Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Ergosterol biosynthesis protein 10; EC 2.3.1.9 (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase
Query= SwissProt::P41338 (398 letters) >NCBI__GCF_001418085.1:WP_055437058.1 Length = 392 Score = 417 bits (1071), Expect = e-121 Identities = 221/400 (55%), Positives = 292/400 (73%), Gaps = 12/400 (3%) Query: 1 MSQNVYIVSTARTPIGSFQGSLSSKTAVELGAVALKGALAKV---PELDASKDFDEIIFG 57 M++ V IVS ARTPIGSF G+LS+ A +LGA+A+KGAL K+ PEL E++ G Sbjct: 1 MNKEVVIVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKINLNPEL-----VQEVLMG 55 Query: 58 NVLSANLGQAPARQVALAAGLSNHIVASTVNKVCASAMKAIILGAQSIKCGNADVVVAGG 117 NV+ A GQAPARQ A+ AG+ N + +T+NKVCAS MK ++ AQSI G+A++VVAGG Sbjct: 56 NVVQAGTGQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGG 115 Query: 118 CESMTNAPYYMPAARAGAKFGQTVLVDGVERDGLNDAYDGLAMGVHAEKCARDWDITREQ 177 E+M+ P+Y A R+ KFG +VDG+++DGL D YD AMGV A+ CA ++ +RE Sbjct: 116 MENMSLIPHYFHA-RSATKFGPATMVDGMQKDGLVDVYDQQAMGVSADACATKYEFSRED 174 Query: 178 QDNFAIESYQKSQKSQKEGKFDNEIVPVTIKGFRGKPDTQVTKDEEPARLHVEKLRSART 237 QD +AI+SY++S + + GKF+NEIVPV + RG D VT+DEE + ++K+ + R Sbjct: 175 QDAYAIQSYKRSAAAWEAGKFNNEIVPVAVPQRRGD-DVIVTEDEEYKNVRMDKIPTLRA 233 Query: 238 VFQKENGTVTAANASPINDGAAAVILVSEKVLKEKNLKPLAIIKGWGEAAHQPADFTWAP 297 F KE GTVTAANAS INDGA A++L+S + E LK LA IKG+ +AAH+P FT AP Sbjct: 234 AFTKE-GTVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAP 292 Query: 298 SLAVPKALKHAGIEDINSVDYFEFNEAFSVVGLVNTKILKLDPSKVNVYGGAVALGHPLG 357 S+A+PKAL AG+ DI VD+FEFNEAFS+VGL N KIL L+ S VNV GGAV+LGHPLG Sbjct: 293 SIALPKALNKAGL-DIKDVDFFEFNEAFSIVGLANMKILGLNDSNVNVNGGAVSLGHPLG 351 Query: 358 CSGARVVVTLLSILQQEGGKIGVAAICNGGGGASSIVIEK 397 CSG R+++TLL++L+Q KIG AAICNGGGGAS++V+E+ Sbjct: 352 CSGVRILITLLNVLEQNDAKIGAAAICNGGGGASALVLER 391 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: 420 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 367 Effective length of database: 361 Effective search space: 132487 Effective search space used: 132487 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_055437058.1 ASC41_RS12920 (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.1430483.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-138 447.6 6.3 2e-138 447.5 6.3 1.0 1 NCBI__GCF_001418085.1:WP_055437058.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055437058.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.5 6.3 2e-138 2e-138 1 385 [] 7 390 .. 7 390 .. 0.98 Alignments for each domain: == domain 1 score: 447.5 bits; conditional E-value: 2e-138 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv+a+Rtpig++ g+l++++a +L+a +ik++le+ +l+pe + ev +Gnv+qag+++++aR+aa+ ag+p++ NCBI__GCF_001418085.1:WP_055437058.1 7 IVSAARTPIGSFLGALSTIPAPKLGAIAIKGALEKINLNPELVQEVLMGNVVQAGTGQAPARQAAIFAGIPNT 79 8************************************************************************ PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 vp +t+n+vCaSg+++v++aaq+i+ G+a++vvaGG+E+mS +p++ +a+ + k+g a++ d ++kd+ NCBI__GCF_001418085.1:WP_055437058.1 80 VPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSLIPHYFHAR---SATKFGPATMVDGMQKDGlv 149 **********************************************9995...7888899************* PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 v+++ +mg++A+ +a+ky++sRe+qD+ya++S++++a+A+e+gkf++eivpv v+++ ++v+ ++++ ++n NCBI__GCF_001418085.1:WP_055437058.1 150 dVYDQQAMGVSADACATKYEFSREDQDAYAIQSYKRSAAAWEAGKFNNEIVPVAVPQRrgDDVIVTEDEEYKN 222 *99*****************************************************99**777777777888* PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 + ++k+ +L++af++ +g tvtA+N+s +nDGA+a++lms+e+a+elgl++la+i ++a a+++pe ++++p NCBI__GCF_001418085.1:WP_055437058.1 223 VRMDKIPTLRAAFTK-EG-TVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTAPS 293 *************96.8*.6***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 A +kaL+kagl+i+d+d++E+nEAF+ + la++k lg l++++vNvnGGA++lGHPlG+sG ri++tll+ L NCBI__GCF_001418085.1:WP_055437058.1 294 IALPKALNKAGLDIKDVDFFEFNEAFSIVGLANMKILG-LNDSNVNVNGGAVSLGHPLGCSGVRILITLLNVL 365 **************************************.88******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 +++++k+G a++C+ggG ++A++le NCBI__GCF_001418085.1:WP_055437058.1 366 EQNDAKIGAAAICNGGGGASALVLE 390 ***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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: 00:00:00.00 # Mc/sec: 22.18 // [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