Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate BPHYT_RS09180 BPHYT_RS09180 3-ketoacyl-CoA thiolase
Query= SwissProt::Q0KBP1 (394 letters) >FitnessBrowser__BFirm:BPHYT_RS09180 Length = 394 Score = 619 bits (1595), Expect = 0.0 Identities = 312/394 (79%), Positives = 349/394 (88%) Query: 1 MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60 M R+VVVVSGVRTAIG FGGSLKD +P +LGA VVRE LARA VSGD+VGHVVFGNV+ T Sbjct: 1 MQRDVVVVSGVRTAIGGFGGSLKDFSPTDLGARVVREVLARANVSGDEVGHVVFGNVVHT 60 Query: 61 EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120 EP+DMYL RVAA+NGGV +APALTVNRLCGSGLQAIVSAAQ++LLGD D+AIGGGAE+M Sbjct: 61 EPKDMYLARVAAINGGVAQHAPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENM 120 Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180 SRAPY PAAR+G RMGDA LVDMM+GAL+DPF IHMGVTAENVA++YDISR QD A Sbjct: 121 SRAPYSMPAARFGQRMGDARLVDMMVGALNDPFQSIHMGVTAENVARKYDISREAQDALA 180 Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240 LESHRRA+ AI +GYFK+QI+P+ +KGDV FDTDEH R A+ +D +KL+PVF KEN Sbjct: 181 LESHRRAANAITSGYFKEQILPITIPSKKGDVVFDTDEHTRMSASPEDFSKLKPVFAKEN 240 Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300 GTVTAGNASG+NDAAAAVV+MER+ AE+RG+KPLARLVSY HAGVDP MGIGPVPAT+ Sbjct: 241 GTVTAGNASGINDAAAAVVLMERSLAEQRGIKPLARLVSYAHAGVDPAYMGIGPVPATRR 300 Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360 ALERAGL V+DLDVIEANEAFAAQACAV+K LG DPAKVNPNGSGISLGHPIGATGALIT Sbjct: 301 ALERAGLTVADLDVIEANEAFAAQACAVSKELGFDPAKVNPNGSGISLGHPIGATGALIT 360 Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 VKAL+EL R+ GRYALVTMCIGGGQGIAAIFERI Sbjct: 361 VKALYELQRIGGRYALVTMCIGGGQGIAAIFERI 394 Lambda K H 0.318 0.134 0.381 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: 574 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate BPHYT_RS09180 BPHYT_RS09180 (3-ketoacyl-CoA thiolase)
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.1959987.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-143 463.8 4.2 2.5e-143 463.6 4.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS09180 BPHYT_RS09180 3-ketoacyl-CoA thi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS09180 BPHYT_RS09180 3-ketoacyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.6 4.2 2.5e-143 2.5e-143 1 385 [] 7 392 .. 7 392 .. 0.99 Alignments for each domain: == domain 1 score: 463.6 bits; conditional E-value: 2.5e-143 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaag 69 +v++vRt+ig +ggslk++s+ dL+a v++e+l+ra+++ +++ +v++Gnv+++ + + +aR aa++ g lcl|FitnessBrowser__BFirm:BPHYT_RS09180 7 VVSGVRTAIGGFGGSLKDFSPTDLGARVVREVLARANVSGDEVGHVVFGNVVHTEPKdMYLARVAAINGG 76 79********99****************************************999888************ PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledq 139 + ++ paltvnr+C+SglqA+ +aaq++ G+ad+++ GG+E+mSr+p++++a+ r + ++g+a+l d+ lcl|FitnessBrowser__BFirm:BPHYT_RS09180 77 VAQHAPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENMSRAPYSMPAA--RFGQRMGDARLVDM 144 ****************************************************98..89***********9 PP TIGR01930 140 llkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvv 205 ++ l + + ++mg+tAen+a+ky+isRe qD++al+Sh++aa+Ai +g+fk++i+p++++ k ++v+ lcl|FitnessBrowser__BFirm:BPHYT_RS09180 145 MVGALndPFQSIHMGVTAENVARKYDISREAQDALALESHRRAANAITSGYFKEQILPITIPSKkgDVVF 214 998889999*****************************************************99999*** PP TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaava 275 ++De+ r + e+ +kLkp+f++++g tvtAgN+s++nD+Aaa++lm+++ a++ g++plar+vs+a+a lcl|FitnessBrowser__BFirm:BPHYT_RS09180 215 DTDEHTRMSASPEDFSKLKPVFAKENG-TVTAGNASGINDAAAAVVLMERSLAEQRGIKPLARLVSYAHA 283 ***************************.6***************************************** PP TIGR01930 276 gvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPl 345 gvdp++mg+gpvpA+++aL++agl++ d+d++E nEAFAaq+ av kelg d++kvN nG+ i+lGHP+ lcl|FitnessBrowser__BFirm:BPHYT_RS09180 284 GVDPAYMGIGPVPATRRALERAGLTVADLDVIEANEAFAAQACAVSKELG-FDPAKVNPNGSGISLGHPI 352 **************************************************.78***************** PP TIGR01930 346 GasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 Ga+Ga i+++ l+eL++ g++y+l+t+C+ggGqG+A+i+e lcl|FitnessBrowser__BFirm:BPHYT_RS09180 353 GATGALITVKALYELQRIGGRYALVTMCIGGGQGIAAIFE 392 **************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (394 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: 29.00 // [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