Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_028311754.1 H566_RS0112785 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000482785.1:WP_028311754.1 Length = 401 Score = 560 bits (1444), Expect = e-164 Identities = 277/397 (69%), Positives = 325/397 (81%), Gaps = 1/397 (0%) Query: 6 YICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGEDN 65 Y+CDA+RTP GR+GGSL+ VRADDL AVP++AL+ RNP VDW+ LD+V GCANQAGEDN Sbjct: 5 YLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGEDN 64 Query: 66 RNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRAP 125 RNV RM+ LLAGLP VPG T+NRLC S +DA +A RAI +GE +LVIAGGVESMSRAP Sbjct: 65 RNVGRMSALLAGLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRAP 124 Query: 126 YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDAF 185 +VMGKA AF R K+EDTTIGWRF+NPLMKA +GVD+MPETA+NVA D+ V+RADQDAF Sbjct: 125 FVMGKATEAFSRSAKVEDTTIGWRFVNPLMKAMHGVDSMPETAENVATDFDVARADQDAF 184 Query: 186 ALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGET-VVDADEHLRPDTTLEALAKLKPVNGP 244 ALRSQQ A AQAAG ++EI PV I K+G+ VV ADEHLRP+TTL ALAKLK V P Sbjct: 185 ALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVSADEHLRPETTLAALAKLKGVVRP 244 Query: 245 DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVR 304 D TVTAGNASGVNDG+ AL+LAS +HGLK RA+++ A AGVAPR+MG GP PA+ Sbjct: 245 DGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRIMGFGPAPAIT 304 Query: 305 KLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGA 364 K+L L + DVIELNEAFAAQ LAVTR G+ADDDARVNPNGGAIALGHPLGASGA Sbjct: 305 KVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASGA 364 Query: 365 RLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 RLV+ A+H+LE++GG+ GLCTMC+GVGQG+AL +ERV Sbjct: 365 RLVIAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401 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: 558 Number of extensions: 19 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_028311754.1 H566_RS0112785 (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.1582781.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-223 726.8 15.1 3.8e-223 726.7 15.1 1.0 1 NCBI__GCF_000482785.1:WP_028311754.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000482785.1:WP_028311754.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 726.7 15.1 3.8e-223 3.8e-223 2 400 .] 3 401 .] 2 401 .] 1.00 Alignments for each domain: == domain 1 score: 726.7 bits; conditional E-value: 3.8e-223 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 ++y++dairtp+GrygGsls vraddl+avp++al+arnps+d+aa+ddvi+GcanqaGednrnv+rm+alla NCBI__GCF_000482785.1:WP_028311754.1 3 HAYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGEDNRNVGRMSALLA 75 89*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glp +vpgttvnrlcgs+lda + aarai+aGe +lviaGGvesmsrapfv+Gka afsrsak+edttiGwr NCBI__GCF_000482785.1:WP_028311754.1 76 GLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRAPFVMGKATEAFSRSAKVEDTTIGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 fvnp +ka++Gvdsmpetaenva++f+v+r+dqdafalrsqqr+aaaqa+G +++ei+pv+i+qk+G++ vv+ NCBI__GCF_000482785.1:WP_028311754.1 149 FVNPLMKAMHGVDSMPETAENVATDFDVARADQDAFALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVS 221 ************************************************************************* PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 +dehlr+ettl alaklk+vvr+dgtvtaGnasGvndGaaalllase ++rhgl+prari+a+a aGv+pr+ NCBI__GCF_000482785.1:WP_028311754.1 222 ADEHLRPETTLAALAKLKGVVRPDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRI 294 ************************************************************************* PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gp+pa+ k+la a+l+l+++dvielneafaaqalav+r+ gladddarvnpnGGaialGhplGasGarlv NCBI__GCF_000482785.1:WP_028311754.1 295 MGFGPAPAITKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASGARLV 367 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400 ++al++le++ggry+l+t+ciGvGqGialvierv NCBI__GCF_000482785.1:WP_028311754.1 368 IAALHELERTGGRYGLCTMCIGVGQGIALVIERV 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.38 // [ok]
This GapMind analysis is from Apr 09 2024. 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