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= 035848
(244 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 7 APTGCFKCGRPGHWSRDC 24
AP CFKC +PGH+S+ C
Sbjct: 18 APKVCFKCKQPGHFSKQC 35
Score = 27.3 bits (59), Expect = 8.3, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 11 CFKCGRPGHWSRDC 24
C+ CG+PGH S C
Sbjct: 3 CYNCGKPGHLSSQC 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 = 30.8 bits (68), Expect = 0.73, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 CFKCGRPGHWSRDC 24
CF+CG+PGH+ ++C
Sbjct: 10 CFRCGKPGHYIKNC 23
>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 = 28.9 bits (63), Expect = 2.8, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 35 GCWKCGKEGHQMKDC 49
>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 = 28.9 bits (63), Expect = 2.8, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 35 GCWKCGKEGHQMKDC 49
>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 = 28.9 bits (63), Expect = 2.9, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 35 GCWKCGKEGHQMKDC 49
>pdb|1NCP|C Chain C, 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 = 18
Score = 28.5 bits (62), Expect = 3.1, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 2 GCWKCGKEGHQMKDC 16
>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 = 28.5 bits (62), Expect = 3.3, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 35 GCWKCGKEGHQMKDC 49
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 28.5 bits (62), Expect = 3.5, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 11 CFKCGRPGHWSRDC 24
CF CG+PGH +R C
Sbjct: 3 CFNCGKPGHTARMC 16
>pdb|2L44|A Chain A, C-Terminal Zinc Knuckle Of The Hivncp7
pdb|2L45|A Chain A, C-Terminal Zinc Knuckle Of The Hivncp7 With Dna
pdb|2L46|A Chain A, C-Terminal Zinc Finger Of The Hivncp7 With Platinated
Dna
Length = 19
Score = 28.5 bits (62), Expect = 3.6, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 2 GCWKCGKEGHQMKDC 16
>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 = 28.5 bits (62), Expect = 3.9, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 24 GCWKCGKEGHQMKDC 38
>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 = 28.5 bits (62), Expect = 4.0, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 25 GCWKCGKEGHQMKDC 39
>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 = 28.5 bits (62), Expect = 4.0, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 24 GCWKCGKEGHQMKDC 38
>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger
1)
Length = 21
Score = 28.1 bits (61), Expect = 4.5, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 11 CFKCGRPGHWSRDC 24
CF CG+ GH RDC
Sbjct: 5 CFSCGKTGHIKRDC 18
>pdb|1Q3Y|A Chain A, Nmr Structure Of The Cys28his Mutant (D Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1.
pdb|1Q3Z|A Chain A, Nmr Structure Of The Cys28his Mutant (e Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1
Length = 42
Score = 27.7 bits (60), Expect = 5.7, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 GCFKCGRPGHWSRDC 24
GC+KCG+ GH +DC
Sbjct: 24 GCWKCGKEGHQMKDC 38
>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 = 27.3 bits (59), Expect = 8.7, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 11 CFKCGRPGHWSRDC 24
CF CG+ GH +R+C
Sbjct: 3 CFNCGKEGHTARNC 16
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 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,628,828
Number of Sequences: 62578
Number of extensions: 194511
Number of successful extensions: 413
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 387
Number of HSP's gapped (non-prelim): 26
length of query: 244
length of database: 14,973,337
effective HSP length: 96
effective length of query: 148
effective length of database: 8,965,849
effective search space: 1326945652
effective search space used: 1326945652
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)