Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_011799496.1 PNAP_RS00315 acetyl-CoA C-acyltransferase
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_000015505.1:WP_011799496.1 Length = 394 Score = 608 bits (1567), Expect = e-178 Identities = 304/394 (77%), Positives = 345/394 (87%) Query: 1 MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60 MTREVVVVSGVRTAIGTFGGSLKD P EL ALVVRE+LARA V G DVGHVVFG+V+ T Sbjct: 1 MTREVVVVSGVRTAIGTFGGSLKDTPPTELAALVVRESLARAGVEGKDVGHVVFGHVVNT 60 Query: 61 EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120 E +DMYL RVAAVNGG PA VNRLCGSGLQAI+SA+Q+ILLGD D+AIGGGAE+M Sbjct: 61 EAKDMYLSRVAAVNGGCAEGTPAFNVNRLCGSGLQAIISASQSILLGDADIAIGGGAENM 120 Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180 SR PY + A R+GAR+GD+ LVDM++GALHDPFH IHMGVTAEN+A ++ I+R +QD A Sbjct: 121 SRGPYASLATRFGARLGDSKLVDMVVGALHDPFHTIHMGVTAENIAAKWGITREEQDALA 180 Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240 ++SH RA AI+AGYFK+QIVPV+ K RKG+V +DTDEH R + T+ DM KL+PVFVKEN Sbjct: 181 VQSHNRAQKAIEAGYFKEQIVPVMLKSRKGEVAYDTDEHFRPNCTLADMAKLKPVFVKEN 240 Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300 GTVTAGNASG+NDAAAAVV+ME AE RGLKPLARLV+Y HAGVDPK MGIGPVPAT++ Sbjct: 241 GTVTAGNASGINDAAAAVVLMEAGVAEARGLKPLARLVAYAHAGVDPKYMGIGPVPATQM 300 Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360 AL++AGL V+DLDVIEANEAFAAQACAVT+ LGLDPAKVNPNGSGISLGHPIGATGALIT Sbjct: 301 ALKKAGLTVNDLDVIEANEAFAAQACAVTRDLGLDPAKVNPNGSGISLGHPIGATGALIT 360 Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394 VKALHEL R+QGRYALVTMCIGGGQGIAAIFER+ Sbjct: 361 VKALHELKRIQGRYALVTMCIGGGQGIAAIFERM 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: 567 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 WP_011799496.1 PNAP_RS00315 (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.17846.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-141 456.3 6.2 4.5e-141 456.2 6.2 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011799496.1 PNAP_RS00315 acetyl-CoA C-acyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011799496.1 PNAP_RS00315 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.2 6.2 4.5e-141 4.5e-141 1 385 [] 7 392 .. 7 392 .. 0.98 Alignments for each domain: == domain 1 score: 456.2 bits; conditional E-value: 4.5e-141 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 +v++vRt+ig++ggslk++++ +L+a v++e l+rag++ +++ +v++G+v+++ ++ + + R aa++ lcl|NCBI__GCF_000015505.1:WP_011799496.1 7 VVSGVRTAIGTFGGSLKDTPPTELAALVVRESLARAGVEGKDVGHVVFGHVVNTEAKdMYLSRVAAVNG 75 79***************************************************99999*********** PP TIGR01930 69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137 g+ e +pa++vnr+C+SglqA+++a q+i G+ad+++ GG+E+mSr p+ + a r +++lg++kl lcl|NCBI__GCF_000015505.1:WP_011799496.1 76 GCAEGTPAFNVNRLCGSGLQAIISASQSILLGDADIAIGGGAENMSRGPYASLAT--RFGARLGDSKLV 142 **************************************************99997..89********** PP TIGR01930 138 dqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 d+++ l + + ++mg+tAen+a+k+gi+ReeqD++a++Sh++a+kAie+g+fk++ivpv +k + + lcl|NCBI__GCF_000015505.1:WP_011799496.1 143 DMVVGALhdPFHTIHMGVTAENIAAKWGITREEQDALAVQSHNRAQKAIEAGYFKEQIVPVMLKSRkgE 211 *8888889999****************************************************999999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 + +++De+ rpn tl+++akLkp+f +++g tvtAgN+s++nD+Aaa++lm+ va++ gl+plar+v+ lcl|NCBI__GCF_000015505.1:WP_011799496.1 212 VAYDTDEHFRPNCTLADMAKLKPVFVKENG-TVTAGNASGINDAAAAVVLMEAGVAEARGLKPLARLVA 279 99****************************.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+agvdp++mg+gpvpA++ aLkkagl+++d+d++E nEAFAaq+ av+++lg ld++kvN nG+ i+ lcl|NCBI__GCF_000015505.1:WP_011799496.1 280 YAHAGVDPKYMGIGPVPATQMALKKAGLTVNDLDVIEANEAFAAQACAVTRDLG-LDPAKVNPNGSGIS 347 ******************************************************.99************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 lGHP+Ga+Ga i+++ l+eLk+ +++y+l+t+C+ggGqG+A+i+e lcl|NCBI__GCF_000015505.1:WP_011799496.1 348 LGHPIGATGALITVKALHELKRIQGRYALVTMCIGGGQGIAAIFE 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.73 // [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