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= 016021
(396 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 = 108 bits (270), Expect = 5e-24, Method: Composition-based stats.
Identities = 50/106 (47%), Positives = 74/106 (69%), Gaps = 3/106 (2%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPDLKRGMF 70
L KG W+ EED+K+ + ++G W+ + K L G R GK CR RW N+L P++K+ +
Sbjct: 5 LVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKG--RLGKQCRERWHNHLNPEVKKSSW 62
Query: 71 SQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
+++E+ +I H+VLGNRWA+IA LPGRTDN +KN WNS +K+K+
Sbjct: 63 TEEEDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVKNHWNSTIKRKV 108
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 63 PDLKRGMFSQQEEDLIISLHEVLGNR-WAQIASQLPGRTDNEIKNFWNSCLKKKLMK 118
PDL +G ++++E+ +I L + G + W IA L GR + + W++ L ++ K
Sbjct: 3 PDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKGRLGKQCRERWHNHLNPEVKK 59
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 104 bits (259), Expect = 1e-22, Method: Composition-based stats.
Identities = 48/107 (44%), Positives = 75/107 (70%), Gaps = 3/107 (2%)
Query: 11 KLRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPDLKRGM 69
+L KG W+ EED+++ ++ ++G WS + K L G R GK CR RW N+L P++K+
Sbjct: 24 ELNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKG--RIGKQCRERWHNHLNPEVKKTS 81
Query: 70 FSQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
++++E+ +I H+ LGNRWA+IA LPGRTDN +KN WNS +++K+
Sbjct: 82 WTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHWNSTMRRKV 128
>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 = 104 bits (259), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 49/106 (46%), Positives = 73/106 (68%), Gaps = 3/106 (2%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPDLKRGMF 70
L KG W+ EED+++ + ++G WS + K L G R GK CR RW N+L P++K+ +
Sbjct: 56 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPEVKKTSW 113
Query: 71 SQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
+++E+ +I H+ LGNRWA+IA LPGRTDN IKN WNS +++K+
Sbjct: 114 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 159
Score = 28.9 bits (63), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 65 LKRGMFSQQEEDLIISLHEVLG-NRWAQIASQLPGRTDNEIKNFWNSCLKKKLMK 118
L + ++++E++ + L E G + W IA+ LP RTD + ++ W L +L+K
Sbjct: 4 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIK 58
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 103 bits (258), Expect = 1e-22, Method: Composition-based stats.
Identities = 49/107 (45%), Positives = 74/107 (69%), Gaps = 3/107 (2%)
Query: 11 KLRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPDLKRGM 69
+L KG W+ EED+++ + ++G WS + K L G R GK CR RW N+L P++K+
Sbjct: 1 ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPEVKKTS 58
Query: 70 FSQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
++++E+ +I H+ LGNRWA+IA LPGRTDN IKN WNS +++K+
Sbjct: 59 WTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 64 DLKRGMFSQQEEDLIISLHEVLG-NRWAQIASQLPGRTDNEIKNFWNSCLKKKLMK 118
+L +G ++++E+ +I L + G RW+ IA L GR + + W++ L ++ K
Sbjct: 1 ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKK 56
>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 = 103 bits (258), Expect = 1e-22, Method: Composition-based stats.
Identities = 49/106 (46%), Positives = 73/106 (68%), Gaps = 3/106 (2%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPDLKRGMF 70
L KG W+ EED+++ + ++G WS + K L G R GK CR RW N+L P++K+ +
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPEVKKTSW 59
Query: 71 SQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
+++E+ +I H+ LGNRWA+IA LPGRTDN IKN WNS +++K+
Sbjct: 60 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 65 LKRGMFSQQEEDLIISLHEVLG-NRWAQIASQLPGRTDNEIKNFWNSCLKKKLMK 118
L +G ++++E+ +I L + G RW+ IA L GR + + W++ L ++ K
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKK 56
>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 = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 37/105 (35%), Positives = 60/105 (57%), Gaps = 5/105 (4%)
Query: 14 KGLWSPEEDEKLYNYITRFGVGCWSSVPKLAGL--QRCGKSCRLRWINYLRPDLKRGMFS 71
KG ++ ED+ + Y+ G W P++ R K CR RW N+L P + + ++
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNW---PRITSFLPNRSPKQCRERWFNHLDPAVVKHAWT 58
Query: 72 QQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
+E++ I + LG++W+ IA +PGRTDN IKN WNS + K++
Sbjct: 59 PEEDETIFRNYLKLGSKWSVIAKLIPGRTDNAIKNRWNSSISKRI 103
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 67 RGMFSQQEEDLIIS-LHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKLMKQGIDP 123
+G F++ E+DLI + E W +I S LP R+ + + W + L ++K P
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNWPRITSFLPNRSPKQCRERWFNHLDPAVVKHAWTP 59
>pdb|1MBJ|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 3
pdb|1MBK|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 3
Length = 53
Score = 62.8 bits (151), Expect = 3e-10, Method: Composition-based stats.
Identities = 26/52 (50%), Positives = 40/52 (76%)
Query: 65 LKRGMFSQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
+K+ ++++E+ +I H+ LGNRWA+IA LPGRTDN IKN WNS +++K+
Sbjct: 1 VKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 52
>pdb|1IDY|A Chain A, Structure Of Myb Transforming Protein, Nmr, Minimized
Average Structure
pdb|1IDZ|A Chain A, Structure Of Myb Transforming Protein, Nmr, 20 Structures
Length = 54
Score = 62.4 bits (150), Expect = 4e-10, Method: Composition-based stats.
Identities = 25/53 (47%), Positives = 41/53 (77%)
Query: 64 DLKRGMFSQQEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFWNSCLKKKL 116
++K+ ++++E+ ++ H+ LGNRWA+IA LPGRTDN IKN WNS +++K+
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 54
>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 = 61.2 bits (147), Expect = 9e-10, Method: Composition-based stats.
Identities = 34/96 (35%), Positives = 50/96 (52%), Gaps = 2/96 (2%)
Query: 13 RKGLWSPEEDEKLYNYITRFGVGCWSSVPKLAGLQRCGKSCRLRWINYLRPDLKRGMFSQ 72
+K ++PEEDE L + + G W + R + CR RW NYL P + ++
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHGSD-WKMIAATFP-NRNARQCRDRWKNYLAPSISHTPWTA 67
Query: 73 QEEDLIISLHEVLGNRWAQIASQLPGRTDNEIKNFW 108
+E+ L++ + G +WA IA PGRTD IKN W
Sbjct: 68 EEDALLVQKIQEYGRQWAIIAKFFPGRTDIHIKNRW 103
>pdb|2K9N|A Chain A, Solution Nmr Structure Of The R2r3 Dna Binding Domain Of
Myb1 Protein From Protozoan Parasite Trichomonas
Vaginalis
pdb|2KDZ|A Chain A, Structure Of The R2r3 Dna Binding Domain Of Myb1 Protein
From Protozoan Parasite Trichomonas Vaginalis In Complex
With Mre-1MRE-2r Dna
Length = 107
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 31/91 (34%), Positives = 50/91 (54%), Gaps = 1/91 (1%)
Query: 18 SPEEDEKLYNYITRFGVGCWSSVPKLAGLQRCGKSCRLRWINYLRPDLKRGMFSQQEEDL 77
+ EED KL + R+G W + +L + R + CR RW NY+ P L+ +S +E+ L
Sbjct: 5 TEEEDLKLQQLVMRYGAKDWIRISQLM-ITRNPRQCRERWNNYINPALRTDPWSPEEDML 63
Query: 78 IISLHEVLGNRWAQIASQLPGRTDNEIKNFW 108
+ + G +W +I+ L R+DN I+N W
Sbjct: 64 LDQKYAEYGPKWNKISKFLKNRSDNNIRNRW 94
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/54 (44%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPD 64
L KG W+ EED++L + ++G WS + K L G R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPE 52
Score = 28.9 bits (63), Expect = 5.2, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 65 LKRGMFSQQEEDLIISLHEVLG-NRWAQIASQLPGRTDNEIKNFWNSCL 112
L +G ++++E+ +I L + G RW+ IA L GR + + W++ L
Sbjct: 1 LIKGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 45.8 bits (107), Expect = 5e-05, Method: Composition-based stats.
Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPD 64
L KG W+ EED+++ + ++G WS + K L G R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPE 52
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 65 LKRGMFSQQEEDLIISLHEVLG-NRWAQIASQLPGRTDNEIKNFWNSCL 112
L +G ++++E+ +I L + G RW+ IA L GR + + W++ L
Sbjct: 1 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|1MBG|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 2
pdb|1MBH|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 2
Length = 53
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPK-LAGLQRCGKSCRLRWINYLRPD 64
L KG W+ EED+++ + ++G WS + K L G R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPE 52
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 65 LKRGMFSQQEEDLIISLHEVLG-NRWAQIASQLPGRTDNEIKNFWNSCL 112
L +G ++++E+ +I L + G RW+ IA L GR + + W++ L
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|2DIM|A Chain A, Solution Structure Of The Myb_dna-Binding Domain Of
Human Cell Division Cycle 5-Like Protein
Length = 70
Score = 35.4 bits (80), Expect = 0.049, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 16 LWSPEEDEKLYNYITRFGVGCWSSVPKLAGLQRCGKSCRLRWINYLRPDLKRGMFS 71
+W EDE L + ++G WS + L ++ K C+ RW +L P +K+ +S
Sbjct: 11 VWRNTEDEILKAAVMKYGKNQWSRIASLLH-RKSAKQCKARWYEWLDPSIKKTEWS 65
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 17 WSPEEDEKLYNYITRFGVGCWSSV 40
W+ EEDEKL + ++G G W+ +
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQI 195
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 17 WSPEEDEKLYNYITRFGVGCWSSV 40
W+ EEDEKL + ++G G W+ +
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQI 194
>pdb|1MBE|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
pdb|1MBF|A Chain A, Mouse C-Myb Dna-Binding Domain Repeat 1
Length = 53
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPKLAGLQRCGKSCRLRWINYLRPD 64
L K W+ EEDEKL + + G W + R C+ RW L P+
Sbjct: 1 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 12 LRKGLWSPEEDEKLYNYITRFGVGCWSSVPKLAGLQRCGKSCRLRWINYLRPD 64
L K W+ EEDEKL + + G W + R C+ RW L P+
Sbjct: 1 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
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
0.315 0.131 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,315,307
Number of Sequences: 62578
Number of extensions: 442080
Number of successful extensions: 876
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 820
Number of HSP's gapped (non-prelim): 44
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)