GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Marinobacter adhaerens HP15

Align Dihydroxy-acid dehydratase, mitochondrial; DAD; 2,3-dihydroxy acid hydrolyase; EC 4.2.1.9 (characterized)
to candidate GFF3421 HP15_3363 dihydroxy-acid dehydratase

Query= SwissProt::P39522
         (585 letters)



>FitnessBrowser__Marino:GFF3421
          Length = 562

 Score =  607 bits (1564), Expect = e-178
 Identities = 304/563 (53%), Positives = 397/563 (70%), Gaps = 11/563 (1%)

Query: 22  KLNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRC 81
           K  KYS  + +  G+ AS+AML A GF  EDFKKPQ+G+ S W +  PCNMH+  L    
Sbjct: 9   KRRKYSAPVVDGIGKSASRAMLRAVGFTDEDFKKPQIGIASTWSNLTPCNMHINQLAEES 68

Query: 82  SQSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIP 141
           +   ++AG K++ FNTI +SDGI+ GT+GM+YSL SRE+IADS ET+   + +D  +AI 
Sbjct: 69  AAGADEAGGKSLIFNTITISDGIANGTEGMKYSLVSREVIADSIETVAGCEGFDGLVAIG 128

Query: 142 SCDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQ 201
            CDKNMPG MM + R NRPS+ VYGGTI+PG           + DI+S F++ G +    
Sbjct: 129 GCDKNMPGCMMGLARLNRPSVFVYGGTIMPGE---------NHTDIISVFEAVGAHARGD 179

Query: 202 FTEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNI 261
               E + + E A PGPGSCGGMYTANTMASA E +G+++P SS+  AVS+ K  +C   
Sbjct: 180 LDLIEVKQIEETAIPGPGSCGGMYTANTMASAIEAMGMSLPGSSAQNAVSETKAEDCRGA 239

Query: 262 GEYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQ 321
           G  +   +E  I P DI+T++AFENAIT V+A GGSTNAVLHL+A+A + GV L  +DF 
Sbjct: 240 GAAVLNLLEKDIKPSDIMTRKAFENAITVVIALGGSTNAVLHLLAMASTVGVDLELEDFV 299

Query: 322 RISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKK 381
            I    P++ D +PSG Y+M++L+ +GG Q ++K L +  +LHG+ +TVTG TLAE    
Sbjct: 300 EIGKRVPVLADLRPSGHYMMSELVAIGGIQPLMKMLLDRGLLHGDCLTVTGQTLAENLAD 359

Query: 382 APSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGA 441
               PEGQ+II    +PIKA+ HL+IL+G+LAP GAV KITGKEGT+F GRARVF  E  
Sbjct: 360 VDPYPEGQDIIHAFDNPIKADSHLRILFGNLAPTGAVAKITGKEGTHFTGRARVFHSEEE 419

Query: 442 FIEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSG 501
             E +  G +  G+  V+VIRYEGP+G PGM EML P+SA+MG GLG DVAL+TDGRFSG
Sbjct: 420 AQERILDGTVVAGD--VLVIRYEGPKGGPGMREMLSPTSAIMGKGLGSDVALITDGRFSG 477

Query: 502 GSHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPR 561
           GSHGF++GHI PEAAEGGPI LV DGD I IDA +N+I+L VSD+E+ +R+Q+W APPPR
Sbjct: 478 GSHGFVVGHITPEAAEGGPIALVEDGDTITIDAVSNRIELDVSDQELERRRQAWQAPPPR 537

Query: 562 YTRGTLSKYAKLVSNASNGCVLD 584
           +TRGTL+KY++ VS+AS G V D
Sbjct: 538 FTRGTLAKYSRTVSSASKGAVTD 560


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: 960
Number of extensions: 33
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: 585
Length of database: 562
Length adjustment: 36
Effective length of query: 549
Effective length of database: 526
Effective search space:   288774
Effective search space used:   288774
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 GFF3421 HP15_3363 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.18864.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18864.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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