Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_043745532.1 AMB_RS21365 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000009985.1:WP_043745532.1 Length = 403 Score = 370 bits (950), Expect = e-107 Identities = 187/386 (48%), Positives = 264/386 (68%), Gaps = 6/386 (1%) Query: 21 TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEE 80 T AVR G RT E EA+F S YV+ +A +A A F G + VYSR+ NPTV FE+ Sbjct: 16 TRAVRGGLSRTNFCETSEAVFMNSGYVYDSAEEAEASFDGTLDRMVYSRFKNPTVAVFEQ 75 Query: 81 RIAALEGAEQAVA-----TASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKR 135 R+A +EGA +A TASGM+A+ A ++ +GD V+ S ++FGS + ++ R Sbjct: 76 RLAEMEGAPPGMAVAARATASGMAAVHAALLCQLRAGDRVVASTALFGSCHWIINELLPR 135 Query: 136 FGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDN 195 +G++ + +DL +WEAA T F+E+PSNP E++D+AA+ E+AH GA + VDN Sbjct: 136 YGVERVFVDGTDLKSWEAALSRPTACVFLETPSNPTLEIIDLAAVCELAHKAGAKVVVDN 195 Query: 196 CFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVG-FLRTAGPTLS 254 F TP LQ PL+LGAD+V++SATK++DGQGR +GG V G E +++G FLR GP LS Sbjct: 196 VFATPILQSPLELGADIVVYSATKHMDGQGRCLGGAVLGSPEFCADILGPFLRNTGPALS 255 Query: 255 PFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQS 314 PFNAW+ LKGLETL +RM+ H A+AL +A +LE +P + RV Y GL SHPQH+LA+RQ Sbjct: 256 PFNAWVLLKGLETLDLRMERHCANALKVARFLEARPEVARVLYPGLESHPQHDLAKRQMR 315 Query: 315 GFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAG 374 G+G++V+ ++KGG+ AA++ ++ ++ I+ NLGD K+ I HP TT+H RLSPED+ G Sbjct: 316 GWGSIVALELKGGKPAAYKLLNGVELIDISNNLGDAKSLITHPWTTTHQRLSPEDKLSMG 375 Query: 375 IGDSLIRVAVGLEDLDDLKADMARGL 400 I + L+R++VGLED DDL D+ R L Sbjct: 376 ITEGLLRLSVGLEDGDDLVEDLGRAL 401 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: 427 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: 403 Length adjustment: 31 Effective length of query: 372 Effective length of database: 372 Effective search space: 138384 Effective search space used: 138384 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