Align Homoserine O-succinyltransferase; HST; EC 2.3.1.46; Homoserine transsuccinylase; HTS (uncharacterized)
to candidate WP_015927464.1 MNOD_RS03535 homoserine O-acetyltransferase
Query= curated2:A0LCI7 (394 letters) >NCBI__GCF_000022085.1:WP_015927464.1 Length = 390 Score = 378 bits (970), Expect = e-109 Identities = 197/379 (51%), Positives = 247/379 (65%), Gaps = 8/379 (2%) Query: 5 PLTASVGIVTPQHVRLFGASTPLQLDGGTLLHSVDVSYETYGTLNQERSNAVLICHALSG 64 P TAS + V FGA PL +D G L V+Y+T GTLN ER+NAVL+CHAL+G Sbjct: 10 PDTASQAVEPASPVAHFGADEPLMMDAGVALAPWQVAYQTTGTLNAERTNAVLVCHALTG 69 Query: 65 NAHAAGYHSKDDKRPGWWDHYIGPGKPFDTNRYFVIASNNLGGCDGTTGPSSIDPATGMP 124 + H A H K PGWW+ +GPGKP DT+RYFVI +N +G C GTTGP+SI+PA G P Sbjct: 70 DQHVAHPHPVTAK-PGWWETMVGPGKPVDTDRYFVICANVVGSCMGTTGPASINPANGHP 128 Query: 125 YGLNFPMITIGDIVRVQHALVRQLGIERLMAVVGGSMGGMQALQWALDYPHMVPASVIIA 184 YGL+FP++TI D+VR Q L+ +LGI L +GGSMGGMQ LQWA YP V A++ IA Sbjct: 129 YGLDFPLVTIRDMVRGQAMLLDRLGIRDLFLCIGGSMGGMQVLQWAASYPDRVFAAMPIA 188 Query: 185 AAPRLTAQNIAFNAVARQAIMADPHFNGGDYYTLPGDPTTKARPESGLALARMMAHITYL 244 R +AQNIAF+ V RQA+MADP ++GG Y + RP GLA+ARM AHITYL Sbjct: 189 TGARHSAQNIAFHEVGRQAVMADPAWHGGRYLDV------GTRPAKGLAVARMGAHITYL 242 Query: 245 SEQGLHERFGRRLQDRDALSYGFETDFAVESYLSYQGSSFVKRFDANSYLYITKAMDYFD 304 SE LH +FGRR QDRDA ++ F+ DF +ESYL +QG SFV+RFDAN+YLY+T+AMDYFD Sbjct: 243 SEPALHRKFGRRFQDRDAPTFSFDADFQIESYLRHQGISFVERFDANAYLYLTRAMDYFD 302 Query: 305 PFPD-AETTVQRLTGVESHFLVMSFDTDWRFDTSRSKELVRILHRSLKDCTFQEFSSPAG 363 D G + F VMSF +DW F T S+ +V L+ + F E S G Sbjct: 303 LAADHGGVLANAFRGTPTRFCVMSFTSDWLFPTPDSRAIVHALNAAAARVAFVEVESDKG 362 Query: 364 HDAFLLPHPSYEKSLGSFL 382 HDAFLL P+ + F+ Sbjct: 363 HDAFLLDEPAMFAAARGFI 381 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: 540 Number of extensions: 21 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: 390 Length adjustment: 31 Effective length of query: 363 Effective length of database: 359 Effective search space: 130317 Effective search space used: 130317 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