Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate WP_020175282.1 A3OQ_RS0110175 hypothetical protein
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_000385335.1:WP_020175282.1 Length = 361 Score = 151 bits (381), Expect = 3e-41 Identities = 117/372 (31%), Positives = 174/372 (46%), Gaps = 28/372 (7%) Query: 5 RRFIELPGPVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMA--DP 62 ++ ELP + G + ++ + +E++G L NA+L+ S ++HAA A D Sbjct: 5 KKTFELPS-FQTQSGRLIKNLCVGWESYGTLNADKSNAILIAHYFSGTSHAAGKYAEEDA 63 Query: 63 SPGWWEYMIGPGKPIDTERFFVIA------INSLGSCFGSTGPASINPATGQPYRLDFPK 116 PG+W+ +IGPGK IDT+R+FV + +N+ +TGPAS++P TG+PY L FP Sbjct: 64 LPGYWDDLIGPGKAIDTDRYFVFSSDTLVNLNARDKNVVTTGPASLDPDTGKPYGLSFPL 123 Query: 117 LSVEDIVAAARGACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATP 176 +S+ D V + LGI +H V G S+GG+ L +A +P I+ + A Sbjct: 124 VSIRDFVGVQKELVDHLGIKKLHAVMGPSMGGLQTLCWASSFPDMMERIVPVICAGVIDA 183 Query: 177 FTIALRSIQREAVRADPAWAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWL---QRFDR 233 + A + + ADPAW G YAP P G+ +A +L L A WL +F R Sbjct: 184 WLTAWLGLWAAPIYADPAWKNGAYAPDAQPVKGLTLALRLVTL---QANHWLWADAQFGR 240 Query: 234 E-RLEGSDDSANPFAMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSL 292 +EG+D A+ A F+V++ + A A DAN LYL +A F Sbjct: 241 AFAVEGADPGAD-LANRFKVEAAIADLAAARAAVSDANHLLYLVKANQTF---------- 289 Query: 293 EAAVRRIDAKRALVAGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDS 352 A + I A R L+ TD +F A + V E+ GH L Sbjct: 290 SADLAAIKA-RTLLLYTPTDQVFRQEHVLATAAAIVQGHAIVETAEILGPYGHLNGLAAL 348 Query: 353 ERFAPMVAEFLA 364 +AEFLA Sbjct: 349 APLGAKIAEFLA 360 Lambda K H 0.320 0.135 0.414 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: 344 Number of extensions: 16 Number of successful extensions: 3 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: 367 Length of database: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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: 49 (23.5 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