Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_004514591.1 GMET_RS10465 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >NCBI__GCF_000012925.1:WP_004514591.1 Length = 391 Score = 391 bits (1004), Expect = e-113 Identities = 210/392 (53%), Positives = 267/392 (68%), Gaps = 2/392 (0%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 M DV ++ + RT +GSF G L+ + AP L A VIR LL+++GL VDEVI+GQVL G Sbjct: 1 MSDVYVIESLRTPLGSFGGELSDVEAPRLAATVIRELLQRSGLPAEGVDEVIVGQVLAGG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQ PARQA A LP ++P++T+NKVCGSGLKAL LGA AIR GD V+IAGGMENMSL Sbjct: 61 TGQAPARQAMRYAELPDSIPAMTINKVCGSGLKALMLGADAIRLGDVGVVIAGGMENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APYVL R G R+G+ ++ID ++ DGL D ++ HMG+ AE +K+GISR QDAFA Sbjct: 121 APYVLSKGRNGYRLGNGELIDLLVNDGLLDPYSGNHMGVIAEATTEKHGISRADQDAFAF 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 S QKA A++ G F DEI P++ RKGD V + DE+P L LK AFKK+G Sbjct: 181 RSYQKAQTAVKEGIFRDEIVPVVKKGRKGD-VTVSDDEEP-FKVDFTKLMGLKSAFKKEG 238 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 ++TAGNAS++NDGAA LL S + K GL AR+ +YA+ + P PV A + Sbjct: 239 TITAGNASTINDGAALTLLASGEAVKKYGLKPRARLVAYASNSLHPDQFTEAPVGAIEKA 298 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 KAG L D+DL E NEAFAA ++ K+L D EKVNVNGGA+AIGHP+GASG R+ Sbjct: 299 CAKAGLKLEDIDLFEINEAFAAVTMLAIKQLGLDPEKVNVNGGAVAIGHPLGASGGRLAA 358 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 TL+ E+ +R A+ GLATLCIGGG+ VA ER Sbjct: 359 TLVRELHRRQARFGLATLCIGGGEAVAAIFER 390 Lambda K H 0.317 0.133 0.378 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: 392 Number of extensions: 12 Number of successful extensions: 3 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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_004514591.1 GMET_RS10465 (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.1170881.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-139 451.0 0.3 1.8e-139 450.9 0.3 1.0 1 NCBI__GCF_000012925.1:WP_004514591.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000012925.1:WP_004514591.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 450.9 0.3 1.8e-139 1.8e-139 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 450.9 bits; conditional E-value: 1.8e-139 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 +++ +Rtp g++gg l++++a L+a+vi+ell+r+gl +e +devi+G+vl g+++++aR+a+ +a+lp+s NCBI__GCF_000012925.1:WP_004514591.1 6 VIESLRTPLGSFGGELSDVEAPRLAATVIRELLQRSGLPAEGVDEVIVGQVLAGGTGQAPARQAMRYAELPDS 78 6899********************************************************************* PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 +pa+t+n+vC+Sgl+A++l+a++i+ G+ vv+aGG+E+mS +p++l++ r++++lg+ +l d l++d+ NCBI__GCF_000012925.1:WP_004514591.1 79 IPAMTINKVCGSGLKALMLGADAIRLGDVGVVIAGGMENMSLAPYVLSKG--RNGYRLGNGELIDLLVNDGll 149 ************************************************97..89******************* PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.kkvvskDegirpnt 215 ++++ +mg+ Ae + +k+gisR +qD++a rS+qka++A++eg f deivpv+ kg+ +v+ +D++ ++ NCBI__GCF_000012925.1:WP_004514591.1 150 dPYSGNHMGVIAEATTEKHGISRADQDAFAFRSYQKAQTAVKEGIFRDEIVPVVKKGRkGDVTVSDDEEPFKV 222 *99**************************************************9999995666666666679* PP TIGR01930 216 tlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvp 288 kL +Lk+afk+ +g t+tAgN+s +nDGAa++ll+s e++k++gl+p ar+v++a +++p++++ +pv NCBI__GCF_000012925.1:WP_004514591.1 223 DFTKLMGLKSAFKK-EG-TITAGNASTINDGAALTLLASGEAVKKYGLKPRARLVAYASNSLHPDQFTEAPVG 293 ************96.8*.6****************************************************** PP TIGR01930 289 AiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLk 361 Aieka +kagl+++didl+EinEAFAa++++++k+lg ld+ekvNvnGGA+A+GHPlGasG+r+ +tl++eL+ NCBI__GCF_000012925.1:WP_004514591.1 294 AIEKACAKAGLKLEDIDLFEINEAFAAVTMLAIKQLG-LDPEKVNVNGGAVAIGHPLGASGGRLAATLVRELH 365 *************************************.99********************************* PP TIGR01930 362 ergkkyGlatlCvggGqGaAvile 385 +r++++GlatlC+ggG ++A+i+e NCBI__GCF_000012925.1:WP_004514591.1 366 RRQARFGLATLCIGGGEAVAAIFE 389 **********************97 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 18.06 // [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