Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Koxy:BWI76_RS16135 Length = 400 Score = 541 bits (1395), Expect = e-158 Identities = 274/401 (68%), Positives = 325/401 (81%), Gaps = 2/401 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M FICDA+RTP GRFGG LA +RADDLAA+PLKAL+E NP + ++D+V +GCANQA Sbjct: 1 MNQAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLPES+PG T+NRLC S +DAIG A RAI SGE +L IAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKAES +SR M++EDTTIGWRFINP MK+ YGVDSMPETA+NVADD+ +SRAD Sbjct: 121 SRAPFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYGVDSMPETAENVADDFAISRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLKP 239 QDAFALRSQ + AAAQ AG FA+E++ V + +KGE ++ RDEH R TT EAL +L+ Sbjct: 181 QDAFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPR-TTTAEALARLRG 239 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 V PD TVTAGNASGVNDGA AL+LAS +A+ + L P ARV+G+A+ GVAPR+MG GP Sbjct: 240 VVRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPA 299 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PAVRK+ + G+ + DVIELNEAFA+Q LAV R+LG+ DDA VNPNGGAIALGHPLG Sbjct: 300 PAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLG 359 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SG RL +TA +QL ++GGR L TMC+GVGQG+AL IERV Sbjct: 360 ASGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 400 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: 543 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 BWI76_RS16135 BWI76_RS16135 (acetyl-CoA 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.29840.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-138 446.3 1.2 5.1e-138 446.1 1.2 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.1 1.2 5.1e-138 5.1e-138 1 385 [] 6 398 .. 6 398 .. 0.95 Alignments for each domain: == domain 1 score: 446.1 bits; conditional E-value: 5.1e-138 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaag 69 i davRtp+g++gg+l++l+a+dL+a +k+ller+ gldp++id+vi+G++ qage+ n+aR+a+l ag lcl|FitnessBrowser__Koxy:BWI76_RS16135 6 ICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNpGLDPARIDDVIYGCANQAGEDnRNVARMALLLAG 76 789*******************************************************9************ PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledql 140 lpesvp+ tvnr+C+S+l+A+ +aa++ik+Ge ++++aGGvEsmSr+p+++ ++ es+ +++++ed++ lcl|FitnessBrowser__Koxy:BWI76_RS16135 77 LPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSRAPFVMGKA---ESAFSRTMRMEDTT 144 *************************************************99997...44444556666633 PP TIGR01930 141 lkdl........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201 + + sm etAen+a++++isR +qD++alrS+ ++a+A+e+g+f+de++ v+v+++ lcl|FitnessBrowser__Koxy:BWI76_RS16135 145 IGWRfinpqmkaLYGVDSMPETAENVADDFAISRADQDAFALRSQLRTAAAQEAGRFADELIAVSVPQRkg 215 333267887887667789*************************************************9999 PP TIGR01930 202 .kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 + +s+De++r +tt+e+La+L+ + + ++g tvtAgN+s++nDGA+alll+se+++++ +l+plar+v+ lcl|FitnessBrowser__Koxy:BWI76_RS16135 216 ePLLFSRDEHPR-TTTAEALARLRGVVR-PDG-TVTAGNASGVNDGACALLLASEQALAANDLQPLARVVG 283 999*********.899***********9.69*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAl 341 +a+agv p++mg+gp+pA++k+L+++gl++ ++d++E+nEAFAaq+lav+++lg+ d + vN nGGAiAl lcl|FitnessBrowser__Koxy:BWI76_RS16135 284 VATAGVAPRIMGFGPAPAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDdAAYVNPNGGAIAL 354 ******************************************************8556999********** PP TIGR01930 342 GHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 GHPlGasG+r+ +t +++L++ g++y+l t+C+g GqG+A+i+e lcl|FitnessBrowser__Koxy:BWI76_RS16135 355 GHPLGASGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIE 398 ******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (400 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: 00:00:00.01 # Mc/sec: 12.35 // [ok]
This GapMind analysis is from Sep 17 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