Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC 2.3.1.89; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate N515DRAFT_4259 N515DRAFT_4259 UDP-2-acetamido-3-amino-2,3-dideoxy-glucuronate N-acetyltransferase
Query= curated2:Q9K9H8 (240 letters) >FitnessBrowser__Dyella79:N515DRAFT_4259 Length = 195 Score = 73.2 bits (178), Expect = 4e-18 Identities = 45/149 (30%), Positives = 72/149 (48%), Gaps = 25/149 (16%) Query: 98 AIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHI--------- 148 AI+ + +IG+ + + + G+ IG+G + NV +G R ++G +C + Sbjct: 9 AIVDEGAQIGEGSRVWHFVHVCGGARIGKGVSLGQNVFVGNRVSIGDHCKVQNNVSVYDN 68 Query: 149 ---------GAGSVLAGVIEPPSA-------KPVVVEDDVVIGANCVILEGVTVGKGAVV 192 G V V P S + +V+ +GANC I+ G+T+G+ A V Sbjct: 69 VTLEEGVFCGPSMVFTNVYNPRSLIERKDEYRDTLVKRGATLGANCTIVCGITIGEYAFV 128 Query: 193 AAGAVVTEDVPPNTVVAGTPARVIKEIDE 221 AGAVVT+DV P ++ G PAR I + E Sbjct: 129 GAGAVVTQDVSPYALMVGVPARQIGWMSE 157 Lambda K H 0.314 0.135 0.372 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: 98 Number of extensions: 8 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: 240 Length of database: 195 Length adjustment: 22 Effective length of query: 218 Effective length of database: 173 Effective search space: 37714 Effective search space used: 37714 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 (21.9 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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