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= 043612
(327 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 = 97.8 bits (242), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 44/89 (49%), Positives = 61/89 (68%), Gaps = 1/89 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQ 73
+G W+ EED+K+I V YG W+ + KH R GK CR RW N+L P++K+ S++ +
Sbjct: 7 KGPWTKEEDQKVIELVKKYGTKQWTLIAKHLK-GRLGKQCRERWHNHLNPEVKKSSWTEE 65
Query: 74 EAALIIELHSILGNRWAQIARHLPGRTDN 102
E +I E H +LGNRWA+IA+ LPGRTDN
Sbjct: 66 EDRIIFEAHKVLGNRWAEIAKLLPGRTDN 94
>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 = 95.1 bits (235), Expect = 4e-20, Method: Composition-based stats.
Identities = 44/92 (47%), Positives = 61/92 (66%), Gaps = 1/92 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQ 73
+G W+ EED+++I V YG WS + KH R GK CR RW N+L P++K+ S++ +
Sbjct: 4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWTEE 62
Query: 74 EAALIIELHSILGNRWAQIARHLPGRTDNEKK 105
E +I + H LGNRWA+IA+ LPGRTDN K
Sbjct: 63 EDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIK 94
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 95.1 bits (235), Expect = 5e-20, Method: Composition-based stats.
Identities = 44/92 (47%), Positives = 61/92 (66%), Gaps = 1/92 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQ 73
+G W+ EED+++I V YG WS + KH R GK CR RW N+L P++K+ S++ +
Sbjct: 4 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWTEE 62
Query: 74 EAALIIELHSILGNRWAQIARHLPGRTDNEKK 105
E +I + H LGNRWA+IA+ LPGRTDN K
Sbjct: 63 EDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIK 94
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 61/89 (68%), Gaps = 1/89 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQ 73
+G W+ EED+++I +V YG WS + KH R GK CR RW N+L P++K+ S++ +
Sbjct: 27 KGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWTEE 85
Query: 74 EAALIIELHSILGNRWAQIARHLPGRTDN 102
E +I + H LGNRWA+IA+ LPGRTDN
Sbjct: 86 EDRIIYQAHKRLGNRWAEIAKLLPGRTDN 114
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 15/103 (14%)
Query: 48 RCGKSCRLRWINYLRPDLKRGSFSPQEAALIIELHSILG-NRWAQIARHLPGRTDNEKKL 106
R C+ RW L P+L +G ++ +E +IE G RW+ IA+HL GR +
Sbjct: 8 RTDVQCQHRWQKVLNPELNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKGRIGKQ--- 64
Query: 107 MSHEIVPALASFPADFHNSLCPEEVGFFSLNTNPNLILNSHQQ 149
+HN L PE +I +H++
Sbjct: 65 -----------CRERWHNHLNPEVKKTSWTEEEDRIIYQAHKR 96
>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 = 92.0 bits (227), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 1/89 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQ 73
+G W+ EED+++I V YG WS + KH R GK CR RW N+L P++K+ S++ +
Sbjct: 58 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPEVKKTSWTEE 116
Query: 74 EAALIIELHSILGNRWAQIARHLPGRTDN 102
E +I + H LGNRWA+IA+ LPGRTDN
Sbjct: 117 EDRIIYQAHKRLGNRWAEIAKLLPGRTDN 145
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 37/134 (27%), Positives = 56/134 (41%), Gaps = 16/134 (11%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQEAA 76
W+ EEDEKL V G W + + R C+ RW L P+L +G ++ +E
Sbjct: 9 WTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPELIKGPWTKEEDQ 67
Query: 77 LIIELHSILG-NRWAQIARHLPGRTDNEKKLMSHEIVPALASFPADFHNSLCPEEVGFFS 135
+I+L G RW+ IA+HL GR + +HN L PE
Sbjct: 68 RVIKLVQKYGPKRWSVIAKHLKGRIGKQ--------------CRERWHNHLNPEVKKTSW 113
Query: 136 LNTNPNLILNSHQQ 149
+I +H++
Sbjct: 114 TEEEDRIIYQAHKR 127
>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 = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 2/95 (2%)
Query: 7 CNKQKVKRGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLK 66
N + K+ ++PEEDE L V +G W + R + CR RW NYL P +
Sbjct: 4 VNLKAAKKQKFTPEEDEMLKRAVAQHGSD-WKMIAATFP-NRNARQCRDRWKNYLAPSIS 61
Query: 67 RGSFSPQEAALIIELHSILGNRWAQIARHLPGRTD 101
++ +E AL+++ G +WA IA+ PGRTD
Sbjct: 62 HTPWTAEEDALLVQKIQEYGRQWAIIAKFFPGRTD 96
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 1/89 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQ 73
+G ++ ED+ + YV G W + R K CR RW N+L P + + +++P+
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNWPRITSFLP-NRSPKQCRERWFNHLDPAVVKHAWTPE 60
Query: 74 EAALIIELHSILGNRWAQIARHLPGRTDN 102
E I + LG++W+ IA+ +PGRTDN
Sbjct: 61 EDETIFRNYLKLGSKWSVIAKLIPGRTDN 89
>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 = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 29/86 (33%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPDLKRGSFSPQEAA 76
++ EED KL V YG W + + + R + CR RW NY+ P L+ +SP+E
Sbjct: 4 FTEEEDLKLQQLVMRYGAKDWIRISQLM-ITRNPRQCRERWNNYINPALRTDPWSPEEDM 62
Query: 77 LIIELHSILGNRWAQIARHLPGRTDN 102
L+ + ++ G +W +I++ L R+DN
Sbjct: 63 LLDQKYAEYGPKWNKISKFLKNRSDN 88
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 51.6 bits (122), Expect = 6e-07, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPD 64
+G W+ EED++LI V YG WS + KH R GK CR RW N+L P+
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPD 64
+G W+ EED+++I V YG WS + KH R GK CR RW N+L P+
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
>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 = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 14 RGLWSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPD 64
+G W+ EED+++I V YG WS + KH R GK CR RW N+L P+
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 65 LKRGSFSPQEAALIIELHSILG-NRWAQIARHLPGR 99
L +G ++ +E +IEL G RW+ IA+HL GR
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGR 36
>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 = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 21/41 (51%), Positives = 30/41 (73%)
Query: 65 LKRGSFSPQEAALIIELHSILGNRWAQIARHLPGRTDNEKK 105
+K+ S++ +E +I + H LGNRWA+IA+ LPGRTDN K
Sbjct: 1 VKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIK 41
>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 = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 20/42 (47%), Positives = 31/42 (73%)
Query: 64 DLKRGSFSPQEAALIIELHSILGNRWAQIARHLPGRTDNEKK 105
++K+ S++ +E ++ + H LGNRWA+IA+ LPGRTDN K
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIK 43
>pdb|2DIM|A Chain A, Solution Structure Of The Myb_dna-Binding Domain Of
Human Cell Division Cycle 5-Like Protein
Length = 70
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 16 LWSPEEDEKLINYVTTYGHGCWSSVPKHAGL--QRCGKSCRLRWINYLRPDLKRGSFS 71
+W EDE L V YG WS + A L ++ K C+ RW +L P +K+ +S
Sbjct: 11 VWRNTEDEILKAAVMKYGKNQWSRI---ASLLHRKSAKQCKARWYEWLDPSIKKTEWS 65
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 34.7 bits (78), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSV 40
W+ EEDEKL+ V YG+G W+ +
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSWTQI 194
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 34.7 bits (78), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSV 40
W+ EEDEKL+ V YG+G W+ +
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSWTQI 195
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1,
Nmr, 18 Structures
Length = 53
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 13 KRGLWSPEEDEKLINYVTTYGHGCWSSVPKH 43
KR W EED+ L + V YG G WS + H
Sbjct: 2 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLH 32
>pdb|1W0T|A Chain A, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna.
pdb|1W0T|B Chain B, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna
Length = 53
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 13 KRGLWSPEEDEKLINYVTTYGHGCWSSVPKH 43
KR W EED+ L + V YG G WS + H
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLH 31
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 13 KRGLWSPEEDEKLINYVTTYGHGCWSSVPKH 43
KR W EED+ L + V YG G WS + H
Sbjct: 10 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLH 40
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
Trf1
Length = 69
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 13 KRGLWSPEEDEKLINYVTTYGHGCWSSVPKH 43
KR W EED+ L + V YG G WS + H
Sbjct: 9 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLH 39
>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 = 30.0 bits (66), Expect = 1.6, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPD 64
W+ EEDEKL V G W + + R C+ RW L P+
Sbjct: 6 WTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 30.0 bits (66), Expect = 1.6, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCRLRWINYLRPD 64
W+ EEDEKL V G W + + R C+ RW L P+
Sbjct: 6 WTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|2ELK|A Chain A, Solution Structure Of The Sant Domain Of Fission Yeast
Spcc24b10.08c Protein
Length = 58
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 17 WSPEEDEKLINYVTTYGHGCWSSVPKHAGLQRCGKSCR 54
W +E+ LI+ T G G W+ + + G R + CR
Sbjct: 12 WGADEELLLIDACETLGLGNWADIADYVGNARTKEECR 49
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
0.319 0.136 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,263,763
Number of Sequences: 62578
Number of extensions: 469847
Number of successful extensions: 825
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 775
Number of HSP's gapped (non-prelim): 34
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)