Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate H281DRAFT_01594 H281DRAFT_01594 3-oxoadipate enol-lactonase
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__Burk376:H281DRAFT_01594 Length = 263 Score = 487 bits (1254), Expect = e-143 Identities = 238/263 (90%), Positives = 251/263 (95%) Query: 1 MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60 MPYAAVNGTELHYRIDG+RHGNAPWIVLSNSLG+DLSMW PQVAALSKHFRVLRYDTRGH Sbjct: 1 MPYAAVNGTELHYRIDGDRHGNAPWIVLSNSLGSDLSMWTPQVAALSKHFRVLRYDTRGH 60 Query: 61 GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120 GHSEAPKGPYTIEQL+GDVLGLMDTLKIARANFCG+SMGGLTGVALAARHA+R ERV L Sbjct: 61 GHSEAPKGPYTIEQLSGDVLGLMDTLKIARANFCGVSMGGLTGVALAARHANRFERVVLA 120 Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180 NTAARIGSPEVWVPRA +ARTEGM AL+DAVLPRWFTADY+EREPVVLAMIRDVFVHTDK Sbjct: 121 NTAARIGSPEVWVPRAARARTEGMLALSDAVLPRWFTADYIEREPVVLAMIRDVFVHTDK 180 Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVELDAS 240 EGYASNC+AIDA DLRPE GIK+P LVISGTHD+AATPAQGRELAQAI GARYVELDAS Sbjct: 181 EGYASNCDAIDATDLRPETHGIKLPVLVISGTHDVAATPAQGRELAQAIPGARYVELDAS 240 Query: 241 HISNIERADAFTKTVVDFLTEQK 263 HISNIE+ADAFTKTV+DFLTE K Sbjct: 241 HISNIEKADAFTKTVIDFLTEPK 263 Lambda K H 0.320 0.134 0.402 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: 372 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: 263 Length of database: 263 Length adjustment: 25 Effective length of query: 238 Effective length of database: 238 Effective search space: 56644 Effective search space used: 56644 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate H281DRAFT_01594 H281DRAFT_01594 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))
# 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/TIGR02427.hmm # target sequence database: /tmp/gapView.27958.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02427 [M=251] Accession: TIGR02427 Description: protocat_pcaD: 3-oxoadipate enol-lactonase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-103 331.4 0.1 1.9e-103 331.2 0.1 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01594 H281DRAFT_01594 3-oxoadipate eno Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01594 H281DRAFT_01594 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 331.2 0.1 1.9e-103 1.9e-103 2 251 .] 11 260 .. 10 260 .. 0.98 Alignments for each domain: == domain 1 score: 331.2 bits; conditional E-value: 1.9e-103 TIGR02427 2 lhyrlegae.adkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedla 66 lhyr++g++ ++p++vl+nSLG+dl++w ++++al+k+frvlryD+rGHG+S++p+gpy+ie+l+ lcl|FitnessBrowser__Burk376:H281DRAFT_01594 11 LHYRIDGDRhGNAPWIVLSNSLGSDLSMWTPQVAALSKHFRVLRYDTRGHGHSEAPKGPYTIEQLS 76 9*****8762589***************************************************** PP TIGR02427 67 ddvlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavrae 132 +dvl+l+D+l+i++a++cG+S+GGl++ aLaar+++r+e++vl+ntaa+ig++e+W +R+a+ r+e lcl|FitnessBrowser__Burk376:H281DRAFT_01594 77 GDVLGLMDTLKIARANFCGVSMGGLTGVALAARHANRFERVVLANTAARIGSPEVWVPRAARARTE 142 ****************************************************************** PP TIGR02427 133 GlaaladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlv 198 G+ al+davl rwFt+++ e+ep l+++r+++v++++egYa++c+Ai ++dlr +++ i++P+lv lcl|FitnessBrowser__Burk376:H281DRAFT_01594 143 GMLALSDAVLPRWFTADYIEREPVVLAMIRDVFVHTDKEGYASNCDAIDATDLRPETHGIKLPVLV 208 ****************************************************************** PP TIGR02427 199 iaGdeDgstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251 i+G++D+++ p++ re+a+++pgar++e++ a+H++n+e+++af+++++dfl+ lcl|FitnessBrowser__Burk376:H281DRAFT_01594 209 ISGTHDVAATPAQGRELAQAIPGARYVELD-ASHISNIEKADAFTKTVIDFLT 260 ******************************.********************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (263 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: 10.46 // [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