GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Paraburkholderia bryophila 376MFSha3.1

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate H281DRAFT_01504 H281DRAFT_01504 3-oxoadipyl-CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Burk376:H281DRAFT_01504
          Length = 400

 Score =  570 bits (1470), Expect = e-167
 Identities = 287/401 (71%), Positives = 336/401 (83%), Gaps = 1/401 (0%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           M EA + DA+RTPIGRYAG+L+SVRADDLGA+PLKAL+ R+  +DWS +DDVIYGCANQA
Sbjct: 1   MTEAFLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKNVDWSVIDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ LLAGLP  VPG+T+NRLCGSG+DAVG AARA++ GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAPFVMGK+  AF R A+I+DTTIGWRFVN LM+Q +G+DSMPET ENVA  +NISRAD
Sbjct: 121 SRAPFVMGKATSAFSRQADIYDTTIGWRFVNPLMKQMYGVDSMPETGENVATDYNISRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ KAA A  +G LA+EIV V IAQ+KG    V  DEHPR +T+LE LAKL  
Sbjct: 181 QDAFALRSQQKAARAQKDGTLAQEIVGVTIAQKKGDPITVSQDEHPR-ETSLETLAKLKG 239

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
             R  G+VTAGNASGVNDGA ALLLA+ E A+R GL  RARV+G+ATAGV PRIMG+GP 
Sbjct: 240 VVRPDGTVTAGNASGVNDGAAALLLANEETAKRFGLTPRARVLGIATAGVAPRIMGMGPA 299

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PA +K++    + +   DVIELNEAFA+QG+AVLR LG+ADDD RVNPNGGAIALGHPLG
Sbjct: 300 PAAQKLMARLNMTIDQFDVIELNEAFASQGIAVLRTLGVADDDARVNPNGGAIALGHPLG 359

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTA+++L+  QGR+ALCTMCIGVGQGIA+ IER+
Sbjct: 360 MSGARLVTTAMYQLQRTQGRFALCTMCIGVGQGIAIAIERV 400


Lambda     K      H
   0.319    0.134    0.384 

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: 549
Number of extensions: 12
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: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate H281DRAFT_01504 H281DRAFT_01504 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.24443.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24443.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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