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= 024873
(261 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 34/118 (28%), Positives = 44/118 (37%), Gaps = 20/118 (16%)
Query: 47 CKNCKRPGHFARECPNVAICHNCG-LPGHIASECTTKALCWNCREPGHMAGNCPNEG--- 102
C NC + GH ++CP++ IC CG H + C C C E GH CP++
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKV 65
Query: 103 ICHTCGKAGHRARDC---------------TAPPLPPGDLRLCNNCYKQGHFAADCTN 145
C C H C P + P C NC +GHF DC
Sbjct: 66 QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE 123
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 41/105 (39%), Gaps = 32/105 (30%)
Query: 149 CNNCRKTGHLARDCPNDPICNLCNVS-GHVARHCPKXXXXXXXXXXXXXXXXXXXXXXXX 207
CNNC + GHL +DCP+ IC+ C + H +RHCPK
Sbjct: 7 CNNCSQRGHLKKDCPH-IICSYCGATDDHYSRHCPK------------------------ 41
Query: 208 XXXXXIVCRNCQQLGHMSRDC--MGPLMVCHNCGGRGHLAYECPS 250
I C C ++GH C + C C + H CPS
Sbjct: 42 ----AIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS 82
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 130 CNNCYKQGHFAADCTNDKACNNCRKTG-HLARDCPNDPICNLCNVSGHVARHCP 182
CNNC ++GH DC + C+ C T H +R CP C+ C+ GH CP
Sbjct: 7 CNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCP 59
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNC-YKQGHFAADCTNDKACNNCRKTGHLARDC 162
C+ C + GH +DC P + +C+ C H++ C C+ C + GH C
Sbjct: 7 CNNCSQRGHLKKDC--PHI------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQC 58
Query: 163 PN---DPICNLCNVSGHVARHCP 182
P+ C LC H CP
Sbjct: 59 PHKWKKVQCTLCKSKKHSKERCP 81
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 65 ICHNCGLPGHIASECTTKALCWNCREPGHMAGNC 98
C+NCG PGH++S+C +C+ C++PGH + C
Sbjct: 2 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 45 NLCKNCKRPGHFARECPNVAICHNCGLPGHIASECTT 81
C NC +PGH + +C +C C PGH + +C +
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 85 CWNCREPGHMAGNCPNEGICHTCGKAGHRARDCTA 119
C+NC +PGH++ C +C C + GH ++ C +
Sbjct: 3 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 128 RLCNNCYKQGHFAADCTNDKACNNCRKTGHLARDC 162
+ C NC K GH ++ C K C C++ GH ++ C
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 7/41 (17%)
Query: 103 ICHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADC 143
C+ CGK GH + C AP ++C C + GHF+ C
Sbjct: 2 TCYNCGKPGHLSSQCRAP-------KVCFKCKQPGHFSKQC 35
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 147 KACNNCRKTGHLARDCPNDPICNLCNVSGHVARHC 181
+ C NC K GHL+ C +C C GH ++ C
Sbjct: 1 QTCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 214 VCRNCQQLGHMSRDCMGPLMVCHNCGGRGHLAYECPS 250
C NC + GH+S C P VC C GH + +C S
Sbjct: 2 TCYNCGKPGHLSSQCRAP-KVCFKCKQPGHFSKQCRS 37
>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 = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH+A NC P + C CGK GH+ +DCT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 52 RPGHFARECPNVAICHNCGLPGHIASECTT--KALCWNCREPGHMAGNCP 99
+ G+F + V C NCG GHIA C K CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH A++C AP C C K+GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCP 163
C NC K+GH A +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTER 52
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + GH++++C P C CG GH +C
Sbjct: 13 VKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTE 51
>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 = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH+A NC P + C CGK GH+ +DCT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 52 RPGHFARECPNVAICHNCGLPGHIASECTT--KALCWNCREPGHMAGNCP 99
+ G+F + V C NCG GHIA C K CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH A++C AP C C K+GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCP 163
C NC K+GH A +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTER 52
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + 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 = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH+A NC P + C CGK GH+ +DCT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 52 RPGHFARECPNVAICHNCGLPGHIASECTT--KALCWNCREPGHMAGNCP 99
+ G+F + V C NCG GHIA C K CW C + GH +C
Sbjct: 2 QKGNFRNQRKTVK-CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH A++C AP C C K+GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKG-----CWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCP 163
C NC K+GH A +C K C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT 50
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTER 52
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + 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 = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH+A NC P + C CGK GH+ +DCT
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCT 50
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH A++C AP R C C K+GH DCT +A
Sbjct: 15 CFNCGKEGHIAKNCRAPR-----KRGCWKCGKEGHQMKDCTERQA 54
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 54 GHFARECPNVAICHNCGLPGHIASECTT--KALCWNCREPGHMAGNCP 99
G+F R + C NCG GHIA C K CW C + GH +C
Sbjct: 4 GNF-RNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCT 50
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH A+ C P C CG GH +CT +
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTER 52
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCP 163
C NC K+GH A +C + C C K GH +DC
Sbjct: 15 CFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCT 50
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
I C NC + GH++++C P C CG GH +C
Sbjct: 13 IKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTE 51
>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 = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH A NC P + C CGK GH+ +DCT
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 40
Score = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH AR+C AP + C C K+GH DCT +A
Sbjct: 5 CFNCGKEGHTARNCRAPR-----KKGCWKCGKEGHQMKDCTERQA 44
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 66 CHNCGLPGHIASECTT--KALCWNCREPGHMAGNCP 99
C NCG GH A C K CW C + GH +C
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 40
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH AR C P C CG GH +CT +
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 42
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + GH +R+C P C CG GH +C
Sbjct: 3 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 41
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCP 163
C NC K+GH A +C K C C K GH +DC
Sbjct: 5 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 40
>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 = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH A NC P + C CGK GH+ +DCT
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTN 145
C CGK GH AR+C AP + C C K+GH DCT
Sbjct: 4 CFNCGKEGHTARNCRAPR-----KKGCWKCGKEGHQMKDCTE 40
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 66 CHNCGLPGHIASECTT--KALCWNCREPGHMAGNCPN 100
C NCG GH A C K CW C + GH +C
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH AR C P C CG GH +CT +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCPN 164
C NC K+GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
Score = 28.1 bits (61), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + 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 = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDCT 118
C+NC + GH A NC P + C CGK GH+ +DCT
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 34.7 bits (78), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH AR+C AP + C C K+GH DCT +A
Sbjct: 4 CFNCGKEGHTARNCRAPR-----KKGCWKCGKEGHQMKDCTERQA 43
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 66 CHNCGLPGHIASECTT--KALCWNCREPGHMAGNCP 99
C NCG GH A C K CW C + GH +C
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASECTTK 82
C NC + GH AR C P C CG GH +CT +
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + GH +R+C P C CG GH +C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCP 163
C NC K+GH A +C K C C K GH +DC
Sbjct: 4 CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 62 NVAICHNCGLPGHIASECTT--KALCWNCREPGHMAGNCPN 100
V C NCG GH A +C + CW C + GH+ CP
Sbjct: 5 KVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCTNDKA 148
C CGK GH AR C AP + C C K GH A C +A
Sbjct: 9 CWNCGKEGHSARQCRAP-----RRQGCWKCGKTGHVMAKCPERQA 48
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGP-LMVCHNCGGRGHLAYECPS 250
I C NC + GH +R C P C CG GH+ +CP
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 30.8 bits (68), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASEC 79
C NC + GH AR+C P C CG GH+ ++C
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 149 CNNCRKTGHLARDC--PNDPICNLCNVSGHVARHCPK 183
C NC K GH AR C P C C +GHV CP+
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 130 CNNCYKQGHFAADCT--NDKACNNCRKTGHLARDCPN 164
C NC K+GH A C + C C KTGH+ CP
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPE 45
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 85 CWNCREPGHMAGNC--PNEGICHTCGKAGHRARDC 117
CWNC + GH A C P C CGK GH C
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKC 43
>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 = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 85 CWNCREPGHMAGN--CPNEGICHTCGKAGHRARDCT 118
C+NC + GH A N P + C CGK GH+ +DCT
Sbjct: 4 CFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCT 39
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/41 (43%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADCT 144
C CGK GH AR+ AP + C C K+GH DCT
Sbjct: 4 CFNCGKEGHTARNHRAPR-----KKGCWKCGKEGHQMKDCT 39
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 65 ICHNCGLPGHIASECTT--KALCWNCREPGHMAGNCPN 100
C NCG PGH A C + CWNC H CP
Sbjct: 2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 213 IVCRNCQQLGHMSRDCMGPLMV-CHNCGGRGHLAYECPS 250
+ C NC + GH +R C P C NCG + H +CP
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 47 CKNCKRPGHFAREC--PNVAICHNCGLPGHIASEC 79
C NC +PGH AR C P C NCG H ++C
Sbjct: 3 CFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQC 37
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 12/54 (22%)
Query: 64 AICHNCGLPGHIASECTTKALCWNCREPGHMAGNCPNEGICHTCGKAGHRARDC 117
+C+ CG PGH ++C K N RE C C GH A+ C
Sbjct: 5 GLCYTCGSPGHYQAQCPKKRKSGNSRE------------RCQLCNGMGHNAKQC 46
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 22/55 (40%), Gaps = 12/55 (21%)
Query: 129 LCNNCYKQGHFAADCTNDKACNNCRKTGHLARDCPNDPICNLCNVSGHVARHCPK 183
LC C GH+ A C + N R+ C LCN GH A+ C K
Sbjct: 6 LCYTCGSPGHYQAQCPKKRKSGNSRER------------CQLCNGMGHNAKQCRK 48
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 9/50 (18%)
Query: 102 GICHTCGKAGHRARDC------TAPPLPPGDLRLCNNCYKQGHFAADCTN 145
G C CGK GH A++C A P PG LC C + H+A +C +
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPG---LCPRCKRGKHWANECKS 48
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADC 143
C+ CG H A++C PP P + C+ C H A C
Sbjct: 27 CYNCGGLDHHAKECKLPPQP----KKCHFCQSISHMVASC 62
>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 = 27.7 bits (60), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADC 143
C+ CG H A++C PP P + C+ C H A C
Sbjct: 98 CYNCGGLDHHAKECKLPPQP----KKCHFCQSINHMVASC 133
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADC 143
C+ CG H A++C PP P + C+ C H A C
Sbjct: 10 CYNCGGLDHHAKECKLPPQP----KKCHFCQSISHMVASC 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 = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 104 CHTCGKAGHRARDCTAPPLPPGDLRLCNNCYKQGHFAADC 143
C+ CG H A++C PP P + C+ C H A C
Sbjct: 100 CYNCGGLDHHAKECKLPPQP----KKCHFCQSINHMVASC 135
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 0.141 0.518
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,948,522
Number of Sequences: 62578
Number of extensions: 254004
Number of successful extensions: 1002
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 632
Number of HSP's gapped (non-prelim): 262
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)