GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Paraburkholderia bryophila 376MFSha3.1

Align dihydroxyacid dehydratase (characterized)
to candidate H281DRAFT_05312 H281DRAFT_05312 dihydroxyacid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__Burk376:H281DRAFT_05312
          Length = 619

 Score =  905 bits (2339), Expect = 0.0
 Identities = 460/621 (74%), Positives = 525/621 (84%), Gaps = 11/621 (1%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS T+T GRNMAGAR+LWRATGM D DF KPIIAVVNSFTQFVPGHVHL+DLG+LV
Sbjct: 1   MPAYRSKTSTAGRNMAGARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSR++IADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSD------QIIKLDLVDAMIQGADP 174
           NCDKITPGMLMA++RLNIPVIFVSGGPMEAGKT+L++      +  KLDLVDAM+  AD 
Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTRLANPKTGTIEFKKLDLVDAMVIAADK 180

Query: 175 KVSDSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLN 234
             SD+   +VERSACPTCGSCSGMFTANSMNCLTEALGLS PGNG+++ATHADR+QLF  
Sbjct: 181 AYSDADVAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLFKR 240

Query: 235 AGKRIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEI 294
           AG+RIVEL ++YYEQ + S LPR +  KA FENAMTLDIAMGGSTNT+LHLLA A+EAEI
Sbjct: 241 AGRRIVELARQYYEQEEASVLPRAVGFKA-FENAMTLDIAMGGSTNTILHLLAIAREAEI 299

Query: 295 DFTMSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLG 354
           DFTM+DID+LSR VPQLCKVAP+T KYH+EDVHRAGG++ ILGELDRAG L  DV  V  
Sbjct: 300 DFTMTDIDRLSRIVPQLCKVAPNTNKYHIEDVHRAGGIMAILGELDRAGKLQTDVPTVHA 359

Query: 355 LTLPQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEH 414
            TL   L+Q+D++ T D+AV+  + AGPAG+ T  AFSQ+ RW +LD DRA GCIRS EH
Sbjct: 360 PTLKDALDQWDIVRTGDEAVRTFYMAGPAGVPTQVAFSQNTRWPSLDLDRAEGCIRSYEH 419

Query: 415 AYSKDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGD 474
           A+SK+GGLAVL GN A +GC+VKTAGVD+SIL F G A V ESQD+AVE IL GKV AGD
Sbjct: 420 AFSKEGGLAVLTGNIALDGCVVKTAGVDESILVFEGTAHVTESQDEAVENILAGKVKAGD 479

Query: 475 VVVIRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAAS 534
           VV++RYEGPKGGPGMQEMLYPTS++KS GLGKACAL+TDGRFSGGTSGLSIGH SPEAA+
Sbjct: 480 VVIVRYEGPKGGPGMQEMLYPTSYIKSQGLGKACALLTDGRFSGGTSGLSIGHCSPEAAA 539

Query: 535 GGSIGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTP-KNRERQVSFAL 593
           GG+IGL+ DGD I IDIPNR I + +SDAELA+RR+ Q+A+G   W P K R R+VS AL
Sbjct: 540 GGAIGLVRDGDKIRIDIPNRTINVLLSDAELASRRDEQNAKG---WKPAKPRPRKVSAAL 596

Query: 594 RAYASLATSADKGAVRDKSKL 614
           +AYA L  SADKGAVRD S L
Sbjct: 597 KAYAKLVMSADKGAVRDLSLL 617


Lambda     K      H
   0.317    0.134    0.386 

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: 1212
Number of extensions: 41
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: 616
Length of database: 619
Length adjustment: 37
Effective length of query: 579
Effective length of database: 582
Effective search space:   336978
Effective search space used:   336978
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate H281DRAFT_05312 H281DRAFT_05312 (dihydroxyacid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.976.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.976.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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