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= 030604
(174 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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 35 RLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN 71
+ C NC KPGH+++ C K C C++ GH ++ C++
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 33.1 bits (74), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 54 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC 88
+ C NC K GH++ C+ VC C GH ++QC
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
Score = 27.7 bits (60), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 10 ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 50
C++CGK GH + C ++C C +PGH + C
Sbjct: 2 TCYNCGKPGHLSSQCRA-------PKVCFKCKQPGHFSKQC 35
>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 = 0.083, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 36 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGD 92
LC C PGH A C + N R+ C LCN GH A+QC K D
Sbjct: 6 LCYTCGSPGHYQAQCPKKRKSGNSRER------------CQLCNGMGHNAKQCRKRD 50
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 19/42 (45%)
Query: 9 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 50
G+C++CG GH C +SG C C GH A C
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 37 CNNCYKPGHIAADCTNDKACKNCRKTG-HIARDCQNEPVCNLCNIAGHVARQCP 89
CNNC + GH+ DC + C C T H +R C C+ C+ GH QCP
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCP 59
Score = 30.0 bits (66), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 128 CRSCNQMGHMSRDCVGPLIICRNCGGR-GHMAYECPSG 164
C +C+Q GH+ +DC P IIC CG H + CP
Sbjct: 7 CNNCSQRGHLKKDC--PHIICSYCGATDDHYSRHCPKA 42
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 25/111 (22%), Positives = 38/111 (34%), Gaps = 38/111 (34%)
Query: 56 CKNCRKTGHIARDCQNEPVCNLCNIAG-HVARQCPKGDSLXXXXXXXXXXXXXXXXXXXX 114
C NC + GH+ +DC + +C+ C H +R CPK
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKA----------------------- 42
Query: 115 XXXXXYVGYHDVICRSCNQMGHMSRDCVGPL--IICRNCGGRGHMAYECPS 163
+ C C+++GH C + C C + H CPS
Sbjct: 43 -----------IQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS 82
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 29/135 (21%), Positives = 44/135 (32%), Gaps = 24/135 (17%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNC-YKPGHIAADCTNDKACKNCRKTGHIARDC 69
C++C + GH +DC H+ +C+ C H + C C C + GH C
Sbjct: 7 CNNCSQRGHLKKDC-PHI-------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQC 58
Query: 70 ---QNEPVCNLCNIAGHVARQCPKGDSLXXXXXXXXXXXXXXXXXXXXXXXXXYVGYHDV 126
+ C LC H +CP + +H +
Sbjct: 59 PHKWKKVQCTLCKSKKHSKERCP------------SIWRAYILVDDNEKAKPKVLPFHTI 106
Query: 127 ICRSCNQMGHMSRDC 141
C +C GH DC
Sbjct: 107 YCYNCGGKGHFGDDC 121
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH AR+C + G C C K GH DCT +A
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 43
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 125 DVICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
+V C +C + GH +R+C P C CG GH +C
Sbjct: 1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
>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 = 32.7 bits (73), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH AR+C + G C C K GH DCT +A
Sbjct: 5 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 44
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 125 DVICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
+V C +C + GH +R+C P C CG GH +C
Sbjct: 2 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 41
Score = 27.7 bits (60), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GH A +C K C C K GH +DC
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 39
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus
Type-2 Nucleocapsid Protein
Length = 49
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH AR C + G C C K GH+ A C +A
Sbjct: 9 CWNCGKEGHSARQCRAPRRQG-----CWKCGKTGHVMAKCPERQA 48
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 126 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
+ C +C + GH +R C P C CG GH+ +CP
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 56 CKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQCPK 90
C NC K GH AR C+ C C GHV +CP+
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 26.6 bits (57), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GH A C + C C KTGH+ C
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
>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 = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 52
C +CGK GH AR+C + G C C K GH DCT
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTE 40
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 126 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
V C +C + GH +R+C P C CG GH +C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
>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 = 31.2 bits (69), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRG-----CWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GHIA +C + C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDC 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 = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 26.9 bits (58), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 126 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
V C +C + GH++++C P C CG GH +C
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTE 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 = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 126 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
V C +C + GH++++C P C CG GH +C
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTE 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 = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 55
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 37 CNNCYKPGHIAADC--TNDKACKNCRKTGHIARDC 69
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 126 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
V C +C + GH++++C P C CG GH +C
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTE 51
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus
(Mpmv)
Length = 60
Score = 30.4 bits (67), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 9 GICHSCGKTGHRARDCSTHVQSGGDLR---LCNNCYKPGHIAADC 50
G C CGK GH A++C H + + + LC C + H A +C
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANEC 46
>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 = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 11 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 52
C +CGK GH AR+ + G C C K GH DCT
Sbjct: 4 CFNCGKEGHTARNHRAPRKKG-----CWKCGKEGHQMKDCTE 40
>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger
1)
Length = 21
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 10 ICHSCGKTGHRARDCSTH 27
+C SCGKTGH RDC
Sbjct: 4 VCFSCGKTGHIKRDCKEE 21
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 55 ACKNCRKTGHIARDCQNE 72
C +C KTGHI RDC+ E
Sbjct: 4 VCFSCGKTGHIKRDCKEE 21
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 26.9 bits (58), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 126 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 163
+ C +C + GH +R C P C NCG + H +CP
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 10 ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 50
C +CGK GH AR C Q G C NC H A C
Sbjct: 2 TCFNCGKPGHTARMCRQPRQEG-----CWNCGSKEHRFAQC 37
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
0.326 0.140 0.497
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,971,073
Number of Sequences: 62578
Number of extensions: 169024
Number of successful extensions: 593
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 385
Number of HSP's gapped (non-prelim): 165
length of query: 174
length of database: 14,973,337
effective HSP length: 92
effective length of query: 82
effective length of database: 9,216,161
effective search space: 755725202
effective search space used: 755725202
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)