Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_097068496.1 CRO22_RS02395 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_900217815.1:WP_097068496.1 Length = 391 Score = 674 bits (1738), Expect = 0.0 Identities = 336/389 (86%), Positives = 361/389 (92%) Query: 1 MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60 MTNVVIVSAARTAVGSFNGAFA+TPAHDLGAAVIEAVVARAGIDKA+VSETILGQVL+AG Sbjct: 1 MTNVVIVSAARTAVGSFNGAFANTPAHDLGAAVIEAVVARAGIDKAEVSETILGQVLSAG 60 Query: 61 QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120 QGQNPARQAHIKAGLP ESAAW INQVCGSGLR VAL AQH+QLGDA IVVAGGQE+MSL Sbjct: 61 QGQNPARQAHIKAGLPIESAAWGINQVCGSGLRTVALGAQHIQLGDADIVVAGGQESMSL 120 Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180 SPHVAHLRAG KMGD+ IDSMIKDGLWDAFNGYHMGQTAENVAA+WQISR+MQD A+A Sbjct: 121 SPHVAHLRAGTKMGDMKMIDSMIKDGLWDAFNGYHMGQTAENVAAQWQISREMQDALALA 180 Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240 SQNKAEAAQKAG+F DEIVPF +KTRKGD+ VDADEYIRHGATL++M KL+PAFIKDGTV Sbjct: 181 SQNKAEAAQKAGKFTDEIVPFTVKTRKGDIVVDADEYIRHGATLESMQKLKPAFIKDGTV 240 Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300 TA NASGINDGAA VL+M+ EEA KRGL+P+ARIAS+ATAGLDPSIMG GPI ASRKALE Sbjct: 241 TAGNASGINDGAAVVLLMTEEEAAKRGLTPMARIASWATAGLDPSIMGCGPIPASRKALE 300 Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360 KAGW DLDL+EANEAFAAQACAVNKDMGWD + VNVNGGAIAIGHPIGASG R+LNTL Sbjct: 301 KAGWTAADLDLIEANEAFAAQACAVNKDMGWDTAKVNVNGGAIAIGHPIGASGCRILNTL 360 Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLE 389 +FEM+R AKKGLATLCIGGGMGVAMCLE Sbjct: 361 VFEMKRSGAKKGLATLCIGGGMGVAMCLE 389 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: 595 Number of extensions: 18 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: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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_097068496.1 CRO22_RS02395 (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.2862469.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-146 473.5 12.8 2.7e-146 473.4 12.8 1.0 1 NCBI__GCF_900217815.1:WP_097068496.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900217815.1:WP_097068496.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.4 12.8 2.7e-146 2.7e-146 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 473.4 bits; conditional E-value: 2.7e-146 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv+a+Rt++g+++g++++++a+dL+aavi+++++rag+d++++ e ilG+vl+ag+++n+aR+a ++aglp + NCBI__GCF_900217815.1:WP_097068496.1 6 IVSAARTAVGSFNGAFANTPAHDLGAAVIEAVVARAGIDKAEVSETILGQVLSAGQGQNPARQAHIKAGLPIE 78 8************************************************************************ PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 +a+ +n+vC+Sgl++val+aq+i+ G+ad+vvaGG EsmS +p++ + r++ k+g++k+ d+++kd+ NCBI__GCF_900217815.1:WP_097068496.1 79 SAAWGINQVCGSGLRTVALGAQHIQLGDADIVVAGGQESMSLSPHVAHL---RAGTKMGDMKMIDSMIKDGlw 148 ********************************************97776...699****************** PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 + ++++mg+tAen+a++++isRe+qD++al+S++ka++A+++gkf deivp++vk++ + vv+ De ir + NCBI__GCF_900217815.1:WP_097068496.1 149 dAFNGYHMGQTAENVAAQWQISREMQDALALASQNKAEAAQKAGKFTDEIVPFTVKTRkgDIVVDADEYIRHG 221 *99*****************************************************999999*********** PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 tle+++kLkpaf + +g tvtAgN+s++nDGAa++llm+ee a++ gltp+ari s+a+ag+dp++mg+gp+ NCBI__GCF_900217815.1:WP_097068496.1 222 ATLESMQKLKPAFIK-DG-TVTAGNASGINDGAAVVLLMTEEEAAKRGLTPMARIASWATAGLDPSIMGCGPI 292 *************95.9*.6***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 pA++kaL+kag+++ d+dl+E nEAFAaq+ av+k++g d++kvNvnGGAiA+GHP+GasG+ri+ tl+ e+ NCBI__GCF_900217815.1:WP_097068496.1 293 PASRKALEKAGWTAADLDLIEANEAFAAQACAVNKDMG-WDTAKVNVNGGAIAIGHPIGASGCRILNTLVFEM 364 **************************************.88******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 k+ g+k GlatlC+ggG+G+A+ le NCBI__GCF_900217815.1:WP_097068496.1 365 KRSGAKKGLATLCIGGGMGVAMCLE 389 **********************987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.81 // [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