Align FAA hydrolase family protein (characterized, see rationale)
to candidate RR42_RS24410 RR42_RS24410 5-carboxymethyl-2-hydroxymuconate isomerase
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Cup4G11:RR42_RS24410 Length = 289 Score = 168 bits (425), Expect = 1e-46 Identities = 89/202 (44%), Positives = 123/202 (60%), Gaps = 2/202 (0%) Query: 71 GKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVV 130 GK + IGLNYADH AES + P + + F K +AV GP ++IP S D+E EL + Sbjct: 77 GKILGIGLNYADHVAESKMEPPTDQLWFAKMPTAVTGPFSAIEIPMVSDALDYEAELAFI 136 Query: 131 IGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVTRDE 190 IG+ ++ + DA + GYC NDVS R++Q R + GK DT P GPW+VT D+ Sbjct: 137 IGRRCRHVSKSDAHKFIFGYCAANDVSVRDWQF-RTTQFLLGKSFDTHAPFGPWIVTADD 195 Query: 191 VADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMG 250 + DP +L + V+G+ Q NT +IF + +LS+ M+L+PGDVI TGTP GVG G Sbjct: 196 INDPHELPIRCFVNGELRQKSNTRNLIFNCYAQIEHLSKVMTLEPGDVIFTGTPGGVGWG 255 Query: 251 VKPEAVYLRAGQTMRLGIDGLG 272 KP LR+G +R+ IDG+G Sbjct: 256 HKPPRP-LRSGDRVRVEIDGIG 276 Lambda K H 0.316 0.138 0.419 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: 257 Number of extensions: 15 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: 281 Length of database: 289 Length adjustment: 26 Effective length of query: 255 Effective length of database: 263 Effective search space: 67065 Effective search space used: 67065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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