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= 038097
(268 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 68 RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQ 121
R K E H + E++RRDK+N + L L+P CN K+DK ++L A+ ++KTL+
Sbjct: 9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 68 RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQ 121
R K E H + E++RRDK+N + L L+P CN K+DK ++L A+ ++KTL+
Sbjct: 5 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 31/40 (77%), Gaps = 1/40 (2%)
Query: 80 ERKRRDKINKKMRALQELIP-NCNKVDKASMLEEAIDYLK 118
E+KRRD+ N ++ L ++P N K+DK+++L+++ID+L+
Sbjct: 20 EKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59
>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 = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 37/58 (63%), Gaps = 3/58 (5%)
Query: 65 KSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQ 121
+S +KRT H E++ R IN K+ L++L+ K++K+++L +AIDY++ LQ
Sbjct: 1 QSRGEKRT--AHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQ 56
>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 = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 32/42 (76%), Gaps = 1/42 (2%)
Query: 78 RYERKRRDKINKKMRALQELIP-NCNKVDKASMLEEAIDYLK 118
+ E+KRRD+ N ++ L ++P N K+DK+++L+++ID+L+
Sbjct: 14 KSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 55
>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 = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQ 121
H ER+RR IN +++ L LIP N + +K ++L+ ++DY++ LQ
Sbjct: 31 HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQ 80
>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 = 35.0 bits (79), Expect = 0.038, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQFQV 124
H ERKRRD I +L++ +P+ K +A +L++A +Y++ ++ +V
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKV 58
>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 = 34.7 bits (78), Expect = 0.060, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQ 121
H ERKRRD I +L++ +P+ K +A +L++A +Y++ ++
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 63
>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 = 34.3 bits (77), Expect = 0.072, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQ 121
H ERKRRD I +L++ +P+ K +A +L++A +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 = 34.3 bits (77), Expect = 0.076, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQ 121
H ERKRRD I +L++ +P+ K +A +L++A +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 = 33.9 bits (76), Expect = 0.085, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQ 121
H ERKRRD I +L++ +P+ K +A +L++A +Y++ ++
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 54
>pdb|1AN4|A Chain A, Structure And Function Of The BHLHZ DOMAIN OF USF
pdb|1AN4|B Chain B, Structure And Function Of The BHLHZ DOMAIN OF USF
Length = 65
Score = 33.1 bits (74), Expect = 0.16, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 76 HKRYERKRRDKINKKMRALQELIPNCNK------VDKASMLEEAIDYLKTLQ 121
H ER+RRDKIN + L ++IP+ + K +L +A DY++ L+
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60
>pdb|1NKP|A Chain A, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|D Chain D, Crystal Structure Of Myc-Max Recognizing Dna
Length = 88
Score = 32.7 bits (73), Expect = 0.23, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 67 NRKKRTPEVHKRYERKRRDKINKKMRALQELIP---NCNKVDKASMLEEAIDYLKTLQ 121
N K+RT H ER+RR+++ + AL++ IP N K K +L++A Y+ ++Q
Sbjct: 4 NVKRRT---HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58
>pdb|1UKL|C Chain C, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|D Chain D, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|E Chain E, Crystal Structure Of Importin-Beta And Srebp-2 Complex
pdb|1UKL|F Chain F, Crystal Structure Of Importin-Beta And Srebp-2 Complex
Length = 61
Score = 30.8 bits (68), Expect = 0.74, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 84 RDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQ 121
R IN K+ L++L+ + K K+ +L +AIDY+K LQ
Sbjct: 1 RSSINDKIIELKDLVXGTDAKXHKSGVLRKAIDYIKYLQ 39
>pdb|1I9W|A Chain A, Crystal Structure Of The Fusion Glycoprotein E1 From
Semliki Forest Virus
Length = 390
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 36/101 (35%), Gaps = 23/101 (22%)
Query: 160 FPPMGIGMDGRM---------QMGAGCNPAQFLMPPIPGATAVPGIQMP-GFP------G 203
FPP G G GR N A L P PG VP Q P GF G
Sbjct: 189 FPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKG 248
Query: 204 QPLPMSMLRTPLGLMHKTNPV----AGVSRAAASMEVKDSA 240
L + P G KTNPV V SM + DSA
Sbjct: 249 TALNT---KAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSA 286
>pdb|1D4T|A Chain A, Crystal Structure Of The Xlp Protein Sap In Complex With
A Slam Peptide
pdb|1D4W|A Chain A, Crystal Structure Of The Xlp Protein Sap In Complex With
Slam Phosphopeptide
pdb|1D4W|B Chain B, Crystal Structure Of The Xlp Protein Sap In Complex With
Slam Phosphopeptide
pdb|1D1Z|A Chain A, Crystal Structure Of The Xlp Protein Sap
pdb|1D1Z|B Chain B, Crystal Structure Of The Xlp Protein Sap
pdb|1D1Z|C Chain C, Crystal Structure Of The Xlp Protein Sap
pdb|1D1Z|D Chain D, Crystal Structure Of The Xlp Protein Sap
pdb|1M27|A Chain A, Crystal Structure Of SapFYNSH3SLAM TERNARY COMPLEX
Length = 104
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 25/56 (44%)
Query: 33 LKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKIN 88
L R E G C C Y + V+ + S + P VHKRY RK ++ I+
Sbjct: 30 LLRDSESVPGVYCLCVLYHGYIYTYRVSQTETGSWSAETAPGVHKRYFRKIKNLIS 85
>pdb|1RER|A Chain A, Crystal Structure Of The Homotrimer Of Fusion Glycoprotein
E1 From Semliki Forest Virus.
pdb|1RER|B Chain B, Crystal Structure Of The Homotrimer Of Fusion Glycoprotein
E1 From Semliki Forest Virus.
pdb|1RER|C Chain C, Crystal Structure Of The Homotrimer Of Fusion Glycoprotein
E1 From Semliki Forest Virus.
pdb|2ALA|A Chain A, Crystal Structure Of The Semliki Forest Virus Envelope
Protein E1 In Its Monomeric Conformation
Length = 391
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 36/101 (35%), Gaps = 23/101 (22%)
Query: 160 FPPMGIGMDGRM---------QMGAGCNPAQFLMPPIPGATAVPGIQMP-GFP------G 203
FPP G G GR N A L P PG VP Q P GF G
Sbjct: 189 FPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKG 248
Query: 204 QPLPMSMLRTPLGLMHKTNPV----AGVSRAAASMEVKDSA 240
L + P G KTNPV V SM + DSA
Sbjct: 249 TALNT---KAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSA 286
>pdb|1KA6|A Chain A, SapSH2D1A BOUND TO PEPTIDE N-Py
pdb|1KA7|A Chain A, SapSH2D1A BOUND TO PEPTIDE N-Y-C
Length = 128
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 25/56 (44%)
Query: 33 LKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKIN 88
L R E G C C Y + V+ + S + P VHKRY RK ++ I+
Sbjct: 30 LLRDSESVPGVYCLCVLYHGYIYTYRVSQTETGSWSAETAPGVHKRYFRKIKNLIS 85
>pdb|4AYA|A Chain A, Crystal Structure Of Id2 Hlh Homodimer At 2.1a Resolution
pdb|4AYA|B Chain B, Crystal Structure Of Id2 Hlh Homodimer At 2.1a Resolution
Length = 97
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 90 KMRALQELIPNCNKVDKASMLEEAIDYLKTLQF 122
K++ L IP KV K +L+ IDY+ LQ
Sbjct: 46 KLKELVPSIPQNKKVSKMEILQHVIDYILDLQI 78
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
0.317 0.131 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,106,544
Number of Sequences: 62578
Number of extensions: 321539
Number of successful extensions: 638
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 624
Number of HSP's gapped (non-prelim): 26
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)