GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Burkholderia phytofirmans PsJN

Align L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 (characterized)
to candidate BPHYT_RS11065 BPHYT_RS11065 threonine dehydratase

Query= SwissProt::P04968
         (514 letters)



>FitnessBrowser__BFirm:BPHYT_RS11065
          Length = 516

 Score =  525 bits (1352), Expect = e-153
 Identities = 268/504 (53%), Positives = 359/504 (71%), Gaps = 6/504 (1%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +YL+  L A VY+ A+ T L++   LS+RL N + +KRED QPV SFK+RGAY  MA ++
Sbjct: 13  DYLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIS 72

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131
            E    GVITASAGNHAQGVA S+AR+GVKA+IV+P  T  +KVDAVR  GG   EV+  
Sbjct: 73  AEALERGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQF 132

Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGG 190
           G ++ +A   A++L +++  T+V PFD P VIAGQGT+A+E+L Q    +  +FVP+GGG
Sbjct: 133 GESYSDAYEHAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGG 192

Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250
           GLAAGVA  +K + P+IKVI V+ +DS  + A+L AG  V L  VGLF++G AVK +G+E
Sbjct: 193 GLAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEE 252

Query: 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310
           TFRLC EYLDD++ V++DA+CAA+KD+F+D R+V EP+G+LA+AG K+Y     I  + L
Sbjct: 253 TFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTL 312

Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370
             I SGAN+NF  +R+V+ER E+GE REA+ AVTIPEE+GSF +FC+L+G RSVTEFNYR
Sbjct: 313 IAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSVTEFNYR 372

Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430
            ADA +A IFVGV++ R   E  +I       G++ VDL+ DE++K H+RYMVGGR    
Sbjct: 373 IADANSAHIFVGVQI-RNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLA 431

Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPD-FE 489
             ERL+ FEFPE PGAL++FL+++   WNISLFHYR+ G DY  +L   ++ D E + F 
Sbjct: 432 HDERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFN 491

Query: 490 TRLNELGYDCHDETNNPAFRFFLA 513
             L  LGY   +ET NP +R FLA
Sbjct: 492 KFLATLGYPNWEETQNPVYRLFLA 515


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: 655
Number of extensions: 27
Number of successful extensions: 6
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: 516
Length adjustment: 35
Effective length of query: 479
Effective length of database: 481
Effective search space:   230399
Effective search space used:   230399
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 BPHYT_RS11065 BPHYT_RS11065 (threonine dehydratase)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.4133.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4133.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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