GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Caulobacter crescentus NA1000

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiolase

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__Caulo:CCNA_02490
          Length = 399

 Score =  567 bits (1462), Expect = e-166
 Identities = 289/396 (72%), Positives = 331/396 (83%), Gaps = 1/396 (0%)

Query: 6   YICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGEDN 65
           YICD +RTPIGR+GGSL+ VRADDLAA+P+KALV RNP +D + +DE+ LG ANQAGEDN
Sbjct: 5   YICDGIRTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQAGEDN 64

Query: 66  RNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRAP 125
           RNVARMALLLAG P SVPGVT+NRLCASG++AVG A RAIASG  +LVIAGGVESMSRAP
Sbjct: 65  RNVARMALLLAGYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESMSRAP 124

Query: 126 YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDAF 185
           +VMGKADSAF R  +I DTTIGWRF+NP M+  YGVD+MPETA+NVA DY V+R DQDAF
Sbjct: 125 FVMGKADSAFSRSAEIFDTTIGWRFVNPAMRKLYGVDSMPETAENVATDYGVNREDQDAF 184

Query: 186 ALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGPD 245
           ALRSQ     AQA G+ A EI PV I GK G T+VD DEH R +TT+EALAKLKP+    
Sbjct: 185 ALRSQARTAAAQANGFLAGEITPVEIPGKAGPTIVDRDEHPR-ETTMEALAKLKPIVREG 243

Query: 246 KTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVRK 305
            TVTAGNASGVNDG+VAL++AS +AVK+HGL  RA++ G ASAGV PRVMGIGPVPAVRK
Sbjct: 244 GTVTAGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASAGVEPRVMGIGPVPAVRK 303

Query: 306 LLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGAR 365
           L+ +  L++ DFDV+ELNEAFAAQGLAV R+LG+ DD A VN NGGAIALGHPLGASGAR
Sbjct: 304 LMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGASGAR 363

Query: 366 LVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           LVLTA+ QLE SGGQRGL T+C+GVGQG ALA ERV
Sbjct: 364 LVLTALRQLEASGGQRGLATLCIGVGQGAALAFERV 399


Lambda     K      H
   0.317    0.134    0.379 

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: 559
Number of extensions: 23
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: 401
Length of database: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_02490 CCNA_02490 (3-ketoacyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.20962.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20962.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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