GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garD in Burkholderia phytofirmans PsJN

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate BPHYT_RS24160 BPHYT_RS24160 D-galactarate dehydratase

Query= reanno::HerbieS:HSERO_RS15800
         (522 letters)



>FitnessBrowser__BFirm:BPHYT_RS24160
          Length = 529

 Score =  786 bits (2031), Expect = 0.0
 Identities = 387/526 (73%), Positives = 447/526 (84%), Gaps = 15/526 (2%)

Query: 12  APRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDV 71
           +P YI ++  DNVAIVVNDGGL  G VFPDGL L +RVPQGHK+AL DL +G+ ++RY+V
Sbjct: 4   SPLYIRVHPNDNVAIVVNDGGLGEGAVFPDGLALRERVPQGHKVALADLAEGDEVIRYNV 63

Query: 72  AIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSVG 131
            IGYA++ +PKG WI E +++MP    L++LPIAT K    PPLEGYTFEGYRNADGSVG
Sbjct: 64  VIGYALKALPKGSWINEHVIRMPSPPGLEDLPIATIKAPDMPPLEGYTFEGYRNADGSVG 123

Query: 132 TRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGIP 191
           +RN+LAITTTVQCVA VV+HAV RI+AELLP+YPNV+DVV+L HTYGCGVAIDAP+A +P
Sbjct: 124 SRNILAITTTVQCVADVVQHAVTRIKAELLPRYPNVDDVVSLGHTYGCGVAIDAPDAMVP 183

Query: 192 IRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPY------------- 238
           IRT+RNISLNPNFGG+ M+VSLGCEKLQP RL+P   IPI                    
Sbjct: 184 IRTVRNISLNPNFGGEVMMVSLGCEKLQPERLMPPGTIPIAAAANVAEVADIGDIEADLN 243

Query: 239 --VVCLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGV 296
             VV LQD  HVGF SMI+SIM MA+  L  LN RRRETCPASDLV+GVQCGGSDAFSG+
Sbjct: 244 GDVVVLQDESHVGFQSMIESIMKMADGHLKRLNNRRRETCPASDLVIGVQCGGSDAFSGL 303

Query: 297 TANPAVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLK 356
           TANPAVG+ATDLLVRAGA+VMFSEVTEVRDG+DQLT+RA N EVA A+IREM WYD+YLK
Sbjct: 304 TANPAVGYATDLLVRAGATVMFSEVTEVRDGVDQLTARAANPEVAAAIIREMQWYDDYLK 363

Query: 357 QGGVDRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPA 416
           +GG DRSANTTPGNKKGGL+NIVEKAMGSI+KSG+S ISGVLSPG+K++QKGLIYAATPA
Sbjct: 364 RGGADRSANTTPGNKKGGLSNIVEKAMGSIIKSGNSAISGVLSPGEKVKQKGLIYAATPA 423

Query: 417 SDFICGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIAS 476
           SDFICGTLQ+AAG+NLH+FTTGRGTPY LA VPVIKVATR+DLARRWHDLMD+NAG IA+
Sbjct: 424 SDFICGTLQVAAGINLHVFTTGRGTPYSLAEVPVIKVATRSDLARRWHDLMDINAGTIAT 483

Query: 477 GEASIEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522
           GE++IE+VGWELF+LMLDVASG+K T AE+ KLHNALTLFNPAPVT
Sbjct: 484 GESTIEEVGWELFRLMLDVASGRKETCAEKLKLHNALTLFNPAPVT 529


Lambda     K      H
   0.317    0.134    0.397 

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: 940
Number of extensions: 33
Number of successful extensions: 2
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: 522
Length of database: 529
Length adjustment: 35
Effective length of query: 487
Effective length of database: 494
Effective search space:   240578
Effective search space used:   240578
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: 52 (24.6 bits)

Align candidate BPHYT_RS24160 BPHYT_RS24160 (D-galactarate dehydratase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.6214.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6214.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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