Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_004308709.1 C665_RS10670 PLP-dependent aspartate aminotransferase family protein
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000310185.1:WP_004308709.1 Length = 382 Score = 201 bits (512), Expect = 2e-56 Identities = 131/348 (37%), Positives = 193/348 (55%), Gaps = 21/348 (6%) Query: 60 GEVPGN-VYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVS 118 G +PG +Y+R +P E + LEG +A ASGM+A A++++L G ++ Sbjct: 43 GSLPGGRIYARDASPAYDPAEALLCELEGGARAALFASGMAAASAVLLAL-KPGARIVAP 101 Query: 119 RSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIA 178 ++ S + + + I +D+ +D A A + L +VE+P+NP E++DIA Sbjct: 102 HDMYWSLRNWMIGFAANWQIALDF--YADAAELAALLQRPADLVWVETPANPTWEILDIA 159 Query: 179 ALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQ 238 AE+AHA GA L VD+ TP +PL LGADVV+HSATKY++G + GV+ R E Sbjct: 160 RAAELAHAAGARLVVDSTVPTPVFTRPLALGADVVMHSATKYLNGHSDVVAGVLVTRAED 219 Query: 239 MKEVVGFLRTA----GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIER 294 + ++TA G L PF AWL +GL TL R++ +ASAL +A+ E P + Sbjct: 220 --DFWARIKTARAAGGAVLGPFEAWLLNRGLRTLFPRVRTAAASALRIAQHFEHHPALLA 277 Query: 295 VYYAGLPSHPQHELARRQ-QSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTT 353 V Y GLPSH H++A RQ + GFGA++S V+GG DAA R A ++ T+LG ++ Sbjct: 278 VLYPGLPSHRGHDIACRQMEGGFGAMLSLRVRGGEDAARRVAGAVKIFRRATSLGSVESL 337 Query: 354 IAHPA-TTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 I H G P D L+R++VG+ED DDL AD+ + L Sbjct: 338 IEHRGPIEGPGTRCPLD---------LLRLSVGIEDSDDLIADLEQAL 376 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: 375 Number of extensions: 18 Number of successful extensions: 5 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: 382 Length adjustment: 31 Effective length of query: 372 Effective length of database: 351 Effective search space: 130572 Effective search space used: 130572 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