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 HSERO_RS09300 HSERO_RS09300 serine O-acetyltransferase
Query= curated2:Q9K9H8 (240 letters) >FitnessBrowser__HerbieS:HSERO_RS09300 Length = 250 Score = 68.2 bits (165), Expect = 1e-16 Identities = 44/109 (40%), Positives = 58/109 (53%), Gaps = 3/109 (2%) Query: 112 IMMGASINIGSVIGEGTMID--MNVVLGGRATVGKNCHIGAGSVLAGVIEPPSAKP-VVV 168 ++ G I+ G+ IG ID M VV+G A VG + I G L G AK + Sbjct: 62 MLTGIEIHPGATIGRRVFIDHGMGVVIGETAIVGDDSTIYQGVTLGGTSLVKGAKRHPTL 121 Query: 169 EDDVVIGANCVILEGVTVGKGAVVAAGAVVTEDVPPNTVVAGTPARVIK 217 V+IGA +L G TVG GA V + AVVT++VP T G PAR+I+ Sbjct: 122 GRGVIIGAGAKVLGGFTVGDGAKVGSNAVVTKEVPAGTTAVGNPARIIE 170 Score = 23.9 bits (50), Expect = 0.003 Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 2/96 (2%) Query: 42 FINGQTGVLFGEWSEI--DAALKANEAKIKDVVVENDRRNSAIPLLDLKNIKARIEPGAI 99 FI+ GV+ GE + + D+ + +V+ +R+ + + A++ G Sbjct: 79 FIDHGMGVVIGETAIVGDDSTIYQGVTLGGTSLVKGAKRHPTLGRGVIIGAGAKVLGGFT 138 Query: 100 IRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVV 135 + D ++G NAV+ +V +I+ N V Sbjct: 139 VGDGAKVGSNAVVTKEVPAGTTAVGNPARIIERNTV 174 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: 149 Number of extensions: 11 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 250 Length adjustment: 24 Effective length of query: 216 Effective length of database: 226 Effective search space: 48816 Effective search space used: 48816 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: 46 (22.3 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