Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate 5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq)
Query= reanno::MR1:200842 (396 letters) >FitnessBrowser__PV4:5209189 Length = 396 Score = 657 bits (1695), Expect = 0.0 Identities = 339/396 (85%), Positives = 358/396 (90%) Query: 1 MSTELLNQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMG 60 MSTE NQEIVIVAAKRTPMG FQGSLS + S +LAATAIK L+ V V+EVLMG Sbjct: 1 MSTEQTNQEIVIVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDAAGVQGGDVNEVLMG 60 Query: 61 CVLPAGLGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGG 120 CVLPAGLGQAPARQATLGA LPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSA VVIAGG Sbjct: 61 CVLPAGLGQAPARQATLGADLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSADVVIAGG 120 Query: 121 MESMSQAPYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQ 180 MESMSQAPYLLDKAR G+RMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTAD+FGITRE Sbjct: 121 MESMSQAPYLLDKARGGMRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADDFGITREA 180 Query: 181 MDAFALSSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAF 240 MD FALSSL+KANAAI SGAFK EIVPVTV+ R+GD+ +DTDEQPGNARPEKIPTLRPAF Sbjct: 181 MDNFALSSLQKANAAIESGAFKAEIVPVTVASRKGDLVVDTDEQPGNARPEKIPTLRPAF 240 Query: 241 AKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGA 300 AKDGTITAANSSSISDGAA LM+ + A + GL VLATIKGHTTH+QEP++FTTAPVGA Sbjct: 241 AKDGTITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTAPVGA 300 Query: 301 MAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGA 360 M KLL V WSKDEVDLFEINEAFAMVTMLA+SELGLD KVNVNGGACALGHPIGCSGA Sbjct: 301 MNKLLDKVNWSKDEVDLFEINEAFAMVTMLAISELGLDEAKVNVNGGACALGHPIGCSGA 360 Query: 361 RLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396 R+LVTLIHALKARGLKRGVASLCIGGGEATAMAIEV Sbjct: 361 RVLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 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: 618 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 5209189 Shew_1667 (acetyl-CoA acetyltransferase (RefSeq))
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.4178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-129 417.7 8.3 2.5e-129 417.5 8.3 1.0 1 lcl|FitnessBrowser__PV4:5209189 Shew_1667 acetyl-CoA acetyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209189 Shew_1667 acetyl-CoA acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.5 8.3 2.5e-129 2.5e-129 1 385 [] 12 395 .. 12 395 .. 0.98 Alignments for each domain: == domain 1 score: 417.5 bits; conditional E-value: 2.5e-129 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpalt 78 iv+a Rtp+g ++gsl+++++ +L+a++ik+l++ ag++ +++ev +G+vl+ag ++++aR+a+l a+lp sv a+t lcl|FitnessBrowser__PV4:5209189 12 IVAAKRTPMGGFQGSLSSVPSPTLAATAIKGLMDAAGVQGGDVNEVLMGCVLPAGLGQAPARQATLGADLPLSVGATT 89 8*********99****************************************************************** PP TIGR01930 79 vnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmge 153 vn+vC+Sg+++v+la + ikaG advv+aGG+EsmS++p+ll+++ r ++++g+ k+ d++ d+ ++t+ +mg+ lcl|FitnessBrowser__PV4:5209189 90 VNKVCGSGMKTVMLAHDLIKAGSADVVIAGGMESMSQAPYLLDKA--RGGMRMGHGKVLDHMFLDGledAYTGGAMGT 165 *******************************************98..89***********9999999*999******* PP TIGR01930 154 tAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafke 229 A+++a+++gi+Re +D++al+S qka++Aie+g fk+eivpv+v + + vv++De++ n ek+ +L+paf++ lcl|FitnessBrowser__PV4:5209189 166 FAQKTADDFGITREAMDNFALSSLQKANAAIESGAFKAEIVPVTVASRkgDLVVDTDEQPG-NARPEKIPTLRPAFAK 242 *********************************************9999778888888876.99************95 PP TIGR01930 230 kkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlv 307 +g t+tA+Nss+++DGAa+l++ms + a + gl++la+i ++++ + +p+ ++++pv A++k+L+k ++s +++dl+ lcl|FitnessBrowser__PV4:5209189 243 -DG-TITAANSSSISDGAAVLMMMSADEASKRGLEVLATIKGHTTHSQEPSMFTTAPVGAMNKLLDKVNWSKDEVDLF 318 .9*.6************************************************************************* PP TIGR01930 308 EinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 EinEAFA ++++++ elg ld++kvNvnGGA AlGHP+G+sGar+++tl+++Lk rg k+G+a+lC+ggG ++A+ +e lcl|FitnessBrowser__PV4:5209189 319 EINEAFAMVTMLAISELG-LDEAKVNVNGGACALGHPIGCSGARVLVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395 ******************.89******************************************************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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.57 // [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