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= 048610
(87 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 = 74.3 bits (181), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 54/78 (69%), Gaps = 1/78 (1%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGN 69
P L KG W EED+++I ++++YG WS++ K+ R GK CR RW N+L P++++ +
Sbjct: 23 PELNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKG-RIGKQCRERWHNHLNPEVKKTS 81
Query: 70 FTQEEDETIIKLHEQLGN 87
+T+EED I + H++LGN
Sbjct: 82 WTEEEDRIIYQAHKRLGN 99
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 48 RCGKSCRLRWMNYLRPDIRRGNFTQEEDETIIKLHEQLG 86
R C+ RW L P++ +G +T+EED+ +I+ ++ G
Sbjct: 8 RTDVQCQHRWQKVLNPELNKGPWTKEEDQRVIEHVQKYG 46
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 73.2 bits (178), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGN 69
P L KG W EED+K+I +++YG W+ + K+ R GK CR RW N+L P++++ +
Sbjct: 3 PDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKG-RLGKQCRERWHNHLNPEVKKSS 61
Query: 70 FTQEEDETIIKLHEQLGN 87
+T+EED I + H+ LGN
Sbjct: 62 WTEEEDRIIFEAHKVLGN 79
>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 = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 52/78 (66%), Gaps = 1/78 (1%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGN 69
P L KG W EED+++I +++YG WS + K+ R GK CR RW N+L P++++ +
Sbjct: 54 PELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-RIGKQCRERWHNHLNPEVKKTS 112
Query: 70 FTQEEDETIIKLHEQLGN 87
+T+EED I + H++LGN
Sbjct: 113 WTEEEDRIIYQAHKRLGN 130
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFT 71
L K W EED KL + + G +W + Y R C+ RW L P++ +G +T
Sbjct: 4 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLPN-RTDVQCQHRWQKVLNPELIKGPWT 62
Query: 72 QEEDETIIKLHEQLG 86
+EED+ +IKL ++ G
Sbjct: 63 KEEDQRVIKLVQKYG 77
>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 = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFT 71
L KG W EED+++I +++YG WS + K+ R GK CR RW N+L P++++ ++T
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-RIGKQCRERWHNHLNPEVKKTSWT 60
Query: 72 QEEDETIIKLHEQLGN 87
+EED I + H++LGN
Sbjct: 61 EEEDRIIYQAHKRLGN 76
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPK 42
P ++K SW EEDR + +R G W+E+ K
Sbjct: 52 PEVKKTSWTEEEDRIIYQAHKRLGN-RWAEIAK 83
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFT 71
L KG W EED+++I +++YG WS + K+ R GK CR RW N+L P++++ ++T
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG-RIGKQCRERWHNHLNPEVKKTSWT 60
Query: 72 QEEDETIIKLHEQLGN 87
+EED I + H++LGN
Sbjct: 61 EEEDRIIYQAHKRLGN 76
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPK 42
P ++K SW EEDR + +R G W+E+ K
Sbjct: 52 PEVKKTSWTEEEDRIIYQAHKRLGN-RWAEIAK 83
>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 = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 14 KGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLL--RCGKSCRLRWMNYLRPDIRRGNFT 71
KG + ED + Y++ G NW P+ L R K CR RW N+L P + + +T
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNW---PRITSFLPNRSPKQCRERWFNHLDPAVVKHAWT 58
Query: 72 QEEDETIIKLHEQLGN 87
EEDETI + + +LG+
Sbjct: 59 PEEDETIFRNYLKLGS 74
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD 64
L KG W EED++LI +++YG WS + K+ R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLK-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 = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD 64
L KG W EED+++I +++YG WS + K+ R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 52
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD 64
L KG W EED+++I +++YG WS + K+ R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLK-GRIGKQCRERWHNHLNPE 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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 14 KGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNFTQE 73
K + EED KL + RYG +W + + + R + CR RW NY+ P +R ++ E
Sbjct: 1 KVKFTEEEDLKLQQLVMRYGAKDWIRISQLM-ITRNPRQCRERWNNYINPALRTDPWSPE 59
Query: 74 EDETIIKLHEQLG 86
ED + + + + G
Sbjct: 60 EDMLLDQKYAEYG 72
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWM 58
P+LR W+PEED L YG W+++ K+ R + R RWM
Sbjct: 49 PALRTDPWSPEEDMLLDQKYAEYGP-KWNKISKFLK-NRSDNNIRNRWM 95
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 11 SLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPDIRRGNF 70
+ +K + PEED L + ++G +W +M R + CR RW NYL P I +
Sbjct: 8 AAKKQKFTPEEDEMLKRAVAQHGS-DW-KMIAATFPNRNARQCRDRWKNYLAPSISHTPW 65
Query: 71 TQEEDETIIKLHEQLG 86
T EED +++ ++ G
Sbjct: 66 TAEEDALLVQKIQEYG 81
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 10 PSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKY 43
PS+ W EED L+ I+ YG W+ + K+
Sbjct: 58 PSISHTPWTAEEDALLVQKIQEYGR-QWAIIAKF 90
>pdb|2ELK|A Chain A, Solution Structure Of The Sant Domain Of Fission Yeast
Spcc24b10.08c Protein
Length = 58
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%)
Query: 6 GSEKPSLRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWM 58
GS S +W +E+ LI G+ NW+++ Y G R + CR ++
Sbjct: 1 GSSGSSGFDENWGADEELLLIDACETLGLGNWADIADYVGNARTKEECRDHYL 53
>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 = 0.059, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 17 WAPEEDRKLIAYIRRYGIWNWSEMPKYAGLL--RCGKSCRLRWMNYLRPDIRRGNFT 71
W ED L A + +YG WS + A LL + K C+ RW +L P I++ ++
Sbjct: 12 WRNTEDEILKAAVMKYGKNQWSRI---ASLLHRKSAKQCKARWYEWLDPSIKKTEWS 65
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 17 WAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYL 61
W EED +L A +R++G +W + + R + C+ RW+ L
Sbjct: 11 WTHEEDEQLRALVRQFGQQDWKFLASHF-PNRTDQQCQYRWLRVL 54
>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 = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD 64
L K W EED KL + + G +W + Y R C+ RW L P+
Sbjct: 1 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 12 LRKGSWAPEEDRKLIAYIRRYGIWNWSEMPKYAGLLRCGKSCRLRWMNYLRPD 64
L K W EED KL + + G +W + Y R C+ RW L P+
Sbjct: 1 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 16 SWAPEEDRKLIAYIRRYGIWNWSEM 40
+W EED KL+ + +YG +W+++
Sbjct: 170 NWTKEEDEKLLIGVFKYGYGSWTQI 194
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 16 SWAPEEDRKLIAYIRRYGIWNWSEM 40
+W EED KL+ + +YG +W+++
Sbjct: 171 NWTKEEDEKLLIGVFKYGYGSWTQI 195
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 13 RKGSWAPEEDRKLIAYIRRYGIWNWSEM 40
++ +W EED+ L + +R+YG NWS++
Sbjct: 10 KRQAWLWEEDKNLRSGVRKYGEGNWSKI 37
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
Trf1
Length = 69
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 13 RKGSWAPEEDRKLIAYIRRYGIWNWSEM 40
++ +W EED+ L + +R+YG NWS++
Sbjct: 9 KRQAWLWEEDKNLRSGVRKYGEGNWSKI 36
>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 = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 13 RKGSWAPEEDRKLIAYIRRYGIWNWSEM 40
++ +W EED+ L + +R+YG NWS++
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKI 28
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1,
Nmr, 18 Structures
Length = 53
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 13 RKGSWAPEEDRKLIAYIRRYGIWNWSEM 40
++ +W EED+ L + +R+YG NWS++
Sbjct: 2 KRQAWLWEEDKNLRSGVRKYGEGNWSKI 29
>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 = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 18/23 (78%)
Query: 65 IRRGNFTQEEDETIIKLHEQLGN 87
+++ ++T+EED I + H++LGN
Sbjct: 1 VKKTSWTEEEDRIIYQAHKRLGN 23
>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 = 25.4 bits (54), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 8/24 (33%), Positives = 19/24 (79%)
Query: 64 DIRRGNFTQEEDETIIKLHEQLGN 87
++++ ++T+EED + + H++LGN
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGN 25
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
0.320 0.138 0.452
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,122,197
Number of Sequences: 62578
Number of extensions: 119384
Number of successful extensions: 256
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 196
Number of HSP's gapped (non-prelim): 44
length of query: 87
length of database: 14,973,337
effective HSP length: 55
effective length of query: 32
effective length of database: 11,531,547
effective search space: 369009504
effective search space used: 369009504
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)