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 Synpcc7942_0931 Synpcc7942_0931 UDP-N-acetylglucosamine acyltransferase
Query= SwissProt::O34981 (236 letters) >FitnessBrowser__SynE:Synpcc7942_0931 Length = 268 Score = 51.6 bits (122), Expect = 2e-11 Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 2/111 (1%) Query: 104 VEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAGSVLAGVIEPPSA 163 V IGD I +IN + GE T+I + +L V NC + V++ + A Sbjct: 81 VRIGDRNRIREYVTINRATKAGEATVIGNDNLLMAYVHVAHNCILHNRIVISNAVS--LA 138 Query: 164 KPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVVAGTPAK 214 +V+E VIG + + + V VG+ A++ + V DV PY +V G PA+ Sbjct: 139 GHIVVESGAVIGGMSGLHQFVHVGRNAMIGGMSRVERDVPPYMLVEGNPAR 189 Score = 34.3 bits (77), Expect = 2e-06 Identities = 31/110 (28%), Positives = 47/110 (42%), Gaps = 8/110 (7%) Query: 92 ARIEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAG 151 A I PGA I V+IG AVI G + IG+ T + + V+ G +G+ I G Sbjct: 9 AIIAPGAEIHPSVQIGPYAVI--GEHVRIGA----HTTVGAHAVIDGWTEIGEENRIFPG 62 Query: 152 SVLAGVIEPPSAKPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVND 201 + + +E K V IG + E VT+ + ++ ND Sbjct: 63 AAIG--LESQDKKTDGSLSVVRIGDRNRIREYVTINRATKAGEATVIGND 110 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: 174 Number of extensions: 14 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 6 Number of HSP's successfully gapped: 2 Length of query: 236 Length of database: 268 Length adjustment: 24 Effective length of query: 212 Effective length of database: 244 Effective search space: 51728 Effective search space used: 51728 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