Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_012047258.1 BBTA_RS35155 hypothetical protein
Query= SwissProt::A9I0E6 (424 letters) >NCBI__GCF_000015165.1:WP_012047258.1 Length = 341 Score = 120 bits (302), Expect = 5e-32 Identities = 110/339 (32%), Positives = 150/339 (44%), Gaps = 40/339 (11%) Query: 42 LASGQSLQSYELAVETYGTLNAGRTNAVLVCHALNASHHVAGLAADDPNDVGWWDNMVGP 101 L SG ++ S LA +TYGTLNA + N +L + +A H D W +VGP Sbjct: 17 LQSGATVPSLRLAYKTYGTLNAAKDNVILYPTSFSAQHV----------DTEW---LVGP 63 Query: 102 GKPLDTNRFFVIGVNNLGSCFGSTGPASINPATGHPWGAAFPVLTVEDWVHAQARLADH- 160 LD++R+F+I N G+ S+ P+ P A FP ++ D V Q RL + Sbjct: 64 ADILDSDRYFIIIPNLFGNGLSSS------PSNTPPADAPFPAISYHDAVAIQRRLVEEQ 117 Query: 161 FGIERFAAVMGGSLGGMQALSWAITCPERVAHCIVIASTPRLSAQNIGFNEVARRAIITD 220 FGI R A V G S+GGMQA WA P+ V V+ + R S N F + + A+I D Sbjct: 118 FGITRIALVYGWSMGGMQAYHWAACHPDMVERAAVVCGSARCSPYNHVFLDAVKAALIAD 177 Query: 221 PDFHGGDYYAHNTVPRRGLSVARMIGHITYLSDDDMAEKFGRTQREPAEGGAYRYGYDVE 280 P + G + A P GL R +G I + M+ +F R + +G A + Sbjct: 178 PAYKNGRFVAK---PVAGL---RAMGRI--YAGWAMSYEFYRDEVWREQGFAAQ------ 223 Query: 281 FEVESYLRYQGEKFSRYFDANTYLLITRALDYFDPAR--GTGGDLARALKPAQADFLLVS 338 E YL + + DAN L D + GGDL RAL A LL+ Sbjct: 224 ---EDYLAATWDTAFAHRDANNLLAQIAIWQNGDISHCSAFGGDLDRALSAITAHMLLMP 280 Query: 339 FSTDWRFPPERSREIVRALLKNGSPVTYAEIDAPHGHDA 377 TD R+ R E L N S I + HGH A Sbjct: 281 GQTD-RYFDWRDNERELPKLVNASSAVLRPIPSIHGHRA 318 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: 347 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: 424 Length of database: 341 Length adjustment: 30 Effective length of query: 394 Effective length of database: 311 Effective search space: 122534 Effective search space used: 122534 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