GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Dinoroseobacter shibae DFL-12

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)

Query= BRENDA::Q97UB2
         (558 letters)



>FitnessBrowser__Dino:3606698
          Length = 577

 Score =  514 bits (1325), Expect = e-150
 Identities = 274/560 (48%), Positives = 366/560 (65%), Gaps = 8/560 (1%)

Query: 4   KLNSPSRY--HGIYNAPHRAFLRSVGLTDEEIGKPLVAIATAWSEAGPCNFHTLALARVA 61
           K   PSR+   G   APHR++  ++G+T+EEI +PLV +AT W+EA PCN      A+  
Sbjct: 8   KSKLPSRHVTEGPSRAPHRSYYYAMGMTEEEIHQPLVGVATCWNEAAPCNIALSRQAQAV 67

Query: 62  KEGTKEAGLSPLAFPTMVVNDNIGMGSEGMRYSLVSRDLIADMVEAQFNAHAFDGLVGIG 121
           K G K+A  +P  F T+ V D I MG EGMR SL SR+ IAD VE     H +D +VG+ 
Sbjct: 68  KMGVKQASGTPREFTTITVTDGIAMGHEGMRSSLASREAIADTVELTMRGHCYDAIVGLA 127

Query: 122 GCDKTTPGILMAMARLNVPSIYIYGGSAEPGYFMGKRLTIEDVHEAIGAYLAKRITENEL 181
           GCDK+ PG++MAM RLNVPS++IYGGS  PG   G+ +T++DV EA+G + A   T+ EL
Sbjct: 128 GCDKSLPGMMMAMVRLNVPSVFIYGGSILPGRLNGEDVTVQDVFEAVGKHQAGNYTDAEL 187

Query: 182 YEIEKRAHPTLGTCSGLFTANTMGSMSEALGMALPGSASPTATSSRRVMYVKETGKALGS 241
             +E+ A P+ G C G FTANTM  +SEA+G+ALP SA   A    R  Y + +G+A+  
Sbjct: 188 EVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQYGEASGRAVMD 247

Query: 242 LIENGIKSREILTFEAFENAITTLMAMGGSTNAVLHLLAIAYEAGVKLTLDDFNRISKRT 301
           LIE GI++R+I+T ++ ENA   +   GGSTNA LHL AIA+EAG++ TL D   I + T
Sbjct: 248 LIEKGIRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFTLQDVCDIFRDT 307

Query: 302 PYIASMKPGGDYVMADLDEVGGVPVVLKKLLDAGLLHGDVLTVTGKTMKQNLEQYKYPNV 361
           PY   +KPGG YV  D+ E GGVPVV+++L  AGL+H D +TVTG ++ + L+  K    
Sbjct: 308 PYFVDLKPGGKYVAKDMYEAGGVPVVMRELRRAGLIHEDCMTVTGYSIGEELD--KVTLE 365

Query: 362 PHSHIVRDVKNPIKPRGGIVILKGSLAPEGAVIKVA--ATNVVKFEGKAKVYNSEDDAFK 419
               ++  V  P+   GG+V L+G+LAPEGA++K+A  + + + F G A+V+  E+DAF+
Sbjct: 366 ADGRVIYPVDTPLSTTGGVVGLEGNLAPEGAIVKIAGMSDDQLVFTGPARVFECEEDAFE 425

Query: 420 GVQSGEVSEGEVVIIRYEGPKGAPGMPEMLRVTAAIMGAGL-NNVALVTDGRFSGATRGP 478
            VQ+   +EG+V +IR EGP G PGM EML  TAA+ G G+   VAL+TDGRFSGATRG 
Sbjct: 426 AVQNRAYAEGDVFVIRNEGPAGGPGMREMLATTAALSGQGMGKKVALITDGRFSGATRGF 485

Query: 479 MVGHVAPEAMVGGPIAIVEDGDTIVIDVESERLDLKLSEEEIKNRLKRWSPPSPR-YKSG 537
            VGHV PEA  GGPIA+++DGD I ID     L + LSE+E+  R   WS P    Y SG
Sbjct: 486 CVGHVGPEAAHGGPIAMLKDGDMITIDALKGELSVALSEDELAARKDAWSGPRETIYASG 545

Query: 538 LLAKYASLVSQASMGAVTRP 557
            L KYA LV  A +GAVT P
Sbjct: 546 ALWKYAQLVGGARLGAVTHP 565


Lambda     K      H
   0.316    0.134    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: 883
Number of extensions: 24
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: 558
Length of database: 577
Length adjustment: 36
Effective length of query: 522
Effective length of database: 541
Effective search space:   282402
Effective search space used:   282402
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 3606698 Dshi_0129 (dihydroxy-acid dehydratase (RefSeq))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.29501.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29501.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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