Align FAA hydrolase family protein (characterized, see rationale)
to candidate Ac3H11_4136 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase.
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4136 Length = 281 Score = 331 bits (848), Expect = 1e-95 Identities = 155/279 (55%), Positives = 201/279 (72%) Query: 1 MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDASLDKIRKLDLESLPAVEGS 60 MKL+RYG G E+PG+LD +G +RDLS + D+ A L+ +L + +D LP V G+ Sbjct: 1 MKLIRYGQPGAERPGLLDATGTLRDLSMLLPDIGPAQLNPRTLSALAAIDASRLPPVYGT 60 Query: 61 PRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKK 120 PR+G+ VG +GK +C+GLNYADHA E+ L PAEPV+F K +A+ GP+DDV+IP G+ K Sbjct: 61 PRLGSPVGGVGKIVCVGLNYADHAREAGLQPPAEPVLFMKAVTALSGPHDDVRIPAGAVK 120 Query: 121 TDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGP 180 TDWEVELG+VIG + + A+ HVAGY + NDVSER +Q+ERGG WDKGK DTF P Sbjct: 121 TDWEVELGIVIGTRARNVAKAQALEHVAGYVLANDVSERAWQMERGGQWDKGKSHDTFAP 180 Query: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVIS 240 IGPWLVT DEV DP + +WLEV+G+R QNG+T IF V +VSY+S FM+L+ GD++ Sbjct: 181 IGPWLVTADEVGDPHAIDLWLEVNGRRVQNGSTRNFIFDVPTVVSYISEFMTLESGDLVL 240 Query: 241 TGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQKTI 279 TGTP GVG+G KP +L+ G MRLG GLGEQ QK + Sbjct: 241 TGTPAGVGLGQKPAPWFLKPGDVMRLGATGLGEQVQKCV 279 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: 315 Number of extensions: 6 Number of successful extensions: 1 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