Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_092055964.1 BQ4888_RS07650 PLP-dependent transferase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_900111775.1:WP_092055964.1 Length = 380 Score = 228 bits (580), Expect = 3e-64 Identities = 139/383 (36%), Positives = 211/383 (55%), Gaps = 15/383 (3%) Query: 21 TLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNV-YSRYTNPTVRTF 78 TL V G R P G ++ S+Y G PG Y+R NP+ R Sbjct: 10 TLLVHQGIDRDPATGASAIPIYQASTY----------HHVGGQPGEYDYARSGNPSRRQV 59 Query: 79 EERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGI 138 E+ IA LEG + A A+GM+AI ++L SGDH++ ++G + GI Sbjct: 60 EDAIALLEGGVRGFAYATGMAAI-GSALALLKSGDHLIAPNDLYGGSWRYLSTVLPEQGI 118 Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198 + ++DL EAA P TK F+E+PSNPL + DI A+ +A +G L +DN F Sbjct: 119 TTSFVDITDLNRIEAAITPATKAIFLETPSNPLFNITDIRAVTALARQRGLLTLLDNTFM 178 Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GPTLSPFN 257 TP LQ+PL+LG DVVIHSATK++ G M G+V Q+ + + + + A G L+PF+ Sbjct: 179 TPLLQRPLELGVDVVIHSATKFLGGHSDLMAGLVTTADPQLAKRLKYFQNAFGAVLAPFD 238 Query: 258 AWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFG 317 ++L +G++TL++R++A SA LAE L+ P + RV++ GL EL Q SG G Sbjct: 239 SFLLARGIKTLKLRLEAAQRSAQDLAERLQDHPAVARVWFPGLVDFAGRELHFSQASGAG 298 Query: 318 AVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGD 377 AV+SF++K A + ++ I +LG +T + H + SH + E + R GI + Sbjct: 299 AVLSFELKEQARVA-PLLQQIKLPIIAPSLGGVETILTHCWSMSHAAIPAETKLRLGIRE 357 Query: 378 SLIRVAVGLEDLDDLKADMARGL 400 +L+R++VG+ED++DL D+A L Sbjct: 358 TLLRISVGIEDVEDLWEDLAAAL 380 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: 341 Number of extensions: 22 Number of successful extensions: 4 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: 380 Length adjustment: 31 Effective length of query: 372 Effective length of database: 349 Effective search space: 129828 Effective search space used: 129828 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