GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Bacteroides thetaiotaomicron VPI-5482

Align acetolactate synthase isozyme 2 large subunit; EC 2.2.1.6 (characterized)
to candidate 351605 BT2077 acetolactate synthase large subunit (NCBI ptt file)

Query= CharProtDB::CH_003896
         (548 letters)



>FitnessBrowser__Btheta:351605
          Length = 565

 Score =  478 bits (1231), Expect = e-139
 Identities = 253/558 (45%), Positives = 360/558 (64%), Gaps = 15/558 (2%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD--GGVEHLLCRHEQGAAMAAIGYA 58
           + GA+ ++ +L  QGV T+FGYPGG+IMP +DALYD    + H+L RHEQGAA AA GYA
Sbjct: 6   ITGAEAMMRSLEHQGVTTIFGYPGGSIMPTFDALYDHQNTLNHILVRHEQGAAHAAQGYA 65

Query: 59  RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118
           R +GK GVC+ TSGPGATN ITG+ADA++DS P+V I GQV   F+GTDAFQEVD++G++
Sbjct: 66  RVSGKVGVCLVTSGPGATNTITGIADAMIDSTPIVVIAGQVGTGFLGTDAFQEVDLVGIT 125

Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTT-VEN 177
               K S+ ++  E++   +A AF +A SGRPGPV++D  K+ Q+     EP     + +
Sbjct: 126 QPIAKWSYQIRRAEDVAWAIARAFYIASSGRPGPVVLDFAKNAQVEKTKYEPTKQEFIRS 185

Query: 178 EVTFPHAE---VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGL 234
            V  P  +   V+ A +++  A++P++ VG GV +  A   LR F+    MPA CTL GL
Sbjct: 186 YVPVPDTDEESVKAAAELINNAERPLVLVGQGVELGSAQEELRIFIEKADMPAGCTLLGL 245

Query: 235 GAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAPHASVIHMD 294
            A+  D+P   GMLGMHG    N    +CD+LIAVG RFDDRVTG L T+A  A VIH D
Sbjct: 246 SALPTDHPLNKGMLGMHGNLGPNINTNKCDVLIAVGMRFDDRVTGNLATYAKQAKVIHFD 305

Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQQPLNQ------YDWQQHCAQLRDEHSWRYD-H 347
           IDPAE+NK  +  +A+ GD    L A+   L +       D  +    + +E   R + H
Sbjct: 306 IDPAEVNKNVKVDIAVLGDCKKTLAAVTGLLKKNRHTEWVDSFKEYEAVEEEKVIRPELH 365

Query: 348 PG-DAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFG 406
           P  D++    +++ +S+    + ++ TDVGQ+QM +A++  +TR  + +TS GLGTMGFG
Sbjct: 366 PATDSLSMGEVVRAVSEATRHEAILVTDVGQNQMISARYFKYTRERSIVTSGGLGTMGFG 425

Query: 407 LPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQ 466
           LPAA+GA   RP+ TV    GDG   MN+QELGT+  ++ P+KI+ L+N  LG VRQWQ 
Sbjct: 426 LPAAIGATFGRPDRTVCVFMGDGGLQMNIQELGTIMEQKAPVKIICLNNNYLGNVRQWQA 485

Query: 467 LFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526
           +FF  RYS T +  NPD++ +ASA+ I  + +  +++++AA+D ML++DG +LL   + E
Sbjct: 486 MFFNRRYSFTPML-NPDYMKIASAYDIPSKRVFSREELKAAIDEMLSTDGAFLLEACVVE 544

Query: 527 LENVWPLVPPGASNSEML 544
             NV P+ PPG S ++ML
Sbjct: 545 EGNVLPMTPPGGSVNQML 562


Lambda     K      H
   0.320    0.135    0.410 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 771
Number of extensions: 32
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 548
Length of database: 565
Length adjustment: 36
Effective length of query: 512
Effective length of database: 529
Effective search space:   270848
Effective search space used:   270848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 351605 BT2077 (acetolactate synthase large subunit (NCBI ptt file))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

Software error:

../bin/blast/fastacmd -i /tmp/list.28787.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28787.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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