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= psy5774
(201 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 = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVL 73
R++ N RER R ++ A LR++VP + +KLSK E LR++ YI L+ +L
Sbjct: 2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL 57
>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 = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVL 73
R+ RER R V+ AF L+R ++P +++L K EILR +IRYI L +L
Sbjct: 6 RRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALL 60
>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 = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 18 RKIFTNTRERWRQQNVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVL 73
R+ RER R V+ AF L+R ++P +++L K EILR +IRYI L +L
Sbjct: 12 RRKAATMRERRRLSKVNEAFETLKRSTSSNP-NQRLPKVEILRNAIRYIEGLQALL 66
>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 = 34.7 bits (78), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 32 NVSGAFGELRRLVPTHPPDKKLSKNEILRMSIRYIRLLNGVLE 74
N++ + +L+ LVP+ P +KK+SK EIL+ I YI L L+
Sbjct: 39 NMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALD 81
>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 = 30.0 bits (66), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 23 NTRERWRQQNVSGAFGELRRLVP-THPPDKKLSKNEILRMSIRYIRLL 69
N ER R+ N++ EL L+P ++ PD + +K IL+ S+ YIR L
Sbjct: 32 NLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKL 79
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 26 ERWRQQNVSGAFGELRRLVPT-HPPDKKLSKNEILRMSIRYIRLLNGV 72
E+ R+ ++ EL LVPT + +KL K +LRM++++++ L G
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA 68
>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 = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 26 ERWRQQNVSGAFGELRRLVPT-HPPDKKLSKNEILRMSIRYIRLLNGV 72
E+ R+ ++ EL LVPT + +KL K +LRM++++++ L G
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA 64
>pdb|4ATH|A Chain A, Mitf Apo Structure
pdb|4ATH|B Chain B, Mitf Apo Structure
Length = 83
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 32 NVSGAFGELRRLVP-THPPDKKLSKNEILRMSIRYIRLL 69
N++ EL L+P ++ PD + +K IL+ S+ YIR L
Sbjct: 6 NINDRIKELGTLIPKSNDPDXRWNKGTILKASVDYIRKL 44
>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 = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 36 AFGELRRLVPTHPPDKKLSKNEILRMSIRYI 66
+ LR LVP P +LS+ EIL+ I YI
Sbjct: 32 CYSRLRELVPGVPRGTQLSQVEILQRVIDYI 62
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
0.314 0.131 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,954,840
Number of Sequences: 62578
Number of extensions: 151876
Number of successful extensions: 201
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 194
Number of HSP's gapped (non-prelim): 9
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)