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= 007230
(612 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 34.3 bits (77), Expect = 0.23, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 323 CFNCGSYSHSLKECPKPRDKDAVNNARKQHK 353
CFNCG H+ + C +PR + N K+H+
Sbjct: 3 CFNCGKPGHTARMCRQPRQEGCWNCGSKEHR 33
>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 = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H+ + C PR K ++ H+ K
Sbjct: 3 KCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMK 36
>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 = 33.1 bits (74), Expect = 0.41, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H+ + C PR K ++ H+ K
Sbjct: 4 KCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMK 37
>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 = 33.1 bits (74), Expect = 0.42, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H+ + C PR K ++ H+ K
Sbjct: 3 KCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMK 36
>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 = 33.1 bits (74), Expect = 0.49, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H K C PR K ++ H+ K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMK 47
>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 = 32.7 bits (73), Expect = 0.54, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H K C PR K ++ H+ K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMK 47
>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 = 32.7 bits (73), Expect = 0.58, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H K C PR K ++ H+ K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMK 47
>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 = 32.0 bits (71), Expect = 1.00, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 322 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 355
+CFNCG H K C PR + ++ H+ K
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMK 47
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 30.4 bits (67), Expect = 3.0, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 322 RCFNCGSYSHSLKECPKPR 340
RC+NCG HS ++C PR
Sbjct: 8 RCWNCGKEGHSARQCRAPR 26
>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 = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 322 RCFNCGSYSHSLKEC---PKPR 340
RC+NCG H KEC P+P+
Sbjct: 99 RCYNCGGLDHHAKECKLPPQPK 120
>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 = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 322 RCFNCGSYSHSLKEC---PKPR 340
RC+NCG H KEC P+P+
Sbjct: 97 RCYNCGGLDHHAKECKLPPQPK 118
>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 = 30.0 bits (66), Expect = 4.4, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 322 RCFNCGSYSHSLKECPKPR 340
RC+NCG HS ++C PR
Sbjct: 8 RCWNCGKEGHSARQCRAPR 26
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 29.3 bits (64), Expect = 7.4, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 322 RCFNCGSYSHSLKEC---PKPR 340
RC+NCG H KEC P+P+
Sbjct: 26 RCYNCGGLDHHAKECKLPPQPK 47
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
0.313 0.133 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,603,586
Number of Sequences: 62578
Number of extensions: 876725
Number of successful extensions: 1239
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1211
Number of HSP's gapped (non-prelim): 29
length of query: 612
length of database: 14,973,337
effective HSP length: 105
effective length of query: 507
effective length of database: 8,402,647
effective search space: 4260142029
effective search space used: 4260142029
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)