Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate HSERO_RS05350 HSERO_RS05350 hypothetical protein
Query= SwissProt::C4XNQ9 (397 letters) >FitnessBrowser__HerbieS:HSERO_RS05350 Length = 359 Score = 90.1 bits (222), Expect = 9e-23 Identities = 76/244 (31%), Positives = 112/244 (45%), Gaps = 30/244 (12%) Query: 35 SGRALGPVVLAYETCGQLNERADNAVLVLHALTGDSHAAGYYEPGDA--KPGWWDLMIGP 92 +G+ L + L Y T G +RA+ AVLVLH G Y+ A + + GP Sbjct: 49 TGQTLENLRLHYVTLG---DRANPAVLVLH---------GTYQSAQAMLSKDFGGQLFGP 96 Query: 93 GKPIDTDRYYVICSNVIGGCMGSTGPSSLDPATGQPYGLTFPVITIGDMVRAQKR-LVEH 151 G+P+D +Y++I + IG G SS P+ G FP DMV AQ R L E Sbjct: 97 GQPLDASKYFIIIPDGIG-----VGKSS-KPSDG--LRAAFPQYNYADMVLAQYRMLTEG 148 Query: 152 LGVTKLLSVVGGSMGGMQALEWSVRYPDMVRTAVPLAT-TTKHSALAIAFNEVARQAIMA 210 +G+T L ++G SMGGMQ W YP VP+A+ T+ ++ + ++I Sbjct: 149 MGITHLRLIIGNSMGGMQTWIWGGTYPGFADGLVPMASQPTEMASRNWMMRRMLVESIKQ 208 Query: 211 DPNWNGGNYYDGVPPAHGLAVGRMI-----GHITYLSDEAMRQKFDRRLQDRCENSFVLE 265 DP WN GN Y PP+ LA + G + Y + + D+ + +R + Sbjct: 209 DPAWNNGN-YTTQPPSLRLANNMFVFATNGGTLAYQAMAGSHAQADKLVDERLAAPVTAD 267 Query: 266 EPDF 269 DF Sbjct: 268 ANDF 271 Lambda K H 0.320 0.135 0.411 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: 363 Number of extensions: 22 Number of successful extensions: 4 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: 397 Length of database: 359 Length adjustment: 30 Effective length of query: 367 Effective length of database: 329 Effective search space: 120743 Effective search space used: 120743 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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