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= 037998
(348 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 = 115 bits (288), Expect = 4e-26, Method: Composition-based stats.
Identities = 51/106 (48%), Positives = 75/106 (70%), Gaps = 3/106 (2%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPDIKRGKF 70
L KGPWT EEDQK++E ++K+G W + K L G R GK CR RW N+L P++K+ +
Sbjct: 5 LVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKG--RLGKQCRERWHNHLNPEVKKSSW 62
Query: 71 SQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+++E++ I H +LGN+W+ IA LPGRTDN +KN WN+ +K+K+
Sbjct: 63 TEEEDRIIFEAHKVLGNRWAEIAKLLPGRTDNAVKNHWNSTIKRKV 108
>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 = 111 bits (278), Expect = 6e-25, Method: Composition-based stats.
Identities = 50/106 (47%), Positives = 74/106 (69%), Gaps = 3/106 (2%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPDIKRGKF 70
L KGPWT EEDQ++++ +QK+G W + K L G R GK CR RW N+L P++K+ +
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPEVKKTSW 59
Query: 71 SQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+++E++ I H LGN+W+ IA LPGRTDN IKN WN+ +++K+
Sbjct: 60 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 111 bits (277), Expect = 7e-25, Method: Composition-based stats.
Identities = 50/106 (47%), Positives = 74/106 (69%), Gaps = 3/106 (2%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPDIKRGKF 70
L KGPWT EEDQ++++ +QK+G W + K L G R GK CR RW N+L P++K+ +
Sbjct: 2 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPEVKKTSW 59
Query: 71 SQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+++E++ I H LGN+W+ IA LPGRTDN IKN WN+ +++K+
Sbjct: 60 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 105
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 50/106 (47%), Positives = 74/106 (69%), Gaps = 3/106 (2%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPDIKRGKF 70
L KGPWT EEDQ+++E +QK+G W + K L G R GK CR RW N+L P++K+ +
Sbjct: 25 LNKGPWTKEEDQRVIEHVQKYGPKRWSDIAKHLKG--RIGKQCRERWHNHLNPEVKKTSW 82
Query: 71 SQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+++E++ I H LGN+W+ IA LPGRTDN +KN WN+ +++K+
Sbjct: 83 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAVKNHWNSTMRRKV 128
>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 = 108 bits (271), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 50/106 (47%), Positives = 74/106 (69%), Gaps = 3/106 (2%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPDIKRGKF 70
L KGPWT EEDQ++++ +QK+G W + K L G R GK CR RW N+L P++K+ +
Sbjct: 56 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPEVKKTSW 113
Query: 71 SQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+++E++ I H LGN+W+ IA LPGRTDN IKN WN+ +++K+
Sbjct: 114 TEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 159
Score = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 34/102 (33%), Positives = 57/102 (55%), Gaps = 2/102 (1%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYLRPDIKRGKFS 71
L K WT EED+KL + ++++G W+ + NR C+ RW L P++ +G ++
Sbjct: 4 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPELIKGPWT 62
Query: 72 QDEEQTILHLHSILG-NKWSAIATHLPGRTDNEIKNFWNTHL 112
++E+Q ++ L G +WS IA HL GR + + W+ HL
Sbjct: 63 KEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 104
Score = 27.7 bits (60), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 69 KFSQDEEQTILHLHSILG-NKWSAIATHLPGRTDNEIKNFWNTHLKKKLIQ 118
+++++E++ + L G + W IA +LP RTD + ++ W L +LI+
Sbjct: 8 RWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIK 58
>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 = 85.5 bits (210), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 42/105 (40%), Positives = 67/105 (63%), Gaps = 5/105 (4%)
Query: 14 KGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGL--NRCGKSCRLRWTNYLRPDIKRGKFS 71
KGP+T ED + E+++++G +W P++ NR K CR RW N+L P + + ++
Sbjct: 2 KGPFTEAEDDLIREYVKENGPQNW---PRITSFLPNRSPKQCRERWFNHLDPAVVKHAWT 58
Query: 72 QDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+E++TI + LG+KWS IA +PGRTDN IKN WN+ + K++
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 = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 37/98 (37%), Positives = 52/98 (53%), Gaps = 2/98 (2%)
Query: 13 KKGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYLRPDIKRGKFSQ 72
KK +TPEED+ L + +HG W+ + NR + CR RW NYL P I ++
Sbjct: 10 KKQKFTPEEDEMLKRAVAQHG-SDWKMIAATFP-NRNARQCRDRWKNYLAPSISHTPWTA 67
Query: 73 DEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNT 110
+E+ ++ G +W+ IA PGRTD IKN W T
Sbjct: 68 EEDALLVQKIQEYGRQWAIIAKFFPGRTDIHIKNRWVT 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 = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 31/95 (32%), Positives = 53/95 (55%), Gaps = 1/95 (1%)
Query: 14 KGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYLRPDIKRGKFSQD 73
K +T EED KL + + ++G W + +L + R + CR RW NY+ P ++ +S +
Sbjct: 1 KVKFTEEEDLKLQQLVMRYGAKDWIRISQLM-ITRNPRQCRERWNNYINPALRTDPWSPE 59
Query: 74 EEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFW 108
E+ + ++ G KW+ I+ L R+DN I+N W
Sbjct: 60 EDMLLDQKYAEYGPKWNKISKFLKNRSDNNIRNRW 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 = 58.9 bits (141), Expect = 4e-09, Method: Composition-based stats.
Identities = 23/52 (44%), Positives = 38/52 (73%)
Query: 65 IKRGKFSQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
+K+ ++++E++ I H LGN+W+ IA LPGRTDN IKN WN+ +++K+
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 = 5e-09, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 39/53 (73%)
Query: 64 DIKRGKFSQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKL 116
++K+ ++++E++ + H LGN+W+ IA LPGRTDN IKN WN+ +++K+
Sbjct: 2 EVKKTSWTEEEDRILYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV 54
>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 = 58.5 bits (140), Expect = 6e-09, Method: Composition-based stats.
Identities = 28/54 (51%), Positives = 36/54 (66%), Gaps = 3/54 (5%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPD 64
L KGPWT EEDQ+++E +QK+G W + K L G R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPE 52
Score = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 67 RGKFSQDEEQTILHLHSILGNK-WSAIATHLPGRTDNEIKNFWNTHL 112
+G ++++E+Q ++ L G K WS IA HL GR + + W+ HL
Sbjct: 3 KGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|1GVD|A Chain A, Crystal Structure Of C-Myb R2 V103l Mutant
Length = 52
Score = 57.8 bits (138), Expect = 8e-09, Method: Composition-based stats.
Identities = 28/54 (51%), Positives = 36/54 (66%), Gaps = 3/54 (5%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPD 64
L KGPWT EEDQ+L++ +QK+G W + K L G R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPE 52
Score = 36.2 bits (82), Expect = 0.031, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 67 RGKFSQDEEQTILHLHSILGNK-WSAIATHLPGRTDNEIKNFWNTHL 112
+G ++++E+Q ++ L G K WS IA HL GR + + W+ HL
Sbjct: 3 KGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>pdb|1GV5|A Chain A, Crystal Structure Of C-Myb R2
Length = 52
Score = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 3/54 (5%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLRPD 64
L KGPWT EEDQ++++ +QK+G W + K L G R GK CR RW N+L P+
Sbjct: 1 LIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKG--RIGKQCRERWHNHLNPE 52
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 67 RGKFSQDEEQTILHLHSILGNK-WSAIATHLPGRTDNEIKNFWNTHL 112
+G ++++E+Q ++ L G K WS IA HL GR + + W+ HL
Sbjct: 3 KGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHL 49
>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 = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYLRPD 64
L K WT EED+KL + ++++G W+ + NR C+ RW L P+
Sbjct: 1 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|1GUU|A Chain A, Crystal Structure Of C-Myb R1
Length = 52
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 12 LKKGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYLRPD 64
L K WT EED+KL + ++++G W+ + NR C+ RW L P+
Sbjct: 1 LGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLP-NRTDVQCQHRWQKVLNPE 52
>pdb|2DIM|A Chain A, Solution Structure Of The Myb_dna-Binding Domain Of
Human Cell Division Cycle 5-Like Protein
Length = 70
Score = 35.8 bits (81), Expect = 0.032, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 17 WTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYLRPDIKRGKFS 71
W ED+ L + K+G W + L + K C+ RW +L P IK+ ++S
Sbjct: 12 WRNTEDEILKAAVMKYGKNQWSRIASLLH-RKSAKQCKARWYEWLDPSIKKTEWS 65
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2
Length = 64
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 10 NGLKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLR 62
N KK WT EE + + +QK+G G+W A+ K +NR + RW R
Sbjct: 7 NITKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 60
>pdb|1W0U|A Chain A, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna.
pdb|1W0U|B Chain B, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna
Length = 55
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 13 KKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLR 62
KK WT EE + + +QK+G G+W A+ K +NR + RW R
Sbjct: 1 KKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 51
>pdb|3SJM|A Chain A, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
pdb|3SJM|B Chain B, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex
Length = 64
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 10 NGLKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLR 62
N KK WT EE + + +QK+G G+W A+ K +NR + RW R
Sbjct: 7 NITKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 60
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2
Length = 63
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 10 NGLKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLR 62
N KK WT EE + + +QK+G G+W A+ K +NR + RW R
Sbjct: 6 NITKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 59
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2
Length = 67
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 10 NGLKKGPWTPEEDQKLVEFIQKHGHGSWRALPK-LAGLNRCGKSCRLRWTNYLR 62
N KK WT EE + + +QK+G G+W A+ K +NR + RW R
Sbjct: 10 NITKKQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFVNRTAVMIKDRWRTMKR 63
>pdb|3TED|A Chain A, Crystal Structure Of The Chd1 Dna-Binding Domain In
Complex With A Dna Duplex
Length = 271
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 17 WTPEEDQKLVEFIQKHGHGSW 37
WT EED+KL+ + K+G+GSW
Sbjct: 172 WTKEEDEKLLIGVFKYGYGSW 192
>pdb|2XB0|X Chain X, Dna-Binding Domain From Saccharomyces Cerevisiae
Chromatin- Remodelling Protein Chd1
Length = 270
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 17 WTPEEDQKLVEFIQKHGHGSW 37
WT EED+KL+ + K+G+GSW
Sbjct: 171 WTKEEDEKLLIGVFKYGYGSW 191
>pdb|2D9A|A Chain A, Solution Structure Of Rsgi Ruh-050, A Myb Dna-Binding
Domain In Mouse Cdna
Length = 60
Score = 32.3 bits (72), Expect = 0.40, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 14 KGPWTPEEDQKLVEFIQKHGHGSWRALPKLAGLNRCGKSCRLRWTNYL 61
K WT EED++L +++ G W+ L NR + C+ RW L
Sbjct: 8 KVKWTHEEDEQLRALVRQFGQQDWKFLASHFP-NRTDQQCQYRWLRVL 54
Score = 28.1 bits (61), Expect = 6.9, Method: Composition-based stats.
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 69 KFSQDEEQTILHLHSILGNK-WSAIATHLPGRTDNEIKNFW 108
K++ +E++ + L G + W +A+H P RTD + + W
Sbjct: 10 KWTHEEDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQYRW 50
>pdb|4FEF|A Chain A, The Crystal Structures Of Several Mutants Of Pleurotus
Eryngii Versatile Peroxidase
Length = 315
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|4FDQ|A Chain A, The Crystal Structures Of Several Mutants Of Pleurotus
Eryngii Versatile Peroxidase
Length = 315
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|4FCS|A Chain A, The Crystal Structures Of Several Mutants Of Pleurotus
Eryngii Versatile Peroxidase
Length = 315
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|4G05|A Chain A, The Crystal Structures Of Several Mutants Of Pleurotus
Eryngii Versatile Peroxidase
Length = 317
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|2W23|A Chain A, Structure Of Mutant W169y Of Pleurotus Eryngii Versatile
Peroxidase (Vp)
Length = 316
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|4FCN|A Chain A, The Crystal Structures Of Several Mutants Of Pleurotus
Eryngii Versatile Peroxidase
Length = 319
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|2VKA|A Chain A, Site-directed Mutagenesis Of The Catalytic Tryptophan
Environment In Pleurotus Eryngii Versatile Peroxidase
Length = 317
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSFVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3FM6|A Chain A, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
Length = 331
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3FM4|A Chain A, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
Length = 331
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|2BOQ|A Chain A, Crystal Structure Of Versatile Peroxidase
Length = 331
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3FJW|A Chain A, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
pdb|3FJW|B Chain B, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
Length = 331
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3FM1|A Chain A, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
Length = 331
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3FKG|A Chain A, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
Length = 331
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3FMU|A Chain A, Crystal Structure Analysis Of Fungal Versatile Peroxidase
From Pleurotus Eryngii
Length = 331
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 255 DPQVPFSFQTSLNN-----NEMGPCSNSFTMVSQDANYPADCSWILPSPPPAV 302
DPQ +Q+ +NN N + ++ QD DCS ++P+PP V
Sbjct: 237 DPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALV 289
>pdb|3AQB|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium
pdb|3AQB|D Chain D, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium
pdb|3AQC|B Chain B, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium And Fpp Analogue
pdb|3AQC|D Chain D, M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate
Synthase In Complex With Magnesium And Fpp Analogue
Length = 325
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 6/90 (6%)
Query: 63 PDIKRGKFSQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKKKLIQMGID 122
DI+ G + I +L +K A+ HL +D+E+ + + +K Q GI+
Sbjct: 229 SDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVK----QYGIE 284
Query: 123 PMTHQPRTDIFASLPHLIAL--ANLKDLLE 150
P R + HL L +N+KD LE
Sbjct: 285 PAELLSRKYGDKAKYHLSQLQDSNIKDYLE 314
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1,
Nmr, 18 Structures
Length = 53
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 13 KKGPWTPEEDQKLVEFIQKHGHGSW-RALPKLAGLNRCGKSCRLRW 57
K+ W EED+ L ++K+G G+W + L NR + RW
Sbjct: 2 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRW 47
>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 = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 13 KKGPWTPEEDQKLVEFIQKHGHGSW-RALPKLAGLNRCGKSCRLRW 57
K+ W EED+ L ++K+G G+W + L NR + RW
Sbjct: 1 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRW 46
>pdb|3DIP|A Chain A, Crystal Structure Of An Enolase Protein From The
Environmental Genome Shotgun Sequencing Of The Sargasso
Sea
pdb|3DIP|B Chain B, Crystal Structure Of An Enolase Protein From The
Environmental Genome Shotgun Sequencing Of The Sargasso
Sea
Length = 410
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 40/90 (44%), Gaps = 10/90 (11%)
Query: 112 LKKKLIQMGIDPMTHQPRTDIFASLPHLIALANLKDLLENQQIDEQAVRIQAEAVQLAKI 171
L + L+ G M P D + PH I+L +LKD LE + +I+A Q +I
Sbjct: 163 LAESLVAEGYAAMKIWPFDDFASITPHHISLTDLKDGLEPFR------KIRAAVGQRIEI 216
Query: 172 QYLQHLL---HSAASL-NTTTPYGQNGITD 197
H L H+AA + N YG + D
Sbjct: 217 MCELHSLWGTHAAARICNALADYGVLWVED 246
>pdb|1NR0|A Chain A, Two Seven-Bladed Beta-Propeller Domains Revealed By The
Structure Of A C. Elegans Homologue Of Yeast Actin
Interacting Protein 1 (Aip1).
pdb|1PEV|A Chain A, Crystal Structure Of The Actin Interacting Protein From
Caenorhabditis Elegans
Length = 611
Score = 28.1 bits (61), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 66 KRGKFSQDEEQTILHLHSILGNKWSAIATHLPGRTDNEIKNFWNTHLKK--KLIQMG 120
K G F D + + H S+ G WS T + + ++ WN K K I +G
Sbjct: 224 KTGVFEDDSLKNVAHSGSVFGLTWSPDGTKIASASADKTIKIWNVATLKVEKTIPVG 280
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1
Length = 70
Score = 27.7 bits (60), Expect = 9.5, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 13 KKGPWTPEEDQKLVEFIQKHGHGSW-RALPKLAGLNRCGKSCRLRW 57
K+ W EED+ L ++K+G G+W + L NR + RW
Sbjct: 10 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRW 55
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human
Trf1
Length = 69
Score = 27.7 bits (60), Expect = 9.9, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 13 KKGPWTPEEDQKLVEFIQKHGHGSW-RALPKLAGLNRCGKSCRLRW 57
K+ W EED+ L ++K+G G+W + L NR + RW
Sbjct: 9 KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRW 54
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
0.315 0.132 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,278,776
Number of Sequences: 62578
Number of extensions: 456106
Number of successful extensions: 1248
Number of sequences better than 100.0: 64
Number of HSP's better than 100.0 without gapping: 29
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 1174
Number of HSP's gapped (non-prelim): 82
length of query: 348
length of database: 14,973,337
effective HSP length: 100
effective length of query: 248
effective length of database: 8,715,537
effective search space: 2161453176
effective search space used: 2161453176
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)