GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Echinicola vietnamensis KMM 6221, DSM 17526

Align Dihydroxy-acid dehydratase, mitochondrial; DAD; 2,3-dihydroxy acid hydrolyase; EC 4.2.1.9 (characterized)
to candidate Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase

Query= SwissProt::P39522
         (585 letters)



>FitnessBrowser__Cola:Echvi_2055
          Length = 561

 Score =  602 bits (1552), Expect = e-176
 Identities = 299/563 (53%), Positives = 404/563 (71%), Gaps = 9/563 (1%)

Query: 23  LNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRCS 82
           L KYS+ I++ +   A+ AMLYATG   +  K+P VGV SC +  NPCNMHL        
Sbjct: 5   LKKYSWEISDNEENPAAMAMLYATGITDKKMKQPFVGVASCGYESNPCNMHLNSFAEDIK 64

Query: 83  QSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIPS 142
            S  +A L    FNTIG+SDG SMGT GMRYSL SRE+IADS E+ ++   +D  + IP 
Sbjct: 65  ASTNQADLSGFIFNTIGISDGQSMGTSGMRYSLPSREVIADSIESFILGHSFDGVVTIPG 124

Query: 143 CDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQF 202
           CDKNMPGV+M M R NRP IMV+GGTI  G+         + ++IVSAF++YG+ I+ Q 
Sbjct: 125 CDKNMPGVVMGMLRVNRPGIMVFGGTIRSGNYK------GEKLNIVSAFEAYGKKINGQI 178

Query: 203 TEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNIG 262
           ++E+   V+++ACPG G+CGGMYTANTM+SA E +GL++P SSS+PA SKEK  EC NIG
Sbjct: 179 SDEDYMGVIKNACPGAGACGGMYTANTMSSAIEAMGLSLPFSSSYPATSKEKREECKNIG 238

Query: 263 EYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQR 322
           +YIK+ + L I P+DI+TK++ ENA+   VA GGSTNA LH++A+A +AG+  + +DF+R
Sbjct: 239 KYIKQLLALDIKPKDIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKR 298

Query: 323 ISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKKA 382
           I+  TP++GDFKPSGK++M DL  +GG  + +KY     +LHG+ +TVTG T+AE  +  
Sbjct: 299 INAETPVLGDFKPSGKFMMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLEDI 358

Query: 383 -PSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGA 441
            P  P  + +I PL +PIK +GHL +L+G+LAP GAV KI+GKEG  F G A+VF++E +
Sbjct: 359 DPVKPSKESVIHPLDNPIKPSGHLCVLHGNLAPEGAVAKISGKEGKSFTGTAKVFDDEPS 418

Query: 442 FIEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSG 501
              A++  EI+KG+  VVVIRY GP+G PGMPEMLKP+S ++G GLG DVAL+TDGRFSG
Sbjct: 419 ANAAMKNKEIQKGD--VVVIRYVGPKGGPGMPEMLKPTSIIIGAGLGSDVALITDGRFSG 476

Query: 502 GSHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPR 561
           G+HGF++GH+ PEA  GGPIGL++DGD I IDA++ +I + VS+ E A+RK++W      
Sbjct: 477 GTHGFVVGHVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERKKNWKNKDLS 536

Query: 562 YTRGTLSKYAKLVSNASNGCVLD 584
           + +GTL KY +LVS AS GCV D
Sbjct: 537 HLQGTLKKYVQLVSTASEGCVTD 559


Lambda     K      H
   0.315    0.134    0.390 

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: 1044
Number of extensions: 50
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: 585
Length of database: 561
Length adjustment: 36
Effective length of query: 549
Effective length of database: 525
Effective search space:   288225
Effective search space used:   288225
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: 53 (25.0 bits)

Align candidate Echvi_2055 Echvi_2055 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.28198.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28198.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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