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= 039494
(140 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 38/66 (57%)
Query: 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVAN 60
+K IEN+ R +TFSKR GI +K EL LT + + LV S++G ++F P E +
Sbjct: 23 IKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVT 82
Query: 61 RFLGLN 66
+ G N
Sbjct: 83 QQEGRN 88
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN----PSIE 56
M+ I+N+ R TFSKR +GI +K EL TLT + + LV S++G ++F P I
Sbjct: 16 MEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMIT 75
Query: 57 AVANRFLGLNC 67
+ + L C
Sbjct: 76 SETGKALIQTC 86
>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 = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN----PSIE 56
M+ I+N+ R TFSKR +GI +K EL TLT + + LV S++G ++F P I
Sbjct: 17 MEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMIT 76
Query: 57 AVANRFLGLNC 67
+ + L C
Sbjct: 77 SETGKALIQTC 87
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 3 KIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRF 62
+I +E R +TF+KR G+ +K EL L IA ++F+ S K F + + ++ V ++
Sbjct: 9 RIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKY 68
Query: 63 LGLN 66
N
Sbjct: 69 TEYN 72
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%)
Query: 3 KIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRF 62
+I +E R +TF+KR G+ +K EL L + IA ++F+ S K F + + ++ V ++
Sbjct: 9 RIMDERNRQVTFTKRKFGLMKKAYELSVLADAEIALIIFNSSNKLFQYASTDMDKVLLKY 68
Query: 63 LGLN 66
N
Sbjct: 69 TEYN 72
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 3 KIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRF 62
+I +E R +TF+KR G+ +K EL L IA ++F+ S K F + + ++ V ++
Sbjct: 9 RIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKY 68
Query: 63 LGLN 66
N
Sbjct: 69 TEYN 72
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 3 KIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVANRF 62
+I +E R +TF+KR G+ +K EL L IA ++F+ S K F + + ++ V ++
Sbjct: 9 RIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKY 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 = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 35/62 (56%)
Query: 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAVAN 60
+ +I ++ R +TF+KR G+ +K EL L IA ++F+ + + F + + ++ V
Sbjct: 8 ISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLL 67
Query: 61 RF 62
++
Sbjct: 68 KY 69
>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 = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 33/58 (56%)
Query: 1 MKKIENEDGRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGNPSIEAV 58
+ +I ++ R +TF+KR G+ +K EL L IA ++F+ + + F + + ++ V
Sbjct: 7 ISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRV 64
>pdb|2E26|A Chain A, Crystal Structure Of Two Repeat Fragment Of Reelin
Length = 725
Score = 30.4 bits (67), Expect = 0.31, Method: Composition-based stats.
Identities = 28/98 (28%), Positives = 39/98 (39%), Gaps = 25/98 (25%)
Query: 9 GRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN----PSIEAVANRFLG 64
G LIT S R G+ + S +T + + + + Q KP F N P + +A RF
Sbjct: 638 GCLITPSNRNQGVLLEYSVNGGITWNLLMEIFYDQYSKP-GFVNILLPPDAKEIATRF-- 694
Query: 65 LNCQMRKRKETQPRWWETPVYEFNHQELLQMDATIDNL 102
RWW+ H L Q D IDN+
Sbjct: 695 -------------RWWQP-----RHDGLDQNDWAIDNV 714
>pdb|3A7Q|A Chain A, Structural Basis For Specific Recognition Of Reelin By Its
Receptors
Length = 725
Score = 30.4 bits (67), Expect = 0.32, Method: Composition-based stats.
Identities = 28/98 (28%), Positives = 39/98 (39%), Gaps = 25/98 (25%)
Query: 9 GRLITFSKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFSFGN----PSIEAVANRFLG 64
G LIT S R G+ + S +T + + + + Q KP F N P + +A RF
Sbjct: 638 GCLITPSNRNQGVLLEYSVNGGITWNLLMEIFYDQYSKP-GFVNILLPPDAKEIATRF-- 694
Query: 65 LNCQMRKRKETQPRWWETPVYEFNHQELLQMDATIDNL 102
RWW+ H L Q D IDN+
Sbjct: 695 -------------RWWQP-----RHDGLDQNDWAIDNV 714
>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 = 26.6 bits (57), Expect = 4.3, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 15 SKRTSGIYRKVSELVTLTVSAIARLVFSQSGKPFS 49
+K +GI RK +L+ IA ++ S+ GKP +
Sbjct: 91 AKERAGILRKWFDLIIANADDIALIMTSEQGKPLA 125
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
0.321 0.134 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,672,752
Number of Sequences: 62578
Number of extensions: 119116
Number of successful extensions: 273
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 263
Number of HSP's gapped (non-prelim): 12
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)