Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_000009985.1:WP_011385133.1 Length = 400 Score = 567 bits (1460), Expect = e-166 Identities = 291/401 (72%), Positives = 329/401 (82%), Gaps = 1/401 (0%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M EALI D RTPIGRYAG+LA VR DDL A P+KAL+ARH LDWS VD+V YGCANQA Sbjct: 1 MTEALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQA 60 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GEDNRNVARMA LLAGLP S+ GTTLNRLCGSG+DAVG AARA+ GEA LM+AGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESM 120 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SRAPFVM K++ AF R A ++DTTIGWRFVN LM++ +G DSMPETAENVA QFNISR D Sbjct: 121 SRAPFVMNKADSAFSRDARLYDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISRED 180 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QDAFA RSQ KA+AA NGR A+EI V + RKG +V HDEHPR +TT+E LAKL Sbjct: 181 QDAFAARSQAKASAAQKNGRFAQEISPVTLPARKGDPVVVSHDEHPR-ETTVEALAKLKA 239 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 PFR GGS+TAGNASGVNDGA ALL+AS AA+ HGL AR++GMATAGVEPRIMGIGPV Sbjct: 240 PFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTPIARILGMATAGVEPRIMGIGPV 299 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PAT+K+L GL +AD+DV+E NEAFAAQ LA R+LGLADDD+RVNPNGGAIALGHPLG Sbjct: 300 PATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVNPNGGAIALGHPLG 359 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 MSGAR+V TA +L + GR AL TMCIGVGQGIA+ IER+ Sbjct: 360 MSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIERV 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: 552 Number of extensions: 18 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 WP_011385133.1 AMB_RS13850 (3-oxoadipyl-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.28427.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-212 689.4 12.7 9e-212 689.2 12.7 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.2 12.7 9e-212 9e-212 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 689.2 bits; conditional E-value: 9e-212 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 e+ i+d rtpiGry+Gsl+ vr+ddlaa p+kal+ar++ ld++ +d+v +GcanqaGednrnvarma lcl|NCBI__GCF_000009985.1:WP_011385133.1 3 EALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQAGEDNRNVARMA 71 789****************************************************************** PP TIGR02430 71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139 +llaGlp+s+ gtt+nrlcgsg+da+g+aara+ +Gea+l+iaGGvesmsrapfv+ kadsafsr+a+l lcl|NCBI__GCF_000009985.1:WP_011385133.1 72 LLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESMSRAPFVMNKADSAFSRDARL 140 ********************************************************************* PP TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208 dttiGwrfvn +++ yG+dsmpetaenvae+f++sredqdafa rsq++++aaq++G fa+ei pv+ lcl|NCBI__GCF_000009985.1:WP_011385133.1 141 YDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISREDQDAFAARSQAKASAAQKNGRFAQEISPVT 209 ********************************************************************* PP TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277 ++ +kG+++vv++deh+r ett+ealaklka++r++g++taGnasGvndGaaall+as a+k+hgltp lcl|NCBI__GCF_000009985.1:WP_011385133.1 210 LPARKGDPVVVSHDEHPR-ETTVEALAKLKAPFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTP 277 ******************.************************************************** PP TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346 aril++a+aGvepr+mG+gpvpa++kllar+gl+++dldv+e+neafaaqala++r+lgladdd+rvn lcl|NCBI__GCF_000009985.1:WP_011385133.1 278 IARILGMATAGVEPRIMGIGPVPATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVN 346 ********************************************************************* PP TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 pnGGaialGhplG+sGar+v ta ql+++ggr+al+t+ciGvGqGia++ierv lcl|NCBI__GCF_000009985.1:WP_011385133.1 347 PNGGAIALGHPLGMSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIERV 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: 11.29 // [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