Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate YP_004140309.1 Mesci_1095 beta-ketoadipyl CoA thiolase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_000185905.1:YP_004140309.1 Length = 401 Score = 565 bits (1456), Expect = e-166 Identities = 284/401 (70%), Positives = 334/401 (83%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M EA I D +RTPIGR+ G+L+SVR+DDLGAIPL+AL R+P +DW A+DDV+YGCANQA Sbjct: 1 MAEAYICDYIRTPIGRFGGSLSSVRSDDLGAIPLRALAERNPGIDWQAIDDVVYGCANQA 60 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GEDNRNVARMA LLAGLP VPG+T+NRLCGSG+DA+ AARA++ GEA LM+AGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPKEVPGSTVNRLCGSGMDALTIAARAIKAGEAELMIAGGVESM 120 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SRAPFVM K++ AF R+AEI+DTTIGWRFVN LM++ +G+DSMPET ENVA F++SRAD Sbjct: 121 SRAPFVMPKADTAFSRNAEIYDTTIGWRFVNPLMKKQYGVDSMPETGENVAEDFSVSRAD 180 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QDAFA+RSQ+KA AA ANGRLAKEI V I QRKG A IV DEHPR +T+E LAKL T Sbjct: 181 QDAFAVRSQNKAVAAQANGRLAKEITPVTILQRKGDALIVSKDEHPRAGSTVEALAKLPT 240 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 PFRQGG+VTAGNASGVNDGA AL++AS A +++GL AR++G A AGV PRIMGIGPV Sbjct: 241 PFRQGGTVTAGNASGVNDGAAALIVASEAAVKKYGLTPIARILGGAAAGVAPRIMGIGPV 300 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PAT+K+ GL DVIELNEAFA+QG+AVLR+LG+A+D E VNPNGGAIALGHPLG Sbjct: 301 PATQKLCARLGLTPKQFDVIELNEAFASQGIAVLRQLGIAEDAEHVNPNGGAIALGHPLG 360 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 MSGAR+ TA EL ER GRYAL TMCIGVGQGIA+ +ER+ Sbjct: 361 MSGARISGTAALELRERGGRYALATMCIGVGQGIAIALERV 401 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: 577 Number of extensions: 13 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: 401 Length of database: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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 YP_004140309.1 Mesci_1095 (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.4095679.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-215 701.5 8.9 1.9e-215 701.3 8.9 1.0 1 NCBI__GCF_000185905.1:YP_004140309.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000185905.1:YP_004140309.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 701.3 8.9 1.9e-215 1.9e-215 2 400 .] 3 401 .] 2 401 .] 1.00 Alignments for each domain: == domain 1 score: 701.3 bits; conditional E-value: 1.9e-215 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 e+yi+d irtpiGr+gGslssvr+ddl+a+pl+al +rnp +d++aiddv++GcanqaGednrnvarma+lla NCBI__GCF_000185905.1:YP_004140309.1 3 EAYICDYIRTPIGRFGGSLSSVRSDDLGAIPLRALAERNPGIDWQAIDDVVYGCANQAGEDNRNVARMALLLA 75 79*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glp++vpg+tvnrlcgsg+dal++aaraikaGea+l+iaGGvesmsrapfv+ kad+afsr+a++ dttiGwr NCBI__GCF_000185905.1:YP_004140309.1 76 GLPKEVPGSTVNRLCGSGMDALTIAARAIKAGEAELMIAGGVESMSRAPFVMPKADTAFSRNAEIYDTTIGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 fvnp +k++yGvdsmpet envae+f+vsr+dqdafa+rsq+++ aaqa+G +a+ei+pv+i q+kG++ +v+ NCBI__GCF_000185905.1:YP_004140309.1 149 FVNPLMKKQYGVDSMPETGENVAEDFSVSRADQDAFAVRSQNKAVAAQANGRLAKEITPVTILQRKGDALIVS 221 ************************************************************************* PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 kdeh+ra +t+ealakl +++r++gtvtaGnasGvndGaaal++ase avk++gltp aril+ a+aGv+pr+ NCBI__GCF_000185905.1:YP_004140309.1 222 KDEHPRAGSTVEALAKLPTPFRQGGTVTAGNASGVNDGAAALIVASEAAVKKYGLTPIARILGGAAAGVAPRI 294 ************************************************************************* PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gpvpa++kl ar+gl+ +++dvielneafa+q++avlr+lg+a+d+++vnpnGGaialGhplG+sGar+ NCBI__GCF_000185905.1:YP_004140309.1 295 MGIGPVPATQKLCARLGLTPKQFDVIELNEAFASQGIAVLRQLGIAEDAEHVNPNGGAIALGHPLGMSGARIS 367 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400 ta +l+++ggryalat+ciGvGqGia+++erv NCBI__GCF_000185905.1:YP_004140309.1 368 GTAALELRERGGRYALATMCIGVGQGIAIALERV 401 *********************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (401 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 22.13 // [ok]
This GapMind analysis is from Sep 24 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