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= 013049
(450 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AGH|A Chain A, Structural Features Of Ssdna Binding Protein Mosub1 From
Magnaporthe Oryzae
Length = 158
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 39/55 (70%)
Query: 98 LSNKRTVAIQEFKGRAFVSIREYFRRDGKLVPTAKGIALTSEQWRAFSKSLPAID 152
+S+KR V I +FK F++IREY+ G++ P KGI LT +Q+ AF K++PAI+
Sbjct: 51 ISDKRRVGISQFKKMDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAIN 105
>pdb|1PCF|A Chain A, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|B Chain B, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|C Chain C, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|D Chain D, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|E Chain E, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|F Chain F, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|G Chain G, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|1PCF|H Chain H, Human Transcriptional Coactivator Pc4 C-Terminal Domain
pdb|2C62|A Chain A, Crystal Structure Of The Human Transcription Cofactor Pc4
In Complex With Single-Stranded Dna
pdb|2C62|B Chain B, Crystal Structure Of The Human Transcription Cofactor Pc4
In Complex With Single-Stranded Dna
pdb|2PHE|A Chain A, Model For Vp16 Binding To Pc4
pdb|2PHE|B Chain B, Model For Vp16 Binding To Pc4
Length = 66
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 97 KLSNKRTVAIQEFKGRAFVSIREYFRR-DGKLVPTAKGIALTSEQWRAFSKSLPAIDEAV 155
++ R V++++FKG+ + IREY+ +G++ P KGI+L EQW + + ID+AV
Sbjct: 4 QIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAV 63
Query: 156 VKM 158
K+
Sbjct: 64 RKL 66
>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 = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
KTV C+NC K+GH+AK+C R
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPR 32
>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 = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
KTV C+NC K+GH+AK+C R
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPR 32
>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 = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 13/22 (59%), Positives = 17/22 (77%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
KTV C+NC K+GH+AK+C R
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPR 32
>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 = 1.0, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
K + C+NC K+GH+AK+C R
Sbjct: 11 KIIKCFNCGKEGHIAKNCRAPR 32
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 422 CYNCRKKGHVAKHCH 436
C+ C KKGH AK+CH
Sbjct: 4 CFKCGKKGHFAKNCH 18
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 83
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 407 SKKRRESEMDSKTVVCYNCRKKGHVAKHCHNKRLHQEINDN 447
++K + + T+ CYNC KGH C KR + N++
Sbjct: 34 NEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSSRVPNED 74
>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 = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
K V C+NC K+GH A++C R
Sbjct: 1 KNVKCFNCGKEGHTARNCRAPR 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 = 30.0 bits (66), Expect = 3.1, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 420 VVCYNCRKKGHVAKHC 435
V C+NC K+GH+A++C
Sbjct: 1 VKCFNCGKEGHIARNC 16
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 29.6 bits (65), Expect = 3.7, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
K + C+NC K+GH A+ C R
Sbjct: 5 KVIRCWNCGKEGHSARQCRAPR 26
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 29.3 bits (64), Expect = 5.1, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 420 VVCYNCRKKGHVAKHCHNKRLHQEINDNC 448
+ C+NC K GH A+ C R QE NC
Sbjct: 1 LTCFNCGKPGHTARMCRQPR--QEGCWNC 27
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 28.9 bits (63), Expect = 6.1, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 400 GPRMREMSKKRRESEMDSKTVVCYNCRKKGHVAKHCHNK 438
G + +RR S++D C C++KGH AK C K
Sbjct: 6 GQKQDRQGGERRRSQLDRDQ--CAYCKEKGHWAKDCPKK 42
>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 = 28.9 bits (63), Expect = 6.4, Method: Composition-based stats.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 420 VVCYNCRKKGHVAKHCHNKR 439
V C+NC K+GH A++C R
Sbjct: 2 VKCFNCGKEGHTARNCRAPR 21
>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 = 28.9 bits (63), Expect = 6.5, Method: Composition-based stats.
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 420 VVCYNCRKKGHVAKHCHNKR 439
V C+NC K+GH A++C R
Sbjct: 2 VKCFNCGKEGHTARNCRAPR 21
>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 = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 418 KTVVCYNCRKKGHVAKHCHNKR 439
K + C+NC K+GH A+ C R
Sbjct: 5 KVIRCWNCGKEGHSARQCRAPR 26
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 28.5 bits (62), Expect = 8.5, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 407 SKKRRESEMDSKTVVCYNCRKKGHVAKHCHNK 438
++K + + T+ CYNC KGH C K
Sbjct: 93 NEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124
>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 = 28.5 bits (62), Expect = 8.6, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 420 VVCYNCRKKGHVAKHC 435
V C+NC K+GH A++C
Sbjct: 1 VKCFNCGKEGHTARNC 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
0.318 0.131 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,252,298
Number of Sequences: 62578
Number of extensions: 467637
Number of successful extensions: 1397
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1370
Number of HSP's gapped (non-prelim): 36
length of query: 450
length of database: 14,973,337
effective HSP length: 102
effective length of query: 348
effective length of database: 8,590,381
effective search space: 2989452588
effective search space used: 2989452588
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)