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= 040998
(117 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 12/19 (63%), Positives = 12/19 (63%)
Query: 87 CFNCGKYGHVSIGCPENGD 105
CF CGK GH CP NGD
Sbjct: 10 CFRCGKPGHYIKNCPTNGD 28
>pdb|2E1X|A Chain A, Nmr Structure Of The Hiv-2 Nucleocapsid Protein
pdb|2IWJ|A Chain A, Solution Structure Of The Zn Complex Of Hiv-2 Ncp(23-49)
Peptide, Encompassing Protein Cchc-Linker, Distal Cchc
Zn- Binding Motif And C-Terminal Tail
Length = 27
Score = 29.3 bits (64), Expect = 0.60, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 87 CFNCGKYGHVSIGCPENGDG 106
C+ CGK GHV CPE G
Sbjct: 8 CWKCGKTGHVMAKCPERQAG 27
>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 = 28.9 bits (63), Expect = 0.77, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH++ C
Sbjct: 1 VKCFNCGKEGHIARNC 16
>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 = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 75 IQKVEY--ESLPINCFNCGKYGHVSIGC 100
IQK + + + CFNCGK GH++ C
Sbjct: 1 IQKGNFRNQRKTVKCFNCGKEGHIAKNC 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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 85 INCFNCGKYGHVSIGC 100
I CFNCGK GH++ C
Sbjct: 13 IKCFNCGKEGHIAKNC 28
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 86 NCFNCGKYGHVSIGCPENGDG 106
C+ CGK GHV CPE G
Sbjct: 29 GCWKCGKTGHVMAKCPERQAG 49
>pdb|1XDF|A Chain A, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2a From Yellow Lupine
pdb|1XDF|B Chain B, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2a From Yellow Lupine
Length = 157
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 75 IQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDENGK 115
I+K+ +E+ + N G G V+I GD +P +E GK
Sbjct: 94 IEKISFETKLVEGANGGSIGKVTIKIETKGDA-QPNEEEGK 133
>pdb|2QIM|A Chain A, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2b From Yellow Lupine In Complex With Cytokinin
pdb|3E85|A Chain A, Crystal Structure Of Pathogenesis-Related Protein
Llpr-10.2b From Yellow Lupine In Complex With
Diphenylurea
Length = 158
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 75 IQKVEYESLPINCFNCGKYGHVSIGCPENGDGEEPQDENGK 115
I+K+ +E+ + N G G V+I GD +P +E GK
Sbjct: 95 IEKISFETKLVEGANGGSIGKVTIKIETKGDA-QPNEEEGK 134
>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 = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH + C
Sbjct: 1 VKCFNCGKEGHTARNC 16
>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 = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH++ C
Sbjct: 13 VKCFNCGKEGHIAKNC 28
>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 = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH++ C
Sbjct: 13 VKCFNCGKEGHIAKNC 28
>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 = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH + C
Sbjct: 3 VKCFNCGKEGHTARNC 18
>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 = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH + C
Sbjct: 2 VKCFNCGKEGHTARNC 17
>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 = 26.2 bits (56), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 85 INCFNCGKYGHVSIGC 100
+ CFNCGK GH + C
Sbjct: 2 VKCFNCGKEGHTARNC 17
>pdb|3H4L|A Chain A, Crystal Structure Of N Terminal Domain Of A Dna Repair
Prote
pdb|3H4L|B Chain B, Crystal Structure Of N Terminal Domain Of A Dna Repair
Prote
Length = 367
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 93 YGHVSIGCPENGDGEEPQD 111
YG SI C +NGDG +P +
Sbjct: 52 YGLESIECSDNGDGIDPSN 70
>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 = 25.8 bits (55), Expect = 6.1, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 87 CFNCGKYGHVSIGC 100
C+NCGK GH+S C
Sbjct: 3 CYNCGKPGHLSSQC 16
>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 = 25.4 bits (54), Expect = 8.3, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 85 INCFNCGKYGHVSIGC 100
I C+NCGK GH + C
Sbjct: 7 IRCWNCGKEGHSARQC 22
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 83
Score = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 69 FLLDGRIQKVEYESLP---INCFNCGKYGHVSIGCPENGDGEEPQDE 112
++L +K + + LP I C+NCG GH C E P ++
Sbjct: 28 YILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSSRVPNED 74
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
0.320 0.139 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,908,209
Number of Sequences: 62578
Number of extensions: 142027
Number of successful extensions: 307
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 272
Number of HSP's gapped (non-prelim): 36
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)