GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Shewanella loihica PV-4

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 5209298 Shew_1776 acetolactate synthase 3 catalytic subunit (RefSeq)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__PV4:5209298
          Length = 573

 Score =  868 bits (2242), Expect = 0.0
 Identities = 422/575 (73%), Positives = 488/575 (84%), Gaps = 3/575 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME LSGA M+VRSLID+GVK +FGYPGG+VLDIYDALH   GI+H+LVRHEQAAVHMADG
Sbjct: 1   MEKLSGASMIVRSLIDEGVKHIFGYPGGSVLDIYDALHQKSGIEHILVRHEQAAVHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+VGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQV ++LIG DAFQECDM+G
Sbjct: 61  YARATGKVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVPSNLIGNDAFQECDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRPVVKHSFLV   +DIP ++KKAF++A++GRPGPVVVD+PKD LNP     Y +P+ +
Sbjct: 121 ISRPVVKHSFLVTDAKDIPAIIKKAFYIASTGRPGPVVVDIPKDCLNPQILHEYQYPDEI 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
           +MRSYNPTTTGHKGQI+R LQ L+ AKKPV+YVGGGA+ +G  QQ+ +  + L LPVV +
Sbjct: 181 NMRSYNPTTTGHKGQIRRGLQALLKAKKPVLYVGGGAVISGADQQILKLSDRLGLPVVST 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP TH  ++GMLGMHG YEANM MHNAD+IF +GVRFDDRTTNN+ KYCPNAT+
Sbjct: 241 LMGLGAFPGTHANSVGMLGMHGCYEANMAMHNADLIFGIGVRFDDRTTNNVEKYCPNATI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQE-SAHQPLDEIRDWWQQIEQWRA 359
           LHIDIDP+SISKTV  DIPIVG A  VL+ ML LL  E S       I  WW +I QWR+
Sbjct: 301 LHIDIDPSSISKTVRVDIPIVGSADSVLDDMLALLDDEPSMKNDEGAIDYWWSEINQWRS 360

Query: 360 RQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGG 419
           R  L YD  SE+IKPQ VIETL +LT GDAYV SDVGQHQMFAALYYPF+KPRRWINSGG
Sbjct: 361 RNSLAYDKSSERIKPQQVIETLHKLTNGDAYVASDVGQHQMFAALYYPFNKPRRWINSGG 420

Query: 420 LGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLG 479
           LGTMGFGLPAA+GVKMA P+ETV+CVTGDGSIQMNIQELSTALQY+ PV ++NLNNR+LG
Sbjct: 421 LGTMGFGLPAAMGVKMAKPDETVICVTGDGSIQMNIQELSTALQYDTPVKIINLNNRFLG 480

Query: 480 MVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNR 539
           MVKQWQDMIYSGRHS SYM S+P+F ++AEAYGHVG+ IS P ELE+ L +AL     ++
Sbjct: 481 MVKQWQDMIYSGRHSHSYMDSVPNFAKIAEAYGHVGMTISDPAELEAGLEKAL--AMKDK 538

Query: 540 LVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           LVFVD++VD +EHVYPMQIRGGGM+EMWLSKTE++
Sbjct: 539 LVFVDISVDETEHVYPMQIRGGGMNEMWLSKTEKS 573


Lambda     K      H
   0.319    0.135    0.403 

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: 1087
Number of extensions: 33
Number of successful extensions: 3
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: 574
Length of database: 573
Length adjustment: 36
Effective length of query: 538
Effective length of database: 537
Effective search space:   288906
Effective search space used:   288906
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 5209298 Shew_1776 (acetolactate synthase 3 catalytic subunit (RefSeq))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

Software error:

../bin/blast/fastacmd -i /tmp/list.5588.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5588.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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