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 HSERO_RS21030 HSERO_RS21030 hypothetical protein
Query= SwissProt::O34981 (236 letters) >FitnessBrowser__HerbieS:HSERO_RS21030 Length = 170 Score = 58.9 bits (141), Expect = 6e-14 Identities = 39/103 (37%), Positives = 53/103 (51%), Gaps = 10/103 (9%) Query: 100 IRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAGSVLAGVIE 159 I D VEIG A+ +G +VIG T I V +G + +G C I S L+G Sbjct: 78 IGDDVEIG--ALCAVGRGTIDDTVIGNNTHIGPQVNIGHNSVIGMRCQIAGRSHLSG--- 132 Query: 160 PPSAKPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVNDV 202 VVIED+ + AN + +GV +G GA V GA+V +DV Sbjct: 133 -----SVVIEDEAKLWANCTLKDGVRIGAGATVGMGALVNHDV 170 Score = 29.3 bits (64), Expect = 5e-05 Identities = 28/93 (30%), Positives = 38/93 (40%), Gaps = 18/93 (19%) Query: 109 NAVIMMGASINIGSVI------GEGTMIDMNVVLGGRATVGKNCHIGAGSVLA----GVI 158 + I G SI G +I GE T I+ ++G + +G IGA +V+ G Sbjct: 1 SVTIAPGVSIGEGVIIEDDVQIGENTRIETGALIGRGSRIGARSRIGARTVIGNEGLGSF 60 Query: 159 EPPSAK--------PVVIEDDVVIGANAVVLEG 183 E + V I DDV IGA V G Sbjct: 61 ETADGQLRNVRHLGNVRIGDDVEIGALCAVGRG 93 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: 179 Number of extensions: 23 Number of successful extensions: 12 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 5 Number of HSP's successfully gapped: 3 Length of query: 236 Length of database: 170 Length adjustment: 21 Effective length of query: 215 Effective length of database: 149 Effective search space: 32035 Effective search space used: 32035 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: 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