Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate BWI76_RS16730 BWI76_RS16730 cystathionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Koxy:BWI76_RS16730 Length = 395 Score = 245 bits (626), Expect = 1e-69 Identities = 147/385 (38%), Positives = 215/385 (55%), Gaps = 10/385 (2%) Query: 21 TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEE 80 TLAV AG + P A+FT TA+ E YSR +NPT + +E Sbjct: 10 TLAVHAGNQSDPVTH---AIFTP----IVTASSFIQPNLYEGGDFCYSRVSNPTRKAYES 62 Query: 81 RIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRF-GIQ 139 +A LEG A ATASGM+A +VM L H++ + V+G T LF+K G+ Sbjct: 63 ALAELEGGIYATATASGMAAT-NIVMELLPKDAHIIAMKGVYGGTWRLFEKLKTHTTGVT 121 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 + Y L+D + + NT L ++E+P+NPL ELVDIA + IA + VDN F + Sbjct: 122 ISYIDLNDEQSLINTIQENTALIWIETPTNPLLELVDIAKVCRIAKERAITTCVDNTFAS 181 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GPTLSPFNA 258 +PL++GAD+V+ S +KY+ G +GG V E + + F++T G SPF+A Sbjct: 182 AWNHKPLEMGADMVMLSTSKYVGGHSDLIGGAVITNNEALASRLDFIKTTLGSIASPFDA 241 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 +L L+G++TL +RM +AL +A++LE P I VYY GLPSHPQH+L R+Q GA Sbjct: 242 YLALRGMKTLDLRMARQCGNALRVAQYLENHPAIASVYYPGLPSHPQHQLCRQQMRSGGA 301 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 VV+ +KG + RFI + +LG ++ I H A+ SHG +S E+R G+ D+ Sbjct: 302 VVTATLKGDIQSLKRFIGGLHYFVLAESLGGVESMINHSASMSHGAMSKEEREAIGVYDT 361 Query: 379 LIRVAVGLEDLDDLKADMARGLAAL 403 +R +VG+E +DDL D+ AA+ Sbjct: 362 TLRFSVGIEHIDDLLQDLESAFAAM 386 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: 342 Number of extensions: 12 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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 09 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