Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate H281DRAFT_05559 H281DRAFT_05559 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q0KBP1 (394 letters) >FitnessBrowser__Burk376:H281DRAFT_05559 Length = 394 Score = 613 bits (1580), Expect = e-180 Identities = 305/393 (77%), Positives = 348/393 (88%) Query: 1 MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60 M+REV VVSGVRTAIG FGGSLKDVAP +LGA VVREAL RA V G+DVGHVVFGNVI T Sbjct: 1 MSREVFVVSGVRTAIGAFGGSLKDVAPTDLGAQVVREALQRASVDGNDVGHVVFGNVIHT 60 Query: 61 EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120 EP+DMYL RVAA++GGV+ +APALTVNRLCGSGLQAI+SAAQ+++LGD D+AIGGGAESM Sbjct: 61 EPKDMYLARVAALDGGVSESAPALTVNRLCGSGLQAIISAAQSVMLGDADIAIGGGAESM 120 Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180 SR+PY PAAR+GARMGDA +VDMM+GAL+DPFHRIHMGVTAENVA+++DISRAQQD A Sbjct: 121 SRSPYAMPAARFGARMGDASMVDMMVGALNDPFHRIHMGVTAENVAQKFDISRAQQDALA 180 Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240 LESHRRA+ A++AGYF +QI+PV K +KG FDTDEHVR DAT D +KL+PVF KEN Sbjct: 181 LESHRRAAHAVEAGYFNEQILPVEVKAKKGVTVFDTDEHVRTDATEADFSKLKPVFAKEN 240 Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300 GTVTAGN+SG+NDAAAAVV+MER + RRG++PL RLV+Y HAGVDPK MGIGPVPATK Sbjct: 241 GTVTAGNSSGINDAAAAVVLMEREQVSRRGVQPLGRLVAYAHAGVDPKIMGIGPVPATKA 300 Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360 AL RAGL + D+DVIEANEAFAAQACAV++ L LDP KVNPNGSGISLGHPIGATGA+IT Sbjct: 301 ALARAGLTIGDMDVIEANEAFAAQACAVSRELELDPHKVNPNGSGISLGHPIGATGAIIT 360 Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFER 393 +KAL+EL R GRYALVTMCIGGGQGIAAIFER Sbjct: 361 IKALYELRRTGGRYALVTMCIGGGQGIAAIFER 393 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: 561 Number of extensions: 8 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 H281DRAFT_05559 H281DRAFT_05559 (acetyl-CoA C-acetyltransferase)
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.3455260.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-142 461.5 8.5 1.2e-142 461.4 8.5 1.0 1 FitnessBrowser__Burk376:H281DRAFT_05559 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Burk376:H281DRAFT_05559 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.4 8.5 1.2e-142 1.2e-142 1 385 [] 7 392 .. 7 392 .. 0.99 Alignments for each domain: == domain 1 score: 461.4 bits; conditional E-value: 1.2e-142 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaag 69 +v++vRt+ig++ggslk++ + dL+a+v++e+l+ra +d +++ +v++Gnv+++ + + +aR aal g FitnessBrowser__Burk376:H281DRAFT_05559 7 VVSGVRTAIGAFGGSLKDVAPTDLGAQVVREALQRASVDGNDVGHVVFGNVIHTEPKdMYLARVAALDGG 76 79***************************************************99988************ PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledq 139 ++es paltvnr+C+SglqA+++aaq+++ G+ad+++ GG+EsmSr+p+ ++a+ r ++++g+a++ d+ FitnessBrowser__Burk376:H281DRAFT_05559 77 VSESAPALTVNRLCGSGLQAIISAAQSVMLGDADIAIGGGAESMSRSPYAMPAA--RFGARMGDASMVDM 144 ****************************************************98..89***********9 PP TIGR01930 140 llkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvv 205 ++ l + + ++mg+tAen+a+k++isR +qD++al+Sh++aa+A+e+g+f+++i+pvevk k +v+ FitnessBrowser__Burk376:H281DRAFT_05559 145 MVGALndPFHRIHMGVTAENVAQKFDISRAQQDALALESHRRAAHAVEAGYFNEQILPVEVKAKkgVTVF 214 999889999*****************************************************999999** PP TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaava 275 ++De++r + t ++ +kLkp+f++++g tvtAgNss++nD+Aaa++lm++e + + g++pl+r+v++a+a FitnessBrowser__Burk376:H281DRAFT_05559 215 DTDEHVRTDATEADFSKLKPVFAKENG-TVTAGNSSGINDAAAAVVLMEREQVSRRGVQPLGRLVAYAHA 283 ***************************.6***************************************** PP TIGR01930 276 gvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPl 345 gvdp++mg+gpvpA+++aL++agl+i d+d++E nEAFAaq+ av +el+ ld++kvN nG+ i+lGHP+ FitnessBrowser__Burk376:H281DRAFT_05559 284 GVDPKIMGIGPVPATKAALARAGLTIGDMDVIEANEAFAAQACAVSRELE-LDPHKVNPNGSGISLGHPI 352 **************************************************.99***************** PP TIGR01930 346 GasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 Ga+Ga+i+++ l+eL++ g++y+l+t+C+ggGqG+A+i+e FitnessBrowser__Burk376:H281DRAFT_05559 353 GATGAIITIKALYELRRTGGRYALVTMCIGGGQGIAAIFE 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: 25.14 // [ok]
This GapMind analysis is from Apr 09 2024. 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