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_086508787.1 BZY95_RS04510 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_002151265.1:WP_086508787.1 Length = 398 Score = 236 bits (603), Expect = 7e-67 Identities = 148/433 (34%), Positives = 220/433 (50%), Gaps = 49/433 (11%) Query: 6 DTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTSN 65 +T+ + AG + + H PI+ T+S+V+ ++ ++ FG E G VYSRF NPT + Sbjct: 14 ETLAIRAGHQRTHEQEHGE---PIFPTSSFVYGSAAEAARKFGGEERGNVYSRFTNPTVH 70 Query: 66 VLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKRF 125 E R+AALEGG +A SSG AA + L GD IV++ L+G T + F F + Sbjct: 71 TFERRLAALEGGERCVATSSGMAAILSTVLALLQAGDEIVASRSLFGSTVSLFDKYFGKL 130 Query: 126 GIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDNT 185 GI R+VE + +E T+ ++ ET NP V D + IAH+H + +DN Sbjct: 131 GITTRYVELSDLAAWEAAITPHTRLLFAETPSNPLSEVVDIAALAEIAHRHQALLAIDNC 190 Query: 186 FGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPAE 245 F QP+ GAD+V HSATK++ G G +GG +V K Sbjct: 191 FLTPA-LQQPLALGADLVIHSATKYLDGQGRAVGGAVVGRDK------------------ 231 Query: 246 GYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENALK 305 E +G ++R GP ++PF +++ +G+ETLSLR H NA Sbjct: 232 -----ELEEVFG-----------VVRTCGPCLSPFNAWIFTKGLETLSLRMRAHCGNAQA 275 Query: 306 LAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKLS 365 LA+WL+ P V+ V Y GL H HE A + + G+G VL F VK A Sbjct: 276 LAEWLQVHPAVARVHYSGLPDHPQHELAGRQQA-GYGAVLGFEVKGGREA---------- 324 Query: 366 GAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFID 425 V+D ++ S N+GD KT + P TTH +L+ +K A+G+++ LIRV+VG+E I+ Sbjct: 325 AWSVIDATRMLSITGNLGDVKTTITHPATTTHGRLSPAQKDAAGISEGLIRVAVGLESIE 384 Query: 426 DIIADFQQSFETV 438 DI D + + + Sbjct: 385 DIRLDLARGLDAL 397 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: 420 Number of extensions: 20 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: 398 Length adjustment: 32 Effective length of query: 412 Effective length of database: 366 Effective search space: 150792 Effective search space used: 150792 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