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= 014781
(419 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 44/170 (25%), Positives = 77/170 (45%), Gaps = 23/170 (13%)
Query: 213 KWTPEELELVRKFYEKHGSD-WKTMADTL-GKHRFHVKDAWRRIKLPNQKKGQWSQEEYQ 270
+WT EE E ++K E++G+D WK +A+ L + + W+++ P KG W++EE Q
Sbjct: 8 RWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIKGPWTKEEDQ 67
Query: 271 KLFALVNMDLRMKASEEKRTKHGMLRDNISWEAISEKLSTRTNAICCMKWYDQLTSPMVA 330
++ LV K+G R W I++ L R C +W++ L +P V
Sbjct: 68 RVIKLVQ-------------KYGPKR----WSVIAKHLKGRIGKQCRERWHNHL-NPEVK 109
Query: 331 EGKWADTDDFHLVNALSGLDACCMDDVDWDNLLEHRSGTFCRKRWNQMVK 380
+ W + +D + A L + LL R+ + WN ++
Sbjct: 110 KTSWTEEEDRIIYQAHKRLGNRWAEIA---KLLPGRTDNAIKNHWNSTMR 156
>pdb|2LLK|A Chain A, Solution Nmr Structure Of The N-Terminal Myb-Like 1 Domain
Of The Human Cyclin-D-Binding Transcription Factor 1
(Hdmp1), Northeast Structural Genomics Consortium (Nesg)
Target Id Hr8011a
Length = 73
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 201 RAHILFERDENR--KWTPEELELVRKFYEKHGSDWKTMADTLGKHRFHVKDAWRRIK 255
R ++ F+ D N K+TPEE+E +++ KHG+DW T+ LG+ VKD R +K
Sbjct: 11 RENLYFQGDRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALGRSASSVKDRCRLMK 67
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 212 RKWTPEELELVRKFYEKHGSDWKTMADTL-GKHRFHVKDAWRRIKLPNQKKGQWSQEE 268
+K+TPEE E++++ +HGSDWK +A T ++ +D W+ P+ W+ EE
Sbjct: 12 QKFTPEEDEMLKRAVAQHGSDWKMIAATFPNRNARQCRDRWKNYLAPSISHTPWTAEE 69
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 50/120 (41%), Gaps = 25/120 (20%)
Query: 137 RGKRFSLEEDEMIKKAVINYIEAHRLGEDGLNMVLHCRSYPEIKHCWKEIGAALPWRPCE 196
+ ++F+ EEDEM+K+AV + G D WK I A P R
Sbjct: 10 KKQKFTPEEDEMLKRAVAQH------GSD-----------------WKMIAATFPNRNAR 46
Query: 197 SIYYR-AHILFERDENRKWTPEELELVRKFYEKHGSDWKTMADTL-GKHRFHVKDAWRRI 254
R + L + WT EE L+ + +++G W +A G+ H+K+ W I
Sbjct: 47 QCRDRWKNYLAPSISHTPWTAEEDALLVQKIQEYGRQWAIIAKFFPGRTDIHIKNRWVTI 106
>pdb|1A5J|A Chain A, Chicken B-Myb Dna Binding Domain, Repeat 2 And Repeat3,
Nmr, 32 Structures
Length = 110
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 31/125 (24%), Positives = 52/125 (41%), Gaps = 21/125 (16%)
Query: 256 LPNQKKGQWSQEEYQKLFALVNMDLRMKASEEKRTKHGMLRDNISWEAISEKLSTRTNAI 315
+P+ KG W++EE QK+ LV K+G + W I++ L R
Sbjct: 2 IPDLVKGPWTKEEDQKVIELVK-------------KYGTKQ----WTLIAKHLKGRLGKQ 44
Query: 316 CCMKWYDQLTSPMVAEGKWADTDDFHLVNALSGLDACCMDDVDWDNLLEHRSGTFCRKRW 375
C +W++ L +P V + W + +D + A L + LL R+ + W
Sbjct: 45 CRERWHNHL-NPEVKKSSWTEEEDRIIFEAHKVLGNRWAEIA---KLLPGRTDNAVKNHW 100
Query: 376 NQMVK 380
N +K
Sbjct: 101 NSTIK 105
>pdb|1H8A|C Chain C, Crystal Structure Of Ternary Protein-Dna Complex3
Length = 128
Score = 33.5 bits (75), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 27/147 (18%)
Query: 234 KTMADTLGKHRFHVKDAWRRIKLPNQKKGQWSQEEYQKLFALVNMDLRMKASEEKRTKHG 293
K D +HR W+++ P KG W++EE Q++ V K+G
Sbjct: 6 KNRTDVQCQHR------WQKVLNPELNKGPWTKEEDQRVIEHVQ-------------KYG 46
Query: 294 MLRDNISWEAISEKLSTRTNAICCMKWYDQLTSPMVAEGKWADTDDFHLVNALSGLDACC 353
R W I++ L R C +W++ L +P V + W + +D + A L
Sbjct: 47 PKR----WSDIAKHLKGRIGKQCRERWHNHL-NPEVKKTSWTEEEDRIIYQAHKRLGNRW 101
Query: 354 MDDVDWDNLLEHRSGTFCRKRWNQMVK 380
+ LL R+ + WN ++
Sbjct: 102 AEIAK---LLPGRTDNAVKNHWNSTMR 125
>pdb|1GV2|A Chain A, Crystal Structure Of C-Myb R2r3
Length = 105
Score = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 49/120 (40%), Gaps = 21/120 (17%)
Query: 261 KGQWSQEEYQKLFALVNMDLRMKASEEKRTKHGMLRDNISWEAISEKLSTRTNAICCMKW 320
KG W++EE Q++ LV K+G R W I++ L R C +W
Sbjct: 4 KGPWTKEEDQRVIKLVQ-------------KYGPKR----WSVIAKHLKGRIGKQCRERW 46
Query: 321 YDQLTSPMVAEGKWADTDDFHLVNALSGLDACCMDDVDWDNLLEHRSGTFCRKRWNQMVK 380
++ L +P V + W + +D + A L + LL R+ + WN ++
Sbjct: 47 HNHL-NPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAK---LLPGRTDNAIKNHWNSTMR 102
>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 = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 29/120 (24%), Positives = 49/120 (40%), Gaps = 21/120 (17%)
Query: 261 KGQWSQEEYQKLFALVNMDLRMKASEEKRTKHGMLRDNISWEAISEKLSTRTNAICCMKW 320
KG W++EE Q++ LV K+G R W I++ L R C +W
Sbjct: 4 KGPWTKEEDQRVIKLVQ-------------KYGPKR----WSVIAKHLKGRIGKQCRERW 46
Query: 321 YDQLTSPMVAEGKWADTDDFHLVNALSGLDACCMDDVDWDNLLEHRSGTFCRKRWNQMVK 380
++ L +P V + W + +D + A L + LL R+ + WN ++
Sbjct: 47 HNHL-NPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAK---LLPGRTDNAIKNHWNSTMR 102
>pdb|2TRC|P Chain P, PhosducinTRANSDUCIN BETA-Gamma Complex
Length = 217
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 134 GFI----RGKRF--SLEEDEMIKKAVINYIEAHRLGEDGLNMVLHCRS--YPEIKHC 182
GF+ G++F ++E+++ + V+N E G D LN L C + YP +K C
Sbjct: 99 GFVYELETGEQFLETIEKEQKVTTIVVNIYEDGVRGCDALNSSLECLAAEYPXVKFC 155
>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 = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 214 WTPEELELVRKFYEKHGSDWKTMADTL-GKHRFHVKDAW 251
WTPEE E + + Y K GS W +A + G+ +K+ W
Sbjct: 57 WTPEEDETIFRNYLKLGSKWSVIAKLIPGRTDNAIKNRW 95
Score = 28.1 bits (61), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 11/92 (11%)
Query: 300 SWEAISEKLSTRTNAICCMKWYDQLTSPMVAEGKWADTDDFHLVNALSGLDACCMDDVDW 359
+W I+ L R+ C +W++ L P V + W +D + L + W
Sbjct: 24 NWPRITSFLPNRSPKQCRERWFNHL-DPAVVKHAWTPEEDETIFRNYLKLGS------KW 76
Query: 360 D---NLLEHRSGTFCRKRWNQMV-KHLGTDGN 387
L+ R+ + RWN + K + T+ N
Sbjct: 77 SVIAKLIPGRTDNAIKNRWNSSISKRISTNSN 108
>pdb|1B9Y|C Chain C, Structural Analysis Of Phosducin And Its Phosphorylation-
Regulated Interaction With Transducin Beta-Gamma
Length = 246
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 134 GFI----RGKRF--SLEEDEMIKKAVINYIEAHRLGEDGLNMVLHCRS--YPEIKHC 182
GF+ G++F ++E+++ + V+N E G D LN L C + YP +K C
Sbjct: 112 GFVYELETGEQFLETIEKEQKVTTIVVNIYEDGVRGCDALNSSLECLAAEYPMVKFC 168
>pdb|1B9X|C Chain C, Structural Analysis Of Phosducin And Its Phosphorylation-
Regulated Interaction With Transducin
Length = 246
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 134 GFI----RGKRF--SLEEDEMIKKAVINYIEAHRLGEDGLNMVLHCRS--YPEIKHC 182
GF+ G++F ++E+++ + V+N E G D LN L C + YP +K C
Sbjct: 112 GFVYELETGEQFLETIEKEQKVTTIVVNIYEDGVRGCDALNSSLECLAAEYPMVKFC 168
>pdb|2V1D|B Chain B, Structural Basis Of Lsd1-Corest Selectivity In Histone H3
Recognition
pdb|2Y48|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A N-
Terminal Snail Peptide
Length = 178
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 211 NRKWTPEELELVRKFYEKHGSDWKTMADTLG-KHRFHVKDAW 251
N +WT EE L + K+G D++ ++D +G K VK+ +
Sbjct: 76 NARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFF 117
>pdb|2IW5|B Chain B, Structural Basis For Corest-dependent Demethylation Of
Nucleosomes By The Human Lsd1 Histone Demethylase
pdb|2UXN|B Chain B, Structural Basis Of Histone Demethylation By Lsd1 Revealed
By Suicide Inactivation
pdb|2UXX|B Chain B, Human Lsd1 Histone Demethylase-Corest In Complex With An
Fad-Tranylcypromine Adduct
Length = 235
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 211 NRKWTPEELELVRKFYEKHGSDWKTMADTLG-KHRFHVKDAW 251
N +WT EE L + K+G D++ ++D +G K VK+ +
Sbjct: 133 NARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFF 174
>pdb|2XAF|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (+)-Cis-2-Phenylcyclopropyl-1-Amine
pdb|2XAG|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
Para-Bromo- (-)-Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAH|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With (+)-
Trans-2-Phenylcyclopropyl-1-Amine
pdb|2XAJ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With
(-)-Trans- 2-Phenylcyclopropyl-1-Amine
pdb|2XAQ|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2584, 13b)
pdb|2XAS|B Chain B, Crystal Structure Of Lsd1-Corest In Complex With A
Tranylcypromine Derivative (Mc2580, 14e)
Length = 482
Score = 28.5 bits (62), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 211 NRKWTPEELELVRKFYEKHGSDWKTMADTLG 241
N +WT EE L + K+G D++ ++D +G
Sbjct: 380 NARWTTEEQLLAVQAIRKYGRDFQAISDVIG 410
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 0.131 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,802,631
Number of Sequences: 62578
Number of extensions: 538914
Number of successful extensions: 1339
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1310
Number of HSP's gapped (non-prelim): 37
length of query: 419
length of database: 14,973,337
effective HSP length: 101
effective length of query: 318
effective length of database: 8,652,959
effective search space: 2751640962
effective search space used: 2751640962
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: 53 (25.0 bits)