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= 026436
(238 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 = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 58 DHVIAERKRREKLNQRFIALSALVPGLK----KTDKASILGDSIKYLKQL---QERVKAL 110
+H + ER+RR +N R L L+P + +K +IL S+ Y+++L Q+R K L
Sbjct: 30 NHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL 89
Query: 111 EEQTSK 116
E + K
Sbjct: 90 ENRQKK 95
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 34.3 bits (77), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 62 AERKRREKLNQRFIALSALVPG-LKKTDKASILGDSIKYLKQLQE 105
+E+KRR++ N L +++PG +K DK+++L SI +L++ +E
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKE 63
>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 = 33.9 bits (76), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 62 AERKRREKLNQRFIALSALVPG-LKKTDKASILGDSIKYLKQLQERVKALE 111
+E+KRR++ N L +++PG +K DK+++L SI +L++ +E LE
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE 65
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGLK--KTDKASILGDSIKYLKQLQERVKALEE 112
H ERKRR+ + F +L VP L+ K +A IL + +Y++ ++ +V L++
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQ 63
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGL----KKTDKASILGDSIKYLKQLQERVKALEEQT 114
H E++RR+K+N L++LVP +K DK ++L +++++K L+ E
Sbjct: 17 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEAN 76
Query: 115 SKKTVES 121
K T S
Sbjct: 77 YKPTFLS 83
>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 = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGLK--KTDKASILGDSIKYLKQLQER 106
H ERKRR+ + F +L VP L+ K +A IL + +Y++ ++ +
Sbjct: 16 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 65
>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 = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 6/53 (11%)
Query: 59 HVIAERKRREKLNQRFIALSALVP--GLKKT----DKASILGDSIKYLKQLQE 105
H ER+RR+K+N + LS ++P ++ T K IL + Y+++L++
Sbjct: 9 HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61
>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 = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 4/50 (8%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGL----KKTDKASILGDSIKYLKQLQ 104
H E++RR+K+N L++LVP +K DK ++L +++++K L+
Sbjct: 13 HSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>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 = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGLKKTDKAS---ILGDSIKYLKQLQ 104
H + ER+RR +L + F AL +P L+ +KA IL + Y+ +Q
Sbjct: 10 HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58
>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 = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGLK--KTDKASILGDSIKYLKQLQER 106
H ERKRR+ + F +L VP L+ K +A IL + +Y++ ++ +
Sbjct: 5 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 54
>pdb|2BO9|B Chain B, Human Carboxypeptidase A4 In Complex With Human Latexin.
pdb|2BO9|D Chain D, Human Carboxypeptidase A4 In Complex With Human Latexin
Length = 222
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 133 TDDETSP-TDINFDAQSNQYLPEIEVRVSDRDVLIRIHCEKNNNKGHLANILSEIENVHH 191
T ET+P + F+ ++ + E + R ++ E N + N+ E+ V H
Sbjct: 79 TGQETAPEVNFTFEGETGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPEMTLVLH 138
Query: 192 LSVLSCNVLPFGNSTVD 208
L+ ++C + + NST D
Sbjct: 139 LAWVACGYIIWQNSTED 155
>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 = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGLK--KTDKASILGDSIKYLKQLQER 106
H ERKRR+ + F +L VP L+ K +A IL + +Y++ ++ +
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 55
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 59 HVIAERKRREKLNQRFIALSALVPGLK--KTDKASILGDSIKYLKQLQER 106
H ERKRR+ + F +L VP L+ K +A IL + +Y++ ++ +
Sbjct: 7 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 56
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
0.315 0.130 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,635,076
Number of Sequences: 62578
Number of extensions: 202100
Number of successful extensions: 602
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 598
Number of HSP's gapped (non-prelim): 25
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
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: 50 (23.9 bits)