Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate RR42_RS06325 RR42_RS06325 serine O-acetyltransferase
Query= SwissProt::O34981 (236 letters) >FitnessBrowser__Cup4G11:RR42_RS06325 Length = 247 Score = 58.5 bits (140), Expect = 1e-13 Identities = 41/121 (33%), Positives = 59/121 (48%), Gaps = 5/121 (4%) Query: 115 GASINIGSVIGEGTMID--MNVVLGGRATVGKNCHIGAGSVLAGVIEPPSAKP-VVIEDD 171 G I+ G+ +G ID M VV+G A +G +C I G L G K + + Sbjct: 65 GIEIHPGAKVGRRVFIDHGMGVVVGETAEIGDDCTIYQGVTLGGTSLYKGVKRHPTLGAN 124 Query: 172 VVIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVVAGTPAKKIKDIDEKTKGKTEIKQ 231 VV+ A A VL G T+G GA + + A+V+ V P G PA+ I + + G+ KQ Sbjct: 125 VVVSAGAKVLGGYTIGDGARIGSNAVVLKPVPPGATAVGIPARII--LPDAPSGQQGAKQ 182 Query: 232 E 232 E Sbjct: 183 E 183 Score = 26.6 bits (57), Expect = 5e-04 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%) Query: 40 KAFINGNTGVVFGEWSEI--QTAIEENQSKIEDYVVENDRRNSAIPMLDLKNIKARIEPG 97 + FI+ GVV GE +EI I + + + + +R+ + + + A++ G Sbjct: 77 RVFIDHGMGVVVGETAEIGDDCTIYQGVTLGGTSLYKGVKRHPTLGANVVVSAGAKVLGG 136 Query: 98 AIIRDQVEIGDNAVIM 113 I D IG NAV++ Sbjct: 137 YTIGDGARIGSNAVVL 152 Lambda K H 0.313 0.134 0.364 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: 135 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: 236 Length of database: 247 Length adjustment: 23 Effective length of query: 213 Effective length of database: 224 Effective search space: 47712 Effective search space used: 47712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 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 Aug 03 2021. The underlying query database was built on Aug 03 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