GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Acidovorax sp. GW101-3H11

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= metacyc::MONOMER-18815
         (557 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_954
          Length = 567

 Score =  875 bits (2260), Expect = 0.0
 Identities = 427/554 (77%), Positives = 491/554 (88%)

Query: 4   NKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADAAID 63
           N+RS NITQG +R+PNRSMYYA+GY++ DF KPMVG+ANGHSTITPCN+GLQ+LADAAI 
Sbjct: 12  NRRSANITQGKSRAPNRSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIA 71

Query: 64  AIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVIGGC 123
            I+ +  N QVFGTPTISDGM+MGTEGMKYSL+SREVI+DCIET   GQWMDGV+V+GGC
Sbjct: 72  GIEEAGGNAQVFGTPTISDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGC 131

Query: 124 DKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQEDFEG 183
           DKNMPGG++ + R NVP IYVYGGTI PG+++GKDL IVS FEAVGE  AG++S  D + 
Sbjct: 132 DKNMPGGLMGMLRANVPAIYVYGGTILPGHYQGKDLNIVSVFEAVGENAAGKLSDFDLKE 191

Query: 184 VEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAI 243
           +EK A P TGSCGGMYTANTMSS+FEALG+SL YSSTMANP  EK++SA ESA+VL+EAI
Sbjct: 192 IEKRAIPGTGSCGGMYTANTMSSAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAI 251

Query: 244 KQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRKVPV 303
           K+DIKPRDI+T+KSIENAVA+IMATGGSTNAVLH+LAIAHAA VEW+IDDFER+R K PV
Sbjct: 252 KKDIKPRDIVTKKSIENAVAVIMATGGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPV 311

Query: 304 ICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTPRAD 363
           +C+LKPSG+Y+A DLH+AGGIPQVMK+LL AG+LHGDCLTI G+T+AE L++VPD PRAD
Sbjct: 312 LCDLKPSGKYLAVDLHRAGGIPQVMKVLLNAGLLHGDCLTIEGKTVAEVLKDVPDQPRAD 371

Query: 364 QDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEAILA 423
           QDVI PI   +YA+GHLAILKGNL+ EGAVAKITGLKNPVITGPARVFEDEQSA+EAILA
Sbjct: 372 QDVIRPINNPMYAQGHLAILKGNLSPEGAVAKITGLKNPVITGPARVFEDEQSALEAILA 431

Query: 424 DKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGH 483
            KI AGD++VLRYLGPKGGPGMPEMLAPT A+IG GLGESVG ITDGRFSGGTWGMVVGH
Sbjct: 432 GKIKAGDVMVLRYLGPKGGPGMPEMLAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGH 491

Query: 484 VAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVLAKF 543
           VAPEA  GGTIA V EGDSITIDA +LLL+LNV++EE+ARRRA W  PAPRYTRGV AKF
Sbjct: 492 VAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSEEEIARRRAAWTAPAPRYTRGVQAKF 551

Query: 544 SKLASTASKGAVTD 557
           +  AS+ASKGAV D
Sbjct: 552 AFNASSASKGAVLD 565


Lambda     K      H
   0.316    0.133    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: 1137
Number of extensions: 42
Number of successful extensions: 1
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: 557
Length of database: 567
Length adjustment: 36
Effective length of query: 521
Effective length of database: 531
Effective search space:   276651
Effective search space used:   276651
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 Ac3H11_954 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.6774.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6774.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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