Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000230695.2:WP_015446959.1 Length = 400 Score = 501 bits (1289), Expect = e-146 Identities = 252/395 (63%), Positives = 307/395 (77%) Query: 6 YICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGEDN 65 ++ DA RTP GR GG+LA VRADDLAA+P+ AL+ R+P +DW+ LDEV LGCANQAGEDN Sbjct: 5 WLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQAGEDN 64 Query: 66 RNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRAP 125 RNVARMA LLAGLP SVP VT+NRLCASG++A+G A RAIA GEAELV+AGGVESMSRAP Sbjct: 65 RNVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAP 124 Query: 126 YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDAF 185 YV+ KAD A+ RGQ++EDTT+GWR +NP M+A YG+D+M +TA+N+A ++ + R QDA+ Sbjct: 125 YVLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDSQDAY 184 Query: 186 ALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGPD 245 ALRSQQ AQA G+ AEEI V K VV DEH R DTT LA LKP+ G Sbjct: 185 ALRSQQRTAHAQAQGWLAEEITAVHAPHGKESLVVQVDEHPRADTTAAKLAALKPLLGAG 244 Query: 246 KTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVRK 305 ++TAGNASG+NDG+ A++LAS A+ ++GL+ A+++GMA+AGVAPRVMGIGPVPA+ K Sbjct: 245 SSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPVPAIHK 304 Query: 306 LLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGAR 365 LL R L +DFD IE+NEAFAAQ LA TR LG+ DD VN NGGAIALGHPLGASGAR Sbjct: 305 LLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGASGAR 364 Query: 366 LVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 L LTA L + R L ++CVGVGQG+ALA+ER Sbjct: 365 LALTAAFALRRHRQHRALVSLCVGVGQGLALALER 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: 506 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_015446959.1 R2APBS1_RS03900 (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.4085530.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-194 630.5 14.0 6.6e-194 630.4 14.0 1.0 1 NCBI__GCF_000230695.2:WP_015446959.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000230695.2:WP_015446959.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 630.4 14.0 6.6e-194 6.6e-194 2 399 .. 3 399 .. 2 400 .] 0.99 Alignments for each domain: == domain 1 score: 630.4 bits; conditional E-value: 6.6e-194 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 ++++vda rtp+Gr gG+l+ vraddlaa+p++al+ar+p+ld+aa+d+vilGcanqaGednrnvarma+lla NCBI__GCF_000230695.2:WP_015446959.1 3 SAWLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQAGEDNRNVARMATLLA 75 589********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glp+svp++tvnrlc+sgl+a+g aarai++Gea+lv+aGGvesmsrap+vl kad a++r ++ledtt+Gwr NCBI__GCF_000230695.2:WP_015446959.1 76 GLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAPYVLAKADVAYARGQQLEDTTLGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 +vnp+++a yG+dsm +taen+a+e+g++r+ qda+alrsqqrta+aqa+G++aeei+ v+ ++ k + vv+ NCBI__GCF_000230695.2:WP_015446959.1 149 LVNPRMQAGYGIDSMTQTAENLAREHGIDRDSQDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGKE-SLVVQ 220 **************************************************************99886.89*** PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 deh+ra+tt +la lk+++ ++ ++taGnasG+ndGaaa+llase a++r+gl+p ari+++a+aGv+prv NCBI__GCF_000230695.2:WP_015446959.1 221 VDEHPRADTTAAKLAALKPLLGAGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRV 293 ************************************************************************* PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gpvpa++kllar+gl +d+d ie+neafaaq la++r+lgl+dd+++vn+nGGaialGhplGasGarl+ NCBI__GCF_000230695.2:WP_015446959.1 294 MGIGPVPAIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGASGARLA 366 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvier 399 lta l+++ +++al++lc+GvGqG+al++er NCBI__GCF_000230695.2:WP_015446959.1 367 LTAAFALRRHRQHRALVSLCVGVGQGLALALER 399 ********************************9 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.29 // [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