Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate H281DRAFT_02214 H281DRAFT_02214 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >FitnessBrowser__Burk376:H281DRAFT_02214 Length = 381 Score = 697 bits (1800), Expect = 0.0 Identities = 335/381 (87%), Positives = 360/381 (94%) Query: 1 MESIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVA 60 MESIG+VAP MHF EPLRLQ+GS L +Y L+VETYG LNAARSNAVLVCHALNASHHVA Sbjct: 1 MESIGIVAPQKMHFTEPLRLQNGSSLASYDLMVETYGTLNAARSNAVLVCHALNASHHVA 60 Query: 61 GVYADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARF 120 GVYAD+ + GWWDNMVGPGKPLDTN+FFVIGVNNLGSCFGSTGPMSIDPATG PYGA F Sbjct: 61 GVYADNLKDIGWWDNMVGPGKPLDTNKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGATF 120 Query: 121 PVVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKL 180 PVVTVEDWV+AQARVAD FGI RFAAVMGGSLGGMQALAWS++YPERV HCI +ASTPKL Sbjct: 121 PVVTVEDWVNAQARVADQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKL 180 Query: 181 SAQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGR 240 SAQNIAFNEVARSAILSDPDFHGG+YYAH VKP+RGLRVARMIGHITYLSDDDMAEKFGR Sbjct: 181 SAQNIAFNEVARSAILSDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGR 240 Query: 241 ALRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNG 300 +LRRA+GALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAF G Sbjct: 241 SLRRAEGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFEG 300 Query: 301 NLSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLD 360 +L+AA+AHT AKYL+ASFTTDWRFAPARSRE+VKALLD++R+V+YAEIDAPHGHDAFLLD Sbjct: 301 DLTAAVAHTTAKYLIASFTTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLD 360 Query: 361 DARYHNLVRAYYERIAEEVGA 381 DARYHNL+RAYYERIA EV A Sbjct: 361 DARYHNLMRAYYERIANEVNA 381 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: 641 Number of extensions: 17 Number of successful extensions: 1 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: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 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 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