Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Putida:PP_1377 Length = 400 Score = 759 bits (1961), Expect = 0.0 Identities = 389/400 (97%), Positives = 392/400 (98%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M DVFICDAIRTPIGRFGGALA VRADDLAAVPLKALIE NP VQWDQVDEVFFGCANQA Sbjct: 1 MHDVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDA+GTAFRAIASGEMEL IAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKAES YSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD Sbjct: 121 SRAPFVMGKAESAYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE IVERDEHLRPETTLEALTKLKPV Sbjct: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGEIIVERDEHLRPETTLEALTKLKPV 240 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 NGPDKTVTAGNASGVNDGAAA+ILASA AVKKHGLTPRARVLGMASGGVAPRVMGIGPVP Sbjct: 241 NGPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 AVRKLTERLG+AVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM Sbjct: 301 AVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV Sbjct: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 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: 671 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 PP_1377 PP_1377 (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.30850.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-139 450.1 2.8 3.5e-139 449.9 2.8 1.0 1 lcl|FitnessBrowser__Putida:PP_1377 PP_1377 beta-ketoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 449.9 2.8 3.5e-139 3.5e-139 1 385 [] 6 398 .. 6 398 .. 0.95 Alignments for each domain: == domain 1 score: 449.9 bits; conditional E-value: 3.5e-139 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpes 73 i da+Rtpig++gg+l++++a+dL+a +k+l+er+ g++ +++dev +G++ qage+ n+aR+a+l aglpes lcl|FitnessBrowser__Putida:PP_1377 6 ICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNpGVQWDQVDEVFFGCANQAGEDnRNVARMALLLAGLPES 80 789*******************************************************9**************** PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.... 144 +p++t+nr+CaSg++Av +a ++i++Ge+++v+aGGvEsmSr+p+++ ++ es+ +++kled+++ lcl|FitnessBrowser__Putida:PP_1377 81 IPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESMSRAPFVMGKA---ESAYSRNMKLEDTTIGWRfinp 152 *********************************************99997...5555566677774443336788 PP TIGR01930 145 ....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirp 213 ++ sm etA+n+a++y++sR +qD++alrS+qkaa+A+++g+f++eivpv++ +k + +v++De++rp lcl|FitnessBrowser__Putida:PP_1377 153 lmksQYGVDSMPETADNVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKkgEIIVERDEHLRP 227 8998778889************************************************9999999********** PP TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvp 288 +ttle+L kLkp+ + + tvtAgN+s++nDGAaa++l+s +++k++gltp ar+ ++a gv p++mg+gpvp lcl|FitnessBrowser__Putida:PP_1377 228 ETTLEALTKLKPVNGP-DK-TVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 **************95.77.7****************************************************** PP TIGR01930 289 AiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltllkeLke 362 A++k+ ++ g+ +sd+d++E+nEAFA+q lav +elg d +vN nGGAiAlGHPlG+sGar+vlt l++L++ lcl|FitnessBrowser__Putida:PP_1377 301 AVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADdAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEK 375 *************************************866789******************************** PP TIGR01930 363 rgkkyGlatlCvggGqGaAvile 385 g++ Glat+Cvg GqG A+ +e lcl|FitnessBrowser__Putida:PP_1377 376 SGGRKGLATMCVGVGQGLALAIE 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.21 // [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