Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011766784.1 AZO_RS15365 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000061505.1:WP_011766784.1 Length = 402 Score = 575 bits (1481), Expect = e-168 Identities = 287/398 (72%), Positives = 336/398 (84%), Gaps = 1/398 (0%) Query: 4 VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63 V++CDAIRTP GR+GG L+ VRADDLAA+P++ALI NP V W+ VD+V +GCANQAGED Sbjct: 5 VYLCDAIRTPFGRYGGLLSSVRADDLAALPIRALIARNPGVDWNLVDDVIYGCANQAGED 64 Query: 64 NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123 NRNVARMA LLAGLP +PG T+NRLC S +DAIG+A RAIA+GE EL IAGGVESMSRA Sbjct: 65 NRNVARMAALLAGLPVEVPGSTVNRLCGSSLDAIGSAARAIAAGEAELMIAGGVESMSRA 124 Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183 PFV+GKA+S +SR+ K+EDTTIGWRF+NPLMK+QYGVDSMPETA+NVA D+ VSRADQDA Sbjct: 125 PFVLGKADSAFSRSAKIEDTTIGWRFVNPLMKAQYGVDSMPETAENVATDFNVSRADQDA 184 Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKPVNG 242 ALRSQQ+ A+A GFFA EIVPV I KKG+ + + DEH RP+TTL+ L KLK V Sbjct: 185 LALRSQQRWASANERGFFAREIVPVDIPRKKGDPVRMTTDEHPRPDTTLDMLAKLKGVVR 244 Query: 243 PDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAV 302 PD TVTAGNASGVNDGAAA++LAS AVK+HGLTPRAR+LG A+ GVAPR+MGIGP PA Sbjct: 245 PDGTVTAGNASGVNDGAAAVLLASEAAVKRHGLTPRARILGSAAAGVAPRIMGIGPAPAS 304 Query: 303 RKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSG 362 KL RLG+ ++ FDVIELNEAFA+Q LAV R LG+ADD +VNPNGGAI++GHPLG SG Sbjct: 305 EKLLARLGMGIARFDVIELNEAFAAQALAVTRRLGLADDDARVNPNGGAISIGHPLGASG 364 Query: 363 ARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 ARLV TAL+QLE SGGR GLATMC+GVGQG+ALAIER+ Sbjct: 365 ARLVTTALNQLETSGGRYGLATMCIGVGQGIALAIERI 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: 549 Number of extensions: 14 Number of successful extensions: 2 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: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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_011766784.1 AZO_RS15365 (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.10305.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-139 451.2 0.8 1.7e-139 451.0 0.8 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011766784.1 AZO_RS15365 3-oxoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011766784.1 AZO_RS15365 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.0 0.8 1.7e-139 1.7e-139 2 385 .] 8 400 .. 7 400 .. 0.95 Alignments for each domain: == domain 1 score: 451.0 bits; conditional E-value: 1.7e-139 TIGR01930 2 vdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaa 68 da+Rtp+g++gg l++++a+dL+a i++l++r+ g+d + +d+vi+G++ qage+ n+aR+aal a lcl|NCBI__GCF_000061505.1:WP_011766784.1 8 CDAIRTPFGRYGGLLSSVRADDLAALPIRALIARNpGVDWNLVDDVIYGCANQAGEDnRNVARMAALLA 76 589******99**********************************************9*********** PP TIGR01930 69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137 glp +vp+ tvnr+C+S+l+A+ +aa++i+aGea++++aGGvEsmSr+p++l ++ +s+ ++ak e lcl|NCBI__GCF_000061505.1:WP_011766784.1 77 GLPVEVPGSTVNRLCGSSLDAIGSAARAIAAGEAELMIAGGVESMSRAPFVLGKA---DSAFSRSAKIE 142 ****************************************************997...45555566666 PP TIGR01930 138 dqllkdl........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvev 198 d+++ ++ sm etAen+a+++++sR +qD++alrS+q+ a+A e+g+f++eivpv++ lcl|NCBI__GCF_000061505.1:WP_011766784.1 143 DTTIGWRfvnplmkaQYGVDSMPETAENVATDFNVSRADQDALALRSQQRWASANERGFFAREIVPVDI 211 644333367888998778889************************************************ PP TIGR01930 199 kgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelglt 264 ++k ++ +++De++rp+ttl+ LakLk + + ++g tvtAgN+s++nDGAaa+ll+se+++k++glt lcl|NCBI__GCF_000061505.1:WP_011766784.1 212 PRKkgdPVRMTTDEHPRPDTTLDMLAKLKGVVR-PDG-TVTAGNASGVNDGAAAVLLASEAAVKRHGLT 278 *999999999**********************9.69*.6****************************** PP TIGR01930 265 plarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekv 332 p ari + a agv p++mg+gp+pA+ek+L++ g+ i +d++E+nEAFAaq+lav++ lg+ d +++v lcl|NCBI__GCF_000061505.1:WP_011766784.1 279 PRARILGSAAAGVAPRIMGIGPAPASEKLLARLGMGIARFDVIELNEAFAAQALAVTRRLGLADdDARV 347 *************************************************************86679*** PP TIGR01930 333 NvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 N nGGAi++GHPlGasGar+v+t l++L+ g++yGlat+C+g GqG+A+ +e lcl|NCBI__GCF_000061505.1:WP_011766784.1 348 NPNGGAISIGHPLGASGARLVTTALNQLETSGGRYGLATMCIGVGQGIALAIE 400 *************************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (402 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: 9.32 // [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