Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate BWI76_RS24210 BWI76_RS24210 cystathionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Koxy:BWI76_RS24210 Length = 381 Score = 254 bits (648), Expect = 4e-72 Identities = 146/383 (38%), Positives = 225/383 (58%), Gaps = 12/383 (3%) Query: 21 TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEE 80 TL+V +G G ++ TS++ A G+ G YSR NPT E Sbjct: 6 TLSVHSGTFTDEHGAVMPPIYATSTF--------AQPAPGQHTGYEYSRSGNPTRHALET 57 Query: 81 RIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRF-GIQ 139 IA LE + A ASG++AI + V+ L H++ V+G T L + +R G++ Sbjct: 58 AIADLESGTRGYAFASGLAAI-STVLELLDKDSHLVAVDDVYGGTYRLIENVRRRSAGLR 116 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 V + DLAA EAA +P+T++ +VE+P+NPL +L D++A+A IA + DN F + Sbjct: 117 VSWVKPDDLAAIEAAIRPDTRMIWVETPTNPLLKLADLSAIAAIARRHNIISVTDNTFAS 176 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGV-VAGRGEQMKEVVGFLRTA-GPTLSPFN 257 PA+ +PL+LG D+V+HSATKY++G + G+ V G + E +G+L+ A G L PF+ Sbjct: 177 PAIHRPLELGFDIVVHSATKYLNGHSDVVAGLAVVGDNAALAEKLGYLQNAVGGVLDPFS 236 Query: 258 AWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFG 317 ++L L+G+ TL +RM+ HS++AL LAEWLE+QP +E+V++ L SHP H+LARRQ + G Sbjct: 237 SFLTLRGIRTLALRMERHSSNALLLAEWLEQQPQVEKVWFPWLASHPHHQLARRQMALPG 296 Query: 318 AVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGD 377 ++S VKG A R I ++ ++ +LG ++ ++ P + +H + E R GI Sbjct: 297 GMISVVVKGDDSYAERIIRKLKLFTLAESLGGVESLVSQPFSMTHASIPLEQRLANGITP 356 Query: 378 SLIRVAVGLEDLDDLKADMARGL 400 LIR++VG+ED DL AD L Sbjct: 357 QLIRLSVGIEDPQDLIADWRHAL 379 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: 362 Number of extensions: 20 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: 381 Length adjustment: 31 Effective length of query: 372 Effective length of database: 350 Effective search space: 130200 Effective search space used: 130200 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