GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Caulobacter crescentus NA1000

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiolase

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



>FitnessBrowser__Caulo:CCNA_02490
          Length = 399

 Score =  564 bits (1454), Expect = e-165
 Identities = 286/400 (71%), Positives = 331/400 (82%), Gaps = 1/400 (0%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M   +ICD IRTPIGR+GG+L+ VRADDLAA+PLKAL+  NP++    +DE+  G ANQA
Sbjct: 1   MTAAYICDGIRTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAG P S+PGVT+NRLCASG++A+G A RAIASG  +L IAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA+S +SR+ ++ DTTIGWRF+NP M+  YGVDSMPETA+NVA DY V+R D
Sbjct: 121 SRAPFVMGKADSAFSRSAEIFDTTIGWRFVNPAMRKLYGVDSMPETAENVATDYGVNRED 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQ + AAAQA GF A EI PV I  K G TIV+RDEH R ETT+EAL KLKP+
Sbjct: 181 QDAFALRSQARTAAAQANGFLAGEITPVEIPGKAGPTIVDRDEHPR-ETTMEALAKLKPI 239

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
                TVTAGNASGVNDGA AL++AS +AVK+HGLTPRAR+ G AS GV PRVMGIGPVP
Sbjct: 240 VREGGTVTAGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASAGVEPRVMGIGPVP 299

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKL  + G+A+ DFDV+ELNEAFA+QGLAVLR+LG+ DD   VN NGGAIALGHPLG 
Sbjct: 300 AVRKLMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGA 359

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLVLTAL QLE SGG++GLAT+C+GVGQG ALA ERV
Sbjct: 360 SGARLVLTALRQLEASGGQRGLATLCIGVGQGAALAFERV 399


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: 551
Number of extensions: 17
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: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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 CCNA_02490 CCNA_02490 (3-ketoacyl-CoA thiolase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.16852.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16852.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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