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= psy9185
(248 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 142 DYKKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLL 199
D +K A RER R+ +N AF+ L+ P ++L K+E LR AIRYI LQ LL
Sbjct: 5 DRRKAATMRERRRLSKVNEAFETLKR--STSSNPNQRLPKVEILRNAIRYIEGLQALL 60
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 147 ACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLLEYG 202
A RER RM +N A D LR ++ PC +KLSKIE+LR+A YI L +L G
Sbjct: 6 ANARERNRMHGLNAALDNLR-KVVPCYSKTQKLSKIETLRLAKNYIWALSEILRSG 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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 142 DYKKTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLL 199
D +K A RER R+ +N AF+ L+ P ++L K+E LR AIRYI LQ LL
Sbjct: 11 DRRKAATMRERRRLSKVNEAFETLKR--STSSNPNQRLPKVEILRNAIRYIEGLQALL 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 = 34.3 bits (77), Expect = 0.069, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
E+ R MN D L + +P C +KL K+ LRMA+++++ L+
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 34.3 bits (77), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 151 ERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQ 196
E+ R MN D L + +P C +KL K+ LRMA+++++ L+
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 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 = 33.9 bits (76), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 145 KTACDRERTRMRDMNRAFDLLRNRLPPCKPPGKKLSKIESLRMAIRYIRHLQCLLE 200
KT D + + +MN + L+ L P P KK+SK+E L+ I YI LQ L+
Sbjct: 27 KTPVDDPMSLLYNMNDCYSKLK-ELVPSIPQNKKVSKMEILQHVIDYILDLQIALD 81
>pdb|3I2W|A Chain A, Crystal Structure Of EfcF-Bar Domain Of Drosophila
SyndapinPACSIN
pdb|3I2W|B Chain B, Crystal Structure Of EfcF-Bar Domain Of Drosophila
SyndapinPACSIN
Length = 290
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 198 LLEYGPEYETILYSSRSVVPSSTNTSYVYP--LDDSCVDCGSAIGQW 242
L+E GPEY T + + V+ S S V+ D+ C D S I W
Sbjct: 55 LIEKGPEYGTTEAAWKGVLTESERISDVHXKIKDNLCNDVNSQIKTW 101
>pdb|1PYT|C Chain C, Ternary Complex Of Procarboxypeptidase A, Proproteinase E,
And Chymotrypsinogen C
Length = 253
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 204 EYE-TILYSSRSVVPSSTNTSYVYPLDDS-CVDCGSAI 239
EY+ ++L S V+P + +V+PL +S CV CG+ I
Sbjct: 70 EYDRSVLQGSEQVIPINAGDLFVHPLWNSNCVACGNDI 107
>pdb|1FON|A Chain A, Crystal Structure Of Bovine Procarboxypeptidase A-S6
Subunit Iii, A Highly Structured Truncated Zymogen E
pdb|1FON|B Chain B, Crystal Structure Of Bovine Procarboxypeptidase A-S6
Subunit Iii, A Highly Structured Truncated Zymogen E
Length = 240
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 204 EYE-TILYSSRSVVPSSTNTSYVYPLDDS-CVDCGSAI 239
EY+ ++L S V+P + +V+PL +S CV CG+ I
Sbjct: 57 EYDRSVLEGSEQVIPINAGDLFVHPLWNSNCVACGNDI 94
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 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,912,636
Number of Sequences: 62578
Number of extensions: 188076
Number of successful extensions: 375
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 367
Number of HSP's gapped (non-prelim): 10
length of query: 248
length of database: 14,973,337
effective HSP length: 96
effective length of query: 152
effective length of database: 8,965,849
effective search space: 1362809048
effective search space used: 1362809048
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)