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= psy7374
(106 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A04|A Chain A, Structure Of The Dna-Bound T-Box Domain Of Human Tbx1, A
Transcription Factor Associated With The Digeorge
Syndrome
pdb|4A04|B Chain B, Structure Of The Dna-Bound T-Box Domain Of Human Tbx1, A
Transcription Factor Associated With The Digeorge
Syndrome
Length = 203
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 20/31 (64%), Positives = 26/31 (83%)
Query: 75 VTCHLETKELWDKFNELGTEMIITKTGRKLF 105
V+ LE K LWD+FN+LGTEMI+TK GR++F
Sbjct: 16 VSVQLEMKALWDEFNQLGTEMIVTKAGRRMF 46
>pdb|1H6F|A Chain A, Human Tbx3, A Transcription Factor Responsible For Ulnar-
Mammary Syndrome, Bound To A Palindromic Dna Site
pdb|1H6F|B Chain B, Human Tbx3, A Transcription Factor Responsible For Ulnar-
Mammary Syndrome, Bound To A Palindromic Dna Site
Length = 193
Score = 48.9 bits (115), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 19/29 (65%), Positives = 26/29 (89%)
Query: 77 CHLETKELWDKFNELGTEMIITKTGRKLF 105
HLE KELWD+F++ GTEM+ITK+GR++F
Sbjct: 7 VHLEAKELWDQFHKRGTEMVITKSGRRMF 35
>pdb|2X6U|A Chain A, Crystal Structure Of Human Tbx5 In The Dna-Free Form
pdb|2X6V|A Chain A, Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna-
Free Form
pdb|2X6V|B Chain B, Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna-
Free Form
Length = 203
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 24/31 (77%)
Query: 75 VTCHLETKELWDKFNELGTEMIITKTGRKLF 105
+ L +ELW KF+E+GTEMIITK GR++F
Sbjct: 6 IKVFLHERELWLKFHEVGTEMIITKAGRRMF 36
>pdb|1XBR|A Chain A, T Domain From Xenopus Laevis Bound To Dna
pdb|1XBR|B Chain B, T Domain From Xenopus Laevis Bound To Dna
Length = 184
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 21/27 (77%)
Query: 79 LETKELWDKFNELGTEMIITKTGRKLF 105
LE ++LW +F EL EMI+TK GR++F
Sbjct: 6 LEERDLWTRFKELTNEMIVTKNGRRMF 32
>pdb|3A9E|B Chain B, Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And
Antagonist- Bound Rxr-Alpha Heterodimer Ligand Binding
Domains
Length = 269
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 83 ELWDKFNELGTEMII 97
+LWDKF+EL T+ II
Sbjct: 71 DLWDKFSELSTKCII 85
>pdb|4DQM|A Chain A, Revealing A Marine Natural Product As A Novel Agonist
For Retinoic Acid Receptors With A Unique Binding Mode
And Antitumor Activity
pdb|4DQM|C Chain C, Revealing A Marine Natural Product As A Novel Agonist
For Retinoic Acid Receptors With A Unique Binding Mode
And Antitumor Activity
Length = 234
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 83 ELWDKFNELGTEMII 97
+LWDKF+EL T+ II
Sbjct: 42 DLWDKFSELSTKCII 56
>pdb|1DKF|B Chain B, Crystal Structure Of A Heterodimeric Complex Of Rar And
Rxr Ligand-Binding Domains
Length = 235
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 83 ELWDKFNELGTEMII 97
+LWDKF+EL T+ II
Sbjct: 42 DLWDKFSELSTKCII 56
>pdb|1XDK|B Chain B, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
pdb|1XDK|F Chain F, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
Length = 303
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 84 LWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 72 LWDKFSELATKCII 85
>pdb|3KMR|A Chain A, Crystal Structure Of Raralpha Ligand Binding Domain In
Complex With An Agonist Ligand (Am580) And A
Coactivator Fragment
pdb|3KMZ|B Chain B, Crystal Structure Of Raralpha Ligand Binding Domain In
Complex With The Inverse Agonist Bms493 And A
Corepressor Fragment
pdb|3KMZ|A Chain A, Crystal Structure Of Raralpha Ligand Binding Domain In
Complex With The Inverse Agonist Bms493 And A
Corepressor Fragment
Length = 266
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 83 ELWDKFNELGTEMII 97
+LWDKF+EL T+ II
Sbjct: 68 DLWDKFSELSTKCII 82
>pdb|1FCY|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The RarbetaGAMMA-
Selective Retinoid Cd564
Length = 236
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 84 LWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 45 LWDKFSELATKCII 58
>pdb|1FCX|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The Rargamma-Selective
Retinoid Bms184394
pdb|1FCZ|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The Panagonist Retinoid
Bms181156
pdb|1FD0|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The Rargamma-Selective
Retinoid Sr11254
Length = 235
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 84 LWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 44 LWDKFSELATKCII 57
>pdb|1XAP|A Chain A, Structure Of The Ligand Binding Domain Of The Retinoic
Acid Receptor Beta
pdb|4DM6|A Chain A, Crystal Structure Of Rarb Lbd Homodimer In Complex With
Ttnpb
pdb|4DM6|B Chain B, Crystal Structure Of Rarb Lbd Homodimer In Complex With
Ttnpb
pdb|4DM8|A Chain A, Crystal Structure Of Rarb Lbd In Complex With 9cis
Retinoic Acid
pdb|4DM8|B Chain B, Crystal Structure Of Rarb Lbd In Complex With 9cis
Retinoic Acid
Length = 267
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 84 LWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 70 LWDKFSELATKCII 83
>pdb|1EXA|A Chain A, Enantiomer Discrimination Illustrated By Crystal
Structures Of The Human Retinoic Acid Receptor
Hrargamma Ligand Binding Domain: The Complex With The
Active R-Enantiomer Bms270394.
pdb|1EXX|A Chain A, Enantiomer Discrimination Illustrated By Crystal
Structures Of The Human Retinoic Acid Receptor
Hrargamma Ligand Binding Domain: The Complex With The
Inactive S-Enantiomer Bms270395
Length = 246
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 84 LWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 49 LWDKFSELATKCII 62
>pdb|2LBD|A Chain A, Ligand-Binding Domain Of The Human Retinoic Acid
Receptor Gamma Bound To All-Trans Retinoic Acid
pdb|3LBD|A Chain A, Ligand-binding Domain Of The Human Retinoic Acid
Receptor Gamma Bound To 9-cis Retinoic Acid
pdb|4LBD|A Chain A, Ligand-binding Domain Of The Human Retinoic Acid
Receptor Gamma Bound To The Synthetic Agonist Bms961
Length = 267
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 84 LWDKFNELGTEMII 97
LWDKF+EL T+ II
Sbjct: 70 LWDKFSELATKCII 83
>pdb|3J0A|A Chain A, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
An Electron Microscopy Single Particle Reconstruction
pdb|3J0A|B Chain B, Homology Model Of Human Toll-Like Receptor 5 Fitted Into
An Electron Microscopy Single Particle Reconstruction
Length = 844
Score = 26.2 bits (56), Expect = 5.2, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 55 QTPPLNPLLQERFNSEELRHVTCHLETKELWDKFNEL 91
QTP NP L++ F E + + ET+ WD F L
Sbjct: 445 QTPSENPSLEQLFLGENMLQLA--WETELCWDVFEGL 479
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
0.318 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,815,353
Number of Sequences: 62578
Number of extensions: 81108
Number of successful extensions: 221
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 206
Number of HSP's gapped (non-prelim): 16
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
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: 45 (21.9 bits)