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= 025602
(250 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 = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 48/108 (44%), Positives = 73/108 (67%), Gaps = 3/108 (2%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPDIKRGNF 74
L +G W ED+ + + +K YG +W I A LK R GK CR RW N+L P++K+ ++
Sbjct: 5 LVKGPWTKEEDQKVIELVKKYGTKQWTLI--AKHLKGRLGKQCRERWHNHLNPEVKKSSW 62
Query: 75 SKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRVDA 122
+++E+ ++ HK+LGNRWA IA LPGRTDN +KN+WN+ + ++VD
Sbjct: 63 TEEEDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVKNHWNSTIKRKVDT 110
>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 = 47/106 (44%), Positives = 74/106 (69%), Gaps = 3/106 (2%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPDIKRGNF 74
LN+G W ED+ + ++++ YG +W I A LK R GK CR RW N+L P++K+ ++
Sbjct: 25 LNKGPWTKEEDQRVIEHVQKYGPKRWSDI--AKHLKGRIGKQCRERWHNHLNPEVKKTSW 82
Query: 75 SKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
+++E+ ++ + HK LGNRWA IA LPGRTDN +KN+WN+ + ++V
Sbjct: 83 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHWNSTMRRKV 128
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 94.7 bits (234), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/106 (44%), Positives = 71/106 (66%), Gaps = 3/106 (2%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPDIKRGNF 74
L +G W ED+ + ++ YG +W I A LK R GK CR RW N+L P++K+ ++
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVI--AKHLKGRIGKQCRERWHNHLNPEVKKTSW 59
Query: 75 SKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
+++E+ ++ + HK LGNRWA IA LPGRTDN IKN+WN+ + ++V
Sbjct: 60 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 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 = 94.4 bits (233), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/106 (44%), Positives = 71/106 (66%), Gaps = 3/106 (2%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPDIKRGNF 74
L +G W ED+ + ++ YG +W I A LK R GK CR RW N+L P++K+ ++
Sbjct: 56 LIKGPWTKEEDQRVIKLVQKYGPKRWSVI--AKHLKGRIGKQCRERWHNHLNPEVKKTSW 113
Query: 75 SKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
+++E+ ++ + HK LGNRWA IA LPGRTDN IKN+WN+ + ++V
Sbjct: 114 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 159
>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 = 94.4 bits (233), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 47/106 (44%), Positives = 71/106 (66%), Gaps = 3/106 (2%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPDIKRGNF 74
L +G W ED+ + ++ YG +W I A LK R GK CR RW N+L P++K+ ++
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVI--AKHLKGRIGKQCRERWHNHLNPEVKKTSW 59
Query: 75 SKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
+++E+ ++ + HK LGNRWA IA LPGRTDN IKN+WN+ + ++V
Sbjct: 60 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 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 = 87.4 bits (215), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 40/111 (36%), Positives = 67/111 (60%), Gaps = 1/111 (0%)
Query: 18 RGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKD 77
+G + ED ++ +Y+K G W I + R K CR RW N+L P + + ++ +
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNWPRI-TSFLPNRSPKQCRERWFNHLDPAVVKHAWTPE 60
Query: 78 EEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRVDANHHHHQ 128
E++ + R + LG++W++IA +PGRTDN IKN WN+ +SKR+ N +H +
Sbjct: 61 EDETIFRNYLKLGSKWSVIAKLIPGRTDNAIKNRWNSSISKRISTNSNHKE 111
>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 = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 50/90 (55%), Gaps = 2/90 (2%)
Query: 25 EDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVIR 84
ED++L + +G W+ I A R + CR RW NYL P I ++ +E+ L+++
Sbjct: 18 EDEMLKRAVAQHG-SDWKMI-AATFPNRNARQCRDRWKNYLAPSISHTPWTAEEDALLVQ 75
Query: 85 LHKLLGNRWALIAGRLPGRTDNDIKNYWNT 114
+ G +WA+IA PGRTD IKN W T
Sbjct: 76 KIQEYGRQWAIIAKFFPGRTDIHIKNRWVT 105
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 25/51 (49%)
Query: 70 KRGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
K+ F+ +E++++ R G+ W +IA P R ++ W L+ +
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHGSDWKMIAATFPNRNARQCRDRWKNYLAPSI 60
>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 = 60.5 bits (145), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 42/53 (79%)
Query: 68 DIKRGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
++K+ +++++E+ ++ + HK LGNRWA IA LPGRTDN IKN+WN+ + ++V
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 54
>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 = 60.5 bits (145), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 25/52 (48%), Positives = 41/52 (78%)
Query: 69 IKRGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120
+K+ +++++E+ ++ + HK LGNRWA IA LPGRTDN IKN+WN+ + ++V
Sbjct: 1 VKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 52
>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 = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 25 EDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVIR 84
ED L + YG W I + + R + CR RW NY+ P ++ +S +E+ L+ +
Sbjct: 8 EDLKLQQLVMRYGAKDWIRISQLM-ITRNPRQCRERWNNYINPALRTDPWSPEEDMLLDQ 66
Query: 85 LHKLLGNRWALIAGRLPGRTDNDIKNYW 112
+ G +W I+ L R+DN+I+N W
Sbjct: 67 KYAEYGPKWNKISKFLKNRSDNNIRNRW 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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPD 68
L +G W ED+ + + ++ YG +W I A LK R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVI--AKHLKGRIGKQCRERWHNHLNPE 52
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 71 RGNFSKDEEDLVIRLHKLLG-NRWALIAGRLPGRTDNDIKNYWNTKLS 117
+G ++K+E+ VI L + G RW++IA L GR + W+ L+
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 50
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPD 68
L +G W ED+ L ++ YG +W I A LK R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRLIKLVQKYGPKRWSVI--AKHLKGRIGKQCRERWHNHLNPE 52
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 71 RGNFSKDEEDLVIRLHKLLG-NRWALIAGRLPGRTDNDIKNYWNTKLS 117
+G ++K+E+ +I+L + G RW++IA L GR + W+ L+
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 20 AWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKR-CGKSCRLRWMNYLRPDIKRGNFS 75
W+ ED+IL + YG+ +W I A+ L R K C+ RW +L P IK+ +S
Sbjct: 11 VWRNTEDEILKAAVMKYGKNQWSRI--ASLLHRKSAKQCKARWYEWLDPSIKKTEWS 65
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLK-RCGKSCRLRWMNYLRPD 68
L +G W ED+ + ++ YG +W I A LK R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIKLVQKYGPKRWSVI--AKHLKGRIGKQCRERWHNHLNPE 52
Score = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 71 RGNFSKDEEDLVIRLHKLLG-NRWALIAGRLPGRTDNDIKNYWNTKLS 117
+G ++K+E+ VI+L + G RW++IA L GR + W+ L+
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLN 50
>pdb|4A17|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|V Chain V, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 239
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 15/85 (17%)
Query: 4 KRKTPCCSKGEGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMN 63
+RK SK + ++A E KI+ + KA G + ++P A + + R+R +N
Sbjct: 36 QRKAEWISKAQKYA-AEYEAAEKKIVDEKRKARKTGAF-YVPAEA---KVAFAIRIRGVN 90
Query: 64 YLRPDIKRGNFSKDEEDLVIRLHKL 88
L PD+KR V+RL +L
Sbjct: 91 QLHPDVKR----------VLRLFRL 105
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
Trf1
Length = 69
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 18 RGAWKAVEDKILTDYIKAYGEGKWRHI 44
R AW EDK L ++ YGEG W I
Sbjct: 10 RQAWLWEEDKNLRSGVRKYGEGNWSKI 36
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 27.3 bits (59), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 18 RGAWKAVEDKILTDYIKAYGEGKWRHI 44
R AW EDK L ++ YGEG W I
Sbjct: 11 RQAWLWEEDKNLRSGVRKYGEGNWSKI 37
>pdb|2ELK|A Chain A, Solution Structure Of The Sant Domain Of Fission Yeast
Spcc24b10.08c Protein
Length = 58
Score = 27.3 bits (59), Expect = 9.0, Method: Composition-based stats.
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 21 WKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWM 62
W A E+ +L D + G G W I G R + CR ++
Sbjct: 12 WGADEELLLIDACETLGLGNWADIADYVGNARTKEECRDHYL 53
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 0.135 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,713,247
Number of Sequences: 62578
Number of extensions: 325243
Number of successful extensions: 2239
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2187
Number of HSP's gapped (non-prelim): 40
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
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)