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 PfGW456L13_3934 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3934 Length = 403 Score = 247 bits (631), Expect = 4e-70 Identities = 154/426 (36%), Positives = 223/426 (52%), Gaps = 49/426 (11%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 FDT+ + AGQ + H P++ T+SYVF + + F EVPG VYSR+ NPT Sbjct: 19 FDTLAVRAGQHRTPEGEHGD---PMFFTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTV 75 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 EERIAALE A+A ++G AA + L GD+++ + ++G T + F+ FKR Sbjct: 76 RAFEERIAALESAEQAVATATGMAAIMAVVMSLCSAGDHVLVSRSVFGSTISLFEKYFKR 135 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 FGIE +V + ++ TK +++E+ NP + D ++ IAH G +VVDN Sbjct: 136 FGIEVDYVPLADLSGWDAAIKANTKLLFVESPSNPLAELVDIAELAKIAHAKGAMLVVDN 195 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 F QP+K GADIV HSATK+I G G +GG++ G+ Sbjct: 196 CFCTPA-LQQPLKMGADIVVHSATKFIDGQGRCMGGVVAGRGE----------------- 237 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 E G LR GP ++PF +++ L+G+ETL+LR + H NA Sbjct: 238 ------QMKEVVG-----------FLRTAGPTLSPFNAWIFLKGLETLNLRMKAHCANAQ 280 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 +LA+WLEQ + V Y GL SH HE A + GFG V+SF VK K Sbjct: 281 QLAEWLEQQDGIEKVHYAGLKSHPQHELALRQ-QKGFGAVVSFEVKG----------GKE 329 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 + +D +L S AN+GD+KT + P T+H +L +E+ A+G+ LIRV+VG+E + Sbjct: 330 GAWRFIDATRLISITANLGDSKTTITHPSTTSHGRLAPQEREAAGIRDSLIRVAVGLEDV 389 Query: 425 DDIIAD 430 D+ AD Sbjct: 390 ADLQAD 395 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: 424 Number of extensions: 18 Number of successful extensions: 4 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: 403 Length adjustment: 32 Effective length of query: 412 Effective length of database: 371 Effective search space: 152852 Effective search space used: 152852 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 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