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))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02430.hmm # target sequence database: /tmp/gapView.2563.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02430 [M=400] Accession: TIGR02430 Description: pcaF: 3-oxoadipyl-CoA thiolase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-227 738.9 11.6 8.2e-227 738.7 11.6 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiola Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02490 CCNA_02490 3-ketoacyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 738.7 11.6 8.2e-227 8.2e-227 2 400 .] 3 399 .] 2 399 .] 1.00 Alignments for each domain: == domain 1 score: 738.7 bits; conditional E-value: 8.2e-227 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 ++yi+d+irtpiGrygGsls+vraddlaa+plkal+arnpsld+aaid+++lG+anqaGednrnvarma+lla lcl|FitnessBrowser__Caulo:CCNA_02490 3 AAYICDGIRTPIGRYGGSLSKVRADDLAAIPLKALVARNPSLDLAAIDEIVLGSANQAGEDNRNVARMALLLA 75 69*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 G+pvsvpg+tvnrlc+sgl+a+g+aarai++G++dlviaGGvesmsrapfv+Gkadsafsrsa+++dttiGwr lcl|FitnessBrowser__Caulo:CCNA_02490 76 GYPVSVPGVTVNRLCASGLEAVGYAARAIASGHNDLVIAGGVESMSRAPFVMGKADSAFSRSAEIFDTTIGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 fvnp++++lyGvdsmpetaenva+++gv+redqdafalrsq+rtaaaqa+Gf+a ei+pvei++k G +t+vd lcl|FitnessBrowser__Caulo:CCNA_02490 149 FVNPAMRKLYGVDSMPETAENVATDYGVNREDQDAFALRSQARTAAAQANGFLAGEITPVEIPGKAG-PTIVD 220 *******************************************************************.9**** PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 +deh+r ett+ealaklk++vre+gtvtaGnasGvndGa+al++ase+avkrhgltprari+++asaGveprv lcl|FitnessBrowser__Caulo:CCNA_02490 221 RDEHPR-ETTMEALAKLKPIVREGGTVTAGNASGVNDGAVALVIASEDAVKRHGLTPRARITGYASAGVEPRV 292 ******.****************************************************************** PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gpvpav+kl+a++gl++ d+dv+elneafaaq+lavlr+lgl+dd+a+vn+nGGaialGhplGasGarlv lcl|FitnessBrowser__Caulo:CCNA_02490 293 MGIGPVPAVRKLMAKTGLAIGDFDVVELNEAFAAQGLAVLRQLGLPDDGAHVNANGGAIALGHPLGASGARLV 365 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400 ltal+qle+sgg+++latlciGvGqG al++erv lcl|FitnessBrowser__Caulo:CCNA_02490 366 LTALRQLEASGGQRGLATLCIGVGQGAALAFERV 399 *********************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (399 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.46 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory