GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaB in Sinorhizobium meliloti 1021

Align 3-Carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2) (characterized)
to candidate SM_b20575 SM_b20575 3-carboxy-cis,cis-muconate cycloisomerase

Query= BRENDA::Q2HNZ1
         (353 letters)



>FitnessBrowser__Smeli:SM_b20575
          Length = 351

 Score =  392 bits (1006), Expect = e-113
 Identities = 206/349 (59%), Positives = 247/349 (70%)

Query: 1   MSLSPFEHPFLSGLFGDSEIIELFSAKADIDAMIRFETALAQAEAEASIFADDEAEAIVS 60
           M+ S F+HP+LSGL GD  +   FS  AD+ AM+ FE ALA+AEA   +  +  A  I  
Sbjct: 1   MTYSAFDHPYLSGLLGDEAVAAEFSVVADVRAMLAFEAALARAEARHGVIPEAAANRIAE 60

Query: 61  GLSEFAADMSALRHGVAKDGVVVPELIRQMRAAVAGQGADKVHFGATSQDVIDTSLMLRL 120
               F+ D+ A+R   A DGVVVPEL+RQ+R AV  + A+ VHFGATSQDV+DTSLMLRL
Sbjct: 61  ACRGFSPDVGAMRRATAIDGVVVPELVRQLRRAVGEEAAEHVHFGATSQDVVDTSLMLRL 120

Query: 121 KMAAEIIATRLGHLIDTLGDLASRDGHKPLTGYTRMQAAIGITVADRAAGWIAPLERHLL 180
           K  AE+ + R+G ++  L       G + LT +TRMQ AI ITVADR   WI PL  H  
Sbjct: 121 KAIAELFSGRVGDVVTALEACGRHWGERALTAHTRMQPAIAITVADRLRSWIEPLLDHQD 180

Query: 181 RLETFAQNGFALQFGGAAGTLEKLGDNAGAVRADLAKRLGLADRPQWHNQRDGIPEFANL 240
           RL+T   + FA+QFGGAAGTLEKL   A  VRA LA+ L L D PQWH+QR  I +FA+L
Sbjct: 181 RLDTTGTDIFAVQFGGAAGTLEKLKGKADIVRATLAEELALVDCPQWHSQRLPIADFAHL 240

Query: 241 LSLVTGTLGKFGQDIALMAEIGSEIRLSGGGGSSAMPHKQNPVNAETLVTLARFNAVQIS 300
           LSLVTG+LGKFGQD+ALMA+ G EI L+GGGGSSAMPHKQNPV AE LVTLARFNA Q+S
Sbjct: 241 LSLVTGSLGKFGQDVALMAQAGDEIVLAGGGGSSAMPHKQNPVAAEVLVTLARFNATQVS 300

Query: 301 ALHQSLVQEQERSGAGWMLEWLTLPQMVTATGTSLLVAERLAAQIDRLG 349
           A+HQSLV EQERSG+ W LEWL LPQMV AT  +L +A  LA  + RLG
Sbjct: 301 AIHQSLVHEQERSGSAWTLEWLILPQMVGATAAALRLAAELAGNVRRLG 349


Lambda     K      H
   0.318    0.133    0.376 

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: 401
Number of extensions: 17
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: 353
Length of database: 351
Length adjustment: 29
Effective length of query: 324
Effective length of database: 322
Effective search space:   104328
Effective search space used:   104328
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: 49 (23.5 bits)

Align candidate SM_b20575 SM_b20575 (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.23367.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23367.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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