Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_013459654.1 SULKU_RS04030 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >NCBI__GCF_000183725.1:WP_013459654.1 Length = 365 Score = 300 bits (767), Expect = 6e-86 Identities = 157/363 (43%), Positives = 221/363 (60%), Gaps = 10/363 (2%) Query: 10 HTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAGVYADDPRS 69 H+ HF PL L+SG +L Y +V ETYGELN AR N +++CHAL SHH AG Y D + Sbjct: 7 HSEHFTNPLYLESGRILEPYDIVYETYGELNEARDNVIVICHALTGSHHAAGTYEGDNKP 66 Query: 70 TGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARFPVVTVEDWV 129 GWWD ++G GK +DT+RFFVI N +GSCFGSTGPMS+ PY +FPV+T+ D V Sbjct: 67 -GWWDGLIGQGKAVDTDRFFVICTNVIGSCFGSTGPMSLRYPYNDPYRYKFPVITILDMV 125 Query: 130 HAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKLSAQNIAFNE 189 AQ + D GI + AV+GGS+GGMQALA+ + +P I +A+T IAFN+ Sbjct: 126 KAQRILFDRLGIHQVHAVIGGSMGGMQALAFGVFFPNFAKKIIAMATTAATQPWAIAFNK 185 Query: 190 VARSAILSDPDFHGGDYYAHGVKPR--RGLRVARMIGHITYLSDDDMAEKFGRALRRADG 247 VA+ AIL DP+F G Y ++ G+ + RM GHI++LS MA+KFGR +R DG Sbjct: 186 VAQEAILKDPEFKNGYYDPEVIRENGLSGMAIGRMAGHISFLSHQSMAKKFGREYKRTDG 245 Query: 248 ALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNGNLSAALA 307 + + +F+VESYL Y G F +FD +YL IT+A++ +D ++ F+ ++ AL Sbjct: 246 LFELFG-----KFQVESYLEYNGYNFTKWFDPLSYLYITKAINIYDLSRGFD-SIEEALN 299 Query: 308 HTKAKYLVASFTTDWRFAPARSREIVKALLD-NRRSVSYAEIDAPHGHDAFLLDDARYHN 366 A+ + F D F P+ I A+L + + Y E+ + +GHDAFL++ + N Sbjct: 300 KINAELYLVGFEKDILFLPSEMESIHTAMLAMGKTNSDYLEVVSDYGHDAFLVEIDKIEN 359 Query: 367 LVR 369 VR Sbjct: 360 YVR 362 Lambda K H 0.322 0.136 0.417 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: 381 Number of extensions: 20 Number of successful extensions: 5 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: 381 Length of database: 365 Length adjustment: 30 Effective length of query: 351 Effective length of database: 335 Effective search space: 117585 Effective search space used: 117585 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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