Align FAA hydrolase family protein (characterized, see rationale)
to candidate N515DRAFT_1252 N515DRAFT_1252 2,4-diketo-3-deoxy-L-fuconate hydrolase
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Dyella79:N515DRAFT_1252 Length = 288 Score = 351 bits (900), Expect = e-101 Identities = 165/277 (59%), Positives = 213/277 (76%), Gaps = 1/277 (0%) Query: 1 MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDASLDKIRKLDLESLPAVEGS 60 MKL+RYG G EKPG++D+ G +RDLS ++ D++ VL ++ +D SLP VEG+ Sbjct: 1 MKLVRYGAHGNEKPGLIDKDGALRDLSEHVADIDPYVLGREGRARLAAIDPASLPEVEGT 60 Query: 61 PRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKK 120 PR GA V + K IC+G+NYA HAAE+ P+PA+PV+F K T+A++GPNDDV IPRGS Sbjct: 61 PRFGAPVAPVSKIICVGMNYARHAAETGQPVPAQPVLFMKATTAIMGPNDDVVIPRGSTC 120 Query: 121 TDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGP 180 TDWEVELGVVIG+ + +A++HVAG+ V+ND+SERE+Q+E GG W KGK CD+FGP Sbjct: 121 TDWEVELGVVIGETARDVSVDEALAHVAGFIVINDLSEREFQLEHGGQWVKGKSCDSFGP 180 Query: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVIS 240 +GPWLVT DEV DPQ L +WLEV+G RYQ+ NTS M+FGVA +VSY+SR+M+L PGDVIS Sbjct: 181 LGPWLVTIDEVPDPQNLHLWLEVNGHRYQDSNTSDMVFGVAKLVSYISRYMTLLPGDVIS 240 Query: 241 TGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQK 277 TGTP GVG+G+KP YLR G + LGIDGLG Q+Q+ Sbjct: 241 TGTPAGVGLGLKP-PTYLRPGDVIELGIDGLGRQRQQ 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: 350 Number of extensions: 10 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: 288 Length adjustment: 26 Effective length of query: 255 Effective length of database: 262 Effective search space: 66810 Effective search space used: 66810 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