Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012334051.1 M446_RS20655 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000019365.1:WP_012334051.1 Length = 432 Score = 217 bits (553), Expect = 5e-61 Identities = 138/418 (33%), Positives = 213/418 (50%), Gaps = 15/418 (3%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T +H+ + ++ PI+ + + ++ A A +F + PGYRY R NPT A LE Sbjct: 5 TIAIHAGYEDDPTTKAVAVPIYQTAAYAFDSAEHGAALFNLEMPGYRYSRIANPTNAVLE 64 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWMTV-GAQGAK 129 ++ ++E G + + ATG AA+ + L G ++VS L+G T++L+ V QG Sbjct: 65 RRVAELEGGVAALSVATGQAALHYAIATLADCGGNIVSVPQLYGTTHTLFAHVLPRQGIH 124 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 + + V I A+TR V+ E+I NP + D+ + E+ G+ VVDNT+ + Sbjct: 125 TRFAASDAPEAVARLIDADTRAVYCESIGNPAGNICDIAALAEVAHAHGVPLVVDNTVAT 184 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNPAPQWG 249 P L RP GA +V+ SLTK +GGHG LGG + D G F W +P + K A G Sbjct: 185 PILMRPLDHGADIVIASLTKFMGGHGTTLGGIIVDGGRFPWLAHPERFPMFCKPDASYHG 244 Query: 250 MA------------QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297 + + R+ R G L P +A + G ET+ALR ER +NA +A+ Sbjct: 245 LVYAERFGASAFAERARSVYQRTTGAVLAPFSAFLLLQGIETVALRVERHVENARKVAEF 304 Query: 298 LQADERVAAVYYPGLESHPQHALS-KALFRSFGSLMSFELKDG-IDCFDYLNRLRLAIPT 355 L+ D RVA V Y G P + ++ K L SL++F ++ G + + L L Sbjct: 305 LRDDPRVAWVNYAGFPDSPHYPMARKYLGGRASSLLTFGVQGGYAGGAAFYDALTLVKRL 364 Query: 356 SNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 N+GD ++L A T +M E + G+ IR+SVG+E +DD++AD QAL+A Sbjct: 365 VNIGDAKSLACHPASTTHRQMSPEEQRHAGVLPEAIRLSVGIEHSDDILADLDQALEA 422 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: 462 Number of extensions: 23 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: 432 Length adjustment: 32 Effective length of query: 381 Effective length of database: 400 Effective search space: 152400 Effective search space used: 152400 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 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