GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Cupriavidus basilensis 4G11

Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate RR42_RS16210 RR42_RS16210 dihydroxy-acid dehydratase

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



>FitnessBrowser__Cup4G11:RR42_RS16210
          Length = 557

 Score = 1065 bits (2754), Expect = 0.0
 Identities = 529/557 (94%), Positives = 552/557 (99%)

Query: 1   MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60
           MA+NKRSQ+ITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCN+GLQRLADA
Sbjct: 1   MAYNKRSQHITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNSGLQRLADA 60

Query: 61  AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120
           A+ AIKASDANPQ+FGTPTISDGMSMGTEGMKYSLISREVIADCIETA QGQWMDGVVVI
Sbjct: 61  AVAAIKASDANPQIFGTPTISDGMSMGTEGMKYSLISREVIADCIETATQGQWMDGVVVI 120

Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180
           GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGR+SQED
Sbjct: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRLSQED 180

Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240
           FEGVEKNACPS+GSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV
Sbjct: 181 FEGVEKNACPSSGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240

Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300
           EAIK+DIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAH+AEVEW+IDDFERIRRK
Sbjct: 241 EAIKKDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHSAEVEWSIDDFERIRRK 300

Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360
           VPVICNLKPSGQYVATDLH+AGGIPQVMKILLKAG++HGDCLTITGRTLAEELENVPDTP
Sbjct: 301 VPVICNLKPSGQYVATDLHRAGGIPQVMKILLKAGLMHGDCLTITGRTLAEELENVPDTP 360

Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420
           RADQDVI+PIEKALY EGHLAILKGNLA+EGAVAKITGLKNPVITGPARVFEDEQSAM+A
Sbjct: 361 RADQDVIMPIEKALYKEGHLAILKGNLAQEGAVAKITGLKNPVITGPARVFEDEQSAMDA 420

Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480
           ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV
Sbjct: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480

Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540
           VGHVAPEA+VGG IALVQEGDS+TIDAHKLLL+LNV++EELA+RRA WKQPAPRYTRGVL
Sbjct: 481 VGHVAPEAHVGGNIALVQEGDSVTIDAHKLLLELNVSEEELAKRRAAWKQPAPRYTRGVL 540

Query: 541 AKFSKLASTASKGAVTD 557
           AKF+KLASTASKGAVTD
Sbjct: 541 AKFAKLASTASKGAVTD 557


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: 1203
Number of extensions: 34
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: 557
Length adjustment: 36
Effective length of query: 521
Effective length of database: 521
Effective search space:   271441
Effective search space used:   271441
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 RR42_RS16210 RR42_RS16210 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.12549.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12549.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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