Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate HSERO_RS16440 HSERO_RS16440 hypothetical protein
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__HerbieS:HSERO_RS16440 Length = 413 Score = 823 bits (2126), Expect = 0.0 Identities = 413/413 (100%), Positives = 413/413 (100%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR Sbjct: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW 120 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW Sbjct: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW 120 Query: 121 MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGIL 180 MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGIL Sbjct: 121 MTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGIL 180 Query: 181 YVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENY 240 YVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENY Sbjct: 181 YVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENY 240 Query: 241 KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQA 300 KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQA Sbjct: 241 KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQA 300 Query: 301 DERVAAVYYPGLESHPQHALSKALFRSFGSLMSFELKDGIDCFDYLNRLRLAIPTSNLGD 360 DERVAAVYYPGLESHPQHALSKALFRSFGSLMSFELKDGIDCFDYLNRLRLAIPTSNLGD Sbjct: 301 DERVAAVYYPGLESHPQHALSKALFRSFGSLMSFELKDGIDCFDYLNRLRLAIPTSNLGD 360 Query: 361 TRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 TRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA Sbjct: 361 TRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 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: 759 Number of extensions: 15 Number of successful extensions: 1 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: 413 Length adjustment: 31 Effective length of query: 382 Effective length of database: 382 Effective search space: 145924 Effective search space used: 145924 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 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