Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate 3607598 Dshi_1007 3-oxoadipate enol-lactonase (RefSeq)
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__Dino:3607598 Length = 268 Score = 189 bits (481), Expect = 4e-53 Identities = 106/262 (40%), Positives = 148/262 (56%), Gaps = 5/262 (1%) Query: 1 MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60 MP +G LHYR +G R G P +V +NSLGTDL +W P + L R++RYD RGH Sbjct: 1 MPEFTRDGVRLHYRDEGPRDG--PVVVFANSLGTDLRLWEPILPLLPPGLRIVRYDMRGH 58 Query: 61 GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120 G S+ P PYT+ L D GL+D L I F GLS+GG+ LA + D + + L Sbjct: 59 GQSDVPPAPYTMGALVSDAEGLLDHLGIRDCVFVGLSIGGMVAQGLAVKRLDLVRAMVLS 118 Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180 NTAARIGSP++W R R G+ AL DA+L RWF+ ++ +P L RD+ + T Sbjct: 119 NTAARIGSPKLWQDRIDGVRAGGVAALTDAILERWFSRAFL-TDP-RLPFWRDMVLATPD 176 Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVEL-DA 239 EGY AI D G+++P L I+G+ D + P RE I G+R+V L A Sbjct: 177 EGYIGCSAAISGTDFYTPTSGLRLPTLGIAGSEDGSTPPDLVRETVNLIPGSRFVLLRRA 236 Query: 240 SHISNIERADAFTKTVVDFLTE 261 H+ ++E+ +A+ + + DFL E Sbjct: 237 GHLPHVEQPEAYAEALTDFLRE 258 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: 204 Number of extensions: 10 Number of successful extensions: 3 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: 268 Length adjustment: 25 Effective length of query: 238 Effective length of database: 243 Effective search space: 57834 Effective search space used: 57834 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 3607598 Dshi_1007 (3-oxoadipate enol-lactonase (RefSeq))
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.30946.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-98 314.8 0.0 2.3e-98 314.6 0.0 1.0 1 lcl|FitnessBrowser__Dino:3607598 Dshi_1007 3-oxoadipate enol-lact Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607598 Dshi_1007 3-oxoadipate enol-lactonase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 314.6 0.0 2.3e-98 2.3e-98 1 251 [] 10 257 .. 10 257 .. 0.99 Alignments for each domain: == domain 1 score: 314.6 bits; conditional E-value: 2.3e-98 TIGR02427 1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallDalg 77 rlhyr eg++ d pv+v+ nSLGtdlrlw+++l+ l + +r++ryD rGHG+Sdvp +py+++ l++d +llD+lg lcl|FitnessBrowser__Dino:3607598 10 RLHYRDEGPR-DGPVVVFANSLGTDLRLWEPILPLLPPGLRIVRYDMRGHGQSDVPPAPYTMGALVSDAEGLLDHLG 85 69********.9***************************************************************** PP TIGR02427 78 iekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFtpafreae 154 i++ +++GlS+GG++aq+La++r d+v+a+vlsntaa+ig+++ W++Ri+ vra G+aal+da+lerwF++af lcl|FitnessBrowser__Dino:3607598 86 IRDCVFVGLSIGGMVAQGLAVKRLDLVRAMVLSNTAARIGSPKLWQDRIDGVRAGGVAALTDAILERWFSRAFL--T 160 *************************************************************************9..5 PP TIGR02427 155 paelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpgarfaeieeaa 231 +l +r+m++++p egY++++aAi +d+++ ++ +++Ptl iaG+eDgstPp+lvre+++l+pg+rf+ ++ a+ lcl|FitnessBrowser__Dino:3607598 161 DPRLPFWRDMVLATPDEGYIGCSAAISGTDFYTPTSGLRLPTLGIAGSEDGSTPPDLVRETVNLIPGSRFVLLRRAG 237 66789************************************************************************ PP TIGR02427 232 Hlpnleqpeafaallrdflk 251 Hlp +eqpea+a++l+dfl+ lcl|FitnessBrowser__Dino:3607598 238 HLPHVEQPEAYAEALTDFLR 257 ******************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (268 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.36 // [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