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= 048263
(207 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus
Type-2 Nucleocapsid Protein
Length = 49
Score = 28.1 bits (61), Expect = 3.3, Method: Composition-based stats.
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 3/25 (12%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFK 24
+C +CG GH++R C A +GC+K
Sbjct: 8 RCWNCGKEGHSARQCRAPRRQGCWK 32
>pdb|2F98|A Chain A, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F98|B Chain B, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F98|C Chain C, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F98|D Chain D, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F99|A Chain A, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F99|B Chain B, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F99|C Chain C, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity.
pdb|2F99|D Chain D, Crystal Structure Of The Polyketide Cyclase Aknh With
Bound Substrate And Product Analogue: Implications For
Catalytic Mechanism And Product Stereoselectivity
Length = 153
Score = 28.1 bits (61), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 58 GEFNGHVDEGREFDGD-VDEGYLSDGPIHTKHE--------RKRGKPWTEAEHR 102
GE G GR F G+ + + DG IH + R+ G+PW E EHR
Sbjct: 98 GEMVGMAPTGRLFSGEQIHLLHFVDGKIHHHRDWPDYQGTYRQLGEPWPETEHR 151
>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 = 27.3 bits (59), Expect = 5.5, Method: Composition-based stats.
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFK 24
KC +CG GH ++ C A KGC+K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKKGCWK 38
>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 = 27.3 bits (59), Expect = 5.9, Method: Composition-based stats.
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFK 24
KC +CG GH ++ C A KGC+K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKKGCWK 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 = 26.9 bits (58), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFKL 25
KC +CG GH +R C A KGC+K
Sbjct: 4 KCFNCGKEGHTARNCRAPRKKGCWKC 29
>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 = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFKL 25
KC +CG GH +R C A KGC+K
Sbjct: 3 KCFNCGKEGHTARNCRAPRKKGCWKC 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 = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFKL 25
KC +CG GH +R C A KGC+K
Sbjct: 3 KCFNCGKEGHTARNCRAPRKKGCWKC 28
>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 = 9.7, Method: Composition-based stats.
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 3 KCSHCGHNGHNSRTCHA---KGCFK 24
KC +CG GH ++ C A +GC+K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKRGCWK 38
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 0.136 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,858,303
Number of Sequences: 62578
Number of extensions: 204636
Number of successful extensions: 451
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 424
Number of HSP's gapped (non-prelim): 27
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
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: 49 (23.5 bits)