Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000018545.1:WP_012709751.1 Length = 393 Score = 616 bits (1588), Expect = 0.0 Identities = 302/388 (77%), Positives = 342/388 (88%) Query: 3 NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62 ++VI SAARTAVGSFNGAF +TPAH+LGA VI+AV+ RAG+D A+V E ILGQVL AG+G Sbjct: 5 SIVIASAARTAVGSFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLPAGEG 64 Query: 63 QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122 QNPARQA IKAG+PQE AW +NQ+CGSGLRAVAL Q + GDASI+VAGG E+MS++P Sbjct: 65 QNPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAP 124 Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182 H AHLR G KMGD ID+MIKDGL DAF GYHMG TAENVA KWQ++R+ QDEFA+ SQ Sbjct: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGTTAENVARKWQLTREEQDEFALRSQ 184 Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242 NKAEAAQKAGRFADEIVPF++KTRKGDVTVD DEYIRHGATL+++AKLRPAF K+GTVTA Sbjct: 185 NKAEAAQKAGRFADEIVPFIVKTRKGDVTVDQDEYIRHGATLESIAKLRPAFDKEGTVTA 244 Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302 NASG+NDGAAA L+M+ EA KRG+ PLARI S+ATAG+DP IMG GPI ASRKALEKA Sbjct: 245 GNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 304 Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362 GW +GD++LVEANEAFAAQACAVNKD+GWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF Sbjct: 305 GWPIGDVELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 364 Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLER 390 EM+RR KGLATLCIGGGMGVAMC+ER Sbjct: 365 EMKRRGVSKGLATLCIGGGMGVAMCVER 392 Lambda K H 0.317 0.130 0.375 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: 542 Number of extensions: 11 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: 391 Length of database: 393 Length adjustment: 31 Effective length of query: 360 Effective length of database: 362 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_012709751.1 NGR_RS27475 (acetyl-CoA C-acetyltransferase)
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.1040369.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-148 480.0 8.1 3.1e-148 479.7 8.1 1.0 1 NCBI__GCF_000018545.1:WP_012709751.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_012709751.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.7 8.1 3.1e-148 3.1e-148 1 385 [] 8 391 .. 8 391 .. 0.98 Alignments for each domain: == domain 1 score: 479.7 bits; conditional E-value: 3.1e-148 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 i +a+Rt++g+++g++ +++a++L+a+vik++lerag+d++++devilG+vl+age++n+aR+aa++ag+p++ NCBI__GCF_000018545.1:WP_012709751.1 8 IASAARTAVGSFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLPAGEGQNPARQAAIKAGVPQE 80 789********************************************************************** PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 a+ +n++C+Sgl+Aval++q+i++G+a+++vaGG+EsmS +p+ + r ++k+g++k+ d+++kd+ NCBI__GCF_000018545.1:WP_012709751.1 81 KTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAPHCAHL---RGGVKMGDYKMIDTMIKDGlt 150 ********************************************97776...69*****************99 PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 + +++mg+tAen+a+k++++ReeqDe+alrS++ka++A+++g+f+deivp+ vk++ +++v++De ir + NCBI__GCF_000018545.1:WP_012709751.1 151 dAFYGYHMGTTAENVARKWQLTREEQDEFALRSQNKAEAAQKAGRFADEIVPFIVKTRkgDVTVDQDEYIRHG 223 98899************************************************99999999************ PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 tle++akL+paf++ +g tvtAgN+s+lnDGAaa+llm+e+ a++ g++plarivs+a+agvdp++mg+gp+ NCBI__GCF_000018545.1:WP_012709751.1 224 ATLESIAKLRPAFDK-EG-TVTAGNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTGPI 294 *************95.8*.6***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 pA++kaL+kag+ i d++lvE nEAFAaq+ av+k+lg d++ vNvnGGAiA+GHP+GasGar++ tll e+ NCBI__GCF_000018545.1:WP_012709751.1 295 PASRKALEKAGWPIGDVELVEANEAFAAQACAVNKDLG-WDPSIVNVNGGAIAIGHPIGASGARVLNTLLFEM 366 **************************************.88******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 k+rg+ GlatlC+ggG+G+A+ +e NCBI__GCF_000018545.1:WP_012709751.1 367 KRRGVSKGLATLCIGGGMGVAMCVE 391 **********************987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.47 // [ok]
This GapMind analysis is from Apr 09 2024. 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