Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate RR42_RS01160 RR42_RS01160 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >FitnessBrowser__Cup4G11:RR42_RS01160 Length = 390 Score = 645 bits (1665), Expect = 0.0 Identities = 310/380 (81%), Positives = 344/380 (90%), Gaps = 5/380 (1%) Query: 2 ESIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAG 61 +S+G+VAP MHF EPL+L++G+ L +Y L+VETYG LNAARSNAVLVCHALNASHHVAG Sbjct: 16 DSVGIVAPQCMHFTEPLKLRNGTSLADYDLMVETYGTLNAARSNAVLVCHALNASHHVAG 75 Query: 62 VYADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARFP 121 VY DPR GWWDNMVGPGKPLDT+RFFVIGVNNLGSCFGSTGPMS +PATG PYGA FP Sbjct: 76 VYEHDPRDVGWWDNMVGPGKPLDTDRFFVIGVNNLGSCFGSTGPMSANPATGQPYGATFP 135 Query: 122 VVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKLS 181 VVTVEDWV+AQARVAD FGI +FAAVMGGSLGGMQALAWSL+YP+R+ HCI +ASTPKLS Sbjct: 136 VVTVEDWVNAQARVADRFGITQFAAVMGGSLGGMQALAWSLMYPDRLRHCIVVASTPKLS 195 Query: 182 AQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGRA 241 AQNIAFNEVARSAILSDPDFHGG+YYAHGVKP+RGLRVARMIGHITYLSD+DMAEKFGR Sbjct: 196 AQNIAFNEVARSAILSDPDFHGGNYYAHGVKPKRGLRVARMIGHITYLSDEDMAEKFGRE 255 Query: 242 LRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNGN 301 L+ D F+FDVEF+VESYLRYQGDKFA+YFDANTYLLITRALDYFDPA AF G+ Sbjct: 256 LK-----TDDIRFSFDVEFQVESYLRYQGDKFAEYFDANTYLLITRALDYFDPALAFGGD 310 Query: 302 LSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDD 361 L+ A++ T+A +LVASFTTDWRFAP RSRE+VKALLDN+R VSYAEIDAPHGHDAFLLDD Sbjct: 311 LTRAVSQTQASFLVASFTTDWRFAPNRSRELVKALLDNKRPVSYAEIDAPHGHDAFLLDD 370 Query: 362 ARYHNLVRAYYERIAEEVGA 381 RYHNL+RAYYERIAEE+GA Sbjct: 371 PRYHNLMRAYYERIAEEIGA 390 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: 613 Number of extensions: 18 Number of successful extensions: 2 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: 390 Length adjustment: 30 Effective length of query: 351 Effective length of database: 360 Effective search space: 126360 Effective search space used: 126360 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 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