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= 024209
(271 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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 69 VCNNCGLPGHIASECTTQARCWNCREPGHMASNCHN 104
C NCG PGH++S+C C+ C++PGH + C +
Sbjct: 2 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 132 RLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN 168
+ C NC KPGH+++ C K C C++ GH ++ C++
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 89 CWNCREPGHMASNCHNEGICHSCGKTGHRARDCST 123
C+NC +PGH++S C +C C + GH ++ C +
Sbjct: 3 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 49 NLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTT 85
C NC +PGH + +C VC C PGH + +C +
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 151 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC 185
+ C NC K GH++ C+ VC C GH ++QC
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 107 ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 147
C++CGK GH + C ++C C +PGH + C
Sbjct: 2 TCYNCGKPGHLSSQCRA-------PKVCFKCKQPGHFSKQC 35
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 51/123 (41%), Gaps = 9/123 (7%)
Query: 51 CNNCKRPGHFARECPNVAVCNNCG-LPGHIASECTTQARCWNCREPGHMASNCHNEGI-- 107
CNNC + GH ++CP++ +C+ CG H + C +C C E GH S C ++
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKV 65
Query: 108 -CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDC 166
C C H C + + L N KP + C NC GH DC
Sbjct: 66 QCTLCKSKKHSKERCPS-IWRAYILVDDNEKAKPKVLPFHTI---YCYNCGGKGHFGDDC 121
Query: 167 QNE 169
+ +
Sbjct: 122 KEK 124
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 134 CNNCYKPGHIAADCTNDKACKNCRKTG-HIARDCQNEPVCNLCNIAGHVARQCP 186
CNNC + GH+ DC + C C T H +R C C+ C+ GH QCP
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCP 59
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 225 CRSCNQMGHMSRDCVGPLIICRNCGGR-GHMAYECPSG 261
C +C+Q GH+ +DC P IIC CG H + CP
Sbjct: 7 CNNCSQRGHLKKDC--PHIICSYCGATDDHYSRHCPKA 42
Score = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 35/152 (23%), Positives = 50/152 (32%), Gaps = 37/152 (24%)
Query: 88 RCWNCREPGHMASNCHNEGICHSCGKT-GHRARDCSTHVQSGGDLRLCNNCYKPGHIAAD 146
+C NC + GH+ +C IC CG T H +R C +Q C+ C + GH +
Sbjct: 6 KCNNCSQRGHLKKDC-PHIICSYCGATDDHYSRHCPKAIQ-------CSKCDEVGHYRSQ 57
Query: 147 CTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLXXXXXXXXXXXXXXX 206
C H + Q C LC H +CP
Sbjct: 58 CP------------HKWKKVQ----CTLCKSKKHSKERCP------------SIWRAYIL 89
Query: 207 XXXXXXXXXXYVGYHDVICRSCNQMGHMSRDC 238
+ +H + C +C GH DC
Sbjct: 90 VDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121
>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 = 34.3 bits (77), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 31.6 bits (70), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 56 RPGHFARECPNVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 102
+ G+F + V C NCG GHIA C + CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 30.8 bits (68), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECT 84
C NC + GH A+ C P C CG GH +CT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
>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 = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 56 RPGHFARECPNVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 102
+ G+F + V C NCG GHIA C + CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 30.8 bits (68), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECT 84
C NC + GH A+ C P C CG GH +CT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
>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 = 33.9 bits (76), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 56 RPGHFARECPNVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 102
+ G+F + V C NCG GHIA C + CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 30.8 bits (68), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECT 84
C NC + GH A+ C P C CG GH +CT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 88 RCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCT 50
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 67 VAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 102
+ C NCG GHIA C + CW C + GH +C
Sbjct: 12 IIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDC 49
Score = 30.8 bits (68), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRG-----CWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GHIA +C + C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDC 49
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 86
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTER 52
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 133 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGD 189
LC C PGH A C + N R+ C LCN GH A+QC K D
Sbjct: 6 LCYTCGSPGHYQAQCPKKRKSGNSRER------------CQLCNGMGHNAKQCRKRD 50
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 19/42 (45%)
Query: 106 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 147
G+C++CG GH C +SG C C GH A C
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 12/54 (22%)
Query: 68 AVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDC 121
+C CG PGH ++C + + N RE C C GH A+ C
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRE------------RCQLCNGMGHNAKQC 46
>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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH A NC + C CGK GH+ +DC+
Sbjct: 3 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 40
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH AR+C + G C C K GH DCT +A
Sbjct: 5 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 44
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 86
C NC + GH AR C P C CG GH +CT +
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 42
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 222 DVICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 260
+V C +C + GH +R+C P C CG GH +C
Sbjct: 2 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 41
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GH A +C K C C K GH +DC
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 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 = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH A NC + C CGK GH+ +DC+
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 149
C +CGK GH AR+C + G C C K GH DCT
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTE 40
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 86
C NC + GH AR C P C CG GH +CT +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
Score = 27.7 bits (60), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
>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 = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 122
+C+NC + GH A NC + C CGK GH+ +DC+
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH AR+C + G C C K GH DCT +A
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 43
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 86
C NC + GH AR C P C CG GH +CT +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 222 DVICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 260
+V C +C + GH +R+C P C CG GH +C
Sbjct: 1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 134 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 166
C NC K GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 152
C +CGK GH AR C + G C C K GH+ A C +A
Sbjct: 9 CWNCGKEGHSARQCRAPRRQG-----CWKCGKTGHVMAKCPERQA 48
Score = 31.2 bits (69), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 66 NVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 102
V C NCG GH A +C R CW C + GH+ + C
Sbjct: 5 KVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 88 RCWNCREPGHMASNCH--NEGICHSCGKTGHRARDC 121
RCWNC + GH A C C CGKTGH C
Sbjct: 8 RCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASEC 83
C NC + GH AR+C P C CG GH+ ++C
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 223 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 260
+ C +C + GH +R C P C CG GH+ +CP
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 153 CKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQCPK 187
C NC K GH AR C+ C C GHV +CP+
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 106 GICHSCGKTGHRARDCSTHVQSGGDLR---LCNNCYKPGHIAADCTN 149
G C CGK GH A++C H + + + LC C + H A +C +
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKS 48
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 69 VCNNCGLPGHIASECTT--QARCWNCREPGHMASNC 102
C NCG PGH A C Q CWNC H + C
Sbjct: 2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQC 37
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASEC 83
C NC +PGH AR C P C NCG H ++C
Sbjct: 3 CFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQC 37
>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 = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 87 ARCWNCREPGHMASN--CHNEGICHSCGKTGHRARDCS 122
+C+NC + GH A N + C CGK GH+ +DC+
Sbjct: 2 VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCT 39
>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger 1)
Length = 21
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 107 ICHSCGKTGHRARDCS 122
+C SCGKTGH RDC
Sbjct: 4 VCFSCGKTGHIKRDCK 19
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
0.325 0.139 0.503
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,229,151
Number of Sequences: 62578
Number of extensions: 264820
Number of successful extensions: 945
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 615
Number of HSP's gapped (non-prelim): 237
length of query: 271
length of database: 14,973,337
effective HSP length: 97
effective length of query: 174
effective length of database: 8,903,271
effective search space: 1549169154
effective search space used: 1549169154
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: 51 (24.3 bits)