Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate AZOBR_RS20475 AZOBR_RS20475 homoserine acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >FitnessBrowser__azobra:AZOBR_RS20475 Length = 394 Score = 249 bits (636), Expect = 9e-71 Identities = 150/361 (41%), Positives = 202/361 (55%), Gaps = 13/361 (3%) Query: 17 PFPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAAANDANPAAG---WWEG 73 P G L VAY+T+G L AD SNAILI L+ D + D +P G WWE Sbjct: 24 PMRLDSGAELGPFEVAYQTYGALNADRSNAILICHALTGDHYVL--DQHPVTGKPGWWEM 81 Query: 74 MVGPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPELSIEDGARAAIEV 133 +VGPGK +DTDR+FV+C N +G C GSTGP +PATG+PY L FP ++I D RA + Sbjct: 82 LVGPGKPVDTDRYFVICSNVIGGCMGSTGPKETDPATGEPYGLGFPVITIGDMVRAQKLL 141 Query: 134 VRAQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPFSIAIRSLQREAI 193 V GI+QL CV+G SMGGM L + +P + V I+ +A+ +IA + R+AI Sbjct: 142 VEHLGIDQLFCVIGGSMGGMQVLQWAVAYPESVFAAVPIATAARHSAQNIAFHEVGRQAI 201 Query: 194 RLDPRWNGGHY-DDDAYPESGMRMARKLGVITYRSALEWDGRFGRVRLDSDQTDDDPFGL 252 DP W GG+Y + P G+ +AR ITY S +FGR L + QT F Sbjct: 202 MADPDWAGGNYLLEGTRPHRGLAVARMAAHITYLSEPALHRKFGR-NLQNRQTVTYGFDA 260 Query: 253 EFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDL-AEYADGDVLAGLAK----IRVEK 307 +FQVESYL FV FD N YLY++R+MD+FDL A+Y G + K V Sbjct: 261 DFQVESYLRHQGITFVERFDANSYLYITRAMDYFDLAADYGGGTLSNAFRKDGKGTPVRF 320 Query: 308 ALAIGANTDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFERFCPAVRGFL 367 LA ++D LFP + + + L A A+ F+ + + +GHD+FL+D F +RGFL Sbjct: 321 CLA-SFSSDWLFPTSESRAIVHALNAVAANVSFVEIRTDKGHDSFLLDEPEFHQVIRGFL 379 Query: 368 D 368 D Sbjct: 380 D 380 Lambda K H 0.322 0.138 0.432 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: 399 Number of extensions: 17 Number of successful extensions: 5 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: 370 Length of database: 394 Length adjustment: 30 Effective length of query: 340 Effective length of database: 364 Effective search space: 123760 Effective search space used: 123760 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 (21.9 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