Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate WP_014147972.1 MEALZ_RS07275 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000968535.2:WP_014147972.1 Length = 396 Score = 257 bits (657), Expect = 4e-73 Identities = 153/425 (36%), Positives = 229/425 (53%), Gaps = 48/425 (11%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T + AG G+ H ++PI+ T+SYVF++++ S F ++PG +YSRF NPT N Sbjct: 12 ETQAIRAGHRRTGEAEH---SIPIFMTSSYVFDSAEEASLKFTGQIPGNIYSRFTNPTVN 68 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 +ER+A +E G LA +SG AA GL +GD++V + ++G T F+ F +F Sbjct: 69 AFQERLAWMENGERCLAFASGMAAIMAVGMGLLKSGDHVVVSRGVFGNTVLMFQNYFAKF 128 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 G+E+ FV + +E T+ ++LET NP + D + + +AH+H ++VDN Sbjct: 129 GVESDFVALTDLAAWEAAIKPNTRFLFLETPSNPLTEIADIQALADLAHRHDCLLIVDNC 188 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F +P+ GADI+ HSATK+I GHG +GG +V S + K Sbjct: 189 FCTPA-LQKPLDLGADIIVHSATKYIDGHGRCVGGAVVASDEIIEK-------------- 233 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 IY LR G M+PF ++ L G+ETL+LR E+H NAL Sbjct: 234 ----AIY---------------PYLRTGGATMSPFNAWAFLSGLETLALRMEKHCANALD 274 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 LA+WLE+ P V V YPGL SH HE AK+ GFGG++SF +K K Sbjct: 275 LARWLERQPGVERVHYPGLVSHPQHELAKRQ-QTGFGGIVSFELKG----------GKEP 323 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 ++D+ ++ S AN+GD K+ + P TTH +L + + A+G+ L+R+SVG+E I+ Sbjct: 324 AWNLIDSTRMISITANLGDVKSTITHPATTTHGRLTPEARDAAGIKDGLVRISVGLENIE 383 Query: 426 DIIAD 430 DI D Sbjct: 384 DIKKD 388 Lambda K H 0.317 0.136 0.402 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: 454 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 396 Length adjustment: 32 Effective length of query: 412 Effective length of database: 364 Effective search space: 149968 Effective search space used: 149968 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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