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 Synpcc7942_1961 Synpcc7942_1961 ferripyochelin binding protein
Query= curated2:Q8TY70 (245 letters) >FitnessBrowser__SynE:Synpcc7942_1961 Length = 182 Score = 68.2 bits (165), Expect = 1e-16 Identities = 47/143 (32%), Positives = 76/143 (53%), Gaps = 26/143 (18%) Query: 89 AVPLADYSEFEDVRIEPGAIIR---EKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVV 145 AV D E V I P A++R E++++G V GAV++ G T+++ + V Sbjct: 24 AVICGDVVLAEGVSIWPTAVLRGDVERIEIGCNSNVQDGAVLH--GDPGQPTILEEDVTV 81 Query: 146 GSRAEVGKNVHIGAGAVIAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGA 205 G RA + + +IGAG++I G A++L GV++G G++V AGA Sbjct: 82 GHRAVI-HSANIGAGSLI--------------------GIGAIVLNGVQIGAGSIVGAGA 120 Query: 206 VVTEDVPPSKVVAGVPARVVKDV 228 VVT+ +P + GVPA+VV+ + Sbjct: 121 VVTKSIPAGSLAMGVPAKVVRSL 143 Lambda K H 0.315 0.136 0.375 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: 109 Number of extensions: 12 Number of successful extensions: 5 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: 245 Length of database: 182 Length adjustment: 21 Effective length of query: 224 Effective length of database: 161 Effective search space: 36064 Effective search space used: 36064 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: 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