Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_004514045.1 GMET_RS10385 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000012925.1:WP_004514045.1 Length = 399 Score = 412 bits (1058), Expect = e-119 Identities = 216/402 (53%), Positives = 286/402 (71%), Gaps = 5/402 (1%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MR+ I DA+RTP+G+F GAL VR+DDLAA + L++ N + + V++V GC NQA Sbjct: 1 MREAVIVDAVRTPVGKFNGALKNVRSDDLAAHCISELVKRNN-LDPNLVEDVVLGCTNQA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNV RMA LLAGLP S+ G T+NRLCASG++AI +A AI GE ++ IAGG ESM Sbjct: 60 GEDNRNVGRMAALLAGLPYSVAGQTINRLCASGLNAINSAAHAIKLGEGDVFIAGGTESM 119 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 +RAPFVM K+ES +SR++++ D+ IGWRF NP M Y + M ETA+NVA Y ++R + Sbjct: 120 TRAPFVMAKSESPFSRDIRVFDSVIGWRFTNPKMTEPYAKEGMGETAENVAVRYGLTRQE 179 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLR-PETTLEALTKLK 238 QD FAL +Q+K AAA AAG F +EIVPV I KKG+ IV RDE R + T+E L KL Sbjct: 180 QDEFALETQRKWAAADAAGKFNDEIVPVVIPQKKGDPIIVSRDEFPRGNDVTMEQLAKLP 239 Query: 239 PVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298 + TVTAGN+SG+NDGAAAL+L AE KK G P ARV+ A G P MG+GP Sbjct: 240 AAFRKEGTVTAGNSSGINDGAAALLLMEAETAKKLGYKPLARVVASAVAGCDPSYMGLGP 299 Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358 +PA++K+ +R G+ + D D+ ELNEAFA+Q + +RELG+ D +VN NGG+IA+GHPL Sbjct: 300 IPAIQKVLQRSGLKIEDIDLFELNEAFAAQSIPCIRELGI--DPAKVNVNGGSIAIGHPL 357 Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 G +GAR+ T +H++++ G R GL ++C+GVGQG+A ERV Sbjct: 358 GSTGARITATLVHEMKRRGSRYGLVSLCIGVGQGIATIFERV 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: 411 Number of extensions: 18 Number of successful extensions: 4 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_004514045.1 GMET_RS10385 (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.25139.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-150 487.0 0.1 2.1e-150 486.9 0.1 1.0 1 lcl|NCBI__GCF_000012925.1:WP_004514045.1 GMET_RS10385 acetyl-CoA C-acyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004514045.1 GMET_RS10385 acetyl-CoA C-acyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 486.9 0.1 2.1e-150 2.1e-150 1 385 [] 6 397 .. 6 397 .. 0.95 Alignments for each domain: == domain 1 score: 486.9 bits; conditional E-value: 2.1e-150 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 ivdavRtp+gk++g+lk+++++dL+a+ i+el++r++ldp+ +++v+lG++ qage+ n++R+aal a lcl|NCBI__GCF_000012925.1:WP_004514045.1 6 IVDAVRTPVGKFNGALKNVRSDDLAAHCISELVKRNNLDPNLVEDVVLGCTNQAGEDnRNVGRMAALLA 74 9********************************************************9*********** PP TIGR01930 69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137 glp+sv++ t+nr+CaSgl+A+++aa++ik Ge dv++aGG Esm+r+p+++ +s ++ s +++ +++ lcl|NCBI__GCF_000012925.1:WP_004514045.1 75 GLPYSVAGQTINRLCASGLNAINSAAHAIKLGEGDVFIAGGTESMTRAPFVMAKSESPFSRDIRVFDSV 143 **************************************************9999855555554444443 PP TIGR01930 138 dqllkdl........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvev 198 +++k mgetAen+a +yg++R+eqDe+al+ ++k a+A ++gkf+deivpv++ lcl|NCBI__GCF_000012925.1:WP_004514045.1 144 I---GWRftnpkmtePYAKEGMGETAENVAVRYGLTRQEQDEFALETQRKWAAADAAGKFNDEIVPVVI 209 3...2225668889999**************************************************** PP TIGR01930 199 kgk...kkvvskDegir.pnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgl 263 ++k + +vs+De +r +++t+e+LakL++af++ +g tvtAgNss++nDGAaalllm+ e+ak+lg+ lcl|NCBI__GCF_000012925.1:WP_004514045.1 210 PQKkgdPIIVSRDEFPRgNDVTMEQLAKLPAAFRK-EG-TVTAGNSSGINDGAAALLLMEAETAKKLGY 276 *999999**********4469************95.8*.6***************************** PP TIGR01930 264 tplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekv 332 +plar+v+ avag+dp++mglgp+pAi+k+L++ gl+i+didl+E+nEAFAaq + +++elg +d++kv lcl|NCBI__GCF_000012925.1:WP_004514045.1 277 KPLARVVASAVAGCDPSYMGLGPIPAIQKVLQRSGLKIEDIDLFELNEAFAAQSIPCIRELG-IDPAKV 344 **************************************************************.88**** PP TIGR01930 333 NvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 NvnGG+iA+GHPlG++Gari++tl++e+k+rg +yGl++lC+g GqG+A+i+e lcl|NCBI__GCF_000012925.1:WP_004514045.1 345 NVNGGSIAIGHPLGSTGARITATLVHEMKRRGSRYGLVSLCIGVGQGIATIFE 397 ***************************************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.58 // [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