Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate SM_b20579 SM_b20579 beta-ketoadipate enol-lactone hydrolase
Query= BRENDA::Q13KT2 (263 letters) >FitnessBrowser__Smeli:SM_b20579 Length = 268 Score = 159 bits (403), Expect = 4e-44 Identities = 93/251 (37%), Positives = 127/251 (50%), Gaps = 2/251 (0%) Query: 1 MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60 M + +N +HYR+ G P +V NSLGTD +W V L+ F ++ YD RGH Sbjct: 1 MQFTRINDVTIHYRVVGAVT-EKPALVFINSLGTDFRIWRDVVLRLAGDFAIVLYDKRGH 59 Query: 61 GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120 G S+ + PY+IE D+ GL+D L + +A CGLS+GGL +L R D + + L Sbjct: 60 GLSDIGQVPYSIEDHATDLAGLLDRLAVKQAIVCGLSVGGLIAQSLYGRRPDLVRALVLS 119 Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180 TA +IG+ E W R G+ A+AD VL RWFT + E + R++ V Sbjct: 120 GTAHKIGTVEFWDARITAIEAHGIEAVADGVLERWFTPAFRRPENLAFTGYRNMLVRQPV 179 Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARY-VELDA 239 GY C AI AD A I VP L + G D + P R A I GAR+ V A Sbjct: 180 PGYVGTCAAIRDADFTEAAGRIAVPVLCVVGDQDGSTPPDLVRSTADLIPGARFEVIRGA 239 Query: 240 SHISNIERADA 250 HI +E+ +A Sbjct: 240 GHIPCVEQPEA 250 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: 203 Number of extensions: 6 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: 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 SM_b20579 SM_b20579 (beta-ketoadipate enol-lactone hydrolase)
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.29615.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-118 378.2 0.0 1e-117 378.0 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SM_b20579 SM_b20579 beta-ketoadipate enol- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b20579 SM_b20579 beta-ketoadipate enol-lactone hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.0 0.0 1e-117 1e-117 1 251 [] 10 260 .. 10 260 .. 0.99 Alignments for each domain: == domain 1 score: 378.0 bits; conditional E-value: 1e-117 TIGR02427 1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallD 74 ++hyr+ ga ++kp+lv+inSLGtd+r+w++v+ +l+ df+++ yDkrGHGlSd++++pysied+a+d+++llD lcl|FitnessBrowser__Smeli:SM_b20579 10 TIHYRVVGAVTEKPALVFINSLGTDFRIWRDVVLRLAGDFAIVLYDKRGHGLSDIGQVPYSIEDHATDLAGLLD 83 59************************************************************************ PP TIGR02427 75 algiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFtp 148 +l +++a vcGlS+GGliaq+L+ rrpd+v+alvls ta+kigt e+W+aRi+a++a+G++a+ad+vlerwFtp lcl|FitnessBrowser__Smeli:SM_b20579 84 RLAVKQAIVCGLSVGGLIAQSLYGRRPDLVRALVLSGTAHKIGTVEFWDARITAIEAHGIEAVADGVLERWFTP 157 ************************************************************************** PP TIGR02427 149 afreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpga 222 afr++e+ +++ +rnmlv+qp+ gY++tcaAirdad++e++++iavP+l+++Gd+DgstPp+lvr++adl+pga lcl|FitnessBrowser__Smeli:SM_b20579 158 AFRRPENLAFTGYRNMLVRQPVPGYVGTCAAIRDADFTEAAGRIAVPVLCVVGDQDGSTPPDLVRSTADLIPGA 231 ************************************************************************** PP TIGR02427 223 rfaeieeaaHlpnleqpeafaallrdflk 251 rf++i++a+H+p++eqpea++++lr+f++ lcl|FitnessBrowser__Smeli:SM_b20579 232 RFEVIRGAGHIPCVEQPEALWSVLRRFFR 260 ***************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.75 // [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