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= 043113
(172 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 2e-04, Method: Compositional matrix adjust.
Identities = 22/39 (56%), Positives = 29/39 (74%)
Query: 3 GKKTKRRQKIEMKKIENEDDRLITFSKRGSGIYKKASEI 41
GKKT+ R KI+M+ I+N+ R TFSKR +GI KKA E+
Sbjct: 6 GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYEL 44
>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 = 2e-04, Method: Compositional matrix adjust.
Identities = 22/39 (56%), Positives = 29/39 (74%)
Query: 3 GKKTKRRQKIEMKKIENEDDRLITFSKRGSGIYKKASEI 41
GKKT+ R KI+M+ I+N+ R TFSKR +GI KKA E+
Sbjct: 5 GKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYEL 43
>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 = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/35 (60%), Positives = 26/35 (74%)
Query: 7 KRRQKIEMKKIENEDDRLITFSKRGSGIYKKASEI 41
K R+KIE+K IEN+ R +TFSKR GI KKA E+
Sbjct: 16 KERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFEL 50
>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 = 34.7 bits (78), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 9 RQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEAIHLCQPSVKAI----ANRFLGMSQ 64
R+KI++ +I ++ +R +TF+KR G+ KKA +E LC + I ANR +
Sbjct: 3 RKKIQISRILDQRNRQVTFTKRKFGLMKKA---YELSVLCDCEIALIIFNSANRLFQYAS 59
Query: 65 LHNDNIHPLVKAYS 78
D + YS
Sbjct: 60 TDMDRVLLKYTEYS 73
>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 = 34.3 bits (77), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 9 RQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEAIHLCQPSVKAI 55
R+KI++ +I +E +R +TF+KR G+ KKA +E LC + I
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKA---YELSVLCDCEIALI 45
>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 = 34.3 bits (77), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 9 RQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEAIHLCQPSVKAI----ANRFLGMSQ 64
R+KI++ +I ++ +R +TF+KR G+ KKA +E LC + I ANR +
Sbjct: 2 RKKIQISRILDQRNRQVTFTKRKFGLMKKA---YELSVLCDCEIALIIFNSANRLFQYAS 58
Query: 65 LHNDNIHPLVKAYS 78
D + YS
Sbjct: 59 TDMDRVLLKYTEYS 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 = 34.3 bits (77), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 9 RQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEAIHLCQPSVKAI 55
R+KI++ +I +E +R +TF+KR G+ KKA +E LC + I
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKA---YELSVLCDCEIALI 45
>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 = 34.3 bits (77), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 9 RQKIEMKKIENEDDRLITFSKRGSGIYKKASEIWEAIHLCQPSVKAI 55
R+KI++ +I +E +R +TF+KR G+ KKA +E LC + I
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKA---YELSVLCDCEIALI 45
>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 = 33.1 bits (74), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 25/33 (75%)
Query: 9 RQKIEMKKIENEDDRLITFSKRGSGIYKKASEI 41
R+KI++ +I +E +R +TF+KR G+ KKA E+
Sbjct: 2 RKKIQITRIMDERNRQVTFTKRKFGLMKKAYEL 34
>pdb|2JMR|A Chain A, Nmr Structure Of The E. Coli Type 1 Pilus Subunit Fimf
Length = 179
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 48 CQPSVKAIANRFLGMSQLHNDNIHPL---VKAYSHARINELNQQHNDL 92
C +V A+ F G++ HN N+ L V A S I LN+Q N +
Sbjct: 57 CGNAVSAVKVGFTGVADSHNANLLALENTVSAASGLGIQLLNEQQNQI 104
>pdb|3BWU|F Chain F, Crystal Structure Of The Ternary Complex Of Fimd
(n-terminal Domain, Fimdn) With Fimc And The
N-terminally Truncated Pilus Subunit Fimf (fimft)
Length = 142
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 48 CQPSVKAIANRFLGMSQLHNDNIHPL---VKAYSHARINELNQQHNDL 92
C +V A+ F G++ HN N+ L V A S I LN+Q N +
Sbjct: 44 CGNAVSAVKVGFTGVADSHNANLLALENTVSAASGLGIQLLNEQQNQI 91
>pdb|3JWN|E Chain E, Complex Of Fimc, Fimf, Fimg And Fimh
pdb|3JWN|F Chain F, Complex Of Fimc, Fimf, Fimg And Fimh
pdb|3JWN|K Chain K, Complex Of Fimc, Fimf, Fimg And Fimh
pdb|3JWN|L Chain L, Complex Of Fimc, Fimf, Fimg And Fimh
Length = 154
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 48 CQPSVKAIANRFLGMSQLHNDNIHPL---VKAYSHARINELNQQHNDL 92
C +V A+ F G++ HN N+ L V A + I LN+Q N +
Sbjct: 56 CGNAVSAVKVGFTGVADSHNANLLALENTVSAAAGLGIQLLNEQQNQI 103
>pdb|3LA4|A Chain A, Crystal Structure Of The First Plant Urease From Jack Bean
(Canavalia Ensiformis)
Length = 840
Score = 26.6 bits (57), Expect = 6.9, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 62 MSQLHNDNIHPLVKAYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWE 121
M H D P A++H+RI + D+L + + + M RV E R W+
Sbjct: 590 MVXHHLDREIPEDLAFAHSRIRKKTIAAEDVLNDIGAISIISSDSQAMGRVGEVISRTWQ 649
Query: 122 TPVDELNLQE-LLQMDSAVDD 141
T D++ Q L+ DS+ +D
Sbjct: 650 T-ADKMKAQTGPLKCDSSDND 669
>pdb|4H9M|A Chain A, The First Jack Bean Urease (Canavalia Ensiformis) Complex
Obtained At 1.52 Resolution
Length = 840
Score = 26.6 bits (57), Expect = 7.3, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 62 MSQLHNDNIHPLVKAYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWE 121
M H D P A++H+RI + D+L + + + M RV E R W+
Sbjct: 590 MVXHHLDREIPEDLAFAHSRIRKKTIAAEDVLNDIGAISIISSDSQAMGRVGEVISRTWQ 649
Query: 122 TPVDELNLQE-LLQMDSAVDD 141
T D++ Q L+ DS+ +D
Sbjct: 650 T-ADKMKAQTGPLKCDSSDND 669
>pdb|4GY7|A Chain A, Crystallographic Structure Analysis Of Urease From Jack
Bean (Canavalia Ensiformis) At 1.49 A Resolution
Length = 840
Score = 26.6 bits (57), Expect = 7.5, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 62 MSQLHNDNIHPLVKAYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRWWE 121
M H D P A++H+RI + D+L + + + M RV E R W+
Sbjct: 590 MVXHHLDREIPEDLAFAHSRIRKKTIAAEDVLNDIGAISIISSDSQAMGRVGEVISRTWQ 649
Query: 122 TPVDELNLQE-LLQMDSAVDD 141
T D++ Q L+ DS+ +D
Sbjct: 650 T-ADKMKAQTGPLKCDSSDND 669
>pdb|4HPQ|C Chain C, Crystal Structure Of The Atg17-Atg31-Atg29 Complex
pdb|4HPQ|F Chain F, Crystal Structure Of The Atg17-Atg31-Atg29 Complex
Length = 413
Score = 26.2 bits (56), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 68 DNIHPLVKAYSHARINELNQQHNDLLRQLDEEKEQQNMLKQMRRVKETQPRW------WE 121
+ I L++ + + + ++ Q N L + E+ N+LK+++R KET + E
Sbjct: 304 EGISALIQKFKASCLEDIRQTRNLLDFYANFERSYHNLLKEVKRRKETAAKLSQILKSCE 363
Query: 122 TPVDELNLQEL 132
T ++++N +L
Sbjct: 364 TQLEQINTADL 374
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
0.316 0.130 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,483,184
Number of Sequences: 62578
Number of extensions: 161554
Number of successful extensions: 600
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 583
Number of HSP's gapped (non-prelim): 36
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
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: 48 (23.1 bits)