GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Burkholderia phytofirmans PsJN

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate BPHYT_RS33975 BPHYT_RS33975 2-methylcitrate dehydratase

Query= BRENDA::P77243
         (483 letters)



>FitnessBrowser__BFirm:BPHYT_RS33975
          Length = 483

 Score =  792 bits (2046), Expect = 0.0
 Identities = 378/483 (78%), Positives = 431/483 (89%)

Query: 1   MSAQINNIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKL 60
           MSA I+N+RP+ D  + DIVDYV +Y I S +A +TA +CL+DTLGCGLEAL YPAC KL
Sbjct: 1   MSAPISNVRPDPDSVLADIVDYVRDYRIDSALALETARHCLIDTLGCGLEALTYPACTKL 60

Query: 61  LGPIVPGTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120
           +GPIVPGT+VPNG +VPGT FQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI
Sbjct: 61  MGPIVPGTIVPNGAKVPGTSFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGI 120

Query: 121 LATADWLSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVAST 180
           LATADWLSR+A+A+GKAPL MK VL AMIKAHEIQGCIALENSFN+VGLDHVLLVK+AST
Sbjct: 121 LATADWLSRSAIAAGKAPLAMKDVLIAMIKAHEIQGCIALENSFNKVGLDHVLLVKLAST 180

Query: 181 AVVAEMLGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAK 240
           AVV ++L LTR+E++NAVS A+VDG +LRTYRHAPNTG+RKSWAAGDATSRAVRLAL++K
Sbjct: 181 AVVGQLLDLTRDELINAVSQAFVDGHALRTYRHAPNTGSRKSWAAGDATSRAVRLALISK 240

Query: 241 TGEMGYPSALTAPVWGFYDVSFKGESFRFQRPYGSYVMENVLFKISFPAEFHSQTAVEAA 300
           TGEMGYPS LTA  WGFYDV FKG +F+FQRPYGSYVMENVLFKISFPAEFH+QTAVEA 
Sbjct: 241 TGEMGYPSVLTAKTWGFYDVLFKGNAFQFQRPYGSYVMENVLFKISFPAEFHAQTAVEAT 300

Query: 301 MTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAIPLLFGR 360
           M L+ Q+ AAG++  DI K+TIRTHEA IRIIDKKGPLNNPADRDHCIQYMVA+PL+ GR
Sbjct: 301 MKLHAQLNAAGRSVDDISKITIRTHEAAIRIIDKKGPLNNPADRDHCIQYMVAVPLIHGR 360

Query: 361 LTAADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEV 420
           LTAADYED++AQD RID LR K+ C EDP FT DYHDPEKR+IANA+T+EF DG+ F+EV
Sbjct: 361 LTAADYEDSIAQDPRIDVLRAKMECVEDPQFTQDYHDPEKRSIANALTIEFNDGSSFDEV 420

Query: 421 VVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMPVNEYLDL 480
           +VEYPIGH RRR+DGIP LV+KFK NLAR+FP +QQ  IL+VSLD+ARLE MPVNEY+DL
Sbjct: 421 IVEYPIGHKRRREDGIPLLVEKFKTNLARRFPVKQQLAILDVSLDQARLEAMPVNEYVDL 480

Query: 481 YVI 483
           YVI
Sbjct: 481 YVI 483


Lambda     K      H
   0.321    0.136    0.406 

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: 787
Number of extensions: 12
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate BPHYT_RS33975 BPHYT_RS33975 (2-methylcitrate dehydratase)
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

Software error:

../bin/blast/fastacmd -i /tmp/list.19949.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19949.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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