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= psy4832
(770 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RWI|B Chain B, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
pdb|1RWI|A Chain A, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
pdb|1RWL|A Chain A, Extracellular Domain Of Mycobacterium Tuberculosis Pknd
Length = 270
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 45/193 (23%), Positives = 79/193 (40%), Gaps = 47/193 (24%)
Query: 129 NFHEGILQKGDGSSLHLKHEFPRTVSVVMGTGLQRPLV---CKDCDGVARDARLLTPVAL 185
N+ EG+ G+ R V + G+ Q L D DGVA D
Sbjct: 108 NYPEGLAVDTQGAVYVADRGNNRVVKLAAGSKTQTVLPFTGLNDPDGVAVDNS------- 160
Query: 186 TSGPDGSLYVGDF--NLVRRLTPEGNVFTVLQLSATQVSYQYYLALSPADGHLYISDAEK 243
G++YV D N V +L E N VL T ++ + +A+ A G +Y+++
Sbjct: 161 -----GNVYVTDTDNNRVVKLEAESNNQVVLPF--TDITAPWGIAVDEA-GTVYVTEHNT 212
Query: 244 HQILRVLSLESVADPSINWEVAVGSGERCIPGDETNCGDNGPALAAKLSHPKGLAIKADK 303
+Q++++L+ + + +P L+ P +A+ +D+
Sbjct: 213 NQVVKLLAGSTTS--------------TVLP-------------FTGLNTPLAVAVDSDR 245
Query: 304 TMFIADGTNIRVV 316
T+++AD N RVV
Sbjct: 246 TVYVADRGNDRVV 258
>pdb|4IJZ|A Chain A, Crystal Structure Of Diaminopimelate Epimerase From
Escherichia Coli
pdb|4IJZ|B Chain B, Crystal Structure Of Diaminopimelate Epimerase From
Escherichia Coli
Length = 280
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 30/136 (22%), Positives = 54/136 (39%), Gaps = 10/136 (7%)
Query: 208 GNVFTVLQLSATQVSYQYYLALSPADGHLYISDAEKHQILRVLSLESVADPSINWEVAVG 267
GN F V+ V + L AD HL + ++L +E DP +++ +
Sbjct: 10 GNDFMVVDAVTQNVFFSPELIRRLADRHLGVG------FDQLLVVEPPYDPELDFHYRIF 63
Query: 268 SGERCIPGDETNCGDNGPALAAKLSHPKGLAIKADKTMFIADGTNIRVVSPEGIIHTLIG 327
+ + G E NG A+ KGL K D + A+G + V+ + ++ +G
Sbjct: 64 NAD----GSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMG 119
Query: 328 HHKHHNIWSPFNCHRS 343
PF +++
Sbjct: 120 EPNFEPSAVPFRANKA 135
>pdb|4IK0|A Chain A, Crystal Structure Of Diaminopimelate Epimerase Y268a
Mutant From Escherichia Coli
pdb|4IK0|B Chain B, Crystal Structure Of Diaminopimelate Epimerase Y268a
Mutant From Escherichia Coli
Length = 280
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 30/136 (22%), Positives = 54/136 (39%), Gaps = 10/136 (7%)
Query: 208 GNVFTVLQLSATQVSYQYYLALSPADGHLYISDAEKHQILRVLSLESVADPSINWEVAVG 267
GN F V+ V + L AD HL + ++L +E DP +++ +
Sbjct: 10 GNDFMVVDAVTQNVFFSPELIRRLADRHLGVG------FDQLLVVEPPYDPELDFHYRIF 63
Query: 268 SGERCIPGDETNCGDNGPALAAKLSHPKGLAIKADKTMFIADGTNIRVVSPEGIIHTLIG 327
+ + G E NG A+ KGL K D + A+G + V+ + ++ +G
Sbjct: 64 NAD----GSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMG 119
Query: 328 HHKHHNIWSPFNCHRS 343
PF +++
Sbjct: 120 EPNFEPSAVPFRANKA 135
>pdb|2R6F|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Uvra
pdb|2R6F|B Chain B, Crystal Structure Of Bacillus Stearothermophilus Uvra
Length = 972
Score = 29.6 bits (65), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 46/171 (26%), Positives = 62/171 (36%), Gaps = 32/171 (18%)
Query: 625 FIDDRVIFKLTNDLKIRALKKGRFDVTYDYDHLDRLSVRKDNYGNITQFFYNNHEYPTQV 684
F D R +F TN+ K+R KKGRF + + D I F + P +V
Sbjct: 724 FDDIRDVFASTNEAKVRGYKKGRFSFNVKGGRCE--ACHGDGIIKIEXHFLPDVYVPCEV 781
Query: 685 THIYSPRY----------GKLISLVYD---ERGFLIFAQMFRHKYYIAT--------DQC 723
H RY GK I+ V D E FA + + K + T +
Sbjct: 782 CH--GKRYNRETLEVTYKGKNIAEVLDXTVEDALDFFASIPKIKRKLETLYDVGLGYXKL 839
Query: 724 GTPVMVFNQYGETVR-----EIMRSPYGHIVYD-SNPYIYLPIDFCGGLLD 768
G P + GE R E+ R G +Y P L +D LLD
Sbjct: 840 GQPATTLSG-GEAQRVKLAAELHRRSNGRTLYILDEPTTGLHVDDIARLLD 889
>pdb|3UWX|A Chain A, Crystal Structure Of Uvra-Uvrb Complex
Length = 972
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 625 FIDDRVIFKLTNDLKIRALKKGRFDVTYDYDHLDRLSVRKDNYGNITQFFYNNHEYPTQV 684
F D R +F TN+ K+R KKGRF + + D I F + P +V
Sbjct: 724 FDDIRDVFASTNEAKVRGYKKGRFSFNVKGGRCE--ACHGDGIIKIEMHFLPDVYVPCEV 781
Query: 685 TH 686
H
Sbjct: 782 CH 783
>pdb|3UX8|A Chain A, Crystal Structure Of Uvra
Length = 670
Score = 29.6 bits (65), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 625 FIDDRVIFKLTNDLKIRALKKGRF 648
F D R +F TN+ K+R KKGRF
Sbjct: 422 FDDIRDVFASTNEAKVRGYKKGRF 445
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 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,258,178
Number of Sequences: 62578
Number of extensions: 1090677
Number of successful extensions: 3993
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 3979
Number of HSP's gapped (non-prelim): 20
length of query: 770
length of database: 14,973,337
effective HSP length: 106
effective length of query: 664
effective length of database: 8,340,069
effective search space: 5537805816
effective search space used: 5537805816
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: 55 (25.8 bits)