GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Phaeobacter inhibens BS107

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF398 PGA1_c04090 beta-ketoadipyl-CoA thiolase PaaJ

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Phaeo:GFF398
          Length = 400

 Score =  533 bits (1374), Expect = e-156
 Identities = 267/399 (66%), Positives = 314/399 (78%), Gaps = 1/399 (0%)

Query: 3   DVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGE 62
           D FICDA RTPIGR+GGAL+ +R DDLAA+P+ AL   NP V W  +D+V  G ANQAGE
Sbjct: 2   DAFICDATRTPIGRYGGALSQLRTDDLAALPIAALAARNPDVDWSSLDDVILGDANQAGE 61

Query: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122
            NRNVARMA LLAGLP ++PG T+NRLCASGMDA+G A R I +G+ ++AIAGGVESMSR
Sbjct: 62  SNRNVARMAALLAGLPTTVPGTTINRLCASGMDAVGMASRGIKAGDYDMAIAGGVESMSR 121

Query: 123 APFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182
           APFVM KA S ++R   + DTTIGWRF+N  M   YG DSMP+TADNVA+DY +SR DQD
Sbjct: 122 APFVMPKATSAFTRANAVYDTTIGWRFVNKKMHEMYGTDSMPQTADNVAEDYGISREDQD 181

Query: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKG-ETIVERDEHLRPETTLEALTKLKPVN 241
           AFA RSQ + AAA  AG F +EI PV I  +KG + +V+ DEH RP T+ E L  LK VN
Sbjct: 182 AFAARSQARWAAAHEAGIFNDEITPVTIPQRKGDDLVVDTDEHPRPGTSAEKLAGLKGVN 241

Query: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301
           GPDK+VTAGNASGVNDGAAA+++A+  A  K+GL P AR++GM + GV PR+MGIGPVPA
Sbjct: 242 GPDKSVTAGNASGVNDGAAAILMANEAAAAKNGLKPMARIVGMTAAGVEPRIMGIGPVPA 301

Query: 302 VRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361
            RK+  R G+ +   DVIELNEAFASQGLA LRELGVADDAP VNPNGGAIALGHPLGMS
Sbjct: 302 TRKVLARTGLTIDQMDVIELNEAFASQGLATLRELGVADDAPHVNPNGGAIALGHPLGMS 361

Query: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GARLVLTA +QL+++GGR  L TMCVGVGQG AL +ERV
Sbjct: 362 GARLVLTAAYQLQRTGGRYALCTMCVGVGQGTALILERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 541
Number of extensions: 10
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 GFF398 PGA1_c04090 (beta-ketoadipyl-CoA thiolase PaaJ)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.3229.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3229.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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