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= psy11118
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QL2|B Chain B, Crystal Structure Of The Basic-Helix-Loop-Helix Domains
Of The Heterodimer E47NEUROD1 BOUND TO DNA
pdb|2QL2|D Chain D, Crystal Structure Of The Basic-Helix-Loop-Helix Domains
Of The Heterodimer E47NEUROD1 BOUND TO DNA
Length = 60
Score = 68.6 bits (166), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 32/56 (57%), Positives = 43/56 (76%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVI 93
RR+++N RER RMH LN A +LR+V+P K ++LSKIETL LAKNYI AL+ ++
Sbjct: 2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL 57
>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 = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 28/40 (70%)
Query: 50 MHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
++++ND + L+E++P + + +++SK+E L +YI+ L
Sbjct: 37 LYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDL 76
>pdb|2QL2|A Chain A, Crystal Structure Of The Basic-Helix-Loop-Helix Domains
Of The Heterodimer E47NEUROD1 BOUND TO DNA
pdb|2QL2|C Chain C, Crystal Structure Of The Basic-Helix-Loop-Helix Domains
Of The Heterodimer E47NEUROD1 BOUND TO DNA
Length = 60
Score = 32.0 bits (71), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSL-REVIPHVKKERRLSKIETLTLAKNYIMAL 89
RR+ +N RER+R+ +N+AF+ L R H+K ++ +K+ L A I+ L
Sbjct: 1 RRMANNARERVRVRDINEAFRELGRMCQLHLKSDKAQTKLLILQQAVQVILGL 53
>pdb|2LFH|A Chain A, Solution Nmr Structure Of The Helix-Loop-Helix Domain Of
Human Id3 Protein, Northeast Structural Genomics
Consortium Target Hr3111a
pdb|2LFH|B Chain B, Solution Nmr Structure Of The Helix-Loop-Helix Domain Of
Human Id3 Protein, Northeast Structural Genomics
Consortium Target Hr3111a
Length = 68
Score = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%)
Query: 50 MHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNV 92
+ +N + LRE++P V + +LS++E L +YI+ L V
Sbjct: 26 LDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQVV 68
>pdb|1MDY|B Chain B, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
pdb|1MDY|C Chain C, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
pdb|1MDY|D Chain D, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
Length = 62
Score = 30.8 bits (68), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICD 95
RR + RER R+ +N+AF++L+ + RL K+E L A YI L ++ D
Sbjct: 6 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQ-RLPKVEILRNAIRYIEGLQALLRD 62
>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 = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
+R N ER R + D+F SLR+ +P ++ E + S+ + L A YI +
Sbjct: 12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYM 62
>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 = 0.31, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
+R N ER R + D+F SLR+ +P ++ E + S+ + L A YI +
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYM 52
>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 = 30.4 bits (67), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVI 93
+R N ER R + D+F SLR+ +P ++ E + S+ + L A YI + +
Sbjct: 4 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRKV 58
>pdb|1MDY|A Chain A, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
Perspectives On Dna Recognition And Implications For
Transcriptional Activation
Length = 68
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICD 95
RR + RER R+ +N+AF++L+ + RL K+E L A YI L ++ D
Sbjct: 12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQ-RLPKVEILRNAIRYIEGLQALLRD 68
>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 = 29.6 bits (65), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
+R N ER R + D+F SLR+ +P ++ E + S+ + L A YI +
Sbjct: 1 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYM 51
>pdb|1AN2|A Chain A, Recognition By Max Of Its Cognate Dna Through A Dimeric
BHLHZ DOMAIN
Length = 86
Score = 29.6 bits (65), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
+R N ER R + D+F SLR+ +P ++ E + S+ + L A YI +
Sbjct: 3 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYM 53
>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 = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%)
Query: 36 NMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
N++R N ER R + L +F +LR+ IP ++ + K+ L A YI+++
Sbjct: 4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 57
>pdb|4HTO|A Chain A, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv
Apo Form
pdb|4HTP|A Chain A, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv
Bound To Artemis Peptide
pdb|4HTP|B Chain B, Crystal Structure Of The Dbd Domain Of Human Dna Ligase Iv
Bound To Artemis Peptide
Length = 240
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 12/74 (16%)
Query: 57 FQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICDMRGEDS----PYVAPDSSTGL 112
+ ++R ++P +++ER I+ LAK YI L N+ D G+D+ Y P TG
Sbjct: 65 YPAMRLILPQLERERMAYGIKETMLAKLYI-ELLNLPRD--GKDALKLLNYRTP---TG- 117
Query: 113 ITSGTQGDTALTAH 126
T G GD A+ A+
Sbjct: 118 -THGDAGDFAMIAY 130
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 0.129 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,197,929
Number of Sequences: 62578
Number of extensions: 97762
Number of successful extensions: 226
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 214
Number of HSP's gapped (non-prelim): 16
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
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: 46 (22.3 bits)