Align Homoserine O-succinyltransferase; HST; EC 2.3.1.46; Homoserine transsuccinylase; HTS (uncharacterized)
to candidate Ga0059261_2301 Ga0059261_2301 homoserine O-acetyltransferase (EC 2.3.1.31)
Query= curated2:A0LCI7 (394 letters) >FitnessBrowser__Korea:Ga0059261_2301 Length = 371 Score = 384 bits (987), Expect = e-111 Identities = 197/368 (53%), Positives = 254/368 (69%), Gaps = 12/368 (3%) Query: 16 QHVRLFGASTPLQLDGGTLLHSVDVSYETYGTLNQERSNAVLICHALSGNAHAAGYHSKD 75 +HV L G PL+LDGG LL V+++YETYGTL + NA+LICHAL+G+ H A H Sbjct: 11 RHVTLPG---PLRLDGGVLLSPVEIAYETYGTLAPDGGNAILICHALTGDQHVASPHPVT 67 Query: 76 DKRPGWWDHYIGPGKPFDTNRYFVIASNNLGGCDGTTGPSSIDPATGMPYGLNFPMITIG 135 K PGWW +GPGKP D +R+F++ +N LG C G++GP++++PATG P+G++FP+ITI Sbjct: 68 GK-PGWWTRMVGPGKPVDPDRHFIVCANVLGSCMGSSGPATVNPATGRPWGMDFPVITIR 126 Query: 136 DIVRVQHALVRQLGIERLMAVVGGSMGGMQALQWALDYPHMVPASVIIAAAPRLTAQNIA 195 D+VR Q L+ LG+ RL AVVGGSMGGMQAL W +P V A V+IA+ R +AQNIA Sbjct: 127 DMVRAQAMLLDHLGVGRLKAVVGGSMGGMQALSWPATFPDRVDAVVVIASTARHSAQNIA 186 Query: 196 FNAVARQAIMADPHFNGGDYYTLPGDPTTKARPESGLALARMMAHITYLSEQGLHERFGR 255 F+ V RQA+MADP +NGG YY GDP P +GLA+ARM AHITYLSE GL E+FGR Sbjct: 187 FHEVGRQAVMADPRWNGGAYY--DGDP-----PAAGLAVARMAAHITYLSEAGLTEKFGR 239 Query: 256 RLQDRDALSYGFETDFAVESYLSYQGSSFVKRFDANSYLYITKAMDYFDPFPD-AETTVQ 314 RLQ R+A S+GF+ DF +ESYL +QG SFV RFDAN+YLYIT+AMDYFD + Sbjct: 240 RLQAREAKSFGFDADFQIESYLRHQGLSFVDRFDANAYLYITRAMDYFDLAEEHGGLLAN 299 Query: 315 RLTGVESHFLVMSFDTDWRFDTSRSKELVRILHRSLKDCTFQEFSSPAGHDAFLLPHPSY 374 + F ++SFDTDW + T S+ +V L+ + +F E SSP GHDAFLL P Sbjct: 300 AFRETRARFCLVSFDTDWLYPTRDSRAIVHALNAAGAPVSFVELSSPFGHDAFLLEAPEL 359 Query: 375 EKSLGSFL 382 + + FL Sbjct: 360 NRVVDGFL 367 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: 535 Number of extensions: 27 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: 371 Length adjustment: 30 Effective length of query: 364 Effective length of database: 341 Effective search space: 124124 Effective search space used: 124124 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