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= 045687
(212 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 33.1 bits (74), Expect = 0.11, Method: Composition-based stats.
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 159 CYVCGKPGHFANKCRYRK 176
CY CGKPGH +++CR K
Sbjct: 3 CYNCGKPGHLSSQCRAPK 20
Score = 29.3 bits (64), Expect = 1.5, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 159 CYVCGKPGHFANKCR 173
C+ C +PGHF+ +CR
Sbjct: 22 CFKCKQPGHFSKQCR 36
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 33.1 bits (74), Expect = 0.12, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 157 GNCYVCGKPGHFANKC-RYRKGDHKPPKANLVDG 189
G CY CG PGH+ +C + RK + + L +G
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNG 38
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 30.4 bits (67), Expect = 0.73, Method: Composition-based stats.
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGKPGH A CR
Sbjct: 3 CFNCGKPGHTARMCR 17
>pdb|2DI2|A Chain A, Nmr Structure Of The Hiv-2 Nucleocapsid Protein
Length = 29
Score = 28.9 bits (63), Expect = 2.3, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A +CR
Sbjct: 9 CWACGKEGHSARQCR 23
>pdb|3O0K|A Chain A, Crystal Structure Of AldoKETO REDUCTASE FROM BRUCELLA
MELITENSIS
pdb|3O0K|B Chain B, Crystal Structure Of AldoKETO REDUCTASE FROM BRUCELLA
MELITENSIS
pdb|3O0K|C Chain C, Crystal Structure Of AldoKETO REDUCTASE FROM BRUCELLA
MELITENSIS
pdb|3O0K|D Chain D, Crystal Structure Of AldoKETO REDUCTASE FROM BRUCELLA
MELITENSIS
Length = 283
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 43 NELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLINDLKNEN 102
+EL + +H A E W+ L + ++ED ++ K V I +H ++ N
Sbjct: 194 DELRLFHGKHDIATEAWSPLGQGKLLEDPTLKSIAEKHAKSVAQIILRWH-----IETGN 248
Query: 103 IILPESF 109
I++P+S
Sbjct: 249 IVIPKSI 255
>pdb|1MFW|A Chain A, Structure Of N-Terminal Doublecortin Domain From Dclk:
Selenomethionine Labeled Protein
Length = 107
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 87 QIHGFHMLINDLK---NENIILPESFMTIDQLEKAKEITSKANIVKNEAH 133
+ F L+ DL ++N+ LP+ TI ++ K+I+S +V+ E++
Sbjct: 33 RFRSFEALLADLTRTLSDNVNLPQGVRTIYTIDGLKKISSXDQLVEGESY 82
>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 = 28.1 bits (61), Expect = 3.2, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 159 CYVCGKPGHFANKC 172
C+ CGKPGH+ C
Sbjct: 10 CFRCGKPGHYIKNC 23
>pdb|2PZI|A Chain A, Crystal Structure Of Protein Kinase Pkng From
Mycobacterium Tuberculosis In Complex With
Tetrahydrobenzothiophene Ax20017
pdb|2PZI|B Chain B, Crystal Structure Of Protein Kinase Pkng From
Mycobacterium Tuberculosis In Complex With
Tetrahydrobenzothiophene Ax20017
Length = 681
Score = 28.1 bits (61), Expect = 3.6, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 86 SQIHGFHMLINDLKNENIILPESFMTIDQLEKAKEITS 123
S +H ++ NDLK ENI+L E + + L I S
Sbjct: 196 SYLHSIGLVYNDLKPENIMLTEEQLKLIDLGAVSRINS 233
>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 = 27.7 bits (60), Expect = 4.8, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A CR
Sbjct: 3 CFNCGKEGHIARNCR 17
>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 = 27.7 bits (60), Expect = 5.0, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A +CR
Sbjct: 9 CWNCGKEGHSARQCR 23
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 27.7 bits (60), Expect = 5.0, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A +CR
Sbjct: 9 CWNCGKEGHSARQCR 23
>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 = 27.3 bits (59), Expect = 7.1, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A CR
Sbjct: 15 CFNCGKEGHIAKNCR 29
>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 = 26.9 bits (58), Expect = 8.6, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A CR
Sbjct: 3 CFNCGKEGHTARNCR 17
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 83
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 159 CYVCGKPGHFANKCRYRKGDHKP 181
CY CG GHF + C+ ++ P
Sbjct: 49 CYNCGGKGHFGDDCKEKRSSRVP 71
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 157 GNCYVCGKPGHFANKC 172
G+C+ CGK GHFA C
Sbjct: 2 GSCFKCGKKGHFAKNC 17
>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 = 26.6 bits (57), Expect = 9.6, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A CR
Sbjct: 15 CFNCGKEGHIAKNCR 29
>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 = 26.6 bits (57), Expect = 9.6, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 159 CYVCGKPGHFANKCR 173
C+ CGK GH A CR
Sbjct: 15 CFNCGKEGHIAKNCR 29
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
0.315 0.132 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,871,257
Number of Sequences: 62578
Number of extensions: 204247
Number of successful extensions: 548
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 518
Number of HSP's gapped (non-prelim): 32
length of query: 212
length of database: 14,973,337
effective HSP length: 95
effective length of query: 117
effective length of database: 9,028,427
effective search space: 1056325959
effective search space used: 1056325959
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)