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 CCNA_01990 CCNA_01990 UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase LpxD
Query= curated2:Q032G9 (257 letters) >FitnessBrowser__Caulo:CCNA_01990 Length = 339 Score = 58.5 bits (140), Expect = 2e-13 Identities = 40/126 (31%), Positives = 61/126 (48%), Gaps = 10/126 (7%) Query: 120 IIRDQVMIGDNAVIMMGAIINIGAEIGEGTMIDMGAVLGGRATVGKNSHIGAGAVLAGVI 179 +I+D V +G N+ + GA + IGE T ID + +G+N + A ++G Sbjct: 211 VIQDNVTLGANSCVDRGAFGD--TTIGENTKIDNLVHVAHNVRIGRNCVLAAYTGVSG-- 266 Query: 180 EPASAEPVRVGDNVLVGANAVVIEGVQVGSGSVVAAGAIVTQDVPENVVVAGVPARTIKE 239 VGD V G A V + + +GSG+ + A A V +DVP+ G PAR +K Sbjct: 267 ------STVVGDGVAFGGKAGVADHLNIGSGASIGAAASVFKDVPDGETWTGFPARPLKR 320 Query: 240 IDEKTA 245 +TA Sbjct: 321 WLRETA 326 Score = 49.7 bits (117), Expect = 8e-11 Identities = 39/126 (30%), Positives = 55/126 (43%), Gaps = 12/126 (9%) Query: 115 IEPGAIIRDQVMIGDNAVIMMGAIINIGAEIGEGTMIDMGAVLG-----------GRATV 163 + P A + D V + N I GA I G IG G +I G V+G G A + Sbjct: 116 LHPDAALEDGVALAPNVTIGQGASIGRGTRIGPGVVIGPGVVIGRYCRIGANAVIGFAML 175 Query: 164 GKNSHIGAGAVLAGVIEPASAEPVRVGDNVLVGANAVVIEGVQVGSGSVVAAGAIVTQDV 223 G N I AGAV+ A+ P + D +G V+ + V +G+ S V GA + Sbjct: 176 GDNVAISAGAVIGEAGFGAALGPRGMVDLPQLG-RVVIQDNVTLGANSCVDRGAFGDTTI 234 Query: 224 PENVVV 229 EN + Sbjct: 235 GENTKI 240 Score = 24.3 bits (51), Expect = 0.004 Identities = 17/69 (24%), Positives = 29/69 (42%) Query: 98 GRNSAVPLLDTRAINARIEPGAIIRDQVMIGDNAVIMMGAIINIGAEIGEGTMIDMGAVL 157 G N+ + L A N RI ++ + + V+ G A + + I GA + Sbjct: 235 GENTKIDNLVHVAHNVRIGRNCVLAAYTGVSGSTVVGDGVAFGGKAGVADHLNIGSGASI 294 Query: 158 GGRATVGKN 166 G A+V K+ Sbjct: 295 GAAASVFKD 303 Lambda K H 0.316 0.134 0.368 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: 208 Number of extensions: 18 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 257 Length of database: 339 Length adjustment: 26 Effective length of query: 231 Effective length of database: 313 Effective search space: 72303 Effective search space used: 72303 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: 41 (21.6 bits) S2: 48 (23.1 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