Align FAA hydrolase family protein (characterized, see rationale)
to candidate SM_b21112 SM_b21112 bifunctional 2-hydroxyhepta-2,4-diene-1, 7-dioatesomerase/5-carboxymethyl-2-oxo-hex-3-ene-1, 7-dioatedecarboxylase
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Smeli:SM_b21112 Length = 281 Score = 387 bits (995), Expect = e-112 Identities = 177/277 (63%), Positives = 222/277 (80%), Gaps = 1/277 (0%) Query: 1 MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDASLDKIRKLDLESLPAVEGS 60 MKLLRYG GQEKPG+L G IRDLS ++ D+ LD + LD++ LD+E+LPAV G+ Sbjct: 1 MKLLRYGEPGQEKPGLLGSDGIIRDLSGHVSDLAAGALDPSKLDELANLDVETLPAVSGN 60 Query: 61 PRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKK 120 PR+G CV GKFICIGLNY+DHAAE+ +P EP++F K TSA+VGPNDD+ +PRGS+K Sbjct: 61 PRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEPIIFMKATSAIVGPNDDLVLPRGSEK 120 Query: 121 TDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGP 180 TDWEVELG+VIGK Y+ E +A+ +VAGYC V+DVSER +Q ER G W KGK CDTFGP Sbjct: 121 TDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKGKSCDTFGP 180 Query: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVIS 240 GPWLVT+DEVADPQ L MWL+V+G+ Q+G+T TM++G AH+VSYLS+FMSL+PGD+IS Sbjct: 181 TGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMSLRPGDIIS 240 Query: 241 TGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQK 277 TGTPPGVGMG+KP YL+AG + LGI+GLG Q+Q+ Sbjct: 241 TGTPPGVGMGMKPPR-YLKAGDVVELGIEGLGSQKQR 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: 378 Number of extensions: 11 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: 281 Length of database: 281 Length adjustment: 26 Effective length of query: 255 Effective length of database: 255 Effective search space: 65025 Effective search space used: 65025 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