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= 045690
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 35.4 bits (80), Expect = 0.023, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 162 KSKGRDMRQ-VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
K R+ R+ V+CF+C + HI NC KK C C K GH +K+C R N
Sbjct: 3 KGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 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 = 35.4 bits (80), Expect = 0.027, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI NC KK C C K GH +K+C R N
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 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 = 35.4 bits (80), Expect = 0.027, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + HI NC KK C C K GH +K+C R N
Sbjct: 11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN 55
>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 = 33.9 bits (76), Expect = 0.065, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 166 RDMRQV-QCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
R+ R++ +CF+C + HI NC K+ C C K GH +K+C R N
Sbjct: 7 RNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQAN 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 = 33.9 bits (76), Expect = 0.068, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 169 RQVQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
+ V+CF+C + H NC KK C C K GH +K+C R N
Sbjct: 1 KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN 45
>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 = 33.5 bits (75), Expect = 0.10, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 171 VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTRPQN 210
V+CF+C + H NC KK C C K GH +K+C R N
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN 44
>pdb|3KK7|A Chain A, Crystal Structure Of Putative Cell Invasion Protein With
MacPERFORIN Domain (Np_812351.1) From Bacteriodes
Thetaiotaomicron Vpi-5482 At 2.46 A Resolution
pdb|3KK7|B Chain B, Crystal Structure Of Putative Cell Invasion Protein With
MacPERFORIN Domain (Np_812351.1) From Bacteriodes
Thetaiotaomicron Vpi-5482 At 2.46 A Resolution
Length = 541
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 7 SVDQSLVLNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQNYLSGIQ 66
+V LNL P+K + V+N D++ K H E I G L++Q S ++
Sbjct: 123 TVKSGFSLNLGPFKFGRQKTIKETFVHNTDDSEKVVHGELSI-EVVNGXLNLQTAPSALR 181
Query: 67 NLWAKYVDMIYV 78
+ A Y+D ++V
Sbjct: 182 KIAADYLDELFV 193
>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 = 32.0 bits (71), Expect = 0.24, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 171 VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTR 207
V+CF+C + H NC KK C C K GH +K+C R
Sbjct: 2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER 41
>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 = 31.2 bits (69), Expect = 0.46, Method: Composition-based stats.
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 191 CNYCKKPGHIIKECPT 206
C C KPGH IK CPT
Sbjct: 10 CFRCGKPGHYIKNCPT 25
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 30.8 bits (68), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 170 QVQCFSCKEY--RHIIVNCAKKFCNYC 194
++QC C EY + +NCA FC+YC
Sbjct: 53 ELQCIICSEYFIEAVTLNCAHSFCSYC 79
>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|G Chain G, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|H Chain H, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|K Chain K, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|L Chain L, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
Length = 149
Score = 30.8 bits (68), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 170 QVQCFSCKEY--RHIIVNCAKKFCNYC 194
++QC C EY + +NCA FC+YC
Sbjct: 64 ELQCIICSEYFIEAVTLNCAHSFCSYC 90
>pdb|4EWG|A Chain A, Crystal Structure Of A Beta-Ketoacyl Synthase From
Burkholderia Phymatum Stm815
pdb|4EWG|B Chain B, Crystal Structure Of A Beta-Ketoacyl Synthase From
Burkholderia Phymatum Stm815
Length = 412
Score = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 139 ATQTILQQNKMHDNAIAYAAAHGKSKGR-DMRQVQCFSCKEYRHIIVNCAKKFCNYCKKP 197
A Q L+ K+ NAIAY AHG S R D+ + Q + + ++ K +
Sbjct: 284 AMQLALEDAKLDANAIAYVNAHGTSTDRGDVAESQATARTFGERMPISSLKSYV------ 337
Query: 198 GHIIKEC 204
GH + C
Sbjct: 338 GHTLGAC 344
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.4 bits (67), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 170 QVQCFSCKEY--RHIIVNCAKKFCNYC 194
++QC C EY + +NCA FC+YC
Sbjct: 53 ELQCIICSEYFIEAVTLNCAHSFCSYC 79
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 30.4 bits (67), Expect = 0.83, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 191 CNYCKKPGHIIKECPTRPQ 209
C YCK+ GH K+CP +P+
Sbjct: 26 CAYCKEKGHWAKDCPKKPR 44
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 30.0 bits (66), Expect = 0.95, Method: Composition-based stats.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 191 CNYCKKPGHIIKECPTRPQ 209
C YCK+ GH K+CP +P+
Sbjct: 13 CAYCKEKGHWAKDCPKKPR 31
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 29.6 bits (65), Expect = 1.2, Method: Composition-based stats.
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 172 QCFSCKEYRHIIVNCA----KKFCNYCKKPGHIIKECPTRPQNCQASQA 216
+C++C H C K C++C+ H++ CP + Q ++Q
Sbjct: 9 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQG 57
>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 = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 173 CFSCKEYRHIIVNC-AKKFCNYCKKPGHIIKEC 204
C++C + H+ C A K C CK+PGH K+C
Sbjct: 3 CYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQC 35
>pdb|2FJ0|A Chain A, Crystal Structure Of Juvenile Hormone Esterase From
Manduca Sexta, With Otfp Covalently Attached
Length = 551
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 15 NLKPYKTAKDMWEYLKKVYNQDNTAKC 41
N+KP+ +DM ++ +YN + T+ C
Sbjct: 523 NVKPHSEQRDMLDFFDSIYNWNGTSYC 549
>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 = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 162 KSKGRDMRQVQCFSCKEYRHIIVNCA----KKFCNYCKKPGHIIKECPTRPQNCQASQA 216
+ KG D +C++C H C K C++C+ H++ CP + Q +SQ
Sbjct: 93 RPKGGD----RCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQGPSSQG 147
>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 = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 162 KSKGRDMRQVQCFSCKEYRHIIVNCA----KKFCNYCKKPGHIIKECPTRPQNCQASQA 216
+ KG D +C++C H C K C++C+ H++ CP + Q +SQ
Sbjct: 91 RPKGGD----RCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQGPSSQG 145
>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 = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 171 VQCFSCKEYRHIIVN---CAKKFCNYCKKPGHIIKECPTR 207
V+CF+C + H N KK C C K GH +K+C R
Sbjct: 2 VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTER 41
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 171 VQCFSCKEYRHIIVNCA---KKFCNYCKKPGHIIKECPTR 207
++C++C + H C ++ C C K GH++ +CP R
Sbjct: 7 IRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPER 46
>pdb|1DG3|A Chain A, Structure Of Human Guanylate Binding Protein-1 In
Nucleotide Free Form
pdb|1F5N|A Chain A, Human Guanylate Binding Protein-1 In Complex With The Gtp
Analogue, Gmppnp
Length = 592
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 78 VQVPIESLADVQGVHEQSKRDQFLMKLRPEYKAARSNLMNRDLSPSLD 125
VQ+P ESL ++ +H S+R+ + +R +K +L ++L+ L+
Sbjct: 343 VQLPTESLQELLDLHRDSEREAIEVFIRSSFKDV-DHLFQKELAAQLE 389
>pdb|2GW1|A Chain A, Crystal Structure Of The Yeast Tom70
pdb|2GW1|B Chain B, Crystal Structure Of The Yeast Tom70
Length = 514
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 5 MGSVDQSLV----LNLKPYKTAKDMWEYLKKVYNQDNTAKCFHLEYEIARYSQGDLSIQN 60
G +D + L+ +P K KD E L V + + F E A Y + + + +
Sbjct: 130 FGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKE 189
Query: 61 YLSGIQNLWAK 71
++G+ NL+ +
Sbjct: 190 LMNGLSNLYKR 200
>pdb|2K78|A Chain A, Solution Structure Of The Isdc Neat Domain Bound To Zinc
Protoporphyrin
Length = 147
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 37 NTAKCFHLEYEIARYSQGDLSIQN-YLSGIQNLWAKYV---DMIYVQVPIESLADVQGVH 92
N A L YE+ +Y+ D SI N Y N AKY+ +YVQ+ + + G+
Sbjct: 24 NAADSGTLNYEVYKYNTNDTSIANDYF----NKPAKYIKKNGKLYVQITVNHSHWITGMS 79
Query: 93 EQSKRDQFLMK 103
+ ++ + K
Sbjct: 80 IEGHKENIISK 90
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 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,322,053
Number of Sequences: 62578
Number of extensions: 241832
Number of successful extensions: 660
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 626
Number of HSP's gapped (non-prelim): 42
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
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: 49 (23.5 bits)