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 HSERO_RS18310 HSERO_RS18310 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__HerbieS:HSERO_RS18310 Length = 429 Score = 416 bits (1070), Expect = e-121 Identities = 205/433 (47%), Positives = 291/433 (67%), Gaps = 13/433 (3%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F+T+ +H G + D R+ AVPIY T ++ F++++HG+ LF L+V G +YSR NPT Sbjct: 9 FETISVHGGYDP--DPTTRAVAVPIYQTVAFAFDDTQHGADLFDLKVQGNIYSRIMNPTQ 66 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 +VLE+R+AALEGG ALA++SGQAA T AIQ +A GDNIVS S LYGGTYN F + + Sbjct: 67 DVLEKRLAALEGGIGALALASGQAAVTYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQ 126 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 +G++ RF + P FE + D+RTKA+Y+E+IGNP N+ D + IAH+HG+P++VDN Sbjct: 127 YGVQTRFADPRQPASFEPLIDDRTKAIYIESIGNPLGNITDIAAVADIAHRHGVPLIVDN 186 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244 T A Y +P ++GADIV HS TK++GGHGTT+GG IVDSGKFPW + ++F + ++P Sbjct: 187 TV-ATPYLLRPFEHGADIVVHSLTKYLGGHGTTLGGAIVDSGKFPWAKHKQRFKRLNEPD 245 Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304 YHG +Y EA G AYI R LR++G ++PF +F +LQG+ETL LR +R N L Sbjct: 246 VSYHGVVYTEALGEAAYIGRARVVPLRNMGAALSPFNAFQILQGIETLGLRLDRITANTL 305 Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPFKL 364 +A++L++ P V WV+Y GL H H A+ Y GVL+FGV + + Sbjct: 306 AVAQYLKRHPKVRWVNYAGLEDHPDHALAQTYFKGRASGVLTFGVAN----------GRE 355 Query: 365 SGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIEFI 424 GA+ D L+L + L N+GDAK+L P TTH+QL+ E +GVT+D +R+S+GIE I Sbjct: 356 GGARFQDALQLFTRLVNIGDAKSLATHPASTTHRQLSPTELEKAGVTEDTVRLSIGIEHI 415 Query: 425 DDIIADFQQSFET 437 DD++AD +Q+ ++ Sbjct: 416 DDLLADLEQALQS 428 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: 570 Number of extensions: 32 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: 444 Length of database: 429 Length adjustment: 32 Effective length of query: 412 Effective length of database: 397 Effective search space: 163564 Effective search space used: 163564 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: 51 (24.3 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