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= psy16574
(152 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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 32/116 (27%), Positives = 45/116 (38%), Gaps = 27/116 (23%)
Query: 59 CYNCSGQGHVAKDCT-----------------VKSSIICYNCNSSGHFARNCPNDSSK-R 100
C NCS +GH+ KDC +I C C+ GH+ CP+ K +
Sbjct: 7 CNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQ 66
Query: 101 CYACHQAGHMAKECPG---------QTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
C C H + CP P+ + ++ CY CG +GH DCK
Sbjct: 67 CTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCK 122
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 30/89 (33%), Gaps = 8/89 (8%)
Query: 5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSG 64
IQC C + GHY+ CP K + C C + H C +
Sbjct: 41 KAIQCSKCDEVGHYRSQCPHKWKK--------VQCTLCKSKKHSKERCPSIWRAYILVDD 92
Query: 65 QGHVAKDCTVKSSIICYNCNSSGHFARNC 93
+I CYNC GHF +C
Sbjct: 93 NEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAG 120
+ I C+NC GH AR C + C+ C + GH+ +CP + AG
Sbjct: 4 RKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQAG 49
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 20/42 (47%)
Query: 57 VTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSS 98
+ C+NC +GH A+ C C+ C +GH CP +
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQA 48
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
I C+ C GH AR+C A C+ C GHV C + +
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQA 48
Score = 25.8 bits (55), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
RC+ C + GH A++C ++P C+ CG GH+ C Q
Sbjct: 8 RCWNCGKEGHSARQC------RAPR-----RQGCWKCGKTGHVMAKCPERQ 47
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
+ ++ C+NC GH A+NC K C+ C + GH K+C + A
Sbjct: 10 RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 55 ESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
++V C+NC +GH+AK+C C+ C GH ++C
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 26 SSADARGDKVGIVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
+ R + + C+ C GH A+ C A C+ C +GH KDCT + +
Sbjct: 2 QKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
+C+ C + GH+AK C ++P C+ CG +GH DC Q
Sbjct: 14 KCFNCGKEGHIAKNC------RAPR-----KKGCWKCGKEGHQMKDCTERQ 53
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 13/59 (22%)
Query: 2 SSTSTIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFARECATESVT 58
+ T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 8 NQRKTVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDCTERQAN 55
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
+ ++ C+NC GH A+NC K C+ C + GH K+C + A
Sbjct: 10 RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 55 ESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
++V C+NC +GH+AK+C C+ C GH ++C
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 26 SSADARGDKVGIVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
+ R + + C+ C GH A+ C A C+ C +GH KDCT + +
Sbjct: 2 QKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
+C+ C + GH+AK C ++P C+ CG +GH DC Q
Sbjct: 14 KCFNCGKEGHIAKNC------RAPR-----KKGCWKCGKEGHQMKDCTERQ 53
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 13/59 (22%)
Query: 2 SSTSTIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFARECATESVT 58
+ T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 8 NQRKTVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDCTERQAN 55
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
+ ++ C+NC GH A+NC K C+ C + GH K+C + A
Sbjct: 10 RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 55 ESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
++V C+NC +GH+AK+C C+ C GH ++C
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDC 49
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 26 SSADARGDKVGIVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
+ R + + C+ C GH A+ C A C+ C +GH KDCT + +
Sbjct: 2 QKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
+C+ C + GH+AK C ++P C+ CG +GH DC Q
Sbjct: 14 KCFNCGKEGHIAKNC------RAPR-----KKGCWKCGKEGHQMKDCTERQ 53
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 13/59 (22%)
Query: 2 SSTSTIQCYNCFDFGHYQYSC--PQKSSADARGDKVGIVCYKCNNYGHFARECATESVT 58
+ T++C+NC GH +C P+K C+KC GH ++C
Sbjct: 8 NQRKTVKCFNCGKEGHIAKNCRAPRKKG-----------CWKCGKEGHQMKDCTERQAN 55
>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 = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 76 SSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
++ C+NC GH ARNC K C+ C + GH K+C + A
Sbjct: 1 KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQA 44
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 55 ESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
++V C+NC +GH A++C C+ C GH ++C
Sbjct: 1 KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 39
Score = 35.4 bits (80), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
+ C+ C GH AR C A C+ C +GH KDCT + +
Sbjct: 3 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQA 44
Score = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
+C+ C + GH A+ C ++P C+ CG +GH DC Q
Sbjct: 4 KCFNCGKEGHTARNC------RAPR-----KKGCWKCGKEGHQMKDCTERQ 43
>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 = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 77 SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
++ C+NC GH ARNC K C+ C + GH K+C + A
Sbjct: 1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQA 43
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
+V C+NC +GH A++C C+ C GH ++C
Sbjct: 1 NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
Score = 35.0 bits (79), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
+ C+ C GH AR C A C+ C +GH KDCT + +
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQA 43
Score = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
+C+ C + GH A+ C ++P C+ CG +GH DC Q
Sbjct: 3 KCFNCGKEGHTARNC------RAPR-----KKGCWKCGKEGHQMKDCTERQ 42
>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 = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 21/37 (56%)
Query: 78 IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKEC 114
+ C+NC GH ARNC K C+ C + GH K+C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 57 VTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
V C+NC +GH A++C C+ C GH ++C
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38
Score = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKS 76
+ C+ C GH AR C A C+ C +GH KDCT +
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ 42
Score = 26.2 bits (56), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 11/51 (21%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
+C+ C + GH A+ C ++P C+ CG +GH DC Q
Sbjct: 3 KCFNCGKEGHTARNC------RAPR-----KKGCWKCGKEGHQMKDCTERQ 42
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 75 KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
+ I C+NC GH A+NC + C+ C + GH K+C + A
Sbjct: 10 RKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQA 54
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 57 VTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
+ C+NC +GH+AK+C C+ C GH ++C
Sbjct: 13 IKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDC 49
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 26 SSADARGDKVGIVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCTVKSS 77
+ R + I C+ C GH A+ C A C+ C +GH KDCT + +
Sbjct: 2 QRGNFRNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQA 54
Score = 29.3 bits (64), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
+C+ C + GH+AK C ++P C+ CG +GH DC
Sbjct: 14 KCFNCGKEGHIAKNC------RAPR-----KRGCWKCGKEGHQMKDC 49
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 9/57 (15%)
Query: 2 SSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVT 58
+ I+C+NC GH +C + RG C+KC GH ++C
Sbjct: 8 NQRKIIKCFNCGKEGHIAKNC---RAPRKRG------CWKCGKEGHQMKDCTERQAN 55
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 75 KSSIICYNCNSSGHFARNCPN-----DSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDM 129
++ +CY C S GH+ CP +S +RC C+ GH AK+C + + P +
Sbjct: 2 RARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRPGKGL 61
Score = 33.5 bits (75), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 9 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 52
CY C GHYQ CP+K + ++ C CN GH A++C
Sbjct: 7 CYTCGSPGHYQAQCPKKRKSGNSRER----CQLCNGMGHNAKQC 46
>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 = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 58 TCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
TCYNC GH++ C ++ +C+ C GHF++ C
Sbjct: 2 TCYNCGKPGHLSSQC--RAPKVCFKCKQPGHFSKQC 35
Score = 33.9 bits (76), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 79 ICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKEC 114
CYNC GH + C + K C+ C Q GH +K+C
Sbjct: 2 TCYNCGKPGHLSSQC--RAPKVCFKCKQPGHFSKQC 35
Score = 29.6 bits (65), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 38 VCYKCNNYGHFARECATESVTCYNCSGQGHVAKDC 72
CY C GH + +C V C+ C GH +K C
Sbjct: 2 TCYNCGKPGHLSSQCRAPKV-CFKCKQPGHFSKQC 35
Score = 29.3 bits (64), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 9 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 54
CYNC GH S+ R KV C+KC GHF+++C +
Sbjct: 3 CYNCGKPGHL--------SSQCRAPKV---CFKCKQPGHFSKQCRS 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 = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 77 SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKEC 114
++ C+NC GH ARN K C+ C + GH K+C
Sbjct: 1 NVKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDC 38
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
+V C+NC +GH A++ C+ C GH ++C
Sbjct: 1 NVKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDC 38
Score = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 37 IVCYKCNNYGHFARE-CATESVTCYNCSGQGHVAKDCTVKS 76
+ C+ C GH AR A C+ C +GH KDCT +
Sbjct: 2 VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ 42
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 34.7 bits (78), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 57 VTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP 94
+TC+NC GH A+ C C+NC S H CP
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38
Score = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 78 IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECP 115
+ C+NC GH AR C + C+ C H +CP
Sbjct: 1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38
>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 = 30.0 bits (66), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 1/64 (1%)
Query: 53 ATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP-NDSSKRCYACHQAGHMA 111
ES+ G + + K CYNC H A+ C K+C+ C HM
Sbjct: 71 GLESIRVTGPGGVFCIGSERRPKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMV 130
Query: 112 KECP 115
CP
Sbjct: 131 ASCP 134
Score = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 31 RGDKVGIVCYKCNNYGHFAREC--ATESVTCYNCSGQGHVAKDCTVKS 76
R K G CY C H A+EC + C+ C H+ C +K+
Sbjct: 90 RRPKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKA 137
>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 = 30.0 bits (66), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 1/64 (1%)
Query: 53 ATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP-NDSSKRCYACHQAGHMA 111
ES+ G + + K CYNC H A+ C K+C+ C HM
Sbjct: 73 GLESIRVTGPGGVFCIGSERRPKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMV 132
Query: 112 KECP 115
CP
Sbjct: 133 ASCP 136
Score = 26.6 bits (57), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 31 RGDKVGIVCYKCNNYGHFAREC--ATESVTCYNCSGQGHVAKDCTVKS 76
R K G CY C H A+EC + C+ C H+ C +K+
Sbjct: 92 RRPKGGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKA 139
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp,
A Rna Surveillance Complex
Length = 83
Score = 29.6 bits (65), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 32/90 (35%), Gaps = 9/90 (10%)
Query: 3 STSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNC 62
S +QC C H + CP A D +N + ++ CYNC
Sbjct: 2 SWKKVQCTLCKSKKHSKERCPSIWRAYILVD---------DNEKAKPKVLPFHTIYCYNC 52
Query: 63 SGQGHVAKDCTVKSSIICYNCNSSGHFARN 92
G+GH DC K S N + S N
Sbjct: 53 GGKGHFGDDCKEKRSSRVPNEDGSAFTGSN 82
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 12/70 (17%)
Query: 78 IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCG 137
+ C C S H CP S R Y AK P+ + ++ CY CG
Sbjct: 6 VQCTLCKSKKHSKERCP--SIWRAYILVDDNEKAK----------PKVLPFHTIYCYNCG 53
Query: 138 HQGHLSYDCK 147
+GH DCK
Sbjct: 54 GKGHFGDDCK 63
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 77 SIICYNCNSSGHFARNCPNDSSKR 100
+I CYNC GHF +C S R
Sbjct: 46 TIYCYNCGGKGHFGDDCKEKRSSR 69
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 29.6 bits (65), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 59 CYNCSGQGHVAKDCTVKSSI-ICYNCNSSGHFARNCP 94
CYNC G H AK+C + C+ C S H +CP
Sbjct: 27 CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 63
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 80 CYNCNSSGHFARNCP-NDSSKRCYACHQAGHMAKECP 115
CYNC H A+ C K+C+ C HM CP
Sbjct: 27 CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 63
Score = 27.3 bits (59), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 23 PQKSSADARGDKVGIVCYKCNNYGHFAREC--ATESVTCYNCSGQGHVAKDCTVKS 76
P+ S R K G CY C H A+EC + C+ C H+ C +K+
Sbjct: 12 PKGKSMQKRRSK-GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKA 66
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 59 CYNCSGQGHVAKDCTVKSSI-ICYNCNSSGHFARNCP 94
CYNC G H AK+C + C+ C S H +CP
Sbjct: 10 CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 46
Score = 25.8 bits (55), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 27 SADARGDKVGIVCYKCNNYGHFAREC--ATESVTCYNCSGQGHVAKDCTVKS 76
S+ + GD+ CY C H A+EC + C+ C H+ C +K+
Sbjct: 2 SSGSSGDR----CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKA 49
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus
(Mpmv)
Length = 60
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 9 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES 56
C+ C GH+ +C + + +A KV +C +C H+A EC +++
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAE-PKVPGLCPRCKRGKHWANECKSKT 50
Score = 26.9 bits (58), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 21/58 (36%), Gaps = 12/58 (20%)
Query: 36 GIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC 93
G C+KC GHFA+ C H + K +C C H+A C
Sbjct: 1 GGSCFKCGKKGHFAKNCHE------------HAHNNAEPKVPGLCPRCKRGKHWANEC 46
Score = 26.9 bits (58), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 80 CYNCNSSGHFARNC----PNDSSKR----CYACHQAGHMAKECPGQT 118
C+ C GHFA+NC N++ + C C + H A EC +T
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKT 50
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike
Domain Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 26.2 bits (56), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 57 VTCYNCSGQGHVAKDC 72
V C+NC +GH+A++C
Sbjct: 1 VKCFNCGKEGHIARNC 16
Score = 25.8 bits (55), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 78 IICYNCNSSGHFARNC 93
+ C+NC GH ARNC
Sbjct: 1 VKCFNCGKEGHIARNC 16
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From
The Human Retinoblastoma-Binding Protein 6
(Retinoblastoma- Binding Q Protein 1, Rbq-1)
Length = 55
Score = 25.8 bits (55), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 76 SSIICYNCNSSGHFARNCPNDSSK 99
S C+ C GH+ +NCP + K
Sbjct: 6 SGYTCFRCGKPGHYIKNCPTNGDK 29
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
0.321 0.132 0.448
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,688,168
Number of Sequences: 62578
Number of extensions: 176965
Number of successful extensions: 591
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 353
Number of HSP's gapped (non-prelim): 191
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)