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= 013677
(438 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 = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 149 CFNCGSYSHSLKECPKPRDKDAVNNARKQHK 179
CFNCG H+ + C +PR + N K+H+
Sbjct: 3 CFNCGKPGHTARMCRQPRQEGCWNCGSKEHR 33
Score = 28.5 bits (62), Expect = 7.6, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 149 CFNCGSYSHSLKECPK 164
C+NCGS H +CPK
Sbjct: 24 CWNCGSKEHRFAQCPK 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 = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+CFNCG H+ + C PR K ++ H+ K
Sbjct: 3 KCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMK 36
>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 = 33.5 bits (75), Expect = 0.27, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+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 = 0.29, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+CFNCG H+ + C PR K ++ H+ K
Sbjct: 4 KCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMK 37
>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 = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+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 = 0.40, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+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 = 0.46, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+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 = 31.6 bits (70), Expect = 0.81, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+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 = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 148 RCFNCGSYSHSLKECPKPR 166
RC+NCG HS ++C PR
Sbjct: 8 RCWNCGKEGHSARQCRAPR 26
>pdb|2W3Z|A Chain A, Structure Of A Streptococcus Mutans Ce4 Esterase
Length = 311
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 51 QQWSEWQAQFGSSSNDPNEGIEFGEQTFFPAIRVGKAKGPAVSFWIDNQTRNQQNKNFIP 110
Q W +WQA+ S+ N PN F + +G G + + ++ +Q+KN I
Sbjct: 5 QHWKKWQAKIFSAKNRPN--------LLFSLLIIGLVLGVVL---VQAKSMQKQHKNHIR 53
Query: 111 S 111
S
Sbjct: 54 S 54
>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 = 28.9 bits (63), Expect = 5.6, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 148 RCFNCGSYSHSLKECPKPR 166
RC+NCG HS ++C PR
Sbjct: 8 RCWNCGKEGHSARQCRAPR 26
>pdb|3EPN|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Imidazole Ribonucleotide
pdb|3EPN|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Imidazole Ribonucleotide
pdb|3EPO|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Hmp-P
pdb|3EPO|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Hmp-P
Length = 612
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 204 DGLRPGAL-----DAETRQLLGLGELDPPPWLHRMRELGYPPGYL 243
DGLRPG+ +A+ +L LGEL W H ++ + PG++
Sbjct: 374 DGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHV 418
>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 = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQ 196
RC+NCG H KEC P +K H + + + P++ Q
Sbjct: 99 RCYNCGGLDHHAKECKLP------PQPKKCHFCQSINHMVASCPLKAQQ 141
>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 = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSKRNQNSASRNPMRYYQ 196
RC+NCG H KEC P +K H + + + P++ Q
Sbjct: 97 RCYNCGGLDHHAKECKLP------PQPKKCHFCQSINHMVASCPLKAQQ 139
>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 = 28.1 bits (61), Expect = 9.0, Method: Composition-based stats.
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 148 RCFNCGSYSHSLKECPKPRDKDAVNNARKQHKSK 181
+CFNCG H+ + PR K ++ H+ K
Sbjct: 3 KCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMK 36
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 28.1 bits (61), Expect = 9.5, Method: Composition-based stats.
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 148 RCFNCGSYSHSLKECPKP 165
RC+NCG H KEC P
Sbjct: 26 RCYNCGGLDHHAKECKLP 43
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 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,691,287
Number of Sequences: 62578
Number of extensions: 600321
Number of successful extensions: 836
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 808
Number of HSP's gapped (non-prelim): 38
length of query: 438
length of database: 14,973,337
effective HSP length: 102
effective length of query: 336
effective length of database: 8,590,381
effective search space: 2886368016
effective search space used: 2886368016
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: 53 (25.0 bits)