Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase
Query= uniprot:D8ITH5 (401 letters) >FitnessBrowser__HerbieS:HSERO_RS20660 Length = 401 Score = 786 bits (2029), Expect = 0.0 Identities = 401/401 (100%), Positives = 401/401 (100%) Query: 1 MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60 MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG Sbjct: 1 MEALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAG 60 Query: 61 EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120 EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT Sbjct: 61 EDNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMT 120 Query: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ Sbjct: 121 RAPFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV Sbjct: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP Sbjct: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA Sbjct: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA 401 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA Sbjct: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERVA 401 Lambda K H 0.320 0.135 0.394 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: 710 Number of extensions: 15 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 HSERO_RS20660 HSERO_RS20660 (acetyl-CoA acetyltransferase)
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.19787.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-225 732.4 9.9 7.9e-225 732.2 9.9 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 732.2 9.9 7.9e-225 7.9e-225 2 400 .] 2 400 .. 1 400 [. 1.00 Alignments for each domain: == domain 1 score: 732.2 bits; conditional E-value: 7.9e-225 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarm 69 e+ i+dairtp+GrygG+l +vraddlaa p++ l++rnp +d++ ++d+++GcanqaGednrnvarm lcl|FitnessBrowser__HerbieS:HSERO_RS20660 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDNRNVARM 69 789***************************************************************** PP TIGR02430 70 aallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsa 137 a llaGlp +vpg+tvnrlcgs+lda+g+aaraik+Ge +l+iaGGvesm+rapfv+Gka+saf+rsa lcl|FitnessBrowser__HerbieS:HSERO_RS20660 70 AGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPFVMGKAESAFARSA 137 ******************************************************************** PP TIGR02430 138 kledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeiv 205 ++dttiGwrfvnp +ka+yG+dsmpetaenva++f+++r+dqdafalrsqqr+aaaqa+Gffa ei+ lcl|FitnessBrowser__HerbieS:HSERO_RS20660 138 AIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAFALRSQQRWAAAQAAGFFAGEIA 205 ******************************************************************** PP TIGR02430 206 pveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrh 273 p++i+qkkG++ vv +deh+r++ttl +laklk+vvr+dgtvtaGnasGvndGa+alllas +a+ + lcl|FitnessBrowser__HerbieS:HSERO_RS20660 206 PLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVRPDGTVTAGNASGVNDGACALLLASPKAADLY 273 ******************************************************************** PP TIGR02430 274 gltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladd 341 +l+prar+l++a+aGv+pr+mG+gp+pav+k+la++gl+l+++dvielneafaaq+lav+r+lgl+dd lcl|FitnessBrowser__HerbieS:HSERO_RS20660 274 RLKPRARVLGMATAGVAPRIMGFGPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDD 341 ******************************************************************** PP TIGR02430 342 darvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 +a+vnpnGGaia+GhplGasGarlv+ta++qle+sggryal+t+ciGvGqGialvierv lcl|FitnessBrowser__HerbieS:HSERO_RS20660 342 AAHVNPNGGAIAIGHPLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 **********************************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 8.32 // [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