Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_013258670.1 DEBA_RS09300 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000143965.1:WP_013258670.1 Length = 395 Score = 404 bits (1038), Expect = e-117 Identities = 216/392 (55%), Positives = 277/392 (70%), Gaps = 4/392 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 MKEAVIV+ RT VG+A +G+L RP+ +G++ ++E +KR G + IDD++IGC+ P Sbjct: 1 MKEAVIVAACRTAVGRAPRGTLRHTRPEYMGSVVLQEVIKRTPGLDPKEIDDVVIGCSFP 60 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQG+NMAR + GLP + IT+NR+CSSGL +I+ AAE+IM+GA D +AGG ES Sbjct: 61 EAEQGMNMARVLIQKLGLPDDISGITINRFCSSGLNAISMAAERIMVGAADVMVAGGVES 120 Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179 MS VPM G++ +A P MG TAE V+ + VSREDQDAFAV S+ A A Sbjct: 121 MSMVPMGGNIMSVEPEIAGSRPWDLEGMGMTAENVSADFNVSREDQDAFAVESNNKALAA 180 Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239 + G FKDEIVP+ VT + +F DE R T + L+ L+PAF V G Sbjct: 181 IKSGAFKDEIVPLTVTKQRQKANGSFELYDEIFDTDECPRG-ATLEGLAKLKPAFKVGGC 239 Query: 240 VTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRAL 299 VTAGN+SQTSDGAAAVMLM +EKA ALGL P+ +R FAVGGVP + MGIGPV+AIP+AL Sbjct: 240 VTAGNASQTSDGAAAVMLMSKEKAKALGLKPMATYRGFAVGGVPGKYMGIGPVKAIPKAL 299 Query: 300 KLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLS 359 K+ GL L DI L ELNEAFA+QA+ IRELG++++ +N +GGAIALGHPLGCTG KLT Sbjct: 300 KITGLSLSDINLIELNEAFAAQALYCIRELGLNKDLINPHGGAIALGHPLGCTGAKLTTQ 359 Query: 360 LIHEMKRRNEQ--FGVVTMCIGGGMGAAGVFE 389 L++EM RR + +G+V+MCIG GMGAAG+FE Sbjct: 360 LLYEMNRRGPECRYGLVSMCIGLGMGAAGIFE 391 Lambda K H 0.316 0.133 0.377 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: 466 Number of extensions: 21 Number of successful extensions: 4 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: 391 Length of database: 395 Length adjustment: 31 Effective length of query: 360 Effective length of database: 364 Effective search space: 131040 Effective search space used: 131040 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_013258670.1 DEBA_RS09300 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))
# 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/TIGR01930.hmm # target sequence database: /tmp/gapView.16491.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01930 [M=385] Accession: TIGR01930 Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-136 441.1 0.4 1.9e-136 440.9 0.4 1.0 1 lcl|NCBI__GCF_000143965.1:WP_013258670.1 DEBA_RS09300 acetyl-CoA C-acyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_013258670.1 DEBA_RS09300 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.9 0.4 1.9e-136 1.9e-136 1 385 [] 6 391 .. 6 391 .. 0.97 Alignments for each domain: == domain 1 score: 440.9 bits; conditional E-value: 1.9e-136 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 iv+a Rt++g + +g+l+++++e +++ v++e+++r+ gldp++id+v++G++++++eq +n+aR + lcl|NCBI__GCF_000143965.1:WP_013258670.1 6 IVAACRTAVGrAPRGTLRHTRPEYMGSVVLQEVIKRTpGLDPKEIDDVVIGCSFPEAEQgMNMARVLIQ 74 8**********99******************************************************** PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 + glp++++++t+nr+C+Sgl+A+++aa++i++G+adv+vaGGvEsmS vp++ + +s++++ a lcl|NCBI__GCF_000143965.1:WP_013258670.1 75 KLGLPDDISGITINRFCSSGLNAISMAAERIMVGAADVMVAGGVESMSMVPMGGNI----MSVEPEIAG 139 ***************************************************97775....588988888 PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 ++ + mg+tAen+++++++sRe+qD++a++S++ka +Ai++g fkdeivp++v ++ lcl|NCBI__GCF_000143965.1:WP_013258670.1 140 SRP-------WDLEGMGMTAENVSADFNVSREDQDAFAVESNNKALAAIKSGAFKDEIVPLTVTKQrqk 201 777.......66789************************************************99999* PP TIGR01930 202 ........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelg 262 ++++++De++r + tle LakLkpafk g vtAgN+sq++DGAaa++lms+e+ak+lg lcl|NCBI__GCF_000143965.1:WP_013258670.1 202 angsfelyDEIFDTDECPR-GATLEGLAKLKPAFKV-GG-CVTAGNASQTSDGAAAVMLMSKEKAKALG 267 *******************.899***********95.78.6**************************** PP TIGR01930 263 ltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlek 331 l+p+a+++++av gv+ ++mg+gpv+Ai+kaLk +gls+sdi+l+E+nEAFAaq+l++++elg l+++ lcl|NCBI__GCF_000143965.1:WP_013258670.1 268 LKPMATYRGFAVGGVPGKYMGIGPVKAIPKALKITGLSLSDINLIELNEAFAAQALYCIRELG-LNKDL 335 ***************************************************************.889** PP TIGR01930 332 vNvnGGAiAlGHPlGasGarivltllkeLker..gkkyGlatlCvggGqGaAvile 385 +N +GGAiAlGHPlG++Ga ++++ll+e+++r +++yGl+++C+g+G+GaA i+e lcl|NCBI__GCF_000143965.1:WP_013258670.1 336 INPHGGAIALGHPLGCTGAKLTTQLLYEMNRRgpECRYGLVSMCIGLGMGAAGIFE 391 ********************************8889*****************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (395 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 6.25 // [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