Align subunit of 3-oxoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate GFF1785 PS417_09080 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase
Query= metacyc::MONOMER-3221 (263 letters) >FitnessBrowser__WCS417:GFF1785 Length = 270 Score = 79.7 bits (195), Expect = 6e-20 Identities = 75/255 (29%), Positives = 113/255 (44%), Gaps = 24/255 (9%) Query: 22 PVLVLSNSLGTDLGMWDTQIPLWSQHFRVLRYDTRGHGASL-VTEGPYSIEQLGRDVLAL 80 PV++L +S D MW QI SQ +RV+ + GHG S + S++ L R L L Sbjct: 20 PVVLLGSSYLWDADMWSPQIEALSQQYRVIVPELWGHGESASLPAQTRSLDDLARQALTL 79 Query: 81 LDGLDIQKAHFVGLSMGGLIGQWLGIHAGERLHSLTLCNT--AAKIANDEVWNTRIDTVL 138 +D LDI + + VGLS+GG+ G L + A ER++SL L +T A+ + + ++ Sbjct: 80 IDQLDIAQINLVGLSVGGMWGARLALRAPERINSLVLMDTYLGAEPEATRQYYFSLFKMI 139 Query: 139 KGGQQAMVDLRDASIARWFTPGF-----------AQAQAEQAQRICQMLAQTSPQGYAGN 187 + L D +F PG Q Q +R+ Q + G Sbjct: 140 EDAGAIPEPLLDVVAPIFFRPGIDRESALYQDFRKQLQGYSKERLLQSIVP------LGR 193 Query: 188 CAAVRDADYREQLGRIQV-PALIVAGTQDVVTTPEHGRFMQAGIQGAEYVDFP-AAHLSN 245 R+ D EQL R+ L++ G QD P M AG+ G + P A H+S Sbjct: 194 LIFSRE-DILEQLPRLDADTTLVMCGEQDKPRPPAESEEM-AGLIGCSLILIPEAGHISA 251 Query: 246 VEIGEAFSRRVLDFL 260 E + + +L FL Sbjct: 252 RENPDFVNEALLTFL 266 Lambda K H 0.321 0.137 0.416 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: 175 Number of extensions: 8 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: 263 Length of database: 270 Length adjustment: 25 Effective length of query: 238 Effective length of database: 245 Effective search space: 58310 Effective search space used: 58310 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