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= 008631
(558 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4ATI|A Chain A, Mitf:m-Box Complex
pdb|4ATI|B Chain B, Mitf:m-Box Complex
pdb|4ATK|A Chain A, Mitf:e-Box Complex
pdb|4ATK|B Chain B, Mitf:e-Box Complex
Length = 118
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 13/108 (12%)
Query: 358 PKEEYIHVRARRGQATNSHSLAERVRREKISERMKFLQDLVPGCSKVT---GKAVMLDEI 414
P E A+ Q ++H+L ER RR I++R+K L L+P + K +L
Sbjct: 13 PTESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKAS 72
Query: 415 INYVQSLQRQ------VEFLSMKLATVNPRLDFNIEELLAKDVLQSRA 456
++Y++ LQR+ +E KL N L ++EL +Q+RA
Sbjct: 73 VDYIRKLQREQQRAKDLENRQKKLEHANRHLLLRVQEL----EMQARA 116
>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
Length = 82
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 369 RGQATNSHSLAERVRREKISERMKFLQDLVPGCSKVTGKAVMLDEIINYVQSLQR----- 423
RG+ +H+ E+ R I++++ L+DLV G K+ +L + I+Y++ LQ
Sbjct: 3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL 62
Query: 424 QVEFLSMKLA 433
+ E LS++ A
Sbjct: 63 KQENLSLRTA 72
>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
Length = 87
Score = 33.1 bits (74), Expect = 0.42, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 376 HSLAERVRREKISERMKFLQDLVPGCS-KVTGKAVMLDEIINYVQSLQRQVEFLSMKL 432
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+V L +
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDI 65
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 36/147 (24%), Positives = 63/147 (42%), Gaps = 18/147 (12%)
Query: 361 EYIHVRARRGQATNSHSLAERVRREKISERMKFLQDLVPGCSKVTGKAVMLDEIINYVQS 420
EY + R A +HS E+ RR+K++ + L LVP C+ ++ K LD++
Sbjct: 2 EYAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRK---LDKL----TV 54
Query: 421 LQRQVEFLSMKLATVNPRLDFNIEELLAKD------VLQSRAGPSSTLGFSPDMPL---- 470
L+ V+ + NP + N + D +L++ G +G L
Sbjct: 55 LRMAVQHMKTLRGATNPYTEANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSE 114
Query: 471 -VYPPVHQSQAGLMHGALPGMGNPSDI 496
V+ ++ SQ L+ +L +P DI
Sbjct: 115 SVFKILNYSQNDLIGQSLFDYLHPKDI 141
>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|E Chain E, Crystal Structure Of Myc-Max Recognizing Dna
Length = 83
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 376 HSLAERVRREKISERMKFLQDLVPGCS-KVTGKAVMLDEIINYVQSLQRQ 424
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 55
>pdb|1NLW|B Chain B, Crystal Structure Of Mad-Max Recognizing Dna
pdb|1NLW|E Chain E, Crystal Structure Of Mad-Max Recognizing Dna
Length = 76
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 376 HSLAERVRREKISERMKFLQDLVPGCS-KVTGKAVMLDEIINYVQSLQRQ 424
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 54
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 376 HSLAERVRREKISERMKFLQDLVPGCS-KVTGKAVMLDEIINYVQSLQRQ 424
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 56
>pdb|3M1R|A Chain A, The Crystal Structure Of Formimidoylglutamase From
Bacillus Subtilis Subsp. Subtilis Str. 168
pdb|3M1R|B Chain B, The Crystal Structure Of Formimidoylglutamase From
Bacillus Subtilis Subsp. Subtilis Str. 168
pdb|3M1R|C Chain C, The Crystal Structure Of Formimidoylglutamase From
Bacillus Subtilis Subsp. Subtilis Str. 168
pdb|3M1R|D Chain D, The Crystal Structure Of Formimidoylglutamase From
Bacillus Subtilis Subsp. Subtilis Str. 168
pdb|3M1R|E Chain E, The Crystal Structure Of Formimidoylglutamase From
Bacillus Subtilis Subsp. Subtilis Str. 168
pdb|3M1R|F Chain F, The Crystal Structure Of Formimidoylglutamase From
Bacillus Subtilis Subsp. Subtilis Str. 168
Length = 322
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 399 PGCSKVTGKAVMLDEIINYVQSLQRQVEFLSMKLATVNPRLDF 441
PGC + + DE++ V+ + +Q +++ V+P LDF
Sbjct: 255 PGCPAIGPGGLYTDELLEAVKYIAQQPNVAGIEIVEVDPTLDF 297
>pdb|1HLO|A Chain A, The Crystal Structure Of An Intact Human Max-Dna Complex:
New Insights Into Mechanisms Of Transcriptional Control
pdb|1HLO|B Chain B, The Crystal Structure Of An Intact Human Max-Dna Complex:
New Insights Into Mechanisms Of Transcriptional Control
Length = 80
Score = 30.0 bits (66), Expect = 3.9, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 376 HSLAERVRREKISERMKFLQDLVPGCS-KVTGKAVMLDEIINYVQSLQRQ 424
H+ ER RR+ I + L+D VP + +A +LD+ Y+Q ++R+
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 65
>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 73
Score = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 366 RARRGQATNSHSLAERVRREKISERMKFLQDLVPGCSKVTGKAVMLDEIINYVQSLQ 422
+ R A +HS E+ RR+K++ + L LVP C+ ++ K L + VQ ++
Sbjct: 3 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 59
>pdb|1FJX|A Chain A, Structure Of Ternary Complex Of Hhai Methyltransferase
Mutant (T250g) In Complex With Dna And Adohcy
pdb|2C7R|A Chain A, Hhai Dna Methyltransferase (T250g Mutant) Complex With
Oligonucleotide Containing 2-Aminopurine As A Target
Base (Gpgc:gmgc) And Sah
Length = 327
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2I9K|A Chain A, Engineered Extrahelical Base Destabilization Enhances
Sequence Discrimination Of Dna Methyltransferase M.Hhai
Length = 327
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2Z6A|A Chain A, S-Adenosyl-L-Methionine-Dependent Methyl Transfer:
Observable Precatalytic Intermediates During Dna
Cytosine Methylation
Length = 327
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2ZCJ|A Chain A, Ternary Structure Of The Glu119gln M.Hhai, C5-Cytosine Dna
Methyltransferase, With Unmodified Dna And Adohcy
Length = 327
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2UYH|A Chain A, Hhai Dna Methyltransferase S87q-Q237s Mutant Complex With
13mer Gcgc-Gmgc Oligonucleotide And Sah
Length = 327
Score = 28.9 bits (63), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|1MHT|A Chain A, Covalent Ternary Structure Of Hhai Methyltransferase, Dna
And S-Adenosyl-L-Homocysteine
pdb|3MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With
Unmodified Dna And Adohcy
pdb|4MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With Native
Dna And Adohcy
pdb|5MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With
Hemimethylated Dna And Adohcy
pdb|6MHT|A Chain A, Ternary Structure Of Hhai Methyltransferase With Adohcy
And Dna Containing 4'-Thio-2'deoxycytidine At The Target
pdb|7MHT|A Chain A, Cytosine-Specific Methyltransferase HhaiDNA COMPLEX
pdb|8MHT|A Chain A, Cytosine-Specific Methyltransferase HhaiDNA COMPLEX
pdb|9MHT|A Chain A, Cytosine-specific Methyltransferase Hhai/dna Complex
pdb|10MH|A Chain A, Ternary Structure Of Hhai Methyltransferase With Adohcy
And Hemimethylated Dna Containing
5,6-Dihydro-5-Azacytosine At The Target
pdb|2HMY|B Chain B, Binary Complex Of Hhai Methyltransferase With Adomet
Formed In The Presence Of A Short Nonpsecific Dna
Oligonucleotide
pdb|1M0E|A Chain A, Zebularine: A Novel Dna Methylation Inhibitor That Forms A
Covalent Complex With Dna Methyltransferase
pdb|1SKM|A Chain A, Hhai Methyltransferase In Complex With Dna Containing An
Abasic South Carbocyclic Sugar At Its Target Site
pdb|2C7O|A Chain A, Hhai Dna Methyltransferase Complex With 13mer
Oligonucleotide Containing 2-Aminopurine Adjacent To The
Target Base (Pcgc:gmgc) And Sah
pdb|2C7P|A Chain A, Hhai Dna Methyltransferase Complex With Oligonucleotide
Containing 2-Aminopurine Opposite To The Target Base (
Gcgc:gmpc) And Sah
pdb|2C7Q|A Chain A, Hhai Dna Methyltransferase Complex With Oligonucleotide
Containing 2-Aminopurine Outside The Recognition
Sequence (Paired With G) And Sah
pdb|2HR1|A Chain A, Ternary Structure Of Wt M.hhai C5-cytosine Dna
Methyltransferase With Unmodified Dna And Adohcy
pdb|1HMY|A Chain A, Crystal Structure Of The Hhai Dna Methyltransferase
Complexed With S- Adenosyl-L-Methionine
pdb|3EEO|A Chain A, M. Hhai Co-Crystallized With Synthetic Dsdna Containing A
Propane Diol In Place Of The Deoxycytidine Residue
Targeted For Methylation
Length = 327
Score = 28.9 bits (63), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2UZ4|A Chain A, Hhai Dna Methyltransferase R165n Mutant Complex With 13mer
Gcgc-Gmgc Oligonucleotide And Sah
Length = 327
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2UYC|A Chain A, Hhai Dna Methyltransferase R163n Mutant Complex With 13mer
Gcgc-Gmgc Oligonucleotide And Sah
Length = 327
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2Z6U|A Chain A, Ternary Structure Of The Glu119ala M.Hhai, C5-Cytosine Dna
Methyltransferase, With Unmodified Dna And Adohcy
Length = 327
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|2Z6Q|A Chain A, Ternary Structure Of Arg165ala M.Hhai C5-Cytosine Dna
Methyltransferase With Unmodified Dna And Adohcy
Length = 327
Score = 28.9 bits (63), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
>pdb|1SVU|A Chain A, Structure Of The Q237w Mutant Of Hhai Dna
Methyltransferase: An Insight Into Protein-Protein
Interactions
pdb|1SVU|B Chain B, Structure Of The Q237w Mutant Of Hhai Dna
Methyltransferase: An Insight Into Protein-Protein
Interactions
Length = 327
Score = 28.9 bits (63), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 519 ANVWEDELHNVVQMSYGTSAPSDSQDVNGSTPPDH 553
+N W+ V +M++G D VN T PDH
Sbjct: 38 SNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDH 72
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
0.309 0.128 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,445,914
Number of Sequences: 62578
Number of extensions: 752087
Number of successful extensions: 1562
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1538
Number of HSP's gapped (non-prelim): 37
length of query: 558
length of database: 14,973,337
effective HSP length: 104
effective length of query: 454
effective length of database: 8,465,225
effective search space: 3843212150
effective search space used: 3843212150
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)