GapMind for catabolism of small carbon sources

 

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

Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate H281DRAFT_03815 H281DRAFT_03815 D-glucarate dehydratase

Query= SwissProt::P42206
         (451 letters)



>FitnessBrowser__Burk376:H281DRAFT_03815
          Length = 468

 Score =  734 bits (1894), Expect = 0.0
 Identities = 352/438 (80%), Positives = 392/438 (89%)

Query: 14  PVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGIRKTLED 73
           P +T+L+VVPVAG DSMLLNLSGAHGP FTRNI+IL DS+GHVGVGEVPGGE IRKT++D
Sbjct: 31  PTVTELRVVPVAGRDSMLLNLSGAHGPYFTRNIVILRDSAGHVGVGEVPGGENIRKTIDD 90

Query: 74  ARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALLDLLGQH 133
           AR  ++ QSIGN Q++LNKVR  FADRD GGRGLQTFDLR  +HAVTA+E+ALLDLLGQH
Sbjct: 91  ARSFVVGQSIGNLQAILNKVRTQFADRDAGGRGLQTFDLRTTIHAVTALEAALLDLLGQH 150

Query: 134 LQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKEALTPES 193
           L VPVAALLGEGQQRDAVEMLGYLFY+GDRNKTDL Y S  +A ++W R+R +EALTPE+
Sbjct: 151 LGVPVAALLGEGQQRDAVEMLGYLFYIGDRNKTDLPYASGADARDDWDRVRTEEALTPEA 210

Query: 194 VVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWSLKEAVA 253
           VV LAEAA  RYGF DFKLKGGVL G+ EI AVTAL+ERFP+AR+TLDPNGAWSL EA+ 
Sbjct: 211 VVRLAEAAQARYGFNDFKLKGGVLPGDAEIEAVTALAERFPNARVTLDPNGAWSLAEAIR 270

Query: 254 LCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHAIQLQSV 313
           LCRD+H VLAYAEDPCGAENGYSGREVMAEFRR+TGL TATNMIATDWRQMGHAIQLQSV
Sbjct: 271 LCRDKHDVLAYAEDPCGAENGYSGREVMAEFRRATGLPTATNMIATDWRQMGHAIQLQSV 330

Query: 314 DIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGNITAIDT 373
           DIPLADPHFWTMQGSVRVAQMCN+WGLTWGSHSNNHFDISLAMFTHVAAAAPG ITAIDT
Sbjct: 331 DIPLADPHFWTMQGSVRVAQMCNDWGLTWGSHSNNHFDISLAMFTHVAAAAPGKITAIDT 390

Query: 374 HWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGARDDATAM 433
           HWIWQDGQRLT+EPLQI GG V+VP+KPGLGVELD D + KAH +Y+  GLGARDD  AM
Sbjct: 391 HWIWQDGQRLTREPLQIVGGKVKVPQKPGLGVELDMDEIEKAHALYQQHGLGARDDGVAM 450

Query: 434 RYLVSGWEFNNKRPCMVR 451
           +YL+  W+F+NKRPC+VR
Sbjct: 451 QYLIPNWKFDNKRPCLVR 468


Lambda     K      H
   0.319    0.135    0.410 

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: 708
Number of extensions: 15
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: 451
Length of database: 468
Length adjustment: 33
Effective length of query: 418
Effective length of database: 435
Effective search space:   181830
Effective search space used:   181830
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_03815 H281DRAFT_03815 (D-glucarate dehydratase)
to HMM TIGR03247 (gudD: glucarate dehydratase (EC 4.2.1.40))

Software error:

../bin/blast/fastacmd -i /tmp/list.18015.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18015.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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