GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaB in Burkholderia phytofirmans PsJN

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2 (characterized, see rationale)
to candidate BPHYT_RS21425 BPHYT_RS21425 3-carboxy-cis,cis-muconate cycloisomerase

Query= uniprot:A0A0C4YE08
         (470 letters)



>FitnessBrowser__BFirm:BPHYT_RS21425
          Length = 459

 Score =  500 bits (1287), Expect = e-146
 Identities = 267/449 (59%), Positives = 311/449 (69%), Gaps = 4/449 (0%)

Query: 1   MPTSSRLTDPMFGSAATLAAFSDTATVQRMLDFEAALARAEASCGVIPADAAEAIAATCR 60
           + +S+RLT  + G+      ++  AT+QRMLD EAALARA A+  VIP  A  AI A C+
Sbjct: 2   LDSSARLTGLLCGTQPMNDIWAPRATLQRMLDVEAALARASAAHQVIPQTAVAAIEAACQ 61

Query: 61  AGEIDFDALAAAAVAGGNLAIPLVRQLTARVAARDAQAARYVHWGATSQDAIDTGMVLQL 120
           A ++D DALA  A  GGNLAIPLV+QLTARV A DA+A++YVHWGATSQD IDT  VLQL
Sbjct: 62  ADQLDADALARDAALGGNLAIPLVKQLTARVKAADAEASKYVHWGATSQDIIDTATVLQL 121

Query: 121 REALQAVDADLKALGHACAALAAQHRDTPMVARTWLQHALPTTFGLKAAGWLDALRRDLR 180
           R+    +D+ L++   A A LAA HR TPM+ RTWLQ ALP T GLK A WLDAL R   
Sbjct: 122 RDTFDLLDSSLQSTCDAVAKLAATHRTTPMIGRTWLQQALPITLGLKFAQWLDALLRHRE 181

Query: 181 RLDAARAQAATLQFGGAAGTLASLGAAAPAVATALGSALSLAVAPTPWHAYRDRMVEVAT 240
           RLDA RA+A  LQFGGAAGTLASL  AAP V  +L   L L V   PWH  RDR+ E A 
Sbjct: 182 RLDALRARALVLQFGGAAGTLASLRDAAPQVTQSLAKELGLTVPTLPWHTQRDRIAETAA 241

Query: 241 TLGMLTGSLGKIARDVSLMMQTEVAEVAEPTGPGRGGSSTMPHKRNPVGCAAVLTAAVRV 300
             GML G+LGKIARD+SL MQTE+ E+AEP   G+GGSSTMPHKRNPVGCAAVLTAA R 
Sbjct: 242 LFGMLIGTLGKIARDISLQMQTEIDELAEPAAAGKGGSSTMPHKRNPVGCAAVLTAATRA 301

Query: 301 PPLVATMLAGMVQEHERALGGWQAEWDTLPQIVTLAAGALRQMLEVVGGLQVDAARMRAN 360
           P LVAT+ AGMVQEHERALGGWQAEWD LP +  LA GAL  + ++  GL V+  R+ AN
Sbjct: 302 PGLVATVFAGMVQEHERALGGWQAEWDALPDLARLAGGALANIEQIAAGLNVNVPRLAAN 361

Query: 361 LGVTHGLILAEAAMLELGGKIGRLPAHHLVEGACRRAVAEGTTLRQALGATLAEDAAHAG 420
           L VTHGLIL EA ML LG  IGRL AHHLVE A + A+ +G TL   L A    D A   
Sbjct: 362 LDVTHGLILGEAVMLALGDSIGRLDAHHLVERASKAAIRDGQTLFDVLAA----DPAVTA 417

Query: 421 LMDAAALDRVCDPANYAGQAAGFVDAVLA 449
            +    L ++ DPA Y GQA  +VDA LA
Sbjct: 418 HLPLERLKQLLDPAQYVGQAHAYVDAALA 446


Lambda     K      H
   0.319    0.130    0.380 

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: 504
Number of extensions: 19
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: 470
Length of database: 459
Length adjustment: 33
Effective length of query: 437
Effective length of database: 426
Effective search space:   186162
Effective search space used:   186162
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 BPHYT_RS21425 BPHYT_RS21425 (3-carboxy-cis,cis-muconate cycloisomerase)
to HMM TIGR02426 (pcaB: 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.1138.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1138.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.