Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate 200842 SO1677 acetyl-CoA acetyltransferase (NCBI ptt file)
Query= reanno::MR1:200842 (396 letters) >FitnessBrowser__MR1:200842 Length = 396 Score = 762 bits (1968), Expect = 0.0 Identities = 396/396 (100%), Positives = 396/396 (100%) Query: 1 MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG 60 MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG Sbjct: 1 MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG 60 Query: 61 CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG 120 CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG Sbjct: 61 CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG 120 Query: 121 MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ 180 MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ Sbjct: 121 MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ 180 Query: 181 MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF 240 MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF Sbjct: 181 MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF 240 Query: 241 AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA 300 AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA Sbjct: 241 AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA 300 Query: 301 MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA 360 MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA Sbjct: 301 MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA 360 Query: 361 RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396 RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV Sbjct: 361 RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396 Lambda K H 0.316 0.131 0.364 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: 682 Number of extensions: 11 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate 200842 SO1677 (acetyl-CoA acetyltransferase (NCBI ptt file))
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.1843944.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-132 425.4 9.2 1.1e-131 425.2 9.2 1.0 1 lcl|FitnessBrowser__MR1:200842 SO1677 acetyl-CoA acetyltransfer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200842 SO1677 acetyl-CoA acetyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.2 9.2 1.1e-131 1.1e-131 1 385 [] 12 395 .. 12 395 .. 0.98 Alignments for each domain: == domain 1 score: 425.2 bits; conditional E-value: 1.1e-131 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpaltv 79 iv+a Rtp+g+++gsl+ +++ +L+a++ik+ll+ +++ p+k+dev +G+vl+ag ++++aR+a+l aglp sv a+tv lcl|FitnessBrowser__MR1:200842 12 IVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGLGQAPARQATLGAGLPLSVGATTV 90 8****************************************************************************** PP TIGR01930 80 nrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmgetA 155 n+vC+Sg+++v+la + ikaG a+vv+aGG+EsmS++p+ll+++ r+++++g+ k+ d++ d+ ++t+ +mg+ A lcl|FitnessBrowser__MR1:200842 91 NKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPYLLDKA--RAGIRMGHGKVLDHMFLDGledAYTGGAMGTFA 167 ******************************************98..89***********9999999*999********* PP TIGR01930 156 enlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkg 232 +++a+++gi+Re++D++al+S +ka++Ai++g fk eivpv+v ++ ++++++De++ n ek+ +L+paf++ +g lcl|FitnessBrowser__MR1:200842 168 QKTADEFGITREQMDAFALSSLEKANAAINSGAFKTEIVPVTVSDRrgDVTIDTDEQPG-NARPEKIPTLRPAFAK-DG 244 ********************************************99*999999999886.99************95.9* PP TIGR01930 233 stvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinE 311 t+tA+Nss+++DGAaal+l++++ a++lglt+la+i ++++ + +p+ ++++pv A+ k+L+ g+s +++dl+EinE lcl|FitnessBrowser__MR1:200842 245 -TITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLSNVGWSKDEVDLFEINE 322 .6***************************************************************************** PP TIGR01930 312 AFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 AFA ++++++ elg ld kvNvnGGA AlGHP+G+sGar+++tl+++Lk rg k+G+a+lC+ggG ++A+ +e lcl|FitnessBrowser__MR1:200842 323 AFAMVTMLAVSELG-LDMTKVNVNGGACALGHPIGCSGARLLVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395 **************.88******************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (396 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: 00:00:00.00 # Mc/sec: 20.59 // [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