Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_011385204.1 AMB_RS14215 FAA hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >NCBI__GCF_000009985.1:WP_011385204.1 Length = 340 Score = 157 bits (396), Expect = 4e-43 Identities = 106/296 (35%), Positives = 150/296 (50%), Gaps = 26/296 (8%) Query: 1 MKLLRYGPVG-QEKPGVLDQSGKIRDLSAYIKDVNGAV-LDDASL-DKIRKLDLESLPA- 56 ++L+ Y G + GV+ SG++ DL A K A+ D AS+ IR D A Sbjct: 39 LRLVTYSAGGVAPRVGVVKASGRVVDLGAAAKARGMALAFDPASMVSLIRAGDFALAQAR 98 Query: 57 --VEGSPRIGACVGNIG----------KFICIGLNYADHAAES------NLPIPAEPVVF 98 ++ P G V + +G NY +H E + +P PV F Sbjct: 99 QLMQEGPETGPLVSEVRLLAPIPEPSRNVYAVGWNYLEHFKEGEAMRLKSADLPEHPVFF 158 Query: 99 NKWTSAVVGPNDDVKIPRG-SKKTDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVS 157 K V GP D + S DWE EL V+IGKGG I E DAM HV G+CV+ND + Sbjct: 159 TKAVGTVNGPYDPIPYDAAVSTSIDWECELAVIIGKGGKNIAEADAMKHVFGFCVINDTT 218 Query: 158 EREYQIER-GGTWDKGKGCDTFGPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTM 216 R+ Q ++ GG W KGK D GP+GPW+V ++ D ++ + V+G Q+ +T M Sbjct: 219 ARDVQQKKHGGQWFKGKSLDGHGPLGPWIVPASDI-DHTRVHLITRVNGVVKQDASTEQM 277 Query: 217 IFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLG 272 F V I++ LS ++L+PGD+I+TGTPPGVG KP +L+ G M I +G Sbjct: 278 YFKVPRIIAELSAGLTLEPGDIIATGTPPGVGGARKPPE-FLKPGDVMETEIVEIG 332 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: 285 Number of extensions: 17 Number of successful extensions: 4 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: 340 Length adjustment: 27 Effective length of query: 254 Effective length of database: 313 Effective search space: 79502 Effective search space used: 79502 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: 48 (23.1 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