query: 55 FS 56
F+
Sbjct: 64 FT 65
>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 = 24/62 (38%), Positives = 37/62 (59%), Gaps = 7/62 (11%)
Query: 2 AEVQRSSGTVKWFSAQKGFGFIAPE-------DGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
++ +G KWF+ + GFGF++ D D+FVHQ+ + EGFR+L EG+ VE
Sbjct: 5 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVE 64
Query: 55 FS 56
F+
Sbjct: 65 FT 66
>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 = 2e-07, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 7/62 (11%)
Query: 2 AEVQRSSGTVKWFSAQKGFGFIAPE-------DGGEDLFVHQTSIKSEGFRTLSEGQTVE 54
++ +G KWF+ + GFGF++ D D+FVHQ+ + EGFR+L EG+ VE
Sbjct: 3 PQLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVE 62
Query: 55 FS 56
F+
Sbjct: 63 FT 64
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 19/30 (63%), Positives = 25/30 (83%)
Query: 6 RSSGTVKWFSAQKGFGFIAPEDGGEDLFVH 35
+ +G VKWF+A KGFGFI P+DG +D+FVH
Sbjct: 16 KMTGIVKWFNADKGFGFITPDDGSKDVFVH 45
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 9 GTVKWFSAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAV 68
G K F KG GFI P DGG D+F+H + ++ E + T + ++ + +AV
Sbjct: 65 GVCKCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAV 124
Query: 69 DV 70
+V
Sbjct: 125 EV 126
>pdb|2YTX|A Chain A, Solution Structure Of The Second Cold-Shock Domain Of
The Human Kiaa0885 Protein (Unr Protein)
Length = 97
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 15 SAQKGFGFIAPEDGGEDLFVHQTSIKSEGFRTLSEGQTVEFSVDVGEDGRTKAVDV 70
+ ++ FGFI D +++F H + K + TL G VEF++ +G+ A DV
Sbjct: 25 AMKEAFGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIK-DRNGKEVATDV 78
>pdb|1KT0|A Chain A, Structure Of The Large Fkbp-like Protein, Fkbp51, Involved
In Steroid Receptor Complexes
Length = 457
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 29 GEDLF-----VHQTSIKSEGFRTLSEGQTVEFSVD 58
GEDLF + +T K EG+ +EG TVE ++
Sbjct: 139 GEDLFEDGGIIRRTKRKGEGYSNPNEGATVEIHLE 173
>pdb|3O5D|A Chain A, Crystal Structure Of A Fragment Of Fkbp51 Comprising The
Fk1 And Fk2 Domains
pdb|3O5D|B Chain B, Crystal Structure Of A Fragment Of Fkbp51 Comprising The
Fk1 And Fk2 Domains
Length = 264
Score = 26.6 bits (57), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 29 GEDLF-----VHQTSIKSEGFRTLSEGQTVEFSVD 58
GEDLF + +T K EG+ +EG TVE ++
Sbjct: 143 GEDLFEDGGIIRRTKRKGEGYSNPNEGATVEIHLE 177
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 26.6 bits (57), Expect = 8.0, Method: Composition-based stats.
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 120 CFNCGRTGHIA 130
CFNCG+ GHIA
Sbjct: 15 CFNCGKEGHIA 25
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc
Stoichiometry
Length = 55
Score = 26.2 bits (56), Expect = 9.4, Method: Composition-based stats.
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 120 CFNCGRTGHIA 130
CFNCG+ GHIA
Sbjct: 15 CFNCGKEGHIA 25
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 26.2 bits (56), Expect = 9.5, Method: Composition-based stats.
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 120 CFNCGRTGHIA 130
CFNCG+ GHIA
Sbjct: 15 CFNCGKEGHIA 25
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
0.319 0.135 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,819,439
Number of Sequences: 62578
Number of extensions: 79182
Number of successful extensions: 240
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 190
Number of HSP's gapped (non-prelim): 37
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
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)