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= 010045
(519 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 = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 285 KARVRARRGQATDPHSIAERLRREKIAERMKNLQELVPNSNKTD----KASMLDEIIDYV 340
+AR A+ Q D H++ ER RR I +R+K L L+P SN D K ++L +DY+
Sbjct: 17 EARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYI 76
Query: 341 KFLQ 344
+ LQ
Sbjct: 77 RKLQ 80
>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 = 36.2 bits (82), Expect = 0.040, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 292 RGQATDPHSIAERLRREKIAERMKNLQELVPNSN-KTDKASMLDEIIDYVKFLQLQVKVL 350
RG+ H+ E+ R I +++ L++LV + K +K+++L + IDY++FLQ + L
Sbjct: 3 RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKL 62
Query: 351 SMSRLGAAGAV 361
L AV
Sbjct: 63 KQENLSLRTAV 73
>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 = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 299 HSIAERLRREKIAERMKNLQELVPN--SNKTDKASMLDEIIDYVKFLQLQVKVL 350
H+ ER RR+ I + +L++ VP+ K +A +LD+ +Y+++++ +V L
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTL 61
>pdb|3JXF|A Chain A, Ca-Like Domain Of Human Ptprz
pdb|3JXF|B Chain B, Ca-Like Domain Of Human Ptprz
Length = 272
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 18/125 (14%)
Query: 311 AERMKNLQELVPNSNKTDKASMLDEI--IDYVKFLQLQVKVLSMSRLGAAGAVLPLI--- 365
A+R + +E V K S+L E+ + + F + V S+SR G A+ P I
Sbjct: 130 ADRFSSFEEAVKGKGKLRALSILFEVGTEENLDFKAIIDGVESVSRFGKQAALDPFILLN 189
Query: 366 -----TDGQAEASKGLSLSPQADQGVD-------ISLNSDQIAFEEEVVKLMESNVTKAM 413
TD + L+ SP VD +S++ Q+A EV+ + +S M
Sbjct: 190 LLPNSTDKYYIYNGSLT-SPPCTDTVDWIVFKDTVSISESQLAVFCEVLTMQQSGYVMLM 248
Query: 414 QYLQN 418
YLQN
Sbjct: 249 DYLQN 253
>pdb|3S97|A Chain A, Ptprz Cntn1 Complex
pdb|3S97|B Chain B, Ptprz Cntn1 Complex
Length = 273
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 18/125 (14%)
Query: 311 AERMKNLQELVPNSNKTDKASMLDEI--IDYVKFLQLQVKVLSMSRLGAAGAVLPLI--- 365
A+R + +E V K S+L E+ + + F + V S+SR G A+ P I
Sbjct: 131 ADRFSSFEEAVKGKGKLRALSILFEVGTEENLDFKAIIDGVESVSRFGKQAALDPFILLN 190
Query: 366 -----TDGQAEASKGLSLSPQADQGVD-------ISLNSDQIAFEEEVVKLMESNVTKAM 413
TD + L+ SP VD +S++ Q+A EV+ + +S M
Sbjct: 191 LLPNSTDKYYIYNGSLT-SPPCTDTVDWIVFKDTVSISESQLAVFCEVLTMQQSGYVMLM 249
Query: 414 QYLQN 418
YLQN
Sbjct: 250 DYLQN 254
>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 = 32.3 bits (72), Expect = 0.70, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 299 HSIAERLRREKIAERMKNLQELVPN--SNKTDKASMLDEIIDYVKFLQ 344
H+ ER RR+ I + +L++ VP+ K +A +LD+ +Y+++++
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 53
>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 = 32.0 bits (71), Expect = 0.88, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 299 HSIAERLRREKIAERMKNLQELVPN--SNKTDKASMLDEIIDYVKFLQ 344
H+ ER RR+ I + +L++ VP+ K +A +LD+ +Y+++++
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 52
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 299 HSIAERLRREKIAERMKNLQELVPN--SNKTDKASMLDEIIDYVKFLQ 344
H+ ER RR+ I + +L++ VP+ K +A +LD+ +Y+++++
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 54
>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 = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 299 HSIAERLRREKIAERMKNLQELVPN--SNKTDKASMLDEIIDYVKFLQ 344
H+ ER RR+ I + +L++ VP+ K +A +LD+ +Y+++++
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 63
>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 = 31.2 bits (69), Expect = 1.5, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 289 RARRGQATDPHSIAERLRREKIAERMKNLQELVPNSN----KTDKASMLDEIIDYVKFLQ 344
+ R A + HS E+ RR+K+ + L LVP N K DK ++L + ++K L+
Sbjct: 3 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 286 ARVRARRGQATDPHSIAERLRREKIAERMKNLQELVPNSN----KTDKASMLDEIIDYVK 341
A + R A + HS E+ RR+K+ + L LVP N K DK ++L + ++K
Sbjct: 4 AEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 63
Query: 342 FLQ 344
L+
Sbjct: 64 TLR 66
>pdb|1Y10|A Chain A, Mycobacterial Adenylyl Cyclase Rv1264, Holoenzyme,
Inhibited State
pdb|1Y10|B Chain B, Mycobacterial Adenylyl Cyclase Rv1264, Holoenzyme,
Inhibited State
pdb|1Y10|C Chain C, Mycobacterial Adenylyl Cyclase Rv1264, Holoenzyme,
Inhibited State
pdb|1Y10|D Chain D, Mycobacterial Adenylyl Cyclase Rv1264, Holoenzyme,
Inhibited State
pdb|1Y11|A Chain A, Mycobacterial Adenylyl Cyclase Rv1264, Holoenzyme, Active
State
Length = 407
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 340 VKFLQLQVKVLSMSRLGAAGAVLPLITDGQAEASKGLSLSPQADQGVDISLNSDQIAFEE 399
++ LQ + + ++R+ AV+ + DG+A A +A + V++ LN DQ+
Sbjct: 80 LELLQRVQRAVGLARVDDPDAVVHMRADGEAAA--------RAQRFVELGLNPDQVVLVV 131
Query: 400 EVVKLMESNVTKAMQY 415
V+ S+ +AM+Y
Sbjct: 132 RVLAEGLSHAAEAMRY 147
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 30.0 bits (66), Expect = 3.5, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 307 REKIAERMKNLQELVPNSNKTD----KASMLDEIIDYVKFLQ 344
R I +R+K L L+P SN D K ++L +DY++ LQ
Sbjct: 4 RFNINDRIKELGTLIPKSNDPDXRWNKGTILKASVDYIRKLQ 45
>pdb|2EV1|A Chain A, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, At Ph 6.0
pdb|2EV1|B Chain B, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, At Ph 6.0
pdb|2EV2|A Chain A, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, At Ph 8.5
pdb|2EV2|B Chain B, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, At Ph 8.5
pdb|2EV3|A Chain A, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, At Ph 5.3
pdb|2EV3|B Chain B, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, At Ph 5.3
pdb|2EV4|A Chain A, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, With A Salt
Precipitant
pdb|2EV4|B Chain B, Structure Of Rv1264n, The Regulatory Domain Of The
Mycobacterial Adenylyl Cylcase Rv1264, With A Salt
Precipitant
Length = 222
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 340 VKFLQLQVKVLSMSRLGAAGAVLPLITDGQAEASKGLSLSPQADQGVDISLNSDQIAFEE 399
++ LQ + + ++R+ AV+ + DG+A A +A + V++ LN DQ+
Sbjct: 92 LELLQRVQRAVGLARVDDPDAVVHMRADGEAAA--------RAQRFVELGLNPDQVVLVV 143
Query: 400 EVVKLMESNVTKAMQY 415
V+ S+ +AM+Y
Sbjct: 144 RVLAEGLSHAAEAMRY 159
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 302 AERLRREKIAERMKNLQELVP-NSNKTDKASMLDEIIDYVK 341
+E+ RR++ +K L ++P N+ K DK+++L + ID+++
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 28.5 bits (62), Expect = 9.8, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 302 AERLRREKIAERMKNLQELVP-NSNKTDKASMLDEIIDYVK 341
+E+ RR++ +K L ++P N+ K DK+++L + ID+++
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 55
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
0.311 0.128 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,406,730
Number of Sequences: 62578
Number of extensions: 579876
Number of successful extensions: 1028
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1025
Number of HSP's gapped (non-prelim): 18
length of query: 519
length of database: 14,973,337
effective HSP length: 103
effective length of query: 416
effective length of database: 8,527,803
effective search space: 3547566048
effective search space used: 3547566048
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)