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= 042438
(89 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MU6|A Chain A, Inhibiting The Binding Of Class Iia Histone Deacetylases
To Myocyte Enhancer Factor-2 By Small Molecules
pdb|3MU6|B Chain B, Inhibiting The Binding Of Class Iia Histone Deacetylases
To Myocyte Enhancer Factor-2 By Small Molecules
pdb|3MU6|C Chain C, Inhibiting The Binding Of Class Iia Histone Deacetylases
To Myocyte Enhancer Factor-2 By Small Molecules
pdb|3MU6|D Chain D, Inhibiting The Binding Of Class Iia Histone Deacetylases
To Myocyte Enhancer Factor-2 By Small Molecules
Length = 71
Score = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 40/70 (57%), Positives = 55/70 (78%), Gaps = 2/70 (2%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61
GR K+++ RI ++ NRQVTF+KRK G++KKA+ELSVLCD EIAL+IF+ S K + YAS
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 HTMDKIIARY 71
MDK++ +Y
Sbjct: 61 --MDKVLLKY 68
>pdb|3KOV|A Chain A, Structure Of Mef2a Bound To Dna Reveals A Completely
Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
RECRUITS Transcription Co-Factors
pdb|3KOV|B Chain B, Structure Of Mef2a Bound To Dna Reveals A Completely
Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
RECRUITS Transcription Co-Factors
pdb|3KOV|I Chain I, Structure Of Mef2a Bound To Dna Reveals A Completely
Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
RECRUITS Transcription Co-Factors
pdb|3KOV|J Chain J, Structure Of Mef2a Bound To Dna Reveals A Completely
Folded Mads-BoxMEF2 DOMAIN THAT RECOGNIZES DNA AND
RECRUITS Transcription Co-Factors
pdb|3P57|A Chain A, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
On Dna
pdb|3P57|B Chain B, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
On Dna
pdb|3P57|C Chain C, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
On Dna
pdb|3P57|D Chain D, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
On Dna
pdb|3P57|I Chain I, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
On Dna
pdb|3P57|J Chain J, Crystal Structure Of The P300 Taz2 Domain Bound To Mef2
On Dna
Length = 90
Score = 86.7 bits (213), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 40/70 (57%), Positives = 55/70 (78%), Gaps = 2/70 (2%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61
GR K+++ RI ++ NRQVTF+KRK G++KKA+ELSVLCD EIAL+IF+ S K + YAS
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 HTMDKIIARY 71
MDK++ +Y
Sbjct: 61 --MDKVLLKY 68
>pdb|1EGW|A Chain A, Crystal Structure Of Mef2a Core Bound To Dna
pdb|1EGW|B Chain B, Crystal Structure Of Mef2a Core Bound To Dna
pdb|1EGW|C Chain C, Crystal Structure Of Mef2a Core Bound To Dna
pdb|1EGW|D Chain D, Crystal Structure Of Mef2a Core Bound To Dna
Length = 77
Score = 86.7 bits (213), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 40/70 (57%), Positives = 55/70 (78%), Gaps = 2/70 (2%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61
GR K+++ RI ++ NRQVTF+KRK G++KKA+ELSVLCD EIAL+IF+ S K + YAS
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 62 HTMDKIIARY 71
MDK++ +Y
Sbjct: 61 --MDKVLLKY 68
>pdb|1TQE|P Chain P, Mechanism Of Recruitment Of Class Ii Histone
Deacetylases By Myocyte Enhancer Factor-2
pdb|1TQE|Q Chain Q, Mechanism Of Recruitment Of Class Ii Histone
Deacetylases By Myocyte Enhancer Factor-2
pdb|1TQE|R Chain R, Mechanism Of Recruitment Of Class Ii Histone
Deacetylases By Myocyte Enhancer Factor-2
pdb|1TQE|S Chain S, Mechanism Of Recruitment Of Class Ii Histone
Deacetylases By Myocyte Enhancer Factor-2
Length = 93
Score = 85.9 bits (211), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 38/71 (53%), Positives = 56/71 (78%), Gaps = 2/71 (2%)
Query: 1 MGRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASD 60
MGR K+++ RI ++ NRQVTF+KRK G++KKA+ELSVLCD EIAL+IF+ + + + YAS
Sbjct: 1 MGRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYAST 60
Query: 61 HHTMDKIIARY 71
MD+++ +Y
Sbjct: 61 D--MDRVLLKY 69
>pdb|1C7U|A Chain A, Complex Of The Dna Binding Core Domain Of The
Transcription Factor Mef2a With A 20mer Oligonucleotide
pdb|1C7U|B Chain B, Complex Of The Dna Binding Core Domain Of The
Transcription Factor Mef2a With A 20mer Oligonucleotide
Length = 85
Score = 84.7 bits (208), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 40/70 (57%), Positives = 55/70 (78%), Gaps = 2/70 (2%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61
GR K+++ RI ++ NRQVTF+KRK G++KKA+ELSVL DAEIAL+IF+ S K + YAS
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTD 60
Query: 62 HTMDKIIARY 71
MDK++ +Y
Sbjct: 61 --MDKVLLKY 68
>pdb|1N6J|A Chain A, Structural Basis Of Sequence-Specific Recruitment Of
Histone Deacetylases By Myocyte Enhancer Factor-2
pdb|1N6J|B Chain B, Structural Basis Of Sequence-Specific Recruitment Of
Histone Deacetylases By Myocyte Enhancer Factor-2
Length = 93
Score = 83.2 bits (204), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 37/70 (52%), Positives = 55/70 (78%), Gaps = 2/70 (2%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61
GR K+++ RI ++ NRQVTF+KRK G++KKA+ELSVLCD EIAL+IF+ + + + YAS
Sbjct: 1 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTD 60
Query: 62 HTMDKIIARY 71
MD+++ +Y
Sbjct: 61 --MDRVLLKY 68
>pdb|1MNM|A Chain A, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|B Chain B, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 100
Score = 68.6 bits (166), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 44/57 (77%)
Query: 3 RGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYAS 59
R K+E+K IENKT R VTFSKRK+GI+KKAFELSVL ++ L++ S +G Y +++
Sbjct: 18 RRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFST 74
>pdb|1K6O|B Chain B, Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dna
Complex
pdb|1K6O|C Chain C, Crystal Structure Of A Ternary Sap-1SRFC-Fos Sre Dna
Complex
Length = 103
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/91 (38%), Positives = 51/91 (56%), Gaps = 11/91 (12%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASDH 61
GR K++++ I+NK R TFSKRK GI+KKA+ELS L ++ L++ S +G Y +A+
Sbjct: 10 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT-- 67
Query: 62 HTMDKIIARYRREVGQ------LNSADQRSR 86
K+ E G+ LNS D R
Sbjct: 68 ---RKLQPMITSETGKALIQTCLNSPDSPPR 95
>pdb|1SRS|A Chain A, Serum Response Factor (Srf) Core Complexed With Specific
Sre Dna
pdb|1SRS|B Chain B, Serum Response Factor (Srf) Core Complexed With Specific
Sre Dna
pdb|1HBX|A Chain A, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
pdb|1HBX|B Chain B, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
pdb|1HBX|D Chain D, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
pdb|1HBX|E Chain E, Ternary Complex Of Sap-1 And Srf With Specific Sre Dna
Length = 92
Score = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 41/58 (70%)
Query: 2 GRGKVELKRIENKTNRQVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYAS 59
GR K++++ I+NK R TFSKRK GI+KKA+ELS L ++ L++ S +G Y +A+
Sbjct: 11 GRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFAT 68
>pdb|3EK1|A Chain A, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|B Chain B, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|C Chain C, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|D Chain D, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|E Chain E, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|F Chain F, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|G Chain G, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
pdb|3EK1|H Chain H, Crystal Structure Of Aldehyde Dehydrogenase From Brucella
Melitensis Biovar Abortus 2308
Length = 504
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 22 SKRKNGILKKAFELSVLCDAEIALVIFSPSGK 53
+K + GIL+K F+L + +IAL++ S GK
Sbjct: 91 AKERAGILRKWFDLIIANADDIALIMTSEQGK 122
>pdb|1RYL|A Chain A, The Crystal Structure Of A Protein Of Unknown Function
Yfbm From Escherichia Coli
pdb|1RYL|B Chain B, The Crystal Structure Of A Protein Of Unknown Function
Yfbm From Escherichia Coli
Length = 167
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 29 LKKAFELSVLCDAEI-ALVIFSPSGKAYHYASDHHTMDKIIARYRREVGQLNSA 81
L+K F + L + EI V FS + +AS M+K+I+ YRR + Q N A
Sbjct: 108 LRKQFSIKRLNEMEIYPGVTFSEELEGQLFASIMLDMEKLISAYRRMLRQGNHA 161
>pdb|4HKM|A Chain A, Crystal Structure Of An Anthranilate
Phosphoribosyltransferase (Target Id Nysgrc-016600) From
Xanthomonas Campestris
pdb|4HKM|B Chain B, Crystal Structure Of An Anthranilate
Phosphoribosyltransferase (Target Id Nysgrc-016600) From
Xanthomonas Campestris
Length = 346
Score = 27.3 bits (59), Expect = 2.3, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 48 FSPSGKAYHYASDHHTMDKIIARYRREVG 76
+ +G + YA HH K++A RRE G
Sbjct: 147 LAQTGIGFXYAPVHHPAXKVVAPVRREXG 175
>pdb|3OKT|A Chain A, Mouse Plexin A2, Extracellular Domains 1-4
pdb|3OKY|A Chain A, Plexin A2 In Complex With Semaphorin 6a
pdb|4GZA|A Chain A, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
pdb|4GZA|B Chain B, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
pdb|4GZA|C Chain C, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
pdb|4GZA|D Chain D, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
pdb|4GZA|E Chain E, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
pdb|4GZA|F Chain F, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
Length = 681
Score = 26.2 bits (56), Expect = 5.5, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 18 QVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASD 60
Q + + L +AF +S D ++ IFS K YH+ D
Sbjct: 280 QAAYLAKPGEALAQAFNIS--SDEDVLFAIFSKGQKQYHHPPD 320
>pdb|3AL8|B Chain B, Plexin A2 SEMAPHORIN 6A COMPLEX
pdb|3AL9|A Chain A, Mouse Plexin A2 Extracellular Domain
pdb|3AL9|B Chain B, Mouse Plexin A2 Extracellular Domain
Length = 539
Score = 26.2 bits (56), Expect = 5.5, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 18 QVTFSKRKNGILKKAFELSVLCDAEIALVIFSPSGKAYHYASD 60
Q + + L +AF +S D ++ IFS K YH+ D
Sbjct: 281 QAAYLAKPGEALAQAFNIS--SDEDVLFAIFSKGQKQYHHPPD 321
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 0.133 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,420,770
Number of Sequences: 62578
Number of extensions: 78023
Number of successful extensions: 150
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 139
Number of HSP's gapped (non-prelim): 15
length of query: 89
length of database: 14,973,337
effective HSP length: 56
effective length of query: 33
effective length of database: 11,468,969
effective search space: 378475977
effective search space used: 378475977
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)