Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_028583513.1 G494_RS0104095 cystathionine beta-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000429965.1:WP_028583513.1 Length = 388 Score = 189 bits (480), Expect = 1e-52 Identities = 127/367 (34%), Positives = 187/367 (50%), Gaps = 11/367 (2%) Query: 40 LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMS 99 L+T S+ + + + GE PG VY P R FE I++LEG+ A SG+S Sbjct: 29 LYTGSTVLLDSYQELLLAERGEYPGIVYGTDRMPPQRAFEAAISSLEGSALTRAFQSGIS 88 Query: 100 AILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNT 159 AI +++ SSGDH+LV +V+G T + ++ ++V++ P A + NT Sbjct: 89 AINQTLLAFTSSGDHILVCDNVYGPTARFCRQVLAKYQVEVEFIPPDAGAEIRDYLRDNT 148 Query: 160 KLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATK 219 +L F+ESP + E+ DI A+ IA KG + +DN + TP P LG D+ IHSATK Sbjct: 149 RLIFLESPGSNTFEIQDIPAITAIARHKGVITILDNTWATPLYCDPFALGVDISIHSATK 208 Query: 220 YIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASA 279 YI G + G V+ + F + SP + L L+GL+TL +R+ HS SA Sbjct: 209 YIGGHSDILLGTVSVSEPYGEAFATFYQLMETFASPQDCALALRGLKTLPLRLSRHSQSA 268 Query: 280 LALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSF--DVKGGRDAAWRFIDA 337 L + +WL R P +ERV + L SHPQH L +R SG + +F + G FI++ Sbjct: 269 LEVGQWLCRHPLVERVLHPALDSHPQHHLWQRDFSGASGLFAFLCTEEYGEGLTADFINS 328 Query: 338 TRMVSITTNLGDTKTTI-AHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADM 396 + I + G K+ I A SH SP G +L R+ +GLED +DL AD+ Sbjct: 329 LDLFGIGYSWGGFKSLITAGRCQRSHS--SPYQ------GRTLFRLNIGLEDPEDLIADL 380 Query: 397 ARGLAAL 403 + L Sbjct: 381 KKAFRIL 387 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: 296 Number of extensions: 11 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: 388 Length adjustment: 31 Effective length of query: 372 Effective length of database: 357 Effective search space: 132804 Effective search space used: 132804 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