Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate Echvi_3285 Echvi_3285 homoserine O-acetyltransferase
Query= SwissProt::A9I0E6 (424 letters) >FitnessBrowser__Cola:Echvi_3285 Length = 351 Score = 211 bits (537), Expect = 3e-59 Identities = 132/365 (36%), Positives = 189/365 (51%), Gaps = 30/365 (8%) Query: 29 VTPQLIRFDTPLPLASGQSLQSYELAVETYGTLNAGRTNAVLVCHALNASHHVAGLAADD 88 +T + + L L SG+SL +E++ T G L + N + + HAL D Sbjct: 12 MTQETFHCEEELNLESGESLPGFEISYTTQGHLTPKKDNVIWILHALTG----------D 61 Query: 89 PNDVGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPASINPATGHPWGAAFPVLTVE 148 N WW +VG K D ++F++ N LGSC+GST P S NP TG P+ FP L+ Sbjct: 62 ANVHEWWSGLVGEDKFFDPTKYFIVCANLLGSCYGSTQPLSDNPKTGKPYYYDFPNLSTR 121 Query: 149 DWVHAQARLADHFGIERFAAVMGGSLGGMQALSWAITCPERVAHCIVIASTPRLSAQNIG 208 D A RL H GI++ ++GGSLGG AL W+ E+V I++AS + S IG Sbjct: 122 DMAKAFDRLRQHLGIQQIDTIIGGSLGGQVALEWSYNLQEQVKKTIIVASNAKTSPWTIG 181 Query: 209 FNEVARRAIITDPDFHGGDYYAHNTVPRRGLSVARMIGHITYLSDDDMAEKFGRTQREPA 268 FNE R AI +D + A ++GL AR IG ++Y D F +Q E Sbjct: 182 FNEAQRMAIESDSTWGQNSPDA----GKKGLEAARAIGMLSYRHQD----IFHASQAETE 233 Query: 269 EGGAYRYGYDVEFEVESYLRYQGEKFSRYFDANTYLLITRALDYFDPARGTGGDLARALK 328 E + F V SYLRYQG+K S F+A +Y ++T+A+D D RG GG A+AL Sbjct: 234 EKTDH-------FRVSSYLRYQGQKLSNRFNALSYWVLTKAMDSHDLGRGRGG-TAKALS 285 Query: 329 PAQADFLLVSFSTDWRFPPERSREIVRALLKNGSPVTYAEIDAPHGHDAFLLDDARYHAV 388 +A L + +TD F E S+ I KN TY EI + +GHDAFL+++ + + + Sbjct: 286 AIKAKVLSIGINTDLLFTKEESQFI----SKNVPNGTYREISSIYGHDAFLVENEQLNYI 341 Query: 389 VRGYY 393 + +Y Sbjct: 342 LTSFY 346 Lambda K H 0.320 0.137 0.427 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: 356 Number of extensions: 20 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: 424 Length of database: 351 Length adjustment: 30 Effective length of query: 394 Effective length of database: 321 Effective search space: 126474 Effective search space used: 126474 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