GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Acidovorax sp. GW101-3H11

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate Ac3H11_4836 Threonine dehydratase (EC 4.3.1.19)

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4836
          Length = 399

 Score =  294 bits (752), Expect = 4e-84
 Identities = 170/396 (42%), Positives = 242/396 (61%), Gaps = 4/396 (1%)

Query: 1   MLPYTLIQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMT 60
           ML    I++A  RL+ +V  T  + S   S+ +G  ++ K ENLQ T +FK RGA N +T
Sbjct: 1   MLTLQDIRDAATRLQGQVLDTPCVESKTLSQIVGAQVFLKFENLQFTASFKERGACNRLT 60

Query: 61  SQPREALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLT 120
               +  A+GV+  SAGNHAQGVA+ A  LG+ + + MP  TP  KV  TR +GAEVVL 
Sbjct: 61  LLSEDERARGVVAMSAGNHAQGVAYHAQRLGLRAVIVMPRFTPAVKVERTRGFGAEVVLH 120

Query: 121 GRNFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGG 180
           G   +EA   A    + +   FVHP+DD  V AGQGT+GLE+LQ +PD+  +++ +GGGG
Sbjct: 121 GDTLEEARQHAYALADAQRLTFVHPYDDEGVAAGQGTLGLEMLQAVPDLDTLVIAVGGGG 180

Query: 181 LIAGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNT 240
           LI+G+ATA +   P + ++GV+T   P+   +++     Q   T T+A+GIAV  PG  T
Sbjct: 181 LISGVATAAKAIKPGIEVVGVQTTRFPAMVNAVKGTHHPQ--GTSTIAEGIAVGTPGKIT 238

Query: 241 FPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTV-C 299
             I++ LVD++VLV+E +I  A++ LLE  K LVEGAGA  LAAL+ R      GK V  
Sbjct: 239 QEIVKRLVDDLVLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALV-RYPERFQGKRVGL 297

Query: 300 VLSGGNIDVKTISVVVERGLVAAGRYLKLKVELDDLPGALARLATEIAEAKANISIITHD 359
           VL GGNID   ++ ++ERG+V +GR  ++KV   D+PG LAR+   +A+A ANI  + H 
Sbjct: 298 VLCGGNIDPLLLAAIIERGMVRSGRLARIKVSARDVPGVLARITATVADAGANIGEVHHQ 357

Query: 360 RRSKSLPIGKTEVLIELETRGFEHIQEVISHLQGVG 395
           R    L     E+ + L+TR   H+ EV+  L+  G
Sbjct: 358 RAFTLLAAQNVEIELVLQTRSKAHVAEVLEQLRTAG 393


Lambda     K      H
   0.319    0.137    0.383 

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: 366
Number of extensions: 13
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: 402
Length of database: 399
Length adjustment: 31
Effective length of query: 371
Effective length of database: 368
Effective search space:   136528
Effective search space used:   136528
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: 50 (23.9 bits)

Align candidate Ac3H11_4836 (Threonine dehydratase (EC 4.3.1.19))
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.20943.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20943.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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