Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_013075085.1 BTUS_RS05310 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000092905.1:WP_013075085.1 Length = 392 Score = 499 bits (1284), Expect = e-146 Identities = 252/390 (64%), Positives = 309/390 (79%), Gaps = 1/390 (0%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYE-GNIDDLIIGCATP 59 M+EAVIVSG RT VGKA KG+L RP+DL + V E L+R E ++D+IIGCA P Sbjct: 1 MREAVIVSGVRTAVGKAPKGALRETRPEDLAGLVVAEALRRVPQVEPAEVEDVIIGCAIP 60 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQG+N+ R + AGLP +VP +TVNR+CSSGLQ+IA AAE+IM G D +AGG ES Sbjct: 61 EAEQGMNLGRIVALRAGLPTSVPGVTVNRFCSSGLQTIAMAAERIMAGFADVIVAGGVES 120 Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179 MS VPM GH RPN L E P+ Y+SMG TAEQVA+++ VSREDQDAFA+RSHQ AA+A Sbjct: 121 MSLVPMTGHTVRPNPYLVEHYPQVYLSMGLTAEQVARRFDVSREDQDAFALRSHQRAARA 180 Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239 + EG +DEIVPV VT T +G+D K ++ F F +DEGVR T+ + L+ LRPAF+ DGT Sbjct: 181 IDEGLCRDEIVPVPVTRTVVGDDGKVVKTSFEFVEDEGVRRDTSLEALAQLRPAFAKDGT 240 Query: 240 VTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRAL 299 VTAGNSSQTSDGAAAV++M E+A LGL P + FRSFAVGGV P++MGIGPVEA+P+AL Sbjct: 241 VTAGNSSQTSDGAAAVVVMSAERAAQLGLEPKLIFRSFAVGGVDPDIMGIGPVEAVPKAL 300 Query: 300 KLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLS 359 K AGL + DI LFELNEAFA+Q++ V+R+LG+D EK NVNGGAIALGHPLGCTG+KLT+S Sbjct: 301 KKAGLSIDDIDLFELNEAFAAQSLAVMRKLGMDPEKTNVNGGAIALGHPLGCTGSKLTVS 360 Query: 360 LIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 L++EM+RR ++GVVTMCIGGGMGAAGVFE Sbjct: 361 LMNEMRRRGSRYGVVTMCIGGGMGAAGVFE 390 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: 496 Number of extensions: 22 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: 391 Length of database: 392 Length adjustment: 31 Effective length of query: 360 Effective length of database: 361 Effective search space: 129960 Effective search space used: 129960 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_013075085.1 BTUS_RS05310 (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.4239.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-149 484.5 0.6 1.3e-149 484.3 0.6 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013075085.1 BTUS_RS05310 acetyl-CoA C-acyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013075085.1 BTUS_RS05310 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 484.3 0.6 1.3e-149 1.3e-149 1 385 [] 6 390 .. 6 390 .. 0.96 Alignments for each domain: == domain 1 score: 484.3 bits; conditional E-value: 1.3e-149 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 iv++vRt++g + +g+l+e+++edL+ v+ e+l+r+ +++p+++++vi+G++++++eq +n++R +al lcl|NCBI__GCF_000092905.1:WP_013075085.1 6 IVSGVRTAVGkAPKGALRETRPEDLAGLVVAEALRRVpQVEPAEVEDVIIGCAIPEAEQgMNLGRIVAL 74 8*********988******************************************************** PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 +aglp+svp++tvnr+C+Sglq++a+aa++i+aG adv+vaGGvEsmS vp+ + ++++ + lcl|NCBI__GCF_000092905.1:WP_013075085.1 75 RAGLPTSVPGVTVNRFCSSGLQTIAMAAERIMAGFADVIVAGGVESMSLVPMTGHT------VRPNPYL 137 ***************************************************96554......3342233 PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +e ++++ lsmg tAe++a+++++sRe+qD++alrShq+aa+Ai+eg deivpv v ++ lcl|NCBI__GCF_000092905.1:WP_013075085.1 138 VE-----HYPQVYLSMGLTAEQVARRFDVSREDQDAFALRSHQRAARAIDEGLCRDEIVPVPVTRTvvg 201 33.....366899*************************************************999899* PP TIGR01930 202 ........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelg 262 + + +Deg+r++t+le+La+L+paf++ +g tvtAgNssq++DGAaa+++ms e+a++lg lcl|NCBI__GCF_000092905.1:WP_013075085.1 202 ddgkvvktSFEFVEDEGVRRDTSLEALAQLRPAFAK-DG-TVTAGNSSQTSDGAAAVVVMSAERAAQLG 268 ***9998878899*********************95.9*.6**************************** PP TIGR01930 263 ltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlek 331 l+p+ ++s+av gvdp++mg+gpv+A++kaLkkaglsi+didl+E+nEAFAaq lav+++lg +d+ek lcl|NCBI__GCF_000092905.1:WP_013075085.1 269 LEPKLIFRSFAVGGVDPDIMGIGPVEAVPKALKKAGLSIDDIDLFELNEAFAAQSLAVMRKLG-MDPEK 336 ***************************************************************.88*** PP TIGR01930 332 vNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 NvnGGAiAlGHPlG++G+ ++++l++e+++rg +yG++t+C+ggG+GaA ++e lcl|NCBI__GCF_000092905.1:WP_013075085.1 337 TNVNGGAIALGHPLGCTGSKLTVSLMNEMRRRGSRYGVVTMCIGGGMGAAGVFE 390 **************************************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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: 10.56 // [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