GapMind for Amino acid biosynthesis

 

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

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate Ac3H11_1528 3-isopropylmalate dehydrogenase (EC 1.1.1.85)

Query= BRENDA::Q56268
         (358 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1528
          Length = 357

 Score =  403 bits (1036), Expect = e-117
 Identities = 219/358 (61%), Positives = 261/358 (72%), Gaps = 10/358 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KIA+  GDGIG EIVA A +VL A+D    L       LVGGAA +A   PLP ++L+LA
Sbjct: 2   KIAVLPGDGIGTEIVAEAVKVLKALD----LKFEMESALVGGAAYEAHGHPLPESTLKLA 57

Query: 63  MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122
             ADA++ GAVG  ++D      RPEQ +L LRK L L+AN RPA  + QL+ AS L+PE
Sbjct: 58  KEADAILFGAVGDWKYDKLDRPLRPEQAILGLRKNLGLFANFRPAICYEQLVGASSLKPE 117

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV-----IDGKRRGFNTMVYDEDEIRRIAHVAFRA 177
           L+  +DIL++RELTGDIYFGQPRG  V       G    F+TM Y   EI RIAHVAF+A
Sbjct: 118 LIAGLDILIIRELTGDIYFGQPRGRRVATDGHFPGAEEAFDTMRYSRPEIERIAHVAFQA 177

Query: 178 AQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDV 237
           A+ R K++ SVDKANVLET + W++VVT+V ++YPDV L HMYVDNAAMQL++AP  FDV
Sbjct: 178 ARKRNKKVTSVDKANVLETFQFWKDVVTDVHKEYPDVELQHMYVDNAAMQLVKAPKAFDV 237

Query: 238 LLTGNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATI 296
           ++TGNMFGDILSDEAS LTGSIGMLPSASL    + +YEP HGSAPDIAG+  ANPLATI
Sbjct: 238 VVTGNMFGDILSDEASMLTGSIGMLPSASLNSSNQGLYEPSHGSAPDIAGKGVANPLATI 297

Query: 297 LSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           LS AMMLR SLN E  AQR+EAAVQ+VL QGLRT DI + GT  +GT  MG AVV AL
Sbjct: 298 LSAAMMLRFSLNQEAAAQRIEAAVQKVLAQGLRTPDIYSEGTTKVGTAQMGDAVVKAL 355


Lambda     K      H
   0.320    0.137    0.396 

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: 392
Number of extensions: 13
Number of successful extensions: 4
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: 358
Length of database: 357
Length adjustment: 29
Effective length of query: 329
Effective length of database: 328
Effective search space:   107912
Effective search space used:   107912
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: 49 (23.5 bits)

Align candidate Ac3H11_1528 (3-isopropylmalate dehydrogenase (EC 1.1.1.85))
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.10429.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10429.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.