GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Cupriavidus basilensis 4G11

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate RR42_RS32050 RR42_RS32050 AraC family transcriptional regulator

Query= BRENDA::Q0SH24
         (400 letters)



>FitnessBrowser__Cup4G11:RR42_RS32050
          Length = 397

 Score =  277 bits (709), Expect = 3e-79
 Identities = 154/376 (40%), Positives = 210/376 (55%), Gaps = 6/376 (1%)

Query: 15  GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74
           G A APV++   SLG++ +MW PQ+ AL  + R++  D RGHG S  P GP SV +L  D
Sbjct: 17  GPASAPVLIFSNSLGTDHTMWAPQVEALGQQFRILRYDTRGHGRSALPPGPSSVAELGSD 76

Query: 75  VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134
           V+AL+D+L +  A F GLSMGG    WLG +AP+R   + L  TA + G  +AW  R   
Sbjct: 77  VIALMDALQIQKAAFCGLSMGGLTGMWLGVNAPQRFTRIVLANTAPRIGTHEAWNTRIEG 136

Query: 135 SRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTAD 194
              DG   L +  + RWF+          +   R+++      GYAA C A+ D D    
Sbjct: 137 VLRDGMTPLVEGSLQRWFTPAFVSAAGNQLDDLRQVLTGLDARGYAANCAAVRDADLREA 196

Query: 195 LSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLRE 254
           +  I  P LVIAG  DPST     + LAD I  AR+  L  AAH++N EQ    T  L +
Sbjct: 197 VKTIPVPVLVIAGSADPSTTAEQGRALADAIPGARYLELE-AAHLSNREQPARFTEALLD 255

Query: 255 HIVG-AGYARGRRA----AHAQGMTVRRSILGDAHVDRSVAGTTDFTAPFQDFITRTAWG 309
            + G A  A GR A     +  G+ VRR++LG AHVDRS+A     T  FQ+ ITR AWG
Sbjct: 256 FLGGDAQQAAGRPANDGERYQAGLAVRRAVLGSAHVDRSLAKLNPLTEEFQNLITRYAWG 315

Query: 310 DIWSRPGLDHELRRLLTIAVLTAVGNEHELDMHIRAALRAGVDADTIGEVLLHTSVYAGV 369
           +IW+R GL    R L+TIA++ A+    EL +H+RAA    V  D + EVLL T++Y GV
Sbjct: 316 EIWTREGLPRHSRSLITIAMMVALNRGEELKLHLRAAANNKVSRDEVKEVLLQTAIYCGV 375

Query: 370 PNSNLGFALGKQALAD 385
           P +N  F + ++  A+
Sbjct: 376 PAANSAFHMAEEVFAE 391


Lambda     K      H
   0.318    0.132    0.392 

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: 411
Number of extensions: 16
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: 400
Length of database: 397
Length adjustment: 31
Effective length of query: 369
Effective length of database: 366
Effective search space:   135054
Effective search space used:   135054
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate RR42_RS32050 RR42_RS32050 (AraC family transcriptional regulator)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

Software error:

../bin/blast/fastacmd -i /tmp/list.2453.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2453.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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