Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate WP_010437977.1 G7G_RS0102510 3-oxoadipate enol-lactonase
Query= BRENDA::Q13KT2 (263 letters) >NCBI__GCF_000192475.1:WP_010437977.1 Length = 262 Score = 176 bits (446), Expect = 4e-49 Identities = 98/262 (37%), Positives = 144/262 (54%), Gaps = 5/262 (1%) Query: 1 MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60 M A + LHYRIDG+ G AP IV +NSLGTD+ +W P + L K R++R+D RGH Sbjct: 1 MRIANLKDVSLHYRIDGDVDG-AP-IVFANSLGTDMRLWDPIIPFLPKGLRIIRFDKRGH 58 Query: 61 GHSEAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALC 120 G S P PY++ L D L+D L++ F GLS+GG+ LA + D++ + L Sbjct: 59 GLSSQPAAPYSMGSLIRDAEQLLDHLEVKDCVFVGLSIGGMIAQGLAVKRMDQVRALVLS 118 Query: 121 NTAARIGSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDK 180 NTAA+IG+P++W R R G+ ALADA + RWF+ + + + R++ V Sbjct: 119 NTAAKIGTPKIWHDRMAAVRAGGIEALADATMERWFSKHFQSGPE--MPLWRNMMVRQPV 176 Query: 181 EGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARYVEL-DA 239 EGY C AI D G+++P L I+G+ D + P RE I G+R+ + A Sbjct: 177 EGYLGCCAAISGTDFYTPTSGLQLPTLGIAGSEDGSTPPDLVRETVDLIPGSRFALIRRA 236 Query: 240 SHISNIERADAFTKTVVDFLTE 261 H+ +ER + + + DFL E Sbjct: 237 GHLPCVERPREYAELLGDFLIE 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: 210 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: 262 Length adjustment: 25 Effective length of query: 238 Effective length of database: 237 Effective search space: 56406 Effective search space used: 56406 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 WP_010437977.1 G7G_RS0102510 (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.2435451.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-102 326.5 0.0 6.2e-102 326.3 0.0 1.0 1 NCBI__GCF_000192475.1:WP_010437977.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010437977.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.3 0.0 6.2e-102 6.2e-102 2 250 .. 11 256 .. 10 257 .. 0.98 Alignments for each domain: == domain 1 score: 326.3 bits; conditional E-value: 6.2e-102 TIGR02427 2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallD 74 lhyr++g+ +++p +v+ nSLGtd+rlwd++++ l k +r++r+DkrGHGlS+ p++pys++ l +d +llD NCBI__GCF_000192475.1:WP_010437977.1 11 LHYRIDGDVDGAP-IVFANSLGTDMRLWDPIIPFLPKGLRIIRFDKRGHGLSSQPAAPYSMGSLIRDAEQLLD 82 9********8888.9********************************************************** PP TIGR02427 75 algiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFt 147 +l++++ +++GlS+GG+iaq+La++r d+v+alvlsntaakigt+++W++R+aavra G++alada++erwF+ NCBI__GCF_000192475.1:WP_010437977.1 83 HLEVKDCVFVGLSIGGMIAQGLAVKRMDQVRALVLSNTAAKIGTPKIWHDRMAAVRAGGIEALADATMERWFS 155 ************************************************************************* PP TIGR02427 148 pafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvp 220 ++f+ + e+ l+rnm+v+qp+egY ++caAi +d+++ ++ +++Ptl iaG+eDgstPp+lvre++dl+p NCBI__GCF_000192475.1:WP_010437977.1 156 KHFQ--SGPEMPLWRNMMVRQPVEGYLGCCAAISGTDFYTPTSGLQLPTLGIAGSEDGSTPPDLVRETVDLIP 226 ***9..566778************************************************************* PP TIGR02427 221 garfaeieeaaHlpnleqpeafaallrdfl 250 g+rfa i+ a+Hlp++e+p ++a+ll dfl NCBI__GCF_000192475.1:WP_010437977.1 227 GSRFALIRRAGHLPCVERPREYAELLGDFL 256 ****************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (262 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: 19.12 // [ok]
This GapMind analysis is from Sep 24 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