Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_019555914.1 F612_RS0101190 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000381085.1:WP_019555914.1 Length = 392 Score = 474 bits (1219), Expect = e-138 Identities = 232/385 (60%), Positives = 298/385 (77%), Gaps = 1/385 (0%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 +TLAVRAG +T E E+ EA+F TSS+ + +AA AAARF+GE GNVYSR+TNPTVR FE Sbjct: 7 ETLAVRAGYDQTQEQENSEAIFPTSSFRYTSAAQAAARFSGEEKGNVYSRFTNPTVRAFE 66 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 R+A +EG E V T+SGM+AIL+ M+L SGDHV+ S+SVFG+T LF+KY +FG++ Sbjct: 67 NRLALMEGGEACVGTSSGMAAILSTFMALYESGDHVICSQSVFGTTKVLFNKYLVKFGLE 126 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 V + +D + W+ A +PNTK FF+E+PSNPL E+ D++ ++ +A A G LL VDNCFCT Sbjct: 127 VTFVSQTDTSEWKKAIQPNTKAFFLETPSNPLTEIADLSTISALAKANGCLLIVDNCFCT 186 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKE-VVGFLRTAGPTLSPFNA 258 P LQ+PL+ GAD++IHSATK++DGQGRG+GG V G E + E V GF+RTAGP++SPFNA Sbjct: 187 PILQRPLEQGADIIIHSATKFLDGQGRGIGGAVVGSNELVDEHVRGFMRTAGPSMSPFNA 246 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 W+FLKGLETL IRM AH SAL LAEWL P +E+V+Y GL SHPQ+ELA +QQS G Sbjct: 247 WIFLKGLETLPIRMAAHCQSALQLAEWLSLHPAVEQVFYPGLKSHPQYELACKQQSAGGG 306 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 +VSF VKG + AW ID T+MVSIT NLGD KT+I HPATT+H R+ P+ R RAGI D+ Sbjct: 307 LVSFKVKGNQAEAWSVIDHTQMVSITANLGDVKTSITHPATTTHVRVEPDARLRAGITDN 366 Query: 379 LIRVAVGLEDLDDLKADMARGLAAL 403 LIR++VGLE ++D+KAD+ARGL L Sbjct: 367 LIRLSVGLESIEDIKADLARGLDLL 391 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: 408 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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