Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate BPHYT_RS20310 BPHYT_RS20310 alpha/beta hydrolase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__BFirm:BPHYT_RS20310 Length = 272 Score = 75.9 bits (185), Expect = 9e-19 Identities = 77/263 (29%), Positives = 112/263 (42%), Gaps = 29/263 (11%) Query: 2 GFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFR-VLRFDTRGHGR 60 G+V+ + Y G APV++L LG + + W Q+PA R V+ D+RGHGR Sbjct: 30 GYVEHEGARIWYASYGAG-APVILLHGGLGHSGN-WGYQVPALLDAGRRVVVVDSRGHGR 87 Query: 61 SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVV--C 118 S PY E + DVLA++D L +ERA G S G + LG A ER+ + C Sbjct: 88 STRDARPYRYELMASDVLAVMDTLQLERAALVGWSDGACVAMVLGATAAERVAGVFFFGC 147 Query: 119 NTAAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAA 178 N DPS P + T + + A A ++ TPD +A + Sbjct: 148 NM-----DPSGTRPFVPTPAIERCFSRHAKDYAQLSA--TPDDFEAFVGA----VSTMMK 196 Query: 179 TSPQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEF 238 T P Y+A LA I VP ++ D P ++ + GAE Sbjct: 197 TEP-NYSAG-----------DLAQIRVPVAIVQSEHDEFIKPEHADYLARSIPGAELILL 244 Query: 239 -YAAHLSNVQAGSAFSDRVLSFL 260 +H + +Q + F+ VL FL Sbjct: 245 PGVSHFAPLQRPAQFNRVVLDFL 267 Lambda K H 0.321 0.136 0.410 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: 193 Number of extensions: 12 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: 266 Length of database: 272 Length adjustment: 25 Effective length of query: 241 Effective length of database: 247 Effective search space: 59527 Effective search space used: 59527 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 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