Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases
Query= SwissProt::P41338 (398 letters) >FitnessBrowser__Cola:Echvi_3705 Length = 393 Score = 409 bits (1052), Expect = e-119 Identities = 214/396 (54%), Positives = 288/396 (72%), Gaps = 5/396 (1%) Query: 3 QNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKVPELDASKDFDEIIFGNVLSA 62 + VYI+S RTP+GSF G LS TAVELGA A+KGAL + + DE+I GNVLSA Sbjct: 2 KEVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGRAQV--TPEQVDEVIMGNVLSA 59 Query: 63 NLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGGCESMT 122 NLGQAPARQ A+ AG+ H+ +TVNKVCAS MK+++ AQSI G +D++VAGG ESM+ Sbjct: 60 NLGQAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMS 119 Query: 123 NAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQQDNFA 182 N PYY+P AR G KFG VDG+ +DGL++ Y MG A+ A++ +I+RE QD +A Sbjct: 120 NVPYYIPKARFGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTAKEKNISREAQDEYA 179 Query: 183 IESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSARTVFQKE 242 I+SY+++ ++ K F +E++PVT K +G+ T V +DEE + EK+ S R VF KE Sbjct: 180 IQSYRRAAEAWKAQAFQDEVIPVTFKSRKGESIT-VDEDEEYQNVLFEKIPSLRPVFDKE 238 Query: 243 NGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAPSLAVP 302 GTVTAANAS +NDGAAA++L+S++ + L+P+A I G+ +AA P FT AP+LA+P Sbjct: 239 -GTVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAPALAIP 297 Query: 303 KALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLGCSGAR 362 KALK+AGI+ +VDY+E NEAFS V L N + L + ++NV+GGAV+LGHPLG SGAR Sbjct: 298 KALKNAGIQ-AEAVDYYEINEAFSAVALANQQELNIPNDRLNVFGGAVSLGHPLGASGAR 356 Query: 363 VVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEKI 398 ++ TL S+L+Q+GGKIGVA ICNGGGGAS++VIE + Sbjct: 357 IMATLHSVLRQKGGKIGVAGICNGGGGASAMVIENL 392 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: 414 Number of extensions: 17 Number of successful extensions: 5 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: 393 Length adjustment: 31 Effective length of query: 367 Effective length of database: 362 Effective search space: 132854 Effective search space used: 132854 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 Echvi_3705 Echvi_3705 (acetyl-CoA acetyltransferases)
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.8432.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-144 465.2 4.6 9.3e-144 465.0 4.6 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3705 Echvi_3705 acetyl-CoA acetyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.0 4.6 9.3e-144 9.3e-144 1 385 [] 6 390 .. 6 390 .. 0.97 Alignments for each domain: == domain 1 score: 465.0 bits; conditional E-value: 9.3e-144 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesv 74 i++avRtp g++gg l+ l+a++L+a++ik++l ra+++pe++devi+Gnvl+a+ ++++aR+aa+ ag++++v lcl|FitnessBrowser__Cola:Echvi_3705 6 IISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGRAQVTPEQVDEVIMGNVLSANLGQAPARQAAIGAGIGYHV 79 89************************************************************************ PP TIGR01930 75 paltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...v 145 p +tvn+vCaSg+++v+ aaq+i++G+ d++vaGG+EsmS+vp++++++ r ++k+g+ + d l+kd+ v lcl|FitnessBrowser__Cola:Echvi_3705 80 PCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMSNVPYYIPKA--RFGYKFGNGEFVDGLAKDGlheV 151 ***********************************************98..89********************9 PP TIGR01930 146 ktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpntt 216 + +++mg++A+n+ak+++isRe qDeya++S+++aa+A+++ f+de++pv++k + + +v++ ++ ++n+ lcl|FitnessBrowser__Cola:Echvi_3705 152 YYNFPMGNCADNTAKEKNISREAQDEYAIQSYRRAAEAWKAQAFQDEVIPVTFKSRkgeSITVDE-DEEYQNVL 224 99****************************************************99995555555.55567*** PP TIGR01930 217 lekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAi 290 ek+ +L+p+f++ +g tvtA+N+s +nDGAaal+lms+e+a++lgl+p+a+i ++a a+ dp ++++p+ Ai lcl|FitnessBrowser__Cola:Echvi_3705 225 FEKIPSLRPVFDK-EG-TVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAPALAI 296 ***********95.8*.6******************************************************** PP TIGR01930 291 ekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkerg 364 +kaLk ag++++ +d++EinEAF+a++la+++el+ + ++++Nv GGA++lGHPlGasGari++tl + L+++g lcl|FitnessBrowser__Cola:Echvi_3705 297 PKALKNAGIQAEAVDYYEINEAFSAVALANQQELN-IPNDRLNVFGGAVSLGHPLGASGARIMATLHSVLRQKG 369 ***********************************.88************************************ PP TIGR01930 365 kkyGlatlCvggGqGaAvile 385 +k+G+a +C+ggG ++A+++e lcl|FitnessBrowser__Cola:Echvi_3705 370 GKIGVAGICNGGGGASAMVIE 390 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6.39 // [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