Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__WCS417:GFF1320 Length = 400 Score = 717 bits (1852), Expect = 0.0 Identities = 363/400 (90%), Positives = 383/400 (95%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MRDVFICDAIRTPIGRFGG L+ VRADDLAA+P+KALIE NP+V W VDEVF GCANQA Sbjct: 1 MRDVFICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKA++ +SR MKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY VSRAD Sbjct: 121 SRAPFVMGKADAAFSRTMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYHVSRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QDAFALRSQQ+ AAAQAAGFFAEEIVPVR+AHKKGET+VE+DEH R +TTLEALTKLKPV Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKKGETVVEQDEHPRADTTLEALTKLKPV 240 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLT RARVLGMAS GVAPRVMGIGPVP Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVP 300 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 AVRKL ERLG+AV+DFDVIELNEAFASQGLAVLRELG+ADDAPQVNPNGGAIALGHPLGM Sbjct: 301 AVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNPNGGAIALGHPLGM 360 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SGARLVLTALHQLEK+GG KGLATMCVGVGQGLALAIER+ Sbjct: 361 SGARLVLTALHQLEKTGGSKGLATMCVGVGQGLALAIERI 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: 655 Number of extensions: 16 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 GFF1320 PS417_06710 (beta-ketoadipyl 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.3320527.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-138 445.5 4.4 8.5e-138 445.4 4.4 1.0 1 FitnessBrowser__WCS417:GFF1320 Domain annotation for each sequence (and alignments): >> FitnessBrowser__WCS417:GFF1320 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.4 4.4 8.5e-138 8.5e-138 1 385 [] 6 398 .. 6 398 .. 0.94 Alignments for each domain: == domain 1 score: 445.4 bits; conditional E-value: 8.5e-138 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpesvpal 77 i da+Rtpig++gg l++++a+dL+a ik+l+er+ +d ++dev lG++ qage+ n+aR+a+l aglpes+p++ FitnessBrowser__WCS417:GFF1320 6 ICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNpSVDWTAVDEVFLGCANQAGEDnRNVARMALLLAGLPESIPGV 84 789*******************************************************9******************** PP TIGR01930 78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl..........vk 146 t+nr+CaSg++A+ +a ++i++Ge+++++aGGvEsmSr+p+++ ++ + + +++kled+++ + ++ FitnessBrowser__WCS417:GFF1320 85 TLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGKADA---AFSRTMKLEDTTI--GwrfinplmkaQY 158 *****************************************9999743...3333444444332..1335677789877 PP TIGR01930 147 tklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakL 223 +m +tA+n+a++y++sR +qD++alrS+q++a+A+++g+f++eivpv+v +k ++vv++De++r++ttle+L kL FitnessBrowser__WCS417:GFF1320 159 GVDAMPQTADNVADDYHVSRADQDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKkgETVVEQDEHPRADTTLEALTKL 237 7889************************************************9999999******************** PP TIGR01930 224 kpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsis 302 kp+ + + tvtAgN+s++nDGAaal+l+s e++k++glt ar+ ++a agv p++mg+gpvpA++k++++ gl ++ FitnessBrowser__WCS417:GFF1320 238 KPVNGP-DK-TVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVPAVRKLVERLGLAVT 314 ****95.77.7******************************************************************** PP TIGR01930 303 didlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380 d+d++E+nEAFA+q lav +elg d +vN nGGAiAlGHPlG+sGar+vlt l++L++ g+ Glat+Cvg GqG FitnessBrowser__WCS417:GFF1320 315 DFDVIELNEAFASQGLAVLRELGIADdAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKTGGSKGLATMCVGVGQGL 393 ***********************866789************************************************** PP TIGR01930 381 Avile 385 A+ +e FitnessBrowser__WCS417:GFF1320 394 ALAIE 398 *9886 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.69 // [ok]
This GapMind analysis is from Apr 09 2024. 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