Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_012112924.1 XAUT_RS04530 3-oxoadipyl-CoA thiolase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000017645.1:WP_012112924.1 Length = 402 Score = 560 bits (1442), Expect = e-164 Identities = 284/402 (70%), Positives = 322/402 (80%), Gaps = 1/402 (0%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M AFICD RTPIGRY GAL VRADDLAA P+R L RNP +D E +DDVILGCANQA Sbjct: 1 MAHAFICDFARTPIGRYAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQA 60 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 GEDNR+VARMA LLAGLP S GTT+NRLCGSGLDA+G ARAI GD DL++AGGVESM Sbjct: 61 GEDNRDVARMAALLAGLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVESM 120 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 +RAPFV GKA AFSRQAE++DTTIGWRFVNPLM Q+G DSMPET ENVAE ++SR D Sbjct: 121 TRAPFVQGKAQEAFSRQAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDFQVSRAD 180 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 QD FA RSQQR AQ +G A EI P+ +K KKG V ++ DEH R ETTLEQL GLKA Sbjct: 181 QDLFAYRSQQRVKAAQDAGFFAREIAPIEVKGKKGAVIRVEADEHPRAETTLEQLAGLKA 240 Query: 241 PFR-ANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 PFR A G +TAGNASGVNDGA ALI+ASE A GLTPRAR+V++ AGV PR+MG+GP Sbjct: 241 PFRKAGGTVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQAGVPPRIMGIGP 300 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 PATR++LE+ GL++ D+D+IELNEAFAAQAL VLR+LGLPDDA HVNPNGGAIALGHPL Sbjct: 301 APATRKLLEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVNPNGGAIALGHPL 360 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 GMSGARLA+ A L R G A+ TMCIGVGQGIA ++ERV Sbjct: 361 GMSGARLAMTAVSALEVRGGTRAVATMCIGVGQGIAALIERV 402 Lambda K H 0.319 0.135 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: 536 Number of extensions: 17 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: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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_012112924.1 XAUT_RS04530 (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.2513442.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-210 685.2 11.8 1.7e-210 685.0 11.8 1.0 1 NCBI__GCF_000017645.1:WP_012112924.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000017645.1:WP_012112924.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 685.0 11.8 1.7e-210 1.7e-210 2 400 .] 3 402 .] 2 402 .] 0.99 Alignments for each domain: == domain 1 score: 685.0 bits; conditional E-value: 1.7e-210 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 +++i+d rtpiGry+G+l vraddlaa p++ l +rnp +d++a+ddvilGcanqaGednr+varmaalla NCBI__GCF_000017645.1:WP_012112924.1 3 HAFICDFARTPIGRYAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQAGEDNRDVARMAALLA 75 79*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glpvs pgttvnrlcgsglda+g++arai +G+adl++aGGvesm+rapfv Gka+ afsr+a++ dttiGwr NCBI__GCF_000017645.1:WP_012112924.1 76 GLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVESMTRAPFVQGKAQEAFSRQAEIYDTTIGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 fvnp +ka+yGvdsmpet envae+f+vsr+dqd fa+rsqqr++aaq +Gffa+ei+p+e+k+kkG v+ NCBI__GCF_000017645.1:WP_012112924.1 149 FVNPLMKAQYGVDSMPETGENVAEDFQVSRADQDLFAYRSQQRVKAAQDAGFFAREIAPIEVKGKKGAVIRVE 221 ************************************************************************* PP TIGR02430 221 kdehlraettlealaklkavvre.dgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvepr 292 +deh+raettle+la lka++r+ +gtvtaGnasGvndGa al+lase a+k++gltprar++++ aGv pr NCBI__GCF_000017645.1:WP_012112924.1 222 ADEHPRAETTLEQLAGLKAPFRKaGGTVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQAGVPPR 294 *******************9986268*********************************************** PP TIGR02430 293 vmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarl 365 +mG+gp+pa++kll++ gl+l+d+d+ielneafaaqalavlr+lgl+dd+++vnpnGGaialGhplG+sGarl NCBI__GCF_000017645.1:WP_012112924.1 295 IMGIGPAPATRKLLEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVNPNGGAIALGHPLGMSGARL 367 ************************************************************************* PP TIGR02430 366 vltalkqleksggryalatlciGvGqGialvierv 400 ++ta++ le +gg +a+at+ciGvGqGia +ierv NCBI__GCF_000017645.1:WP_012112924.1 368 AMTAVSALEVRGGTRAVATMCIGVGQGIAALIERV 402 **********************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (402 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: 24.98 // [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