Align FAA hydrolase family protein (characterized, see rationale)
to candidate CA265_RS08350 CA265_RS08350 ureidoglycolate lyase
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Pedo557:CA265_RS08350 Length = 284 Score = 318 bits (814), Expect = 1e-91 Identities = 152/277 (54%), Positives = 199/277 (71%), Gaps = 2/277 (0%) Query: 1 MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDASLDKIRK-LDLESLPAVEG 59 MKL+R+G G EKPGV+ D+SA +KD N L+K++ + LP V+ Sbjct: 1 MKLIRFGEAGAEKPGVIINDNYF-DVSALVKDYNEEFFGGDGLEKLKTAVQSADLPQVDK 59 Query: 60 SPRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSK 119 R+G + K IC+GLNY DHAAE+N PIP+EP++F K TSA+VGPNDD+ IP+ SK Sbjct: 60 GVRLGPALARPSKIICVGLNYKDHAAETNAPIPSEPILFFKATSAIVGPNDDLIIPKNSK 119 Query: 120 KTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFG 179 KTDWEVEL +VIGK SY+ E++A+ H+AGY + ND SERE+QIER G W KGK CDTF Sbjct: 120 KTDWEVELAIVIGKKASYVTEENALDHIAGYVLHNDYSEREFQIERNGQWVKGKSCDTFA 179 Query: 180 PIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVI 239 PIGP++ T+DE+AD L +WL V+GK Q+GNTS +IF V +++Y+S+FM+L PGDVI Sbjct: 180 PIGPFIATQDEIADVHNLRLWLTVNGKTMQDGNTSNLIFNVPFMIAYISQFMTLLPGDVI 239 Query: 240 STGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQ 276 +TGTP GVG+G KPE YL+AG + LGIDGLG +Q Sbjct: 240 TTGTPAGVGLGQKPEPWYLKAGDVVELGIDGLGTSKQ 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: 302 Number of extensions: 6 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: 284 Length adjustment: 26 Effective length of query: 255 Effective length of database: 258 Effective search space: 65790 Effective search space used: 65790 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