Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Putida:PP_1377 Length = 400 Score = 759 bits (1961), Expect = 0.0 Identities = 389/400 (97%), Positives = 392/400 (98%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M DVFICDAIRTPIGRFGGALA VRADDLAAVPLKALIE NP VQWDQVDEVFFGCANQA Sbjct: 1 MHDVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDA+GTAFRAIASGEMEL IAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKAES YSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD Sbjct: 121 SRAPFVMGKAESAYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE IVERDEHLRPETTLEALTKLKPV Sbjct: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGEIIVERDEHLRPETTLEALTKLKPV 240 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 NGPDKTVTAGNASGVNDGAAA+ILASA AVKKHGLTPRARVLGMASGGVAPRVMGIGPVP Sbjct: 241 NGPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 AVRKLTERLG+AVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM Sbjct: 301 AVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV Sbjct: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 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: 671 Number of extensions: 18 Number of successful extensions: 1 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 PP_1377 PP_1377 (beta-ketoadipyl-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.8492.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-225 732.0 8.7 1e-224 731.8 8.7 1.0 1 lcl|FitnessBrowser__Putida:PP_1377 PP_1377 beta-ketoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 731.8 8.7 1e-224 1e-224 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 731.8 bits; conditional E-value: 1e-224 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaGl 76 +v+i+dairtpiGr+gG+l+svraddlaavplkal++rnp ++++++d+v++GcanqaGednrnvarma+llaGl lcl|FitnessBrowser__Putida:PP_1377 3 DVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQAGEDNRNVARMALLLAGL 77 79************************************************************************* PP TIGR02430 77 pvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnp 151 p+s+pg+t+nrlc+sg+da+g+a+rai++Ge +lviaGGvesmsrapfv+Gka+sa+sr+ kledttiGwrf+np lcl|FitnessBrowser__Putida:PP_1377 78 PESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESMSRAPFVMGKAESAYSRNMKLEDTTIGWRFINP 152 *************************************************************************** PP TIGR02430 152 klkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlr 226 +k++yGvdsmpeta+nva++++vsr+dqdafalrsqq++aaaqa+Gffaeeivpv+i++kkG e +v++dehlr lcl|FitnessBrowser__Putida:PP_1377 153 LMKSQYGVDSMPETADNVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKG-EIIVERDEHLR 226 ***************************************************************.899******** PP TIGR02430 227 aettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpa 301 +ettleal+klk+v+ +d+tvtaGnasGvndGaaa++las+ avk+hgltprar+l++as Gv+prvmG+gpvpa lcl|FitnessBrowser__Putida:PP_1377 227 PETTLEALTKLKPVNGPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301 *************************************************************************** PP TIGR02430 302 vkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleks 376 v+kl +r+g++++d+dvielneafa+q+lavlrelg+add+ +vnpnGGaialGhplG+sGarlvltal+qleks lcl|FitnessBrowser__Putida:PP_1377 302 VRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKS 376 *************************************************************************** PP TIGR02430 377 ggryalatlciGvGqGialvierv 400 ggr +lat+c+GvGqG+al+ierv lcl|FitnessBrowser__Putida:PP_1377 377 GGRKGLATMCVGVGQGLALAIERV 400 ***********************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (400 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: 9.90 // [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