Align Homoserine O-succinyltransferase; HST; EC 2.3.1.46; Homoserine transsuccinylase; HTS (uncharacterized)
to candidate WP_013011985.1 DACET_RS13820 homoserine O-acetyltransferase
Query= curated2:A0LCI7 (394 letters) >NCBI__GCF_000025725.1:WP_013011985.1 Length = 369 Score = 335 bits (859), Expect = 1e-96 Identities = 172/377 (45%), Positives = 239/377 (63%), Gaps = 11/377 (2%) Query: 6 LTASVGIVTPQHVRLFGASTPLQLDGGTLLHSVDVSYETYGTLNQERSNAVLICHALSGN 65 ++ SVG+V Q F + G +L SV V+YETYG LN+ R NA+L+CHAL+GN Sbjct: 1 MSGSVGVVKTQ---FFTLKEEFFFESGRVLSSVTVAYETYGKLNEARDNAILVCHALTGN 57 Query: 66 AHAAGYHSKDDKRPGWWDHYIGPGKPFDTNRYFVIASNNLGGCDGTTGPSSIDPATGMPY 125 AHAAG++ +DD+RPGWWD IGPGK FDT++YFVI+SN LG C GTTGPSS+DP T Y Sbjct: 58 AHAAGFNREDDQRPGWWDSMIGPGKAFDTDKYFVISSNFLGSCFGTTGPSSVDPQTKKRY 117 Query: 126 GLNFPMITIGDIVRVQHALVRQLGIERLMAVVGGSMGGMQALQWALDYPHMVPASVIIAA 185 GL FP++T+ D+V++Q L+ LGIE L +V GGSMGGMQAL+W +P+ + + IAA Sbjct: 118 GLKFPVVTVRDMVKLQKKLIDHLGIEVLHSVAGGSMGGMQALEWGATFPYATKSIIPIAA 177 Query: 186 APRLTAQNIAFNAVARQAIMADPHFNGGDYYTLPGDPTTKARPESGLALARMMAHITYLS 245 + +T IAFNA+A+ AIM DP++ GGDYY P GLA+ARM HITY+S Sbjct: 178 SAAVTPMAIAFNAIAKFAIMKDPNWRGGDYY-------DDVAPLDGLAIARMAGHITYMS 230 Query: 246 EQGLHERFGRRLQDRDALSYGFETDFAVESYLSYQGSSFVKRFDANSYLYITKAMDYFDP 305 + H +FGRR + + Y F+ F VE+YL Y G F + +D N+YLY+ KAMD F+ Sbjct: 231 DASFHSKFGRRYATFEGI-YDFKGLFEVENYLRYNGYKFTEFYDPNTYLYVLKAMDIFEL 289 Query: 306 FPDAETTVQRLTGVESHFLVMSFDTDWRFDTSRSKELVRILHRSLKDCTFQEFSSPAGHD 365 L + S L ++F +D+ F +++ELV ++ + ++ S GHD Sbjct: 290 AYGRNGLKDALRLITSKALFITFTSDFLFPPYQTEELVTLMKEIGNEPRWENIESDYGHD 349 Query: 366 AFLLPHPSYEKSLGSFL 382 AFLL + + + +FL Sbjct: 350 AFLLEFEAQTEIIKNFL 366 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: 456 Number of extensions: 16 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: 369 Length adjustment: 30 Effective length of query: 364 Effective length of database: 339 Effective search space: 123396 Effective search space used: 123396 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