Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_055435026.1 ASC41_RS02340 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_001418085.1:WP_055435026.1 Length = 404 Score = 415 bits (1066), Expect = e-120 Identities = 209/402 (51%), Positives = 286/402 (71%), Gaps = 2/402 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M++ +I D IRTPIG + G L+ VR DDL A+ + +++ NP++ + D+V GCANQA Sbjct: 1 MKEAYIIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNPSIPKEAYDDVIMGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARM+ LLAGLP ++PG T+NRLC+SG+ AI A RAI +G+ ++ I+GGVE+M Sbjct: 61 GEDNRNVARMSSLLAGLPFTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 +R P+VM K + + + K+ D+T GWRFINP M++ YG D M TA+N+ + Y +SR D Sbjct: 121 TRGPYVMAKPSTAFGGDSKMYDSTFGWRFINPKMQALYGTDGMGNTAENLVEKYNISRED 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239 QD FAL SQQKA AQ +G A+EIV V I +K + I +DE ++P ++LE L KL+ Sbjct: 181 QDKFALWSQQKATKAQESGRLAKEIVTVEIPQRKKDPIQFSKDEFIKPTSSLEVLGKLRA 240 Query: 240 V-NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298 +VTAGN+SG+NDGAAA I+ASA+AVKK+ L P AR++ A GV PR+MGIGP Sbjct: 241 AFKKEGGSVTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVGVEPRIMGIGP 300 Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358 V A K + G+ + D D+IELNEAFA+Q LA +R G+AD+ P++NPNGGAIA+GHPL Sbjct: 301 VQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADNDPRINPNGGAIAIGHPL 360 Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 G++GAR+ +A +L+ + L TMC+GVGQG A IE V Sbjct: 361 GVTGARVAHSAALELQNQNKKYALITMCIGVGQGYAAIIENV 402 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: 429 Number of extensions: 16 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: 400 Length of database: 404 Length adjustment: 31 Effective length of query: 369 Effective length of database: 373 Effective search space: 137637 Effective search space used: 137637 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_055435026.1 ASC41_RS02340 (3-oxoadipyl-CoA thiolase)
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.3155216.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-142 459.6 1.1 4.6e-142 459.4 1.1 1.0 1 NCBI__GCF_001418085.1:WP_055435026.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055435026.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.4 1.1 4.6e-142 4.6e-142 1 385 [] 6 400 .. 6 400 .. 0.96 Alignments for each domain: == domain 1 score: 459.4 bits; conditional E-value: 4.6e-142 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 i+d++Rtpig+++g+l+ ++ +dL+a vi+e+++r+ + +e+ d+vi+G++ qage+ n+aR+ l aglp NCBI__GCF_001418085.1:WP_055435026.1 6 IIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNpSIPKEAYDDVIMGCANQAGEDnRNVARMSSLLAGLP 78 89********99************************999999****************9************** PP TIGR01930 72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144 +vp+ tvnr+C+Sgl A++ a ++ikaG+ dv+++GGvE+m+r p+++ + +++ g++k++d++ + NCBI__GCF_001418085.1:WP_055435026.1 79 FTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENMTRGPYVMAKP---STAFGGDSKMYDST---F 145 ***********************************************99987...45555677777744...2 PP TIGR01930 145 ...........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kk 203 + mg+tAenl +ky+isRe+qD++al S+qka+kA+e+g++++eiv ve++++ + NCBI__GCF_001418085.1:WP_055435026.1 146 gwrfinpkmqaLYGTDGMGNTAENLVEKYNISREDQDKFALWSQQKATKAQESGRLAKEIVTVEIPQRkkdPI 218 34578888888778889*************************************************9999999 PP TIGR01930 204 vvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavag 276 ++skDe i+p+++le L+kL++afk++ gs vtAgNss+lnDGAaa++++s +++k+++l+plarivs av+g NCBI__GCF_001418085.1:WP_055435026.1 219 QFSKDEFIKPTSSLEVLGKLRAAFKKEGGS-VTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVG 290 9************************99996.****************************************** PP TIGR01930 277 vdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGas 348 v+p++mg+gpv+A++kaL+kagl+++did++E+nEAFAaq+la+++++g d + ++N nGGAiA+GHPlG++ NCBI__GCF_001418085.1:WP_055435026.1 291 VEPRIMGIGPVQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADnDPRINPNGGAIAIGHPLGVT 363 *************************************************877899****************** PP TIGR01930 349 GarivltllkeLkergkkyGlatlCvggGqGaAvile 385 Gar+ + + eL++++kky+l+t+C+g GqG A+i+e NCBI__GCF_001418085.1:WP_055435026.1 364 GARVAHSAALELQNQNKKYALITMCIGVGQGYAAIIE 400 ***********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (404 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: 17.40 // [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