GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Shewanella loihica PV-4

Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate 5207757 Shew_0278 branched-chain amino acid aminotransferase (RefSeq)

Query= SwissProt::O31461
         (356 letters)



>FitnessBrowser__PV4:5207757
          Length = 363

 Score =  295 bits (756), Expect = 1e-84
 Identities = 152/343 (44%), Positives = 221/343 (64%), Gaps = 5/343 (1%)

Query: 16  KPDPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKA 75
           KP+ +++GFG   TD+MF+MDY +G  W  PR+ PY P  + P +   HYGQ++FEG KA
Sbjct: 19  KPE-TNVGFGNLRTDHMFLMDYRDG-EWRDPRVVPYGPFEMAPGAMALHYGQSIFEGAKA 76

Query: 76  YRTDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSL 135
           +  DDG +  FR ++N +RLN S E + +PP+ E + L  +  L+++++ W P + G  L
Sbjct: 77  FMHDDGEIYTFRLNKNAERLNLSGEVVCIPPVPEAMQLAGINALIDVDRLWFPMQDGACL 136

Query: 136 YIRPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGF 195
           YIRPFV ATE  L V  S+ YTF ++LSP G+YY D   K +R+ + + + RAV+GG G 
Sbjct: 137 YIRPFVFATEDRLSVSPSQQYTFCVMLSPSGAYYADGFDKAIRLLITERFHRAVSGGTGA 196

Query: 196 AKTAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVI-NGEAVTPALSG 254
           +K AGNYAASL+A + A E G  QVL+LDA   K +EEVG+MN F V+ +G  + P  + 
Sbjct: 197 SKAAGNYAASLRAGKAAAEYGAAQVLYLDA-NNKQIEEVGAMNHFHVLKDGTIIIPKFTD 255

Query: 255 SILSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGELN 314
           +IL  +T  S +EL  + G  VR+E + +D+  A    GE+ E  G GTAAVV+PVG   
Sbjct: 256 TILKSITSQSIMELGEALGCEVRQETVMLDQFIADIESGEIVEAGGFGTAAVVSPVGSYI 315

Query: 315 IHGKTVI-VGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356
                V+ VGDGQ+G+ ++++Y+ +TDIQ GK +GP  W  +V
Sbjct: 316 FEDHRVLTVGDGQVGEHTRRIYQVLTDIQKGKRQGPEGWMQKV 358


Lambda     K      H
   0.317    0.137    0.400 

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: 359
Number of extensions: 27
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: 356
Length of database: 363
Length adjustment: 29
Effective length of query: 327
Effective length of database: 334
Effective search space:   109218
Effective search space used:   109218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate 5207757 Shew_0278 (branched-chain amino acid aminotransferase (RefSeq))
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.27905.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27905.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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