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 SMc02093 SMc02093 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase
Query= curated2:Q032G9 (257 letters) >FitnessBrowser__Smeli:SMc02093 Length = 354 Score = 57.8 bits (138), Expect = 3e-13 Identities = 39/127 (30%), Positives = 61/127 (48%), Gaps = 10/127 (7%) Query: 120 IIRDQVMIGDNAVIMMGAIINIGAEIGEGTMIDMGAVLGGRATVGKNSHIGAGAVLAGVI 179 II+D V IG N I G + + IGEGT ID +G +G+ I + +AG Sbjct: 221 IIQDHVEIGANTTIDRGTMDD--TVIGEGTKIDNLVQIGHNVRIGRYCGIVSQVGIAG-- 276 Query: 180 EPASAEPVRVGDNVLVGANAVVIEGVQVGSGSVVAAGAIVTQDVPENVVVAGVPARTIKE 239 ++GD V++G V + +G G+ +AA + V DVP G+PAR +++ Sbjct: 277 ------STQIGDGVMIGGGVGVNGHITIGDGAQIAAMSGVASDVPAGERYGGIPARPMRD 330 Query: 240 IDEKTAQ 246 A+ Sbjct: 331 FLRDVAE 337 Score = 43.9 bits (102), Expect = 5e-09 Identities = 30/115 (26%), Positives = 51/115 (44%), Gaps = 16/115 (13%) Query: 115 IEPGAIIRDQVMIGDNAVIMMGAIINIGAEIGEGTMIDMGAVLGGRATVGKNSHIGAGAV 174 + P A + + + A+I GAEIG GT I GA++G +G++ I AGA Sbjct: 119 VAPEAFVDPTARLEAGVEVEPMAVIGAGAEIGSGTRIAAGAMIGQGVRIGRDCTISAGAS 178 Query: 175 LAGVIEPASAEPVRVGDNVLVGANAVV-------IEGVQVGSGSVVAAGAIVTQD 222 + + +G+NV++ A + G + G +V G ++ QD Sbjct: 179 ILCAL---------IGNNVIIHPGARIGQDGFGYAPGPKGGMIKIVQVGRVIIQD 224 Score = 38.9 bits (89), Expect = 1e-07 Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 21/122 (17%) Query: 113 ARIEPGAIIRDQVMIGDNAVIMMGAIINIGAEIGEGTMIDMGAVLGGRAT-----VGKNS 167 AR+E G + +IG A I G I GA IG+G I + A+ +G N Sbjct: 129 ARLEAGVEVEPMAVIGAGAEIGSGTRIAAGAMIGQGVRIGRDCTISAGASILCALIGNNV 188 Query: 168 HIGAGAVL------------AGVIEPASAEPVRVGDNVLVGANAVVIEGVQ----VGSGS 211 I GA + G+I+ V + D+V +GAN + G +G G+ Sbjct: 189 IIHPGARIGQDGFGYAPGPKGGMIKIVQVGRVIIQDHVEIGANTTIDRGTMDDTVIGEGT 248 Query: 212 VV 213 + Sbjct: 249 KI 250 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: 217 Number of extensions: 16 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 257 Length of database: 354 Length adjustment: 27 Effective length of query: 230 Effective length of database: 327 Effective search space: 75210 Effective search space used: 75210 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