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= psy12999
(191 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4ABM|A Chain A, Crystal Structure Of Chmp4b Hairpin
pdb|4ABM|B Chain B, Crystal Structure Of Chmp4b Hairpin
pdb|4ABM|C Chain C, Crystal Structure Of Chmp4b Hairpin
pdb|4ABM|D Chain D, Crystal Structure Of Chmp4b Hairpin
Length = 79
Score = 100 bits (250), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 51/63 (80%), Positives = 56/63 (88%)
Query: 1 MLIKKQEFLEKKIGEEINIARTNGTKNKRAAIQALKRKKRYEKQLQQIDGTLSTIEMQRE 60
ML KKQEFLEKKI +E+ A+ +GTKNKRAA+QALKRKKRYEKQL QIDGTLSTIE QRE
Sbjct: 17 MLSKKQEFLEKKIEQELTAAKKHGTKNKRAALQALKRKKRYEKQLAQIDGTLSTIEFQRE 76
Query: 61 ALE 63
ALE
Sbjct: 77 ALE 79
>pdb|3UM3|B Chain B, Crystal Structure Of The Brox Bro1 Domain In Complex With
The C- Terminal Tail Of Chmp4b
Length = 104
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/104 (34%), Positives = 54/104 (51%), Gaps = 5/104 (4%)
Query: 88 HMDVNQVHDMMDDIAEQQDVAKEISEAISNPVAFGHDVXXXXXXXXXXXXXXXXXXXXXX 147
+MD+++V ++M DIA+QQ++A+EIS AIS PV FG +
Sbjct: 2 NMDIDKVDELMQDIADQQELAEEISTAISKPVGFGEEFDEDELMAELEELEQEELDKNLL 61
Query: 148 XXSTPGG-ELPEIPSTAPKDKPKEKASTKERSVEDEIRELEAWA 190
S P LP +PS A KP + K+ +D+++ELE WA
Sbjct: 62 EISGPETVPLPNVPSIALPSKP----AKKKEEEDDDMKELENWA 101
>pdb|2JMG|A Chain A, Solution Structure Of V7r Mutant Of Hiv-1 Myristoylated
Matrix Protein
Length = 131
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREAL----EGANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 48 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 107
Query: 106 DVAK 109
+ +K
Sbjct: 108 NKSK 111
>pdb|2LYA|A Chain A, Structure Of Hiv-1 Myr(-) Matrix Protein In Complex With
1,2- Dioctanoyl-sn-phosphatidylcholine
pdb|2LYB|A Chain A, Structure Of Hiv-1 Myr(-) Matrix Protein In Complex With
1,2- Dioctanoyl-sn-phosphatidyl-l-serine
Length = 137
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREALE----GANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 48 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 107
Query: 106 DVAK 109
+ +K
Sbjct: 108 NKSK 111
>pdb|2H3I|A Chain A, Solution Structure Of The Hiv-1 Myristoylated Matrix
Protein
pdb|2H3Q|A Chain A, Solution Structure Of Hiv-1 Myrma Bound To Di-C4-
Phosphatidylinositol-(4,5)-Bisphosphate
Length = 131
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREAL----EGANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 48 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 107
Query: 106 DVAK 109
+ +K
Sbjct: 108 NKSK 111
>pdb|1UPH|A Chain A, Hiv-1 Myristoylated Matrix
Length = 132
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREALE----GANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 49 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 108
Query: 106 DVAK 109
+ +K
Sbjct: 109 NKSK 112
>pdb|2H3F|A Chain A, Solution Structure Of The Hiv-1 Ma Protein
pdb|2H3V|A Chain A, Structure Of The Hiv-1 Matrix Protein Bound To Di-C8-
Phosphatidylinositol-(4,5)-Bisphosphate
pdb|2H3Z|A Chain A, Structure Of The Hiv-1 Matrix Protein Bound To Di-C4-
Phosphatidylinositol-(4,5)-Bisphosphate
Length = 131
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREALE----GANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 48 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 107
Query: 106 DVAK 109
+ +K
Sbjct: 108 NKSK 111
>pdb|2NV3|A Chain A, Solution Structure Of L8a Mutant Of Hiv-1 Myristoylated
Matrix Protein
Length = 131
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREAL----EGANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 48 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 107
Query: 106 DVAK 109
+ +K
Sbjct: 108 NKSK 111
>pdb|1HIW|A Chain A, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|B Chain B, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|C Chain C, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|Q Chain Q, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|R Chain R, Trimeric Hiv-1 Matrix Protein
pdb|1HIW|S Chain S, Trimeric Hiv-1 Matrix Protein
pdb|2GOL|A Chain A, Xray Structure Of Gag278
Length = 133
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREAL----EGANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 50 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 109
Query: 106 DVAK 109
+ +K
Sbjct: 110 NKSK 113
>pdb|2HMX|A Chain A, Human Immunodeficiency Virus Type 1 Matrix Protein
Length = 133
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREAL----EGANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 50 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 109
Query: 106 DVAK 109
+ +K
Sbjct: 110 NKSK 113
>pdb|3AKJ|A Chain A, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKJ|B Chain B, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKK|A Chain A, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKK|B Chain B, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKK|C Chain C, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKK|D Chain D, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKL|A Chain A, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKL|B Chain B, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKL|C Chain C, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
pdb|3AKL|D Chain D, Crystal Structure Of A Helicobacter Pylori Proinflammatory
Kinase Ctka
Length = 325
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 73 TTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQDVAKEI 111
T K+ DAL + +D+N++H ++D+ ++ KE
Sbjct: 232 TNNKDCLDALLRIYPRIDMNKIHSIIDNTPFMSEIHKEF 270
>pdb|1L6N|A Chain A, Structure Of The N-Terminal 283-Residue Fragment Of The
Hiv- 1 Gag Polyprotein
Length = 289
Score = 27.3 bits (59), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 50 GTLSTIEMQREAL----EGANTNTAVLTTMKNAADALKAAHKHMDVNQVHDMMDDIAEQQ 105
G L T E R+ L T + L ++ N L H+ +DV + +D I E+Q
Sbjct: 49 GLLETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEALDKIEEEQ 108
Query: 106 DVAK 109
+ +K
Sbjct: 109 NKSK 112
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
0.307 0.123 0.326
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,621,498
Number of Sequences: 62578
Number of extensions: 141090
Number of successful extensions: 385
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 371
Number of HSP's gapped (non-prelim): 14
length of query: 191
length of database: 14,973,337
effective HSP length: 93
effective length of query: 98
effective length of database: 9,153,583
effective search space: 897051134
effective search space used: 897051134
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 48 (23.1 bits)