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= 041991
(325 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 = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 44/105 (41%), Positives = 66/105 (62%), Gaps = 1/105 (0%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPE 75
+G W+ EED K+I+ +K++G W + K R GK CR RW N+L P++K+ + E
Sbjct: 7 KGPWTKEEDQKVIELVKKYGTKQWTLIAKHLK-GRLGKQCRERWHNHLNPEVKKSSWTEE 65
Query: 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQS 120
E I + H + GN+WA IA LPGRTDN +KN WN+ +K+ + +
Sbjct: 66 EDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVKNHWNSTIKRKVDT 110
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 92.4 bits (228), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 42/103 (40%), Positives = 65/103 (63%), Gaps = 1/103 (0%)
Query: 14 MKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFA 73
+ +G W+ EED ++I++++++G W + K R GK CR RW N+L P++K+ +
Sbjct: 25 LNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWT 83
Query: 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116
EE I Q H GN+WA IA LPGRTDN +KN WN+ +++
Sbjct: 84 EEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHWNSTMRR 126
>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 = 92.0 bits (227), Expect = 4e-19, Method: Composition-based stats.
Identities = 43/103 (41%), Positives = 64/103 (62%), Gaps = 1/103 (0%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPE 75
+G W+ EED ++I+ ++++G W + K R GK CR RW N+L P++K+ + E
Sbjct: 4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWTEE 62
Query: 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118
E I Q H GN+WA IA LPGRTDN IKN WN+ +++ +
Sbjct: 63 EDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
Score = 34.3 bits (77), Expect = 0.100, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 69 RGPFAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119
+GP+ EE +I+L +G K W+ IA HL GR + W+ L ++
Sbjct: 4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVK 55
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 91.7 bits (226), Expect = 5e-19, Method: Composition-based stats.
Identities = 43/106 (40%), Positives = 66/106 (62%), Gaps = 1/106 (0%)
Query: 13 KMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPF 72
++ +G W+ EED ++I+ ++++G W + K R GK CR RW N+L P++K+ +
Sbjct: 1 ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPEVKKTSW 59
Query: 73 APEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118
EE I Q H GN+WA IA LPGRTDN IKN WN+ +++ +
Sbjct: 60 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
Score = 34.3 bits (77), Expect = 0.094, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 66 DIKRGPFAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTRLKKHLQ 119
++ +GP+ EE +I+L +G K W+ IA HL GR + W+ L ++
Sbjct: 1 ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVK 55
>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 = 90.1 bits (222), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 43/101 (42%), Positives = 63/101 (62%), Gaps = 1/101 (0%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPE 75
+G W+ EED ++I+ ++++G W + K R GK CR RW N+L P++K+ + E
Sbjct: 58 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWTEE 116
Query: 76 EVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116
E I Q H GN+WA IA LPGRTDN IKN WN+ +++
Sbjct: 117 EDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRR 157
>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 = 82.0 bits (201), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 45/111 (40%), Positives = 65/111 (58%), Gaps = 6/111 (5%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGIL--RSGKSCRLRWMNYLRPDIKRGPFA 73
+G ++ ED + +Y+KE+G W P+ L RS K CR RW N+L P + + +
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNW---PRITSFLPNRSPKQCRERWFNHLDPAVVKHAWT 58
Query: 74 PEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHLQSMNHN 124
PEE TI + + G+KW+ IA +PGRTDN IKN WN+ + K + S N N
Sbjct: 59 PEEDETIFRNYLKLGSKWSVIAKLIPGRTDNAIKNRWNSSISKRI-STNSN 108
>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 = 74.3 bits (181), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 40/106 (37%), Positives = 58/106 (54%), Gaps = 6/106 (5%)
Query: 9 CDMEKMKRGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGIL--RSGKSCRLRWMNYLRPD 66
+++ K+ ++PEED L + + +HG W+ + A R+ + CR RW NYL P
Sbjct: 4 VNLKAAKKQKFTPEEDEMLKRAVAQHG-SDWKMI---AATFPNRNARQCRDRWKNYLAPS 59
Query: 67 IKRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNT 112
I P+ EE A ++Q +G +WA IA PGRTD IKN W T
Sbjct: 60 ISHTPWTAEEDALLVQKIQEYGRQWAIIAKFFPGRTDIHIKNRWVT 105
>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 = 71.2 bits (173), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 34/91 (37%), Positives = 52/91 (57%), Gaps = 1/91 (1%)
Query: 20 SPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPDIKRGPFAPEEVAT 79
+ EED KL Q + +G W + Q I R+ + CR RW NY+ P ++ P++PEE
Sbjct: 5 TEEEDLKLQQLVMRYGAKDWIRIS-QLMITRNPRQCRERWNNYINPALRTDPWSPEEDML 63
Query: 80 IIQLHGLFGNKWAAIASHLPGRTDNDIKNLW 110
+ Q + +G KW I+ L R+DN+I+N W
Sbjct: 64 LDQKYAEYGPKWNKISKFLKNRSDNNIRNRW 94
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 24/52 (46%), Positives = 33/52 (63%)
Query: 67 IKRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKKHL 118
+K+ + EE I Q H GN+WA IA LPGRTDN IKN WN+ +++ +
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 = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 66 DIKRGPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKNLWNTRLKK 116
++K+ + EE + Q H GN+WA IA LPGRTDN IKN WN+ +++
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRR 52
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPD 66
+G W+ EED +LI+ ++++G W + K R GK CR RW N+L P+
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 69 RGPFAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTRL 114
+GP+ EE +I+L +G K W+ IA HL GR + W+ L
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPD 66
+G W+ EED ++I+ ++++G W + K R GK CR RW N+L P+
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 34.3 bits (77), Expect = 0.086, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 69 RGPFAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTRL 114
+GP+ EE +I+L +G K W+ IA HL GR + W+ L
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 16 RGVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILRSGKSCRLRWMNYLRPD 66
+G W+ EED ++I+ ++++G W + K R GK CR RW N+L P+
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 34.3 bits (77), Expect = 0.099, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 69 RGPFAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLWNTRL 114
+GP+ EE +I+L +G K W+ IA HL GR + W+ L
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|1P4W|A Chain A, Solution Structure Of The Dna-Binding Domain Of The
Erwinia Amylovora Rcsb Protein
Length = 99
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 17 GVWSPEEDAKLIQYIKEHGHGTWRHLPKQAGILR 50
G ++PE AKL++ I G+G R PK++ +LR
Sbjct: 11 GSYTPESVAKLLEKISAGGYGDKRLSPKESEVLR 44
>pdb|2DIM|A Chain A, Solution Structure Of The Myb_dna-Binding Domain Of
Human Cell Division Cycle 5-Like Protein
Length = 70
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 18 VWSPEEDAKLIQYIKEHGHGTWRHLPKQAGIL--RSGKSCRLRWMNYLRPDIKRGPFA 73
VW ED L + ++G W + A +L +S K C+ RW +L P IK+ ++
Sbjct: 11 VWRNTEDEILKAAVMKYGKNQWSRI---ASLLHRKSAKQCKARWYEWLDPSIKKTEWS 65
>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 = 31.6 bits (70), Expect = 0.68, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 9/52 (17%)
Query: 19 WSPEEDAKLIQYIKEHGHGTWR----HLPKQAGILRSGKSCRLRWMNYLRPD 66
W+ EED KL + ++++G W+ +LP R+ C+ RW L P+
Sbjct: 6 WTREEDEKLKKLVEQNGTDDWKVIANYLPN-----RTDVQCQHRWQKVLNPE 52
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 31.6 bits (70), Expect = 0.68, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 9/52 (17%)
Query: 19 WSPEEDAKLIQYIKEHGHGTWR----HLPKQAGILRSGKSCRLRWMNYLRPD 66
W+ EED KL + ++++G W+ +LP R+ C+ RW L P+
Sbjct: 6 WTREEDEKLKKLVEQNGTDDWKVIANYLPN-----RTDVQCQHRWQKVLNPE 52
>pdb|2LLK|A Chain A, Solution Nmr Structure Of The N-Terminal Myb-Like 1 Domain
Of The Human Cyclin-D-Binding Transcription Factor 1
(Hdmp1), Northeast Structural Genomics Consortium (Nesg)
Target Id Hr8011a
Length = 73
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 70 GPFAPEEVATIIQLHGLFGNKWAAIASHLPGRTDNDIKN 108
G + PEE+ + +L GN WA I + L GR+ + +K+
Sbjct: 24 GKYTPEEIEKLKELRIKHGNDWATIGAAL-GRSASSVKD 61
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 19 WSPEEDAKLIQYIKEHGHGTWR----HLPKQAGILRSGKSCRLRWMNYL 63
W+ EED +L +++ G W+ H P R+ + C+ RW+ L
Sbjct: 11 WTHEEDEQLRALVRQFGQQDWKFLASHFPN-----RTDQQCQYRWLRVL 54
Score = 27.7 bits (60), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 72 FAPEEVATIIQLHGLFGNK-WAAIASHLPGRTDNDIKNLW 110
+ EE + L FG + W +ASH P RTD + W
Sbjct: 11 WTHEEDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQYRW 50
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 19 WSPEEDAKLIQYIKEHGHGTWRHL 42
W+ EED KL+ + ++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 = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 19 WSPEEDAKLIQYIKEHGHGTWRHL 42
W+ EED KL+ + ++G+G+W +
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQI 194
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
0.313 0.130 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,803,440
Number of Sequences: 62578
Number of extensions: 384114
Number of successful extensions: 738
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 694
Number of HSP's gapped (non-prelim): 40
length of query: 325
length of database: 14,973,337
effective HSP length: 99
effective length of query: 226
effective length of database: 8,778,115
effective search space: 1983853990
effective search space used: 1983853990
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)