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= psy16623
(93 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus
Nucleocapsid Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 35.8 bits (81), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 44 CYNCFDFGHYQYSCPQK-SSADARGDKVGIVCYKCNNYGHFAREC 87
CY C GHYQ CP+K S ++R C CN GH A++C
Sbjct: 7 CYTCGSPGHYQAQCPKKRKSGNSR-----ERCQLCNGMGHNAKQC 46
>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 = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 89
CYNC GH S+ R KV C+KC GHF+++C +
Sbjct: 3 CYNCGKPGHL--------SSQCRAPKV---CFKCKQPGHFSKQCRS 37
>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 = 28.9 bits (63), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 13/53 (24%)
Query: 37 SSTSTIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
+ T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 8 NQRKTVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDC 49
>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 = 28.9 bits (63), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 13/53 (24%)
Query: 37 SSTSTIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
+ T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 8 NQRKTVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDC 49
>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 = 28.9 bits (63), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 13/53 (24%)
Query: 37 SSTSTIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
+ T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 8 NQRKTVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDC 49
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus
(Mpmv)
Length = 60
Score = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES 91
C+ C GH+ +C + + +A KV +C +C H+A EC +++
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAE-PKVPGLCPRCKRGKHWANECKSKT 50
Score = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 71 GIVCYKCNNYGHFAREC 87
G C+KC GHFA+ C
Sbjct: 1 GGSCFKCGKKGHFAKNC 17
>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 = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 9/51 (17%)
Query: 37 SSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
+ I+C+NC GH +C + RG C+KC GH ++C
Sbjct: 8 NQRKIIKCFNCGKEGHIAKNC---RAPRKRG------CWKCGKEGHQMKDC 49
>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 = 3.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 13/50 (26%)
Query: 40 STIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
++C+NC GH +C P+K C+KC GH ++C
Sbjct: 1 KNVKCFNCGKEGHTARNCRAPRKKG-----------CWKCGKEGHQMKDC 39
>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 = 3.4, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 13/48 (27%)
Query: 42 IQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
++C+NC GH +C P+K C+KC GH ++C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKG-----------CWKCGKEGHQMKDC 38
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 39 TSTIQCYNCFDFGHYQYSCPQK 60
IQC C + GHY+ CP K
Sbjct: 40 PKAIQCSKCDEVGHYRSQCPHK 61
Score = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 40 STIQCYNCFDFGHYQYSCPQ------KSSAD--ARGDKVGIVCYKCNNYGHFARECA 88
+ +C NC GH + CP ++ D +R I C KC+ GH+ +C
Sbjct: 3 AAPKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCP 59
>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 = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 13/48 (27%)
Query: 42 IQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
++C+NC GH +C P+K C+KC GH ++C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKG-----------CWKCGKEGHQMKDC 38
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp,
A Rna Surveillance Complex
Length = 83
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 8 SLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSA 63
S+W Y+L + + VL TI CYNC GH+ C +K S+
Sbjct: 23 SIWRAYIL-----VDDNEKAKPKVLPFH-----TIYCYNCGGKGHFGDDCKEKRSS 68
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus
Type-2 Nucleocapsid Protein
Length = 49
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 13/50 (26%)
Query: 40 STIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFAREC 87
I+C+NC GH C P++ C+KC GH +C
Sbjct: 5 KVIRCWNCGKEGHSARQCRAPRRQG-----------CWKCGKTGHVMAKC 43
>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger
1)
Length = 21
Score = 25.0 bits (53), Expect = 9.9, Method: Composition-based stats.
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 71 GIVCYKCNNYGHFARECATE 90
G VC+ C GH R+C E
Sbjct: 2 GPVCFSCGKTGHIKRDCKEE 21
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
0.323 0.136 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,737,286
Number of Sequences: 62578
Number of extensions: 89654
Number of successful extensions: 242
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 204
Number of HSP's gapped (non-prelim): 46
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)