Align O-acetylhomoserine sulfhydrylase protein; EC 2.3.1.31 (characterized, see rationale)
to candidate GFF659 HP15_641 homocysteine synthase
Query= uniprot:D8J1Y3_HERSS (413 letters) >FitnessBrowser__Marino:GFF659 Length = 425 Score = 236 bits (603), Expect = 7e-67 Identities = 145/417 (34%), Positives = 229/417 (54%), Gaps = 15/417 (3%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH+ + + PI+ + ++ ++D + A++F K G Y R NPT A LE Sbjct: 5 TLALHAGFKSDPTTRAATTPIYQTTSYTFDDTQHGADLFDLKVQGNIYTRIMNPTNAVLE 64 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 +++ ++E G + A+GMAAI +Q + + G+++VS++ L+G T +L+ ++ QG + Sbjct: 65 ERMAELEGGVGALAVASGMAAITYALQTICKVGNNIVSTSQLYGGTYNLFAHSLPNQGIE 124 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 MV D VE AI NTR +F E+I NP V D++R E+ + GI +VDNT+ + Sbjct: 125 CKMVRHDDFDAVEKAIDENTRALFCESIGNPAGNVVDIQRWAEIAHKHGIPLMVDNTVAT 184 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW----TRYPHIAEN------ 239 P+L RP GA +V++SLTK IGGHG + G + D+G+FDW ++P + E Sbjct: 185 PFLCRPIEHGADIVIHSLTKYIGGHGTTVAGVVVDSGKFDWKASADKFPMLNEPDPSYHG 244 Query: 240 --YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297 Y P + + R LR+ G +L P A I G ET+ALR ER C+NA +A Sbjct: 245 VVYTDALGPAAFIGRCRVVPLRNTGAALAPFNAFLIMQGLETLALRMERHCENAEKVANF 304 Query: 298 LQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGIDC-FDYLNRLRLAIPT 355 LQ V V Y L + P A + + S ++SF +K G + +++ L L + Sbjct: 305 LQEHPSVEWVNYATLANSPYKATCEKISGGKASGILSFGIKGGREAGAKFIDALELILRL 364 Query: 356 SNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 N+GD ++L A T ++ E S G++E L+R+S+G+E DD++AD QALD Sbjct: 365 VNIGDAKSLACHPATTTHRQLNPEELKSAGVSEDLVRLSIGIEHVDDIIADITQALD 421 Lambda K H 0.319 0.134 0.391 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: 449 Number of extensions: 26 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: 413 Length of database: 425 Length adjustment: 32 Effective length of query: 381 Effective length of database: 393 Effective search space: 149733 Effective search space used: 149733 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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