GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Cupriavidus basilensis 4G11

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate RR42_RS09905 RR42_RS09905 fumarylacetoacetase

Query= SwissProt::P25093
         (419 letters)



>FitnessBrowser__Cup4G11:RR42_RS09905
          Length = 437

 Score =  338 bits (868), Expect = 1e-97
 Identities = 191/427 (44%), Positives = 254/427 (59%), Gaps = 25/427 (5%)

Query: 7   AEDSDFPIQNLPYGVFSTQSNPKP-RIGVAIGDQILDLSVIKHLFTGPVL----SKHQHV 61
           A   DFP+QNLP  VF  + + +  R GVAIGDQI+DL  ++ L   P L    ++    
Sbjct: 20  AAGCDFPLQNLPLSVFRRKGSTEAWRGGVAIGDQIVDLGALQSL---PGLQDSAAEAVRA 76

Query: 62  FDETTLNSFMGLGQAAWKEARASLQNLLSASQAQLRDDKELRQRAFTSQASATMHLPATI 121
               TLN  + LG  +W+  R  L  LL +  +  R  +E    A   Q  A   +P  I
Sbjct: 77  AAAPTLNGLLELGPESWRALRHGLYGLLQSGSSLARQVRE----ALVPQLDAEHAVPVRI 132

Query: 122 GDYTDFYSSLQHATNVGIMFRGKENALLPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMR 181
           GDYTDFY+SL HA N    F  + N   PN+  LP+ YHGR SS+ VSG  + RP GQ R
Sbjct: 133 GDYTDFYTSLDHAVNCCRQFGIEVN---PNFDWLPIAYHGRVSSIDVSGQQVYRPAGQYR 189

Query: 182 PDNSKPPVYGASKRLDMELEMAFFVGPGNRFGEPIPISKAQEHIFGMVLMNDWSARDIQQ 241
            D S  PVYG  +RLD ELE+   +G GN  G PIP++ AQ+HIFG+ L+NDWSARDIQ 
Sbjct: 190 TDPSSAPVYGPCQRLDYELEVGAVIGIGNARGTPIPLANAQQHIFGLCLLNDWSARDIQT 249

Query: 242 WEYVPLGPFLGKSFGTTISPWVVPMDALMPFVV--PNPKQDPKPLPYL---CHSQPYTFD 296
           WE  PLGPFL K+F TT+SPW+V ++AL+P+        + P+PL YL    ++    FD
Sbjct: 250 WEMQPLGPFLAKNFATTLSPWIVTLEALLPYRTGWTRAPERPQPLDYLRSADNAAAGAFD 309

Query: 297 INLSVA-LKGEGMSQAA---TICRSNFKHMYWTILQQLTHHSVNGCNLRPGDLLASGTIS 352
           I L V+ L     +Q      + R++F+H YWT+ Q + HH+V GCNL+PGDLL SGT+S
Sbjct: 310 IQLEVSILSARRQAQGRPPHKLTRTSFQHQYWTLGQMIAHHTVGGCNLQPGDLLGSGTVS 369

Query: 353 GSDPESFGSMLELSWKGTKAIDVGQGQTRTFLLDGDEVIITGHCQGDGY-RVGFGQCAGK 411
           G +P   G+++EL+  GT   D+G G+ R FL DGD V+  G C+ + Y R+GFG     
Sbjct: 370 GPNPWEAGALIELTVSGTHPADIGDGEQRGFLKDGDTVVFRGWCEREDYARIGFGVNYAT 429

Query: 412 VLPALSP 418
           VLPA  P
Sbjct: 430 VLPAPGP 436


Lambda     K      H
   0.320    0.136    0.422 

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: 582
Number of extensions: 29
Number of successful extensions: 7
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: 419
Length of database: 437
Length adjustment: 32
Effective length of query: 387
Effective length of database: 405
Effective search space:   156735
Effective search space used:   156735
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 RR42_RS09905 RR42_RS09905 (fumarylacetoacetase)
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.21334.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21334.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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