Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_052664421.1 NITAL_RS02035 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000969705.1:WP_052664421.1 Length = 424 Score = 226 bits (576), Expect = 1e-63 Identities = 138/404 (34%), Positives = 221/404 (54%), Gaps = 25/404 (6%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ +V + ++DA+ A++F PG Y R NPT LE ++ +E G + + ++G Sbjct: 24 PIYQTVAYEFDDAQHGADLFNLAVPGNIYTRIMNPTQDVLEQRLAALEGGVAALATSSGQ 83 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWMTV-GAQGAKVSMVDATDVKNVEAAITAN 148 AAI +Q + R GD++V+ L+G T +L+ + AQG V + + + A I Sbjct: 84 AAITYAIQTITRAGDNIVTVPLLYGGTYTLFKHMFPAQGVDVRFAEDDSAEALGALIDER 143 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ V++ETI NP + DL+ I ++ + G+ +VD+T+ +P L +P GA +V++SLT Sbjct: 144 TKAVYLETIGNPAGNIPDLEAIAKVAHDAGVPVIVDSTVATPILMKPIEWGADIVIHSLT 203 Query: 209 KSIGGHGNALGGALTDTGEFDWT----RYPHIAENYKKNPAPQWG-------------MA 251 K IGGHGN++GG + D+G+F W+ R+P + P P + + Sbjct: 204 KFIGGHGNSIGGIIVDSGKFPWSEHADRFPQL-----NTPEPAYHGVVYTEALGEAAFIG 258 Query: 252 QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPG 311 + R LR+ G ++ P A G +T+ALR ER +NA +A+ L A +V V Y G Sbjct: 259 RARTVPLRNTGSAISPFNAWQFIQGLQTLALRIERHVENAQKVAEHLAAHPKVTHVEYAG 318 Query: 312 LESHPQHA-LSKALFRSFGSLMSFELKDGID-CFDYLNRLRLAIPTSNLGDTRTLVIPVA 369 L S P HA +K SLM+F ++ G D + + L+L N+GDT++LV A Sbjct: 319 LPSSPYHANANKYTGGKPSSLMTFHVEGGYDAAVKFHDALQLFTRLVNIGDTKSLVNHPA 378 Query: 370 HTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 T ++ E A+ G+ IR++VG+E DD++AD QALDA Sbjct: 379 STTHRQLSEEELATAGVKPDAIRLNVGIEHIDDILADLDQALDA 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: 421 Number of extensions: 18 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: 424 Length adjustment: 32 Effective length of query: 381 Effective length of database: 392 Effective search space: 149352 Effective search space used: 149352 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