Align Amidohydrolase 2 (characterized, see rationale)
to candidate N515DRAFT_1254 N515DRAFT_1254 L-fuconolactonase (EC 3.1.1.-)
Query= uniprot:B2T9V4 (276 letters) >FitnessBrowser__Dyella79:N515DRAFT_1254 Length = 296 Score = 253 bits (647), Expect = 3e-72 Identities = 134/276 (48%), Positives = 164/276 (59%), Gaps = 3/276 (1%) Query: 3 IDAHQHYWDPARGDYEWLTPELKILYRTFGPEDLKPLRERAGIERTVVVQAAPTIDETRY 62 IDAHQHYW RGDY WL +L R F P +L P R AG+ R ++VQAAPT ETR+ Sbjct: 9 IDAHQHYWRVQRGDYGWLADAPHVLRRDFLPFELDPHRAAAGVTRAILVQAAPTEAETRF 68 Query: 63 LLDLARHEPSIAGVVGWVPLLLPTAPQVIEALAHEPK--FKGVRPMLQDLPDDTWIANPD 120 L +LAR + ++AGVVGWV I AL + G+RPM QD+ D W+A P+ Sbjct: 69 LFELARADRAVAGVVGWVDFEATDVDARIAALVRDGDGLLLGLRPMAQDIEDPHWLARPE 128 Query: 121 LTPAIEALIAHDLAFDALIYARHVEPFETFATRFPALRIVVDHGAKPPIRYGRAGYQSWA 180 L A +L H LAFDAL+ + R P LR V+DHG KP I G AG+ +WA Sbjct: 129 LDAAFASLQRHGLAFDALVRPDQLPALLARLEREPQLRAVLDHGGKPAID-GVAGFDAWA 187 Query: 181 DAITRLAQLPHVHCKLSGLVTEASPGWTEETLHPYVEHLLKSFGPARLMWGSDWPVLDLN 240 I LAQ + CK SGL+T+ +P E L PYVEHL FGP+RL+WGSDWPVL L Sbjct: 188 APIAALAQRSSLQCKFSGLLTQLAPNLPESALAPYVEHLFACFGPSRLLWGSDWPVLTLR 247 Query: 241 GDYLLWHSVANTLLTSLSDAERDAVFGGNAAAFYRL 276 GDY W +A L+ A+FGGNAAAFYRL Sbjct: 248 GDYAHWIDLARAYAHRLAPGHEAAIFGGNAAAFYRL 283 Lambda K H 0.322 0.139 0.448 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: 340 Number of extensions: 16 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: 276 Length of database: 296 Length adjustment: 26 Effective length of query: 250 Effective length of database: 270 Effective search space: 67500 Effective search space used: 67500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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