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_011814583.1 HHAL_RS09065 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P06106 (444 letters) >NCBI__GCF_000015585.1:WP_011814583.1 Length = 397 Score = 230 bits (586), Expect = 7e-65 Identities = 140/429 (32%), Positives = 221/429 (51%), Gaps = 48/429 (11%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F++ + AGQ + ++ PIY T+S+ FE++ + F E PG VYSRF NPT Sbjct: 14 FESRAVRAGQVRTDA---QEQSEPIYPTSSFTFESAAQAAARFSGEDPGNVYSRFTNPTV 70 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +R+AALEGG A + +SG +A GL GD++V++ L+G T + R Sbjct: 71 RTFCDRLAALEGGQACVGTASGMSAVLATCLGLLQAGDHVVASRTLFGTTLSLLTKYLPR 130 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 +GIE +V + + T+ ++ ET NP V D ++ +AH H + +DN Sbjct: 131 WGIEVSWVPLSDERAWADAVQPNTRLLFAETPSNPLNEVVDIRRLAEVAHAHEALLAIDN 190 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 F +P++ GAD+V HSATK++ G G +GG +V + + Sbjct: 191 CFCTPA-LQRPLEMGADLVIHSATKYLDGQGRCVGGAVVGDAQ--------------RVG 235 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 E HG +R GP M+PF +++ L+G+ETLSLR H NA Sbjct: 236 EEIHG-------------------FIRTAGPCMSPFNAWVFLKGLETLSLRMHAHSRNAQ 276 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 ++A+WL+ P V V Y GL H HH A S GFGG+++F +LP + Sbjct: 277 QVAEWLQGHPGVERVHYAGLPDHPHHRLAAAQQS-GFGGIVAF---ELPGG-------RE 325 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 + +++D+ ++ S N+GD K+ + P TTH ++D+ + A+G+ + L+RVSVG+E Sbjct: 326 AAWRLIDSTRMLSITGNLGDTKSTITHPATTTHGTISDELRAAAGIREGLVRVSVGLEDP 385 Query: 425 DDIIADFQQ 433 DII D ++ Sbjct: 386 ADIIRDLER 394 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: 465 Number of extensions: 24 Number of successful extensions: 4 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: 444 Length of database: 397 Length adjustment: 32 Effective length of query: 412 Effective length of database: 365 Effective search space: 150380 Effective search space used: 150380 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