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= 001333
(1097 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OLS|A Chain A, The Crystal Structure Of The Phosphoenolpyruvate Synthase
From Neisseria Meningitidis
Length = 794
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 80/348 (22%), Positives = 141/348 (40%), Gaps = 76/348 (21%)
Query: 794 VGAKSCNI-KFLRERVPSWIKIPTSVAIPFGAFETVLSENINKDIANKISRLYKFINGGD 852
VG K+ ++ + + + +++P A A+ L+ N ++ +IS ++ D
Sbjct: 20 VGGKNASLGEMISQLTEKGVRVPGGFATTAEAYRAFLAHN---GLSERISAALAKLDVED 76
Query: 853 LSKL----QEIQEAVLQMSAPLSLIYELK---NKM-------------RSSG----MP-- 886
+++L +EI++ +L P L E++ NKM RSS +P
Sbjct: 77 VAELARVGKEIRQWILDTPFPEQLDAEIEAAWNKMVADAGGADISVAVRSSATAEDLPDA 136
Query: 887 -WPGDE-------GWNLAWRSIKKVWASKWNERAFISCRKANLNHDNLCMAVLIQETICG 938
+ G + G + ++ V+AS +N+RA HD + ++ +Q +
Sbjct: 137 SFAGQQETFLNINGLDNVKEAMHHVFASLYNDRAISYRVHKGFEHDIVALSAGVQRMVRS 196
Query: 939 D--YAFVIHTKNPLSGDNSEIYTEIVKGLGETLV-GAYPGRAMSFVTKKNNLKSPIVTCY 995
D + V+ T + SG + ++ GLGE +V GA F K LK+
Sbjct: 197 DSGASGVMFTLDTESGYDQVVFVTSSYGLGENVVQGAV--NPDEFYVFKPTLKA------ 248
Query: 996 PSKLIGLYGKPSIIFRSDSNGEDLEKYAGAGLYDSVIMNDPEKVVLDYSRDPMVGDK--- 1052
GKP+I L K G+ + + E + D D+
Sbjct: 249 --------GKPAI----------LRKTMGSKHIKMIFTDKAEAGKSVTNVDVPEEDRNRF 290
Query: 1053 SFQTSVFSKIAETGKIIESLYGYPQDIE----GVLKDGLIYVVQARPQ 1096
S +++A IE YG P DIE G+ DG +Y++QARP+
Sbjct: 291 SITDEEITELAHYALTIEKHYGRPMDIEWGRDGL--DGKLYILQARPE 336
>pdb|2HBH|A Chain A, Crystal Structure Of Vitamin D Nuclear Receptor Ligand
Binding Domain Bound To A Locked Side-Chain Analog Of
Calcitriol And Src-1 Peptide
pdb|2HC4|A Chain A, Crystal Structure Of The Lbd Of Vdr Of Danio Rerio In
Complex With Calcitriol
pdb|2HCD|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The
Vitamin D Nuclear Receptor In Complex With Gemini And A
Coactivator Peptide
pdb|3DR1|A Chain A, Side-Chain Fluorine Atoms Of Non-Steroidal Vitamin D3
Analogs Stabilize Helix 12 Of Vitamin D Receptor
pdb|3O1D|A Chain A, Structure-Function Study Of Gemini Derivatives With Two
Different Side Chains At C-20, Gemini-0072 And
Gemini-0097.
pdb|3O1E|A Chain A, Structure-Function Of Gemini Derivatives With Two
Different Side Chains At C-20, Gemini-0072 And
Gemini-0097
Length = 302
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 681 RITGEEEIPVGVVAVLTPDMPDVLSHVSIRARNNKVC 717
++ EE + + + +L+PD P V HV I A +++C
Sbjct: 201 KLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLC 237
>pdb|4FHH|A Chain A, Development Of Synthetically Accessible Non-Secosteroidal
Hybrid Molecules Combining Vitamin D Receptor Agonism
And Histone Deacetylase Inhibition
pdb|4FHI|A Chain A, Development Of Synthetically Accessible Non-Secosteroidal
Hybrid Molecules Combining Vitamin D Receptor Agonism
And Histone Deacetylase Inhibition
pdb|4G1D|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
pdb|4G1Y|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
pdb|4G1Z|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
pdb|4G20|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
pdb|4G21|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
pdb|4G2H|A Chain A, Structural Basis For The Accommodation Of Bis- And
Tris-Aromatic Derivatives In Vitamin D Nuclear Receptor
Length = 300
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 681 RITGEEEIPVGVVAVLTPDMPDVLSHVSIRARNNKVC 717
++ EE + + + +L+PD P V HV I A +++C
Sbjct: 199 KLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLC 235
>pdb|2B2C|A Chain A, Cloning, Expression, Characterisation And Three-
Dimensional Structure Determination Of The
Caenorhabditis Elegans Spermidine Synthase
pdb|2B2C|B Chain B, Cloning, Expression, Characterisation And Three-
Dimensional Structure Determination Of The
Caenorhabditis Elegans Spermidine Synthase
Length = 314
Score = 29.6 bits (65), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 950 LSGDNSEIYTEIVKGLGETLVGAYPGRAMSFVTKK 984
++G + E T+++K G+ + GA+PG+A S KK
Sbjct: 20 MNGASDEEPTKVLKSDGQEMGGAWPGQAFSLQVKK 54
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
0.320 0.136 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,198,709
Number of Sequences: 62578
Number of extensions: 1262638
Number of successful extensions: 3012
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 3007
Number of HSP's gapped (non-prelim): 6
length of query: 1097
length of database: 14,973,337
effective HSP length: 109
effective length of query: 988
effective length of database: 8,152,335
effective search space: 8054506980
effective search space used: 8054506980
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)