GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Shewanella amazonensis SB2B

Align L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 (characterized)
to candidate 6939184 Sama_3278 threonine dehydratase (RefSeq)

Query= SwissProt::P04968
         (514 letters)



>FitnessBrowser__SB2B:6939184
          Length = 531

 Score =  604 bits (1557), Expect = e-177
 Identities = 308/506 (60%), Positives = 382/506 (75%), Gaps = 10/506 (1%)

Query: 16  YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75
           YL+ +L + VY+ A+VTPL  M KLS+RL   I +KRED QPVHSFKLRGAY  ++ LT+
Sbjct: 24  YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQ 83

Query: 76  EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135
            +   GV+ ASAGNHAQGVA S++  G+ A+IVMPT T DIK+DAVR  GG VLLHG +F
Sbjct: 84  PECERGVVCASAGNHAQGVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESF 143

Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAG 195
           D+A A A  L+Q +G  ++ PFD   VIAGQGT+A E+LQQ   L+ VFVPVGGGGL AG
Sbjct: 144 DQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTVAQEMLQQQRDLELVFVPVGGGGLVAG 203

Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255
           +A   K + P +K+I VE ED+ACLKAA+ AG PV L +VGLFA+GVAVKRIG E FR+ 
Sbjct: 204 IAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVKRIGAEPFRIA 263

Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIR-------GE 308
           + Y+D+++TV SD ICAA+KD+FED RA+AEP+GAL+LAG+KKY+A              
Sbjct: 264 KHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTTPALAEAGKPAR 323

Query: 309 RLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFN 368
           ++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE  GSFLKFC+LLG R++TEFN
Sbjct: 324 KVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFN 383

Query: 369 YRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPS 428
           YRF+   +A +F G+RLS G  E KEI+  L  GG+ V DLS DE AKLHVRYMVGG P+
Sbjct: 384 YRFSGRDSAVVFAGIRLSGGQSELKEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGHPT 443

Query: 429 HPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL--GDHEP 486
            PL ERL+SFEFPE PGALL+FL TLG+ WNISLFHYR+HG  +GRVLA FE+  GD+E 
Sbjct: 444 EPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHGAAFGRVLAGFEVPEGDNEA 503

Query: 487 DFETRLNELGYDCHDETNNPAFRFFL 512
            F   L ELG+   +ET++PA+R FL
Sbjct: 504 -FGRFLTELGFVWQEETHSPAYRLFL 528


Lambda     K      H
   0.321    0.138    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: 746
Number of extensions: 30
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: 514
Length of database: 531
Length adjustment: 35
Effective length of query: 479
Effective length of database: 496
Effective search space:   237584
Effective search space used:   237584
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: 52 (24.6 bits)

Align candidate 6939184 Sama_3278 (threonine dehydratase (RefSeq))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.17669.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17669.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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