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= 040841
(280 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 100 bits (250), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 68/105 (64%), Gaps = 1/105 (0%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNIT 71
L +GPWT ED + E++Q +G W + K R GK CR RW N+L P++K+ + T
Sbjct: 25 LNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKG-RIGKQCRERWHNHLNPEVKKTSWT 83
Query: 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
+ED +I + H LGNRW+ IA LPGRTDN +KN+WN+ + +++
Sbjct: 84 EEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHWNSTMRRKV 128
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 99.8 bits (247), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 68/105 (64%), Gaps = 1/105 (0%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNIT 71
L +GPWT ED + E ++ +G W +L K R GK CR RW N+L P++K+ + T
Sbjct: 5 LVKGPWTKEEDQKVIELVKKYGTKQW-TLIAKHLKGRLGKQCRERWHNHLNPEVKKSSWT 63
Query: 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
+ED +I H +LGNRW+ IA LPGRTDN +KN+WN+ + +++
Sbjct: 64 EEEDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVKNHWNSTIKRKV 108
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 63 PDIKRGNITPDEDDLIIRLHSLLGNR-WSLIAGRLPGRTDNEIKNYWNTHLSKRLR 117
PD+ +G T +ED +I L G + W+LIA L GR + + W+ HL+ ++
Sbjct: 3 PDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKGRLGKQCRERWHNHLNPEVK 58
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 96.7 bits (239), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 47/105 (44%), Positives = 68/105 (64%), Gaps = 1/105 (0%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNIT 71
L +GPWT ED + + +Q +G W S+ K R GK CR RW N+L P++K+ + T
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRW-SVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWT 60
Query: 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
+ED +I + H LGNRW+ IA LPGRTDN IKN+WN+ + +++
Sbjct: 61 EEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
Score = 35.4 bits (80), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 64 DIKRGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLS 113
++ +G T +ED +I+L G RWS+IA L GR + + W+ HL+
Sbjct: 1 ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 51
>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 = 96.3 bits (238), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 47/105 (44%), Positives = 68/105 (64%), Gaps = 1/105 (0%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNIT 71
L +GPWT ED + + +Q +G W S+ K R GK CR RW N+L P++K+ + T
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRW-SVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWT 60
Query: 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
+ED +I + H LGNRW+ IA LPGRTDN IKN+WN+ + +++
Sbjct: 61 EEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
>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 = 96.3 bits (238), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 47/105 (44%), Positives = 68/105 (64%), Gaps = 1/105 (0%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNIT 71
L +GPWT ED + + +Q +G W S+ K R GK CR RW N+L P++K+ + T
Sbjct: 56 LIKGPWTKEEDQRVIKLVQKYGPKRW-SVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWT 114
Query: 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
+ED +I + H LGNRW+ IA LPGRTDN IKN+WN+ + +++
Sbjct: 115 EEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 159
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 33/100 (33%), Positives = 51/100 (51%), Gaps = 6/100 (6%)
Query: 17 WTPREDTLLTEYIQVHGEGHWRSLPKKAGLL--RCGKSCRLRWMNYLRPDIKRGNITPDE 74
WT ED L + ++ +G W+ + A L R C+ RW L P++ +G T +E
Sbjct: 9 WTREEDEKLKKLVEQNGTDDWKVI---ANYLPNRTDVQCQHRWQKVLNPELIKGPWTKEE 65
Query: 75 DDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLS 113
D +I+L G RWS+IA L GR + + W+ HL+
Sbjct: 66 DQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 105
>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 = 95.1 bits (235), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 47/105 (44%), Positives = 68/105 (64%), Gaps = 5/105 (4%)
Query: 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLL--RCGKSCRLRWMNYLRPDIKRGNIT 71
+GP+T ED L+ EY++ +G +W P+ L R K CR RW N+L P + + T
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNW---PRITSFLPNRSPKQCRERWFNHLDPAVVKHAWT 58
Query: 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
P+ED+ I R + LG++WS+IA +PGRTDN IKN WN+ +SKR+
Sbjct: 59 PEEDETIFRNYLKLGSKWSVIAKLIPGRTDNAIKNRWNSSISKRI 103
>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 = 67.4 bits (163), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 42/114 (36%), Positives = 58/114 (50%), Gaps = 11/114 (9%)
Query: 18 TPREDTLLTEYIQVHGEGHWRSLPKKAGLL--RCGKSCRLRWMNYLRPDIKRGNITPDED 75
TP ED +L + HG W+ + A R + CR RW NYL P I T +ED
Sbjct: 15 TPEEDEMLKRAVAQHG-SDWKMI---AATFPNRNARQCRDRWKNYLAPSISHTPWTAEED 70
Query: 76 DLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKL 129
L+++ G +W++IA PGRTD IKN W T +S +L + P T + L
Sbjct: 71 ALLVQKIQEYGRQWAIIAKFFPGRTDIHIKNRWVT-ISNKLGI----PQTQQML 119
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%)
Query: 66 KRGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113
K+ TP+ED+++ R + G+ W +IA P R + ++ W +L+
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHGSDWKMIAATFPNRNARQCRDRWKNYLA 57
>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 = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 38/52 (73%)
Query: 65 IKRGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
+K+ + T +ED +I + H LGNRW+ 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 = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 39/53 (73%)
Query: 64 DIKRGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116
++K+ + T +ED ++ + H LGNRW+ IA LPGRTDN IKN+WN+ + +++
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 54
>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 = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 49/91 (53%), Gaps = 1/91 (1%)
Query: 18 TPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDL 77
T ED L + + +G W + + + R + CR RW NY+ P ++ +P+ED L
Sbjct: 5 TEEEDLKLQQLVMRYGAKDWIRISQ-LMITRNPRQCRERWNNYINPALRTDPWSPEEDML 63
Query: 78 IIRLHSLLGNRWSLIAGRLPGRTDNEIKNYW 108
+ + ++ G +W+ I+ L R+DN I+N W
Sbjct: 64 LDQKYAEYGPKWNKISKFLKNRSDNNIRNRW 94
>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: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPD 64
L +GPWT ED + E +Q +G W + K R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 67 RGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLS 113
+G T +ED +I L G RWS+IA L GR + + W+ HL+
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 50
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPD 64
L +GPWT ED L + +Q +G W + K R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 67 RGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLS 113
+G T +ED +I+L G RWS+IA L GR + + W+ HL+
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 50
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPD 64
L +GPWT ED + + +Q +G W + K R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 67 RGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLS 113
+G T +ED +I+L G RWS+IA L GR + + W+ HL+
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 50
>pdb|2DIM|A Chain A, Solution Structure Of The Myb_dna-Binding Domain Of
Human Cell Division Cycle 5-Like Protein
Length = 70
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 17 WTPREDTLLTEYIQVHGEGHWRSLPKKAGLL--RCGKSCRLRWMNYLRPDIKR 67
W ED +L + +G+ W + A LL + K C+ RW +L P IK+
Sbjct: 12 WRNTEDEILKAAVMKYGKNQWSRI---ASLLHRKSAKQCKARWYEWLDPSIKK 61
>pdb|1M1S|A Chain A, Structure Of Wr4, A C.Elegans Msp Family Member
Length = 116
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 8 SKVGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAG 45
SK+ + R P P+ED ++ +Y +V E P KAG
Sbjct: 66 SKLDINRLPGPPKEDKIVIQYAEVPAEETDPXAPFKAG 103
>pdb|3ZTV|A Chain A, Structure Of Haemophilus Influenzae Nad Nucleotidase
(Nadn)
pdb|3ZU0|A Chain A, Structure Of Haemophilus Influenzae Nad Nucleotidase
(Nadn)
pdb|3ZU0|B Chain B, Structure Of Haemophilus Influenzae Nad Nucleotidase
(Nadn)
Length = 579
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 171 LPKPIRVTTTY-LLPRNESFARTTFSQGGEGVLAAHVLEEVPSYSLKDGDDGA 222
LP + Y LP F T ++ EG L VLE+ ++L DG GA
Sbjct: 417 LPGNVTFNDAYTFLP----FGNTLYTYKMEGSLVKQVLEDAMQFALVDGSTGA 465
>pdb|3D8K|A Chain A, Crsytal Structure Of A Phosphatase From A Toxoplasma
Gondii
pdb|3D8K|B Chain B, Crsytal Structure Of A Phosphatase From A Toxoplasma
Gondii
pdb|3D8K|C Chain C, Crsytal Structure Of A Phosphatase From A Toxoplasma
Gondii
pdb|3D8K|D Chain D, Crsytal Structure Of A Phosphatase From A Toxoplasma
Gondii
Length = 377
Score = 27.3 bits (59), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 182 LLPRNESFARTTFSQGGEGVLAAHVLEEVP---SYSLKDGDDGAAGFLVADHHL 232
++P +F F +GG+G L ++ VP ++ GDD AG A H
Sbjct: 223 VVPXTRAFGSFDFKKGGQGKLQQDLVSAVPDVTTFFAYPGDDIVAGTAGAFAHF 276
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
0.318 0.137 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,151,036
Number of Sequences: 62578
Number of extensions: 399530
Number of successful extensions: 810
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 763
Number of HSP's gapped (non-prelim): 41
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
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: 51 (24.3 bits)