Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate WP_065397633.1 BBI00_RS04415 acetyl-CoA C-acyltransferase
Query= SwissProt::P41338 (398 letters) >NCBI__GCF_001684965.1:WP_065397633.1 Length = 391 Score = 347 bits (889), Expect = e-100 Identities = 183/396 (46%), Positives = 271/396 (68%), Gaps = 7/396 (1%) Query: 3 QNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKVPELDASKDFDEIIFGNVLSA 62 + V+I++ RTP+G F GSLS TA +LGA A++ A V A + D + GNVLSA Sbjct: 2 KEVFIIAAKRTPVGGFMGSLSGLTAPQLGAAAIQNAYESVQL--APEYIDSVYMGNVLSA 59 Query: 63 NLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGGCESMT 122 LGQ+PARQ A+ A + A+T+NKVCAS MKA +LGAQ I+ G +V+ GG ESM+ Sbjct: 60 GLGQSPARQAAVFAEIPVDKDAATINKVCASGMKATMLGAQQIQLGLEKIVMTGGMESMS 119 Query: 123 NAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQQDNFA 182 N P+Y R G K G +VL DG+ +DGL D Y+ MG AE + + +TR+Q D++A Sbjct: 120 NVPHYADV-RQGKKLGDSVLTDGLIKDGLWDVYNDFHMGSAAELGVKKYGLTRQQLDDYA 178 Query: 183 IESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSARTVFQKE 242 + SYQ++Q++ + KF NE++ ++++G +G + +++DE+ +L EK+ + F+ + Sbjct: 179 LLSYQRAQEATSKNKFSNELISISVEGRKGT--SVISRDEDIDKLIPEKIALLKPAFEND 236 Query: 243 NGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAPSLAVP 302 G +TAAN+S +NDGAAA++L S + +++ L PLA I + +AA P FT +PS+A+ Sbjct: 237 -GALTAANSSNLNDGAAAILLGSSEAVQQHELVPLARIIAYADAAQSPEWFTTSPSIAIN 295 Query: 303 KALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLGCSGAR 362 K LK AG+ + +DY E NEA+S V L N +IL D ++VNVYGGAVALGHP+G SGAR Sbjct: 296 KVLKQAGLS-LADIDYLEINEAYSSVILSNQQILGYDLNRVNVYGGAVALGHPIGASGAR 354 Query: 363 VVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEKI 398 ++ TL+++L+QE G+ G+AAICNGGGGAS+++IE + Sbjct: 355 IIATLINVLRQEKGRYGIAAICNGGGGASAVLIENM 390 Lambda K H 0.315 0.131 0.372 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: 398 Number of extensions: 12 Number of successful extensions: 6 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: 398 Length of database: 391 Length adjustment: 31 Effective length of query: 367 Effective length of database: 360 Effective search space: 132120 Effective search space used: 132120 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: 42 (22.0 bits) S2: 50 (23.9 bits)
Align candidate WP_065397633.1 BBI00_RS04415 (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.1789370.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-127 412.2 2.7 1.1e-127 412.1 2.7 1.0 1 NCBI__GCF_001684965.1:WP_065397633.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001684965.1:WP_065397633.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.1 2.7 1.1e-127 1.1e-127 1 385 [] 6 388 .. 6 388 .. 0.98 Alignments for each domain: == domain 1 score: 412.1 bits; conditional E-value: 1.1e-127 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 i++a Rtp+g + gsl+ l+a +L+aa+i+++ e ++l pe id v++Gnvl+ag ++++aR+aa+ a++p + NCBI__GCF_001684965.1:WP_065397633.1 6 IIAAKRTPVGGFMGSLSGLTAPQLGAAAIQNAYESVQLAPEYIDSVYMGNVLSAGLGQSPARQAAVFAEIPVD 78 89********99************************************************************* PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 +a t+n+vCaSg++A +l+aq+i+ G +++v++GG+EsmS+vp++ + + ++ klg++ l d l+kd+ NCBI__GCF_001684965.1:WP_065397633.1 79 KDAATINKVCASGMKATMLGAQQIQLGLEKIVMTGGMESMSNVPHYADVR---QGKKLGDSVLTDGLIKDGlw 148 ********************************************999985...89999*************** PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 v+++++mg Ae kkyg++R+++D+yal S+q+a++A++++kf++e++ ++v+g+ + v+s+De i + NCBI__GCF_001684965.1:WP_065397633.1 149 dVYNDFHMGSAAELGVKKYGLTRQQLDDYALLSYQRAQEATSKNKFSNELISISVEGRkgTSVISRDEDID-K 220 *99******************************************************9999999******8.8 PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 + ek+a Lkpaf+ ++g tA+Nss+lnDGAaa+ll s+e++++++l plari+++a a+ +pe ++++p NCBI__GCF_001684965.1:WP_065397633.1 221 LIPEKIALLKPAFE-NDGA-LTAANSSNLNDGAAAILLGSSEAVQQHELVPLARIIAYADAAQSPEWFTTSPS 291 99***********9.59*6.***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 Ai+k+Lk+agls+ did+ EinEA+++++l +++ lg dl++vNv+GGA+AlGHP+GasGari++tl++ L NCBI__GCF_001684965.1:WP_065397633.1 292 IAINKVLKQAGLSLADIDYLEINEAYSSVILSNQQILG-YDLNRVNVYGGAVALGHPIGASGARIIATLINVL 363 **************************************.88******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 ++++++yG+a++C+ggG ++Av++e NCBI__GCF_001684965.1:WP_065397633.1 364 RQEKGRYGIAAICNGGGGASAVLIE 388 **********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (391 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.17 // [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