Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_083786418.1 MNOD_RS14540 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000022085.1:WP_083786418.1 Length = 429 Score = 260 bits (665), Expect = 5e-74 Identities = 143/337 (42%), Positives = 208/337 (61%), Gaps = 2/337 (0%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 YSR NPT + IA LEG AV ASGM+A L L +S + GD ++ +G T Sbjct: 92 YSRLGNPTRDQLADTIAKLEGGAHAVVVASGMAA-LDLALSPVAPGDLLVAPHDCYGGTH 150 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 L + + +V + +D A AA +L +E+PSNPL +VDI +A A A Sbjct: 151 RLLSQRSAKGHYRVAFVDQTDENALAAALVERPRLVLIETPSNPLMRIVDIRRVAARAKA 210 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGG-VVAGRGEQMKEVVGF 245 GALL VDN F +PALQQP+ LGAD+V+HS TK+++G +GG VVA + +++ + Sbjct: 211 VGALLVVDNTFLSPALQQPISLGADLVVHSTTKFLNGHSDVIGGAVVAADAKLGEDLAAW 270 Query: 246 LRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305 T G T SPF+A+L L+G+ TL R++ SA A+A +L P + RV+Y GLP HP Sbjct: 271 ANTIGVTGSPFDAYLTLRGIRTLFARVERQQQSAAAIAAFLAAHPAVARVHYPGLPEHPG 330 Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365 H +A+ QQSGFGA++SF++ GGR+A ++ R+ ++ +LG ++ IAHP + +H + Sbjct: 331 HAIAKAQQSGFGAMLSFELAGGREAIRAVVERLRVFTLAESLGGIESLIAHPVSMTHAAM 390 Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402 PE R RAG+GD L+R++VGLE +DL D+A+ L A Sbjct: 391 DPEARRRAGVGDGLLRLSVGLEAEEDLLDDLAQALDA 427 Lambda K H 0.319 0.133 0.392 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: 416 Number of extensions: 20 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: 403 Length of database: 429 Length adjustment: 31 Effective length of query: 372 Effective length of database: 398 Effective search space: 148056 Effective search space used: 148056 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