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_RS16440 HSERO_RS16440 hypothetical protein
Query= SwissProt::P06106 (444 letters) >FitnessBrowser__HerbieS:HSERO_RS16440 Length = 413 Score = 237 bits (605), Expect = 5e-67 Identities = 144/435 (33%), Positives = 232/435 (53%), Gaps = 34/435 (7%) Query: 5 FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64 F T LH+ ++ + H S PI+ + ++ +E+++ +++F + PGY Y R NPT Sbjct: 9 FTTTILHSDRQKGIE--HGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66 Query: 65 NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124 LE++I +E G + + ++G AA +QGL GD++VS+++L+G T N ++ Sbjct: 67 AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGA 125 Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184 G + V+ + + E T+ V++ETI NP+ V D ++I + + GI VVDN Sbjct: 126 QGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDN 185 Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYP---EKFPQFS 241 T Y +P GA +V +S TK IGGHG +GG + D+G+F W YP E + + Sbjct: 186 TM-TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNP 244 Query: 242 QPAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGE 301 P G + +R + LRD G + P A+ + G ET++LR ER + Sbjct: 245 APQWG---------------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECK 289 Query: 302 NALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDP 361 NAL LA+ L+ V+ V YPGL SH H K L FG ++SF +KD Sbjct: 290 NALALAQMLQADERVAAVYYPGLESHPQHA-LSKALFRSFGSLMSFELKD---------- 338 Query: 362 FKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGI 421 + ++ L+LA +N+GD +TLVI T ++ + + + G+ + LIRVSVG+ Sbjct: 339 -GIDCFDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGL 397 Query: 422 EFIDDIIADFQQSFE 436 E DD++ADF+Q+ + Sbjct: 398 EDTDDLVADFRQALD 412 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: 446 Number of extensions: 28 Number of successful extensions: 5 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: 413 Length adjustment: 32 Effective length of query: 412 Effective length of database: 381 Effective search space: 156972 Effective search space used: 156972 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