Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_039103773.1 FPB0191_RS02510 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >NCBI__GCF_000807275.1:WP_039103773.1 Length = 280 Score = 139 bits (349), Expect = 9e-38 Identities = 91/283 (32%), Positives = 144/283 (50%), Gaps = 24/283 (8%) Query: 1 MKLLRYGPVGQEKPGVLDQSG----------KIRDLSAYIKDVNGAVLDDASLDKIRKLD 50 MKL+ Y G+ G+L Q G K DL + + D G + L+ +D Sbjct: 1 MKLVSYLVSGRASFGLLTQHGIVDLGKKLGDKYTDLKSLLADEKGLAIAKTYLNDPSDID 60 Query: 51 LESLPAVEGSPRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPND 110 + + + P N K +C+G+NYA+ AE N A P +F ++ + G Sbjct: 61 EKDITYLPVIP-------NPNKILCVGMNYAEKRAEFNETSSA-PTLFVRFPDSQTGHKT 112 Query: 111 DVKIPRGSKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTW- 169 ++ P + + D+E EL +VIGK G I ++DA+S+VAGY D S R++Q TW Sbjct: 113 NIIKPAITNELDYEGELAIVIGKSGFRIKQEDALSYVAGYSCYMDGSIRDWQY----TWF 168 Query: 170 DKGKGCDTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSR 229 GK + G GP L T DE+ DP+ L + ++G+ Q + + ++ V ++SY+S Sbjct: 169 TAGKNWPSTGAFGPCLTTTDEIPDPKALTLVTYLNGQEMQRDSVNNLVHTVPELISYIST 228 Query: 230 FMSLQPGDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLG 272 F L PGDVI TG+P GVG P ++++ G + + I G+G Sbjct: 229 FTHLSPGDVILTGSPGGVGKKRNP-PIFMKDGDKIEVEITGIG 270 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: 239 Number of extensions: 12 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: 280 Length adjustment: 26 Effective length of query: 255 Effective length of database: 254 Effective search space: 64770 Effective search space used: 64770 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 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