Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_086508787.1 BZY95_RS04510 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_002151265.1:WP_086508787.1 Length = 398 Score = 531 bits (1368), Expect = e-155 Identities = 257/386 (66%), Positives = 316/386 (81%) Query: 18 AFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 A +TLA+RAG +RT E EHGE +F TSS+V+ +AA+AA +F GE GNVYSR+TNPTV T Sbjct: 12 ALETLAIRAGHQRTHEQEHGEPIFPTSSFVYGSAAEAARKFGGEERGNVYSRFTNPTVHT 71 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 FE R+AALEG E+ VAT+SGM+AIL+ V++L +GD ++ SRS+FGST+SLFDKYF + G Sbjct: 72 FERRLAALEGGERCVATSSGMAAILSTVLALLQAGDEIVASRSLFGSTVSLFDKYFGKLG 131 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 I Y LSDLAAWEAA P+T+L F E+PSNPL+E+VDIAALAEIAH ALLA+DNCF Sbjct: 132 ITTRYVELSDLAAWEAAITPHTRLLFAETPSNPLSEVVDIAALAEIAHRHQALLAIDNCF 191 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFN 257 TPALQQPL LGAD+VIHSATKY+DGQGR +GG V GR ++++EV G +RT GP LSPFN Sbjct: 192 LTPALQQPLALGADLVIHSATKYLDGQGRAVGGAVVGRDKELEEVFGVVRTCGPCLSPFN 251 Query: 258 AWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFG 317 AW+F KGLETL +RM+AH +A ALAEWL+ P + RV+Y+GLP HPQHELA RQQ+G+G Sbjct: 252 AWIFTKGLETLSLRMRAHCGNAQALAEWLQVHPAVARVHYSGLPDHPQHELAGRQQAGYG 311 Query: 318 AVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGD 377 AV+ F+VKGGR+AAW IDATRM+SIT NLGD KTTI HPATT+HGRLSP + AGI + Sbjct: 312 AVLGFEVKGGREAAWSVIDATRMLSITGNLGDVKTTITHPATTTHGRLSPAQKDAAGISE 371 Query: 378 SLIRVAVGLEDLDDLKADMARGLAAL 403 LIRVAVGLE ++D++ D+ARGL AL Sbjct: 372 GLIRVAVGLESIEDIRLDLARGLDAL 397 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: 507 Number of extensions: 12 Number of successful extensions: 1 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: 398 Length adjustment: 31 Effective length of query: 372 Effective length of database: 367 Effective search space: 136524 Effective search space used: 136524 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