GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Pseudomonas fluorescens FW300-N1B4

Align L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 (characterized)
to candidate Pf1N1B4_2280 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= SwissProt::P04968
         (514 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2280
          Length = 504

 Score =  529 bits (1362), Expect = e-154
 Identities = 263/500 (52%), Positives = 359/500 (71%), Gaps = 2/500 (0%)

Query: 15  EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74
           +Y++ +L + VY+ A  TPLQ   +LS RL N I +KRED QPV SFK+RGAY  +  L+
Sbjct: 4   QYVKKILTSRVYDVAVETPLQTARQLSERLGNDIWLKREDLQPVFSFKIRGAYNKLTQLS 63

Query: 75  EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134
           +E++A GV+TASAGNHAQG+A ++  LGVKA IVMP  T +IKV+ VR  GG+V+LHG +
Sbjct: 64  DEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDS 123

Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLA 193
           F EA A +++L  ++G+ ++ P+D P  IAGQGT+A+E+L+Q    LD +FVPVGGGGL 
Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLI 183

Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253
           AG+A  +K L P IK+I VE +DS CL+AA+ AG  V LP VGLFA+GVAV +IG  TF 
Sbjct: 184 AGIAAYVKYLRPDIKIIGVEPDDSNCLQAAMAAGERVVLPTVGLFADGVAVAQIGQHTFD 243

Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313
           +C++Y+D++ITV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+    + G     I
Sbjct: 244 ICKDYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVEQRGVTGHTFVAI 303

Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373
            SGANVNF  LR+V+ER ELGE REA++AVTIPE+ GSF  FC+ +G R +TEFNYR+  
Sbjct: 304 DSGANVNFDRLRHVAERAELGEGREAIIAVTIPEKPGSFKAFCEAIGKRQITEFNYRYNT 363

Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433
              A IFVGV+     + R  +L  L++ G+ V+DL+D+E+AKLH+R+MVGGR  H + E
Sbjct: 364 GSEAHIFVGVQTHPENDPRSALLASLSEQGFPVLDLTDNELAKLHIRHMVGGRAVHVVDE 423

Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDF-ETRL 492
            +  FEFPE PGAL  FLN LG  WNIS+FHYR+HG   GRV+A  ++   E       L
Sbjct: 424 VVLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPHDERHLVPAAL 483

Query: 493 NELGYDCHDETNNPAFRFFL 512
            E+GY   DE++NPA++ FL
Sbjct: 484 EEIGYPYWDESDNPAYQLFL 503


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: 710
Number of extensions: 38
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: 504
Length adjustment: 34
Effective length of query: 480
Effective length of database: 470
Effective search space:   225600
Effective search space used:   225600
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 Pf1N1B4_2280 (Threonine dehydratase biosynthetic (EC 4.3.1.19))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.4092.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4092.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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