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= psy13668
(513 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SVJ|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Amide
Length = 203
Score = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 288 MALVGGIG--ALSGTVSPYLVGVLTPNWLAKQICNSVTYKMRTILSGPTLTSPFDFSASV 345
M L GG+G A +S ++ VL PN + + Y + I+ P + S A++
Sbjct: 65 MGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAAL 124
Query: 346 GPGLGILAASYS 357
G G G L+ +
Sbjct: 125 GEGEGXLSVDRN 136
>pdb|1LM6|A Chain A, Crystal Structure Of Peptide Deformylase From
Streptococcus Pneumoniae
Length = 215
Score = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 288 MALVGGIG--ALSGTVSPYLVGVLTPNWLAKQICNSVTYKMRTILSGPTLTSPFDFSASV 345
M L GG+G A +S ++ VL PN + + Y + I+ P + S A++
Sbjct: 77 MGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAAL 136
Query: 346 GPGLGILAASYS 357
G G G L+ +
Sbjct: 137 GEGEGXLSVDRN 148
>pdb|3STR|P Chain P, Strep Peptide Deformylase With A Time Dependent
Thiazolidine Hydroxamic Acid
pdb|3SW8|P Chain P, Strep Peptide Deformylase With A Time Dependent
Dichlorobenzamide- Reverse Hydroxamic Acid
pdb|4EOX|P Chain P, X-Ray Structure Of Polypeptide Deformylase Bound To A
Acylprolinamide Inhibitor
Length = 203
Score = 32.7 bits (73), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 288 MALVGGIG--ALSGTVSPYLVGVLTPNWLAKQICNSVTYKMRTILSGPTLTSPFDFSASV 345
M L GG+G A +S ++ VL PN + + Y + I+ P + S A++
Sbjct: 65 MGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAAL 124
Query: 346 GPGLGILAASYS 357
G G G L+ +
Sbjct: 125 GEGEGCLSVDRN 136
>pdb|2AIE|P Chain P, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
505684
Length = 203
Score = 32.7 bits (73), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 288 MALVGGIG--ALSGTVSPYLVGVLTPNWLAKQICNSVTYKMRTILSGPTLTSPFDFSASV 345
M L GG+G A +S ++ VL PN + + Y + I+ P + S A++
Sbjct: 65 MGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAAL 124
Query: 346 GPGLGILAASYS 357
G G G L+ +
Sbjct: 125 GEGEGCLSVDRN 136
>pdb|2AI7|A Chain A, S.Pneumoniae Polypeptide Deformylase Complexed With Sb-
485345
pdb|2AIA|A Chain A, S.Pneumoniae Pdf Complexed With Sb-543668
Length = 203
Score = 32.7 bits (73), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 288 MALVGGIG--ALSGTVSPYLVGVLTPNWLAKQICNSVTYKMRTILSGPTLTSPFDFSASV 345
M L GG+G A +S ++ VL PN + + Y + I+ P + S A++
Sbjct: 65 MGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAAL 124
Query: 346 GPGLGILAASYS 357
G G G L+ +
Sbjct: 125 GEGEGCLSVDRN 136
>pdb|3LY1|A Chain A, Crystal Structure Of Putative Histidinol-Phosphate
Aminotransferase (Yp_050345.1) From Erwinia Carotovora
Atroseptica Scri1043 At 1.80 A Resolution
pdb|3LY1|B Chain B, Crystal Structure Of Putative Histidinol-Phosphate
Aminotransferase (Yp_050345.1) From Erwinia Carotovora
Atroseptica Scri1043 At 1.80 A Resolution
pdb|3LY1|C Chain C, Crystal Structure Of Putative Histidinol-Phosphate
Aminotransferase (Yp_050345.1) From Erwinia Carotovora
Atroseptica Scri1043 At 1.80 A Resolution
pdb|3LY1|D Chain D, Crystal Structure Of Putative Histidinol-Phosphate
Aminotransferase (Yp_050345.1) From Erwinia Carotovora
Atroseptica Scri1043 At 1.80 A Resolution
Length = 354
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 36/90 (40%), Gaps = 2/90 (2%)
Query: 344 SVGPGLGILAA--SYSGCNRLAVTVSFTLGMGTMGAFLPSLKVNALDLSPNYAGTLMALV 401
+ G GI AA +Y+ V T G G A + KV + N+A + L
Sbjct: 74 TAGSSEGIRAAIEAYASLEAQLVIPELTYGDGEHFAKIAGXKVTKVKXLDNWAFDIEGLK 133
Query: 402 GGIGALSGTVSPYLVGVLTPNGTLLEWRVV 431
+ A SG YLV P GT+ V+
Sbjct: 134 AAVAAYSGPSIVYLVNPNNPTGTITPADVI 163
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
0.322 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,261,376
Number of Sequences: 62578
Number of extensions: 642481
Number of successful extensions: 1437
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1428
Number of HSP's gapped (non-prelim): 32
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)