Align BadK (characterized)
to candidate WP_015931972.1 MNOD_RS26135 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_000022085.1:WP_015931972.1 Length = 263 Score = 157 bits (398), Expect = 2e-43 Identities = 101/263 (38%), Positives = 146/263 (55%), Gaps = 6/263 (2%) Query: 1 MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60 M+ +L E + +ITLNRP+ LNA N A+ AL AL A AD+ A+++ G R Sbjct: 1 MADEVVLNEPRDGYRVITLNRPERLNAFNPAMHAALRQALDAAAADESCRALILTGAGRG 60 Query: 61 FAAGADIAS--MAAWSYSDVYGSNFITRNWETIRQIRK---PVLAAVAGLAYGGGCELAL 115 F AG D++ A D+ + N +RQ+R PV+ AV G+A G G +AL Sbjct: 61 FCAGQDLSDRDFRAGEIPDLSATLDTLYN-PLVRQLRDLPMPVVCAVNGVAAGAGANIAL 119 Query: 116 ACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYG 175 ACDIV+A RSA+F ++GL+P +GGT LPR +G+A+A + L A P+ A +A+ +G Sbjct: 120 ACDIVLAARSARFIQAFARIGLVPDSGGTWLLPRLVGRARARALALLAEPVPAPQAEAWG 179 Query: 176 LVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARF 235 ++ R V+D+ L E LA +A L +K++L+ A + L + ER Sbjct: 180 MIWRAVEDESLMAEAHQLAAHLAVQPTAGLALIKQALDAAETNDLDAQLDLERDLQGRAG 239 Query: 236 ASADAREGIQAFLEKRAPCFSHR 258 S D EG+ AFLEKR P FS R Sbjct: 240 RSPDYAEGVAAFLEKRPPRFSGR 262 Lambda K H 0.321 0.135 0.389 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: 144 Number of extensions: 4 Number of successful extensions: 2 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: 258 Length of database: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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 (21.9 bits) S2: 47 (22.7 bits)
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