Align Homoserine O-succinyltransferase; HST; EC 2.3.1.46; Homoserine transsuccinylase; HTS (uncharacterized)
to candidate WP_012049205.1 SWIT_RS15195 homoserine O-acetyltransferase
Query= curated2:A0LCI7 (394 letters) >NCBI__GCF_000016765.1:WP_012049205.1 Length = 378 Score = 379 bits (972), Expect = e-109 Identities = 199/362 (54%), Positives = 247/362 (68%), Gaps = 15/362 (4%) Query: 26 PLQLDGGTLLHSVDVSYETYGTLNQERSNAVLICHALSGNAHAAGYHSKDDKRPGWWDHY 85 PL+LDGG L V+++YETYG+L+ + NAVLICHAL+G+ H A H K PGWW Sbjct: 21 PLRLDGGARLAPVEIAYETYGSLDADGGNAVLICHALTGDQHVASTHPITGK-PGWWTRM 79 Query: 86 IGPGKPFDTNRYFVIASNNLGGCDGTTGPSSIDPATGMPYGLNFPMITIGDIVRVQHALV 145 +G GKP D R+F+I +N LG C G++GP +IDPATG PY + FP+ITI D+VR Q L+ Sbjct: 80 VGAGKPIDPARHFIICANVLGSCLGSSGPGTIDPATGAPYAMRFPVITIRDMVRAQAILL 139 Query: 146 RQLGIERLMAVVGGSMGGMQALQWALDYPHMVPASVIIAAAPRLTAQNIAFNAVARQAIM 205 LG+ L A VGGSMGGMQ LQWA YP + ++V IA+ R +AQNIAF+ V RQAIM Sbjct: 140 DHLGVGTLAAAVGGSMGGMQVLQWAATYPDRLRSAVAIASTARHSAQNIAFHEVGRQAIM 199 Query: 206 ADPHFNGGDYYTLPGDPTTKARPESGLALARMMAHITYLSEQGLHERFGRRLQDRDALSY 265 ADP + GGDYY GDP P +GLA+ARM AHITYLSE GL E+FGRRLQ RDA S+ Sbjct: 200 ADPKWAGGDYYA-AGDP-----PAAGLAVARMAAHITYLSEAGLTEKFGRRLQARDAKSF 253 Query: 266 GFETDFAVESYLSYQGSSFVKRFDANSYLYITKAMDYFDPFPDAETTVQRLTGV-----E 320 GF+ DF +ESYL +QG SFV RFDANSYLYIT+AMDYFD AE L G Sbjct: 254 GFDADFQIESYLRHQGISFVDRFDANSYLYITRAMDYFDL---AEEHGGLLAGAFQGAKR 310 Query: 321 SHFLVMSFDTDWRFDTSRSKELVRILHRSLKDCTFQEFSSPAGHDAFLLPHPSYEKSLGS 380 + F ++SFDTDW + T+ S+ +V L+ + +F E SSP GHDAFLL P + + Sbjct: 311 TRFCLVSFDTDWLYPTAESRAIVHALNAAGAPVSFVELSSPFGHDAFLLDVPELNRVVDG 370 Query: 381 FL 382 FL Sbjct: 371 FL 372 Lambda K H 0.320 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: 515 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: 394 Length of database: 378 Length adjustment: 30 Effective length of query: 364 Effective length of database: 348 Effective search space: 126672 Effective search space used: 126672 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 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