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= 026649
(235 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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 33 VCNNCGLPGHIASECTTQARCWNCREPGHMASNCHN 68
C NCG PGH++S+C C+ C++PGH + C +
Sbjct: 2 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 96 RLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN 132
+ C NC KPGH+++ C K C C++ GH ++ C++
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 53 CWNCREPGHMASNCHNEGICHSCGKTGHRARDCST 87
C+NC +PGH++S C +C C + GH ++ C +
Sbjct: 3 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 13 NLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTT 49
C NC +PGH + +C VC C PGH + +C +
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 115 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC 149
+ C NC K GH++ C+ VC C GH ++QC
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 71 ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 111
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: 15 CNNCKRPGHFARECPNVAVCNNCG-LPGHIASECTTQARCWNCREPGHMASNCHNEGI-- 71
CNNC + GH ++CP++ +C+ CG H + C +C C E GH S C ++
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKV 65
Query: 72 -CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDC 130
C C H C + + L N KP + C NC GH DC
Sbjct: 66 QCTLCKSKKHSKERCPS-IWRAYILVDDNEKAKPKVLPFHTI---YCYNCGGKGHFGDDC 121
Query: 131 QNE 133
+ +
Sbjct: 122 KEK 124
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 98 CNNCYKPGHIAADCTNDKACKNCRKTG-HIARDCQNEPVCNLCNIAGHVARQCP 150
CNNC + GH+ DC + C C T H +R C C+ C+ GH QCP
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCP 59
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 189 CRSCNQMGHMSRDCVGPLIICRNCGGR-GHMAYECPSG 225
C +C+Q GH+ +DC P IIC CG H + CP
Sbjct: 7 CNNCSQRGHLKKDC--PHIICSYCGATDDHYSRHCPKA 42
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 35/152 (23%), Positives = 50/152 (32%), Gaps = 37/152 (24%)
Query: 52 RCWNCREPGHMASNCHNEGICHSCGKT-GHRARDCSTHVQSGGDLRLCNNCYKPGHIAAD 110
+C NC + GH+ +C IC CG T H +R C +Q C+ C + GH +
Sbjct: 6 KCNNCSQRGHLKKDC-PHIICSYCGATDDHYSRHCPKAIQ-------CSKCDEVGHYRSQ 57
Query: 111 CTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLXXXXXXXXXXXXXXX 170
C H + Q C LC H +CP
Sbjct: 58 CP------------HKWKKVQ----CTLCKSKKHSKERCP------------SIWRAYIL 89
Query: 171 XXXXXXXXXXYVGYHDVICRSCNQMGHMSRDC 202
+ +H + C +C GH DC
Sbjct: 90 VDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121
>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 = 0.064, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 86
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 20 RPGHFARECPNVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 66
+ G+F + V C NCG GHIA C + CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 30.8 bits (68), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTER 52
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 187 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 224
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 = 33.9 bits (76), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 86
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 20 RPGHFARECPNVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 66
+ G+F + V C NCG GHIA C + CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 31.2 bits (69), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 9 MSQGNL--------CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
M +GN C NC + GH A+ C P C CG GH +CT +
Sbjct: 1 MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTER 52
>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 = 0.073, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 86
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 20 RPGHFARECPNVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 66
+ G+F + V C NCG GHIA C + CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 30.8 bits (68), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
C NC K GHIA +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTER 52
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 187 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 224
V C +C + GH++++C P C CG GH +C
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTE 51
>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 = 0.11, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 52 RCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCST 87
+C+NC + GH+A NC + C CGK GH+ +DC+
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTE 51
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 31 VAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 66
+ C NCG GHIA C + CW C + GH +C
Sbjct: 12 IIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDC 49
Score = 31.2 bits (69), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH A++C + G C C K GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRG-----CWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
C NC K GHIA +C + C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDC 49
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 9 MSQGNL--------CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
M +GN C NC + GH A+ C P C CG GH +CT +
Sbjct: 1 MQRGNFRNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTER 52
>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 = 0.13, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 97 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGD 153
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 = 2.6, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 19/43 (44%)
Query: 69 EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC 111
G+C++CG GH C +SG C C GH A C
Sbjct: 4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQC 46
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 12/54 (22%)
Query: 32 AVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDC 85
+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 = 0.22, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 86
+C+NC + GH A NC + C CGK GH+ +DC+
Sbjct: 3 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 40
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH AR+C + G C C K GH DCT +A
Sbjct: 5 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 44
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
C NC + GH AR C P C CG GH +CT +
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 42
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 186 DVICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 224
+V C +C + GH +R+C P C CG GH +C
Sbjct: 2 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 41
Score = 27.3 bits (59), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
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 = 0.22, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 86
+C+NC + GH A NC + C CGK GH+ +DC+
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 113
C +CGK GH AR+C + G C C K GH DCT
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTE 40
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
C NC + GH AR C P C CG GH +CT +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
C NC K GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
Score = 26.9 bits (58), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 187 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 224
V C +C + GH +R+C P C CG GH +C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 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 = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH AR+C + G C C K GH DCT +A
Sbjct: 4 CFNCGKEGHTARNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 43
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASNCH--NEGICHSCGKTGHRARDCS 86
+C+NC + GH A NC + C CGK GH+ +DC+
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECTTQ 50
C NC + GH AR C P C CG GH +CT +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 186 DVICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 224
+V C +C + GH +R+C P C CG GH +C
Sbjct: 1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 98 CNNCYKPGHIAADCT--NDKACKNCRKTGHIARDC 130
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 = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKA 116
C +CGK GH AR C + G C C K GH+ A C +A
Sbjct: 9 CWNCGKEGHSARQCRAPRRQG-----CWKCGKTGHVMAKCPERQA 48
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 30 NVAVCNNCGLPGHIASECTTQAR--CWNCREPGHMASNC 66
V C NCG GH A +C R CW C + GH+ + C
Sbjct: 5 KVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 52 RCWNCREPGHMASNCH--NEGICHSCGKTGH 80
RCWNC + GH A C C CGKTGH
Sbjct: 8 RCWNCGKEGHSARQCRAPRRQGCWKCGKTGH 38
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASEC 47
C NC + GH AR+C P C CG GH+ ++C
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 187 VICRSCNQMGHMSRDCVGPLII-CRNCGGRGHMAYECPS 224
+ C +C + GH +R C P C CG GH+ +CP
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 117 CKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQCPK 151
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 = 1.1, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 70 GICHSCGKTGHRARDCSTHVQSGGDLR---LCNNCYKPGHIAADCTN 113
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 = 1.4, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 33 VCNNCGLPGHIASECTT--QARCWNCREPGHMASNC 66
C NCG PGH A C Q CWNC H + C
Sbjct: 2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQC 37
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 15 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASEC 47
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 = 2.7, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 51 ARCWNCREPGHMASN--CHNEGICHSCGKTGHRARDCS 86
+C+NC + GH A N + C CGK GH+ +DC+
Sbjct: 2 VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCT 39
Score = 27.3 bits (59), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 72 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 113
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 = 7.1, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 71 ICHSCGKTGHRARDCSTH 88
+C SCGKTGH RDC
Sbjct: 4 VCFSCGKTGHIKRDCKEE 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
0.325 0.139 0.498
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,983,582
Number of Sequences: 62578
Number of extensions: 255239
Number of successful extensions: 906
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 575
Number of HSP's gapped (non-prelim): 235
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
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: 50 (23.9 bits)