Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_017597122.1 D471_RS0102240 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000341125.1:WP_017597122.1 Length = 390 Score = 277 bits (708), Expect = 4e-79 Identities = 146/366 (39%), Positives = 215/366 (58%), Gaps = 2/366 (0%) Query: 37 GEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATAS 96 G ++ ++ F AA F G VY+RY NPTV E+ +A LEG A+A+ S Sbjct: 24 GVPIYQAHTFAFPDTETMAASFQGAGSPFVYARYGNPTVAALEDAVADLEGGAGAIASGS 83 Query: 97 GMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACK 156 GM AI A + +L +G HV+ ++G T +L +R+G++V D AA +AA + Sbjct: 84 GMGAITATLWALLGTGGHVVAQERLYGGTQALLTTLRERWGVEVTQVDAGDPAAVDAALR 143 Query: 157 PNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHS 216 P+T++ +E+ +NP ++ D+ AL +A G + VDN F TP L +P++ GAD+V+HS Sbjct: 144 PDTRVLVLETIANPTGQVADLPALTALARRHGTTVIVDNTFATPLLCRPIEHGADIVVHS 203 Query: 217 ATKYIDGQGRGMGGV-VAGRGEQMKEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAH 275 ATKY+ G +GGV V + V G + PF AWL +GL TL +RM+ H Sbjct: 204 ATKYMGGHSDTIGGVAVFADAGTLTRVRERTNEFGAVMEPFAAWLINRGLSTLGVRMRRH 263 Query: 276 SASALALAEWLERQPGIERVYYAGLPSHPQHELARR-QQSGFGAVVSFDVKGGRDAAWRF 334 A+A LA L+R P + RV+YAGLP HP H AR GFG V++F++ GG +A F Sbjct: 264 CANAEELARRLDRHPAVTRVHYAGLPDHPGHATARELLDGGFGGVLAFELAGGLEAGRSF 323 Query: 335 IDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKA 394 + R+ + +LGD +T + HPA+TSH L E ARAG+ + LIR++ G+ED++DL A Sbjct: 324 AERVRLAVLAPSLGDVRTLVMHPASTSHRMLDAEGLARAGVSEGLIRLSAGIEDVEDLWA 383 Query: 395 DMARGL 400 D+ R L Sbjct: 384 DLERAL 389 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: 406 Number of extensions: 17 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: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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 Jul 25 2024. The underlying query database was built on Jul 25 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