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= 040653
(228 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%)
Query: 1 CGKSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDN 54
GK CR RW N+L P++K+ + + W+ IA LPGRTDN
Sbjct: 41 LGKQCRERWHNHLNPEVKKSSWTEEEDRIIFEAHKVLGNRWAEIAKLLPGRTDN 94
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 27/53 (50%)
Query: 2 GKSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDN 54
GK CR RW N+L P++K+ + + W+ IA LPGRTDN
Sbjct: 62 GKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDN 114
>pdb|1H88|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H89|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex2
Length = 159
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%)
Query: 1 CGKSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDN 54
GK CR RW N+L P++K+ + + W+ IA LPGRTDN
Sbjct: 92 IGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDN 145
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%)
Query: 1 CGKSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDN 54
GK CR RW N+L P++K+ + + W+ IA LPGRTDN
Sbjct: 38 IGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDN 91
>pdb|1MSE|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition
Helices
pdb|1MSF|C Chain C, Solution Structure Of A Specific Dna Complex Of The Myb
Dna- Binding Domain With Cooperative Recognition
Helices
Length = 105
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%)
Query: 1 CGKSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDN 54
GK CR RW N+L P++K+ + + W+ IA LPGRTDN
Sbjct: 38 IGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDN 91
>pdb|3ZQC|A Chain A, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
pdb|3ZQC|D Chain D, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
pdb|3ZQC|G Chain G, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
pdb|3ZQC|J Chain J, Structure Of The Trichomonas Vaginalis Myb3 Dna-Binding
Domain Bound To A Promoter Sequence Reveals A Unique C-
Terminal Beta-Hairpin Conformation
Length = 131
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 24/52 (46%)
Query: 3 KSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDN 54
K CR RW N+L P + + + WS+IA +PGRTDN
Sbjct: 38 KQCRERWFNHLDPAVVKHAWTPEEDETIFRNYLKLGSKWSVIAKLIPGRTDN 89
>pdb|3OSF|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSF|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-2f-13 Dna
pdb|3OSG|A Chain A, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-1-12 Dna
pdb|3OSG|D Chain D, The Structure Of Protozoan Parasite Trichomonas Vaginalis
Myb2 In Complex With Mre-1-12 Dna
Length = 126
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 2 GKSCRLRWLNYLRPDIKRGNISHXXXXXXXXXXXXXXXXWSLIAGRLPGRTDNENMKSRI 61
+ CR RW NYL P I + W++IA PGRTD ++K+R
Sbjct: 45 ARQCRDRWKNYLAPSISHTPWTAEEDALLVQKIQEYGRQWAIIAKFFPGRTDI-HIKNRW 103
Query: 62 IGAPTLENK 70
+ T+ NK
Sbjct: 104 V---TISNK 109
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
0.317 0.133 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,738,270
Number of Sequences: 62578
Number of extensions: 246090
Number of successful extensions: 487
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 473
Number of HSP's gapped (non-prelim): 11
length of query: 228
length of database: 14,973,337
effective HSP length: 95
effective length of query: 133
effective length of database: 9,028,427
effective search space: 1200780791
effective search space used: 1200780791
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)