Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_038211315.1 Q392_RS19580 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000745855.1:WP_038211315.1 Length = 429 Score = 242 bits (617), Expect = 2e-68 Identities = 147/424 (34%), Positives = 228/424 (53%), Gaps = 15/424 (3%) Query: 5 KTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNP 64 + + F T +H+ ++ PI+ +V + ++ A+ A++F K PG Y R NP Sbjct: 3 ENWKFETRSVHAGYSPEPTTKAVVPPIYQTVAYAFDSAQHGADLFDLKVPGNIYTRIMNP 62 Query: 65 TVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TV 123 T LE ++ +E G + + A+G AI +Q + GD++VSS L+G T +L+ T+ Sbjct: 63 TQDVLEQRVAALEGGIAALALASGQMAITYAIQTITEAGDNIVSSTALYGGTYNLFAHTL 122 Query: 124 GAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVV 183 G V D D + I T+ VFVE++ NP + D+ I + + G+ +V Sbjct: 123 PQFGIHVRFADHRDPASFGKLIDERTKAVFVESLGNPAGNITDIAAIAAIAHQHGVPLIV 182 Query: 184 DNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRY---------P 234 DNT+ SPYL RP GA +VV+SLTK +GGHG ++GGA+ D+G+F W ++ P Sbjct: 183 DNTVPSPYLLRPIEHGADIVVHSLTKYLGGHGTSVGGAIVDSGKFPWAQHKERFRRLNEP 242 Query: 235 HIAEN---YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNA 291 ++ + Y + P + + R LR+ GG++ P A I G ET+ALR +R C N Sbjct: 243 DVSYHGVVYTEALGPAAYIGRARVVPLRNTGGAISPFNAFLILQGIETLALRMDRICDNT 302 Query: 292 LALAQMLQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDG-IDCFDYLNRL 349 L +A+ L+A V V Y GLE HP HAL+K S L++F + G + +L+ L Sbjct: 303 LRVARHLKAHPAVRWVNYAGLEDHPDHALAKKYMGGRASGLLTFGIGGGRAEGAKFLDAL 362 Query: 350 RLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQ 409 +L N+GD R+L A T ++ E A G++E +R+ VG+E DDL+AD Q Sbjct: 363 QLFTRLVNIGDVRSLATHPASTTHRQLSPEELAKAGVSEETVRLCVGIEHIDDLLADLDQ 422 Query: 410 ALDA 413 AL A Sbjct: 423 ALAA 426 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: 480 Number of extensions: 28 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: 429 Length adjustment: 32 Effective length of query: 381 Effective length of database: 397 Effective search space: 151257 Effective search space used: 151257 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