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= 012460
(463 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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/39 (46%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 424 TCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
TC NCGK HTA C+ +Q + C+ CGS +HR+ C +
Sbjct: 2 TCFNCGKPGHTARMCRQPRQ-EGCWNCGSKEHRFAQCPK 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 = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE HTA C+ ++ K C+ CG H+ K+C +
Sbjct: 4 CFNCGKEGHTARNCRAPRK-KGCWKCGKEGHQMKDCTE 40
>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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE HTA C+ ++ K C+ CG H+ K+C +
Sbjct: 4 CFNCGKEGHTARNCRAPRK-KGCWKCGKEGHQMKDCTE 40
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 17/38 (44%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE HTA C+ ++ K C+ CG H+ K+C +
Sbjct: 5 CFNCGKEGHTARNCRAPRK-KGCWKCGKEGHQMKDCTE 41
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 21/42 (50%)
Query: 419 GWNSETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNC 460
G + + C NCG +H A CK+ Q K C C S H +C
Sbjct: 4 GSSGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASC 45
>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 = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 423 ETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNC 460
+ C NCG +H A CK+ Q K C C S H +C
Sbjct: 98 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASC 135
>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 = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 423 ETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNC 460
+ C NCG +H A CK+ Q K C C S H +C
Sbjct: 96 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASC 133
>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 = 38.5 bits (88), Expect = 0.009, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE H A C+ ++ K C+ CG H+ K+C +
Sbjct: 15 CFNCGKEGHIAKNCRAPRK-KGCWKCGKEGHQMKDCTE 51
>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 = 38.1 bits (87), Expect = 0.011, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE H A C+ ++ K C+ CG H+ K+C +
Sbjct: 15 CFNCGKEGHIAKNCRAPRK-KGCWKCGKEGHQMKDCTE 51
>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 = 38.1 bits (87), Expect = 0.011, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE H A C+ ++ K C+ CG H+ K+C +
Sbjct: 15 CFNCGKEGHIAKNCRAPRK-KGCWKCGKEGHQMKDCTE 51
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 423 ETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNC 460
+ C NCG +H A CK+ Q K C C S H +C
Sbjct: 25 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASC 62
>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 = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE H A C+ ++ + C+ CG H+ K+C +
Sbjct: 15 CFNCGKEGHIAKNCRAPRK-RGCWKCGKEGHQMKDCTE 51
>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 = 35.8 bits (81), Expect = 0.054, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE HTA + ++ K C+ CG H+ K+C +
Sbjct: 4 CFNCGKEGHTARNHRAPRK-KGCWKCGKEGHQMKDCTE 40
>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 = 35.4 bits (80), Expect = 0.076, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 423 ETCSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCK 461
+TC NCGK H ++ C+ K CF C H K C+
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKV---CFKCKQPGHFSKQCR 36
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQ 462
C NCGKE H+A C+ ++ + C+ CG H C +
Sbjct: 9 CWNCGKEGHSARQCRAPRR-QGCWKCGKTGHVMAKCPE 45
>pdb|2O1X|A Chain A, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
Deinococcus Radiodurans
pdb|2O1X|B Chain B, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
Deinococcus Radiodurans
pdb|2O1X|C Chain C, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
Deinococcus Radiodurans
pdb|2O1X|D Chain D, 1-deoxy-d-xylulose 5-phosphate Synthase (dxs) From
Deinococcus Radiodurans
Length = 629
Score = 32.7 bits (73), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 45/109 (41%), Gaps = 23/109 (21%)
Query: 233 KVVE-VSKPESVLTTEMDGSRHLFIDPAKDNEGASMGEPMPMVRVVGGNDGGNSFEVIDL 291
K VE VSKP + + S F DPA N A+MG VR VG DG N E++ L
Sbjct: 216 KAVEAVSKPLADFMSRAKNSTRHFFDPASVNPFAAMG-----VRYVGPVDGHNVQELVWL 270
Query: 292 CLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLY 340
LER V+ G + T G G+ E + +Y
Sbjct: 271 ---------------LERLVDLDGPTILHIVTTKG--KGLSYAEADPIY 302
>pdb|4A1F|A Chain A, Crystal Structure Of C-Terminal Domain Of Helicobacter
Pylori Dnab Helicase
pdb|4A1F|B Chain B, Crystal Structure Of C-Terminal Domain Of Helicobacter
Pylori Dnab Helicase
Length = 338
Score = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 9/66 (13%)
Query: 283 GNSFEVIDLCLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVEMNNLYSL 342
G + ++++ LS+ +DD+ V+ SLE S E + A++ + +T S+ M++L S
Sbjct: 58 GKTSLMMNMVLSALNDDRGVAVFSLEMSAEQL--ALRALSDLT-------SINMHDLESG 108
Query: 343 RLEDDK 348
RL+DD+
Sbjct: 109 RLDDDQ 114
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 29.6 bits (65), Expect = 3.4, Method: Composition-based stats.
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 425 CSNCGKENHTAATCKMQKQNKPCFLCGSFKHRWKNCKQV 463
CS C + H + C + + C LC S KH + C +
Sbjct: 45 CSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPSI 83
>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 = 29.3 bits (64), Expect = 5.4, Method: Composition-based stats.
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 425 CSNCGKENHTAATCK 439
C NCGKE HTA C+
Sbjct: 3 CFNCGKEGHTARNCR 17
>pdb|2OWM|A Chain A, Motor Domain Of Neurospora Crassa Kinesin-3 (Nckin3)
pdb|2OWM|B Chain B, Motor Domain Of Neurospora Crassa Kinesin-3 (Nckin3)
pdb|2OWM|C Chain C, Motor Domain Of Neurospora Crassa Kinesin-3 (Nckin3)
pdb|2OWM|D Chain D, Motor Domain Of Neurospora Crassa Kinesin-3 (Nckin3)
Length = 443
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 5/54 (9%)
Query: 282 GGNSFEVIDLCLSSTDDDKSVSGVSLERSVEDMGKAVQTTATITGANDGVKSVE 335
GGNS + C+S TD D+++S + D K ++T A + DGV + E
Sbjct: 381 GGNSKTAMIACISPTDYDETLSTLRY----ADQAKRIRTRAVVNQV-DGVSAAE 429
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
0.312 0.130 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,603,874
Number of Sequences: 62578
Number of extensions: 372174
Number of successful extensions: 628
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 583
Number of HSP's gapped (non-prelim): 45
length of query: 463
length of database: 14,973,337
effective HSP length: 102
effective length of query: 361
effective length of database: 8,590,381
effective search space: 3101127541
effective search space used: 3101127541
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)