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= 047168
(258 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 69.3 bits (168), Expect = 2e-12, Method: Composition-based stats.
Identities = 31/71 (43%), Positives = 49/71 (69%), Gaps = 1/71 (1%)
Query: 2 AQLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEA 61
+ +++ G V WF+ +KG+GFI P+DG D+FVH +I+++G++TL E Q VEF++ A
Sbjct: 1 SHMSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGA 60
Query: 62 DGKYQALDVTA 72
G A +VTA
Sbjct: 61 KGP-SAANVTA 70
>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 = 69.3 bits (168), Expect = 2e-12, Method: Composition-based stats.
Identities = 34/66 (51%), Positives = 44/66 (66%), Gaps = 1/66 (1%)
Query: 7 STGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQ 66
+TG V WF+ AKG+GFI PD+GG DLF H +I +G++TL E Q V FDV GK Q
Sbjct: 2 ATGIVKWFNDAKGFGFITPDEGGEDLFAHFSAINXEGFKTLKEGQRVSFDVTTGPKGK-Q 60
Query: 67 ALDVTA 72
A ++ A
Sbjct: 61 AANIQA 66
>pdb|2L15|A Chain A, Solution Structure Of Cold Shock Protein Cspa Using
Combined Nmr And Cs-Rosetta Method
Length = 70
Score = 66.6 bits (161), Expect = 1e-11, Method: Composition-based stats.
Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
+ TG V WF+ KG+GFI PDDG D+FVH +I++DGY++L E Q V F ++ A G
Sbjct: 4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61
>pdb|1MJC|A Chain A, Crystal Structure Of Cspa, The Major Cold Shock Protein
Of Escherichia Coli
Length = 69
Score = 66.2 bits (160), Expect = 2e-11, Method: Composition-based stats.
Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
+ TG V WF+ KG+GFI PDDG D+FVH +I++DGY++L E Q V F ++ A G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60
>pdb|3MEF|A Chain A, Major Cold-Shock Protein From Escherichia Coli Solution
Nmr Structure
Length = 69
Score = 66.2 bits (160), Expect = 2e-11, Method: Composition-based stats.
Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADG 63
+ TG V WF+ KG+GFI PDDG D+FVH +I++DGY++L E Q V F ++ A G
Sbjct: 3 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 60
>pdb|1G6P|A Chain A, Solution Nmr Structure Of The Cold Shock Protein From
The Hyperthermophilic Bacterium Thermotoga Maritima
Length = 66
Score = 65.1 bits (157), Expect = 4e-11, Method: Composition-based stats.
Identities = 29/50 (58%), Positives = 38/50 (76%), Gaps = 1/50 (2%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQ 58
GKV WFD KGYGFI D+GG D+FVH +I+ +G++TL E Q VEF++Q
Sbjct: 3 GKVKWFDSKKGYGFITKDEGG-DVFVHWSAIEMEGFKTLKEGQVVEFEIQ 51
>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 = 60.5 bits (145), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 2 AQLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVE 54
+Q+ R TG WF+ G+GFI P D D+FVHQ + +G+R+L E + VE
Sbjct: 4 SQVLRGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVE 63
Query: 55 FDVQLEADGKYQALDVTAPGGAP 77
F + + G +++ VT PGG+P
Sbjct: 64 FTFKKSSKG-LESIRVTGPGGSP 85
>pdb|2LSS|A Chain A, Solution Structure Of The R. Rickettsii Cold Shock-like
Protein
Length = 70
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK 64
T GKV W++ K +GFI D+GG D+FVH+ ++ + G +L E Q V FD++ E GK
Sbjct: 3 TNIVGKVKWYNSTKNFGFIEQDNGGKDVFVHKSAVDAAGLHSLEEGQDVIFDLE-EKQGK 61
Query: 65 YQALDV 70
A+++
Sbjct: 62 AYAVNL 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 = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 8/82 (9%)
Query: 3 QLTRSTGKVTWFDGAKGYGFIR-------PDDGGADLFVHQKSIKSDGYRTLYENQSVEF 55
Q+ R +G WF+ G+GFI P + D+FVHQ + +G+R+L E + VEF
Sbjct: 5 QVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQSKLYMEGFRSLKEGEPVEF 64
Query: 56 DVQLEADGKYQALDVTAPGGAP 77
+ + G +++L VT PGG P
Sbjct: 65 TFKKSSKG-FESLRVTGPGGNP 85
>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 = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 29/63 (46%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
GKV WF+ KGYGFI + GG+D+FVH +I+ +G++TL E Q V F++ ++ + QA
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI-VQGNRGPQAA 61
Query: 69 DVT 71
+VT
Sbjct: 62 NVT 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 = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 25/49 (51%), Positives = 37/49 (75%), Gaps = 1/49 (2%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
GKV WF+ KGYGFI + GG+D+FVH +I+ +G++TL E Q+V F++
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEI 51
>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 = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 31/64 (48%), Positives = 42/64 (65%), Gaps = 2/64 (3%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGK-YQA 67
G+V WF+ KGYGFI +G D+FVH +I + G+RTL E V FDV+ +GK QA
Sbjct: 4 GRVKWFNAEKGYGFIE-REGDTDVFVHYTAINAKGFRTLNEGDIVTFDVEPGRNGKGPQA 62
Query: 68 LDVT 71
++VT
Sbjct: 63 VNVT 66
>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 = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 25/49 (51%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
GKV WF+ KGYGFI + GG+D+FVH +I+ +G++TL E Q V F++
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI 51
>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 = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 25/49 (51%), Positives = 37/49 (75%), Gaps = 1/49 (2%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
GKV WF+ KGYGFI + GG+D+FVH +I+ +G++TL E Q+V F++
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQAVSFEI 51
>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 = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 25/49 (51%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
GKV WF+ KGYGFI + GG+D+FVH +I+ +G++TL E Q V F++
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI 51
>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 = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 5/74 (6%)
Query: 5 TRSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDG----YRTLYENQSVEFDVQLE 60
T+ G V WF+ GYGFI +D D+FVHQ +IK + R++ + ++VEFDV +E
Sbjct: 7 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDV-VE 65
Query: 61 ADGKYQALDVTAPG 74
+ +A +VT PG
Sbjct: 66 GEKGAEAANVTGPG 79
>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 = 57.8 bits (138), Expect = 6e-09, Method: Composition-based stats.
Identities = 25/49 (51%), Positives = 36/49 (73%), Gaps = 1/49 (2%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV 57
GKV WF+ KGYGFI + GG+D+FVH +I+ +G++TL E Q V F++
Sbjct: 4 GKVKWFNNEKGYGFIEVE-GGSDVFVHFTAIQGEGFKTLEEGQEVSFEI 51
>pdb|2I5L|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Variant Bs-Cspb M1rE3KK65I
Length = 67
Score = 56.6 bits (135), Expect = 1e-08, Method: Composition-based stats.
Identities = 29/66 (43%), Positives = 44/66 (66%), Gaps = 2/66 (3%)
Query: 6 RSTGKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKY 65
R GKV WF+ KG+GFI + G D+FVH +I+ +G++TL E Q+V F++ +E +
Sbjct: 1 RLKGKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEI-VEGNRGP 58
Query: 66 QALDVT 71
QA +VT
Sbjct: 59 QAANVT 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 = 55.8 bits (133), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/63 (44%), Positives = 43/63 (68%), Gaps = 2/63 (3%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
GKV WF+ KG+GFI + G D+FVH +I+ +G++TL E Q+V F++ +E + QA
Sbjct: 4 GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQAVSFEI-VEGNRGPQAA 61
Query: 69 DVT 71
+VT
Sbjct: 62 NVT 64
>pdb|2I5M|X Chain X, Crystal Structure Of Bacillus Subtilis Cold Shock
Protein Cspb Variant A46k S48r
Length = 67
Score = 55.5 bits (132), Expect = 3e-08, Method: Composition-based stats.
Identities = 28/63 (44%), Positives = 42/63 (66%), Gaps = 2/63 (3%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQAL 68
GKV WF+ KG+GFI + G D+FVH +I+ +G++TL E Q V F++ +E + QA
Sbjct: 4 GKVKWFNSEKGFGFIEVE-GQDDVFVHFSAIQGEGFKTLEEGQKVRFEI-VEGNRGPQAA 61
Query: 69 DVT 71
+VT
Sbjct: 62 NVT 64
>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 = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 3 QLTRSTGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEF 55
QL G WF+ G+GF+ D D+FVHQ + +G+R+L E ++VEF
Sbjct: 6 QLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEF 65
Query: 56 DVQLEADGKYQALDVTAPGGA 76
+ A G +++ VT PGG
Sbjct: 66 TFKKSAKG-LESIRVTGPGGV 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 = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 3 QLTRSTGKVTWFDGAKGYGFIRPD-------DGGADLFVHQKSIKSDGYRTLYENQSVEF 55
QL G WF+ G+GF+ D D+FVHQ + +G+R+L E ++VEF
Sbjct: 4 QLLHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVHQSKLHMEGFRSLKEGEAVEF 63
Query: 56 DVQLEADGKYQALDVTAPGGA 76
+ A G +++ VT PGG
Sbjct: 64 TFKKSAKG-LESIRVTGPGGV 83
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/33 (57%), Positives = 23/33 (69%)
Query: 3 QLTRSTGKVTWFDGAKGYGFIRPDDGGADLFVH 35
Q + TG V WF+ KG+GFI PDDG D+FVH
Sbjct: 13 QSGKMTGIVKWFNADKGFGFITPDDGSKDVFVH 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 = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 17 AKGYGFIRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDV--QLEADGKYQALDVTAPG 74
+KG+GFI P DGG D+F+H + +G E V + + + K QA++V
Sbjct: 73 SKGHGFITPADGGPDIFLHISDV--EGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITH 130
Query: 75 GAP 77
AP
Sbjct: 131 LAP 133
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 239 SCFNCGKPGHFAREC 253
+CFNCGKPGH AR C
Sbjct: 2 TCFNCGKPGHTARMC 16
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From The
Human Retinoblastoma-Binding Protein 6 (Retinoblastoma-
Binding Q Protein 1, Rbq-1)
Length = 55
Score = 29.6 bits (65), Expect = 1.9, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 239 SCFNCGKPGHFAREC 253
+CF CGKPGH+ + C
Sbjct: 9 TCFRCGKPGHYIKNC 23
>pdb|1QRI|A Chain A, X-Ray Structure Of The Dna-Eco Ri Endonuclease Complexes
With An E144d Mutation At 2.7 A
Length = 261
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 23 IRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71
I PD GG LFV SIK DG ++ E+ V L A+ K+Q D+
Sbjct: 57 IDPDLGGT-LFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDII 104
>pdb|1QPS|A Chain A, The Crystal Structure Of A Post-Reactive Cognate Dna-Eco
Ri Complex At 2.50 A In The Presence Of Mn2+ Ion
Length = 261
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 23 IRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71
I PD GG LFV SIK DG ++ E+ V L A+ K+Q D+
Sbjct: 57 IDPDLGGT-LFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDII 104
>pdb|1QRH|A Chain A, X-Ray Structure Of The Dna-Eco Ri Endonuclease Complexes
With An R145k Mutation At 2.7 A
Length = 261
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 23 IRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71
I PD GG LFV SIK DG ++ E+ V L A+ K+Q D+
Sbjct: 57 IDPDLGGT-LFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDII 104
>pdb|2OXV|A Chain A, Structure Of The A138t Promiscuous Mutant Of The Ecori
Restriction Endonuclease Bound To Its Cognate
Recognition Site
Length = 277
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 23 IRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71
I PD GG LFV SIK DG ++ E+ V L A+ K+Q D+
Sbjct: 73 IDPDLGGT-LFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDII 120
>pdb|1ERI|A Chain A, X-Ray Structure Of The Dna-Eco Ri Endonuclease-Dna
Recognition Complex: The Recognition Network And The
Integration Of Recognition And Cleavage
pdb|1CKQ|A Chain A, Pre-Transition State Eco Ri EndonucleaseCOGNATE DNA
(Tcgcgaattcgcg) Complex
pdb|1CL8|A Chain A, A Pre-Transition State Eco Ri EndonucleaseCOGNATE DNA
(Tcgcgapttcgcg) Complex With Dna Base Analog Purine (P)
pdb|1QC9|A Chain A, The Crystallographic Structure Of Restriction Endonuclease
Eco Ri At 3.3 A In The Absense Of Dna
pdb|1QC9|B Chain B, The Crystallographic Structure Of Restriction Endonuclease
Eco Ri At 3.3 A In The Absense Of Dna
pdb|1QC9|C Chain C, The Crystallographic Structure Of Restriction Endonuclease
Eco Ri At 3.3 A In The Absense Of Dna
Length = 276
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 23 IRPDDGGADLFVHQKSIKSDGYRTLYENQSVEFDVQLEADGKYQALDVT 71
I PD GG LFV SIK DG ++ E+ V L A+ K+Q D+
Sbjct: 72 IDPDLGGT-LFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDII 119
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 239 SCFNCGKPGHFAREC 253
+C+NCGKPGH + +C
Sbjct: 2 TCYNCGKPGHLSSQC 16
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 239 SCFNCGKPGHFARECTKVA 257
SCF CGK GHFA+ C + A
Sbjct: 3 SCFKCGKKGHFAKNCHEHA 21
>pdb|2KCM|A Chain A, Solution Nmr Structure Of The N-Terminal Ob-Domain Of
So_1732 From Shewanella Oneidensis. Northeast
Structural Genomics Consortium Target Sor210a
Length = 74
Score = 28.1 bits (61), Expect = 4.9, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 9 GKVTWFDGAKGYGFIRPDDGGADLFVHQKSI---KSDGYRTLYENQSVEFD 56
GKV + AK YGFI+ DDG + F+H + K +G L + V FD
Sbjct: 3 GKVVSYLAAKKYGFIQGDDGES-YFLHFSELLDKKDEG--KLVKGSMVHFD 50
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus Type-2
Nucleocapsid Protein, 15 Structures
Length = 29
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 240 CFNCGKPGHFAREC 253
C+NCGK GH AR+C
Sbjct: 9 CWNCGKEGHSARQC 22
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 28.1 bits (61), Expect = 5.3, Method: Composition-based stats.
Identities = 11/14 (78%), Positives = 11/14 (78%)
Query: 240 CFNCGKPGHFAREC 253
CFNCGK GH AR C
Sbjct: 3 CFNCGKEGHIARNC 16
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 239 SCFNCGKPGHFAREC 253
CFNCGK GH AR C
Sbjct: 4 KCFNCGKEGHTARNC 18
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55))
Complexed With The Dna (-) Primer Binding Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And Destabilises
The (-)primer Binding Site During Reverse Transcription
Length = 44
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 239 SCFNCGKPGHFAREC 253
CFNCGK GH AR C
Sbjct: 3 KCFNCGKEGHTARNC 17
>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 = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 239 SCFNCGKPGHFAREC 253
CFNCGK GH A+ C
Sbjct: 14 KCFNCGKEGHIAKNC 28
>pdb|1NCP|N Chain N, Structural Characterization Of A 39 Residue Synthetic
Peptide Containing The Two Zinc Binding Domains From The
Hiv-1 P7 Nucleocapsid Protein By Cd And Nmr Spectroscopy
Length = 17
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/14 (78%), Positives = 11/14 (78%)
Query: 240 CFNCGKPGHFAREC 253
CFNCGK GH AR C
Sbjct: 3 CFNCGKEGHTARNC 16
>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 = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 239 SCFNCGKPGHFAREC 253
CFNCGK GH A+ C
Sbjct: 14 KCFNCGKEGHIAKNC 28
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr,
30 Structures
Length = 55
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 239 SCFNCGKPGHFAREC 253
CFNCGK GH A+ C
Sbjct: 14 KCFNCGKEGHIAKNC 28
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 239 SCFNCGKPGHFAREC 253
CFNCGK GH AR C
Sbjct: 3 KCFNCGKEGHTARNC 17
>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 = 27.7 bits (60), Expect = 6.6, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 240 CFNCGKPGHFAREC 253
CFNCGK GH A+ C
Sbjct: 15 CFNCGKEGHIAKNC 28
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 240 CFNCGKPGHFAREC 253
C+NCGK GH AR+C
Sbjct: 9 CWNCGKEGHSARQC 22
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
0.321 0.138 0.455
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,098,583
Number of Sequences: 62578
Number of extensions: 143115
Number of successful extensions: 450
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 51
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 334
Number of HSP's gapped (non-prelim): 101
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)