Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__Smeli:SM_b20589 Length = 400 Score = 566 bits (1459), Expect = e-166 Identities = 286/400 (71%), Positives = 330/400 (82%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M +AYICD IRTPIGR+GG+L VRADDLGA+P+KAL+ RN VDW AVDDVI+GCANQA Sbjct: 1 MREAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQA 60 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 GEDNRN+ARMS LLAGLP PG TINRLCGSGMDAV AARAIK GEA+LMIAGGVESM Sbjct: 61 GEDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESM 120 Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180 +RAPFV+ KA SAF+R AEI+DTTIGWRFVNPLMK QYGVDSMPET ENVAE + +SR D Sbjct: 121 SRAPFVLPKAESAFSRNAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDYKVSRED 180 Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240 QDAFAL SQ KAA AQ +G LA EIV V I Q+KG + + DEHPR T++E+LA LK Sbjct: 181 QDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRDEHPRATTIEALAGLKTP 240 Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300 R GTVTAGNASGVNDGA AL+IAS++AA ++GLR AR++G A+AGV PRIMG+GP P Sbjct: 241 FREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGMGPVP 300 Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360 A+Q+L+ +LG T D+ DVIELNEAFASQGLAVLR LG+ DDDPRVN NGGAIALGHPLG Sbjct: 301 ASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPLGM 360 Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 SGAR+ TA +L + GR +L TMCIGVGQGIA+ +ER+ Sbjct: 361 SGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALERV 400 Lambda K H 0.319 0.134 0.386 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: 528 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 SM_b20589 SM_b20589 (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.29841.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-213 695.6 10.3 1.1e-213 695.5 10.3 1.0 1 lcl|FitnessBrowser__Smeli:SM_b20589 SM_b20589 beta-ketoadipyl CoA th Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 695.5 10.3 1.1e-213 1.1e-213 1 400 [] 2 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 695.5 bits; conditional E-value: 1.1e-213 TIGR02430 1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 +e+yi+d irtpiGr+gGsl+svraddl+a+plkal++rn s+d++a+ddvi+GcanqaGednrn+arm++lla lcl|FitnessBrowser__Smeli:SM_b20589 2 REAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQAGEDNRNIARMSLLLA 75 69************************************************************************ PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrf 148 Glpv+vpgtt+nrlcgsg+da+ aaraik+Gea+l+iaGGvesmsrapfvl ka+safsr+a++ dttiGwrf lcl|FitnessBrowser__Smeli:SM_b20589 76 GLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESMSRAPFVLPKAESAFSRNAEIYDTTIGWRF 149 ************************************************************************** PP TIGR02430 149 vnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkd 222 vnp +ka+yGvdsmpet envae+++vsredqdafalrsq+++aaaqa+G +a+eiv v+i+q+kG ++v+d+d lcl|FitnessBrowser__Smeli:SM_b20589 150 VNPLMKAQYGVDSMPETGENVAEDYKVSREDQDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRD 223 ************************************************************************** PP TIGR02430 223 ehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGl 296 eh+r tt+eala lk+++re+gtvtaGnasGvndGaaal++aseea+++hgl+p aril+ asaGv pr+mG+ lcl|FitnessBrowser__Smeli:SM_b20589 224 EHPR-ATTIEALAGLKTPFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGM 296 ****.89******************************************************************* PP TIGR02430 297 gpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltal 370 gpvpa ++l++r+g + + +dvielneafa+q+lavlr+lg+addd rvn nGGaialGhplG+sGar+ ta lcl|FitnessBrowser__Smeli:SM_b20589 297 GPVPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPLGMSGARITGTAA 370 ************************************************************************** PP TIGR02430 371 kqleksggryalatlciGvGqGialvierv 400 +l+++ggr +l+t+ciGvGqGia+++erv lcl|FitnessBrowser__Smeli:SM_b20589 371 LELAETGGRTSLSTMCIGVGQGIAVALERV 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.25 // [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