Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_058860019.1 AS188_RS15780 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_001482365.1:WP_058860019.1 Length = 399 Score = 399 bits (1025), Expect = e-116 Identities = 212/402 (52%), Positives = 284/402 (70%), Gaps = 5/402 (1%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M + F+ RTP+GR+GGAL+ VR DDLAA+ +K + + + VDEV G AN A Sbjct: 1 MTEAFLVGGARTPVGRYGGALSSVRPDDLAALVVKHAVT-DAGIDPHDVDEVILGNANGA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GE+NRNVARMA LLAG P+++PG+T+NRLCAS + AI A I +G ++ +AGGVESM Sbjct: 60 GEENRNVARMAWLLAGFPDTVPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESM 119 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVD-SMPETADNVADDYQVSRA 179 SRAP+VM K + +++ ++ DT+IGWRF NP K + SMPETA+ VA ++R Sbjct: 120 SRAPWVMEKPATAFAKPGEVFDTSIGWRFTNPEFKKHDKMTYSMPETAEEVAAVDGITRE 179 Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKG-ETIVERDEHLRPETTLEALTKLK 238 D DAFA+ S +KA AA AG FA+EIVPV + +KG ET+V+ DE RP TT++ L KL+ Sbjct: 180 DADAFAVASHEKAIAAIDAGRFADEIVPVTVKGRKGAETVVDTDEGPRPGTTMDVLAKLR 239 Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298 PV VTAGN+S +NDGA+A+++ S A +K+GLT RAR++ AS GVAP +MG+GP Sbjct: 240 PVVTHGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGVAPEIMGLGP 299 Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358 VPA +K+ ER G + D +ELNEAFASQ LA +R LG+ D VN +GGAIALGH L Sbjct: 300 VPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLGL--DEGIVNNDGGAIALGHAL 357 Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 G SG+RLV+T L ++E+ G +GLATMCVGVGQG A+ +E++ Sbjct: 358 GSSGSRLVVTLLGRMEREGAERGLATMCVGVGQGTAMLVEKI 399 Lambda K H 0.318 0.134 0.383 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: 445 Number of extensions: 21 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: 400 Length of database: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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_058860019.1 AS188_RS15780 (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.2980870.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-142 459.2 3.0 6e-142 459.0 3.0 1.0 1 NCBI__GCF_001482365.1:WP_058860019.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001482365.1:WP_058860019.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.0 3.0 6e-142 6e-142 2 385 .] 7 397 .. 6 397 .. 0.97 Alignments for each domain: == domain 1 score: 459.0 bits; conditional E-value: 6e-142 TIGR01930 2 vdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpes 73 v+++Rtp+g++gg+l++++++dL+a v+k+++ ag+dp+++devilGn+ age+ n+aR+a l ag+p++ NCBI__GCF_001482365.1:WP_058860019.1 7 VGGARTPVGRYGGALSSVRPDDLAALVVKHAVTDAGIDPHDVDEVILGNANGAGEEnRNVARMAWLLAGFPDT 79 89*******99*********************************************9**************** PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 vp++tvnr+CaS+l A+++a ++ikaG+advvvaGGvEsmSr+p+++++ +++ +k+g+ + + + + NCBI__GCF_001482365.1:WP_058860019.1 80 VPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESMSRAPWVMEKP-ATAFAKPGEVFDTSIGWR-Ftn 150 *********************************************99997.788888877766663333.258 PP TIGR01930 145 ......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskD 208 +k +sm etAe++a+ gi+Re+ D++a++Sh+ka +Ai++g+f+deivpv+vkg+ ++vv++D NCBI__GCF_001482365.1:WP_058860019.1 151 pefkkhDKMTYSMPETAEEVAAVDGITREDADAFAVASHEKAIAAIDAGRFADEIVPVTVKGRkgaETVVDTD 223 899999999*****************************************************9**999***** PP TIGR01930 209 egirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpee 281 eg+rp+tt++ LakL+p+ + +gs+vtAgNss+lnDGA+a+l++se++a+++glt ariv+ a agv pe+ NCBI__GCF_001482365.1:WP_058860019.1 224 EGPRPGTTMDVLAKLRPVVT--HGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGVAPEI 294 *******************7..799************************************************ PP TIGR01930 282 mglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivl 354 mglgpvpA++k+L+++g+ i d+ +vE+nEAFA+q la+++ lg ld+ vN GGAiAlGH lG+sG+r+v+ NCBI__GCF_001482365.1:WP_058860019.1 295 MGLGPVPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLG-LDEGIVNNDGGAIALGHALGSSGSRLVV 366 ********************************************.88************************** PP TIGR01930 355 tllkeLkergkkyGlatlCvggGqGaAvile 385 tll +++++g+++Glat+Cvg GqG+A+++e NCBI__GCF_001482365.1:WP_058860019.1 367 TLLGRMEREGAERGLATMCVGVGQGTAMLVE 397 ****************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (399 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 26.28 // [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