Align Acetylornithine deacetylase (EC:3.5.1.16) (characterized)
to candidate 202842 SO3749 hypothetical protein (NCBI ptt file)
Query= reanno::MR1:202842 (275 letters) >FitnessBrowser__MR1:202842 Length = 275 Score = 563 bits (1450), Expect = e-165 Identities = 275/275 (100%), Positives = 275/275 (100%) Query: 1 MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA 60 MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA Sbjct: 1 MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA 60 Query: 61 AKSGLPSLLICAGFHGEESAGPWGLLHFLSEASVELFERVNLSILPLVNPTGFKRGHRFN 120 AKSGLPSLLICAGFHGEESAGPWGLLHFLSEASVELFERVNLSILPLVNPTGFKRGHRFN Sbjct: 61 AKSGLPSLLICAGFHGEESAGPWGLLHFLSEASVELFERVNLSILPLVNPTGFKRGHRFN 120 Query: 121 KFGENPNRGFEFENGKPKANEGTSVEGKLLLEHAQLLIAASRDGILTCHEDVLSHDAYVY 180 KFGENPNRGFEFENGKPKANEGTSVEGKLLLEHAQLLIAASRDGILTCHEDVLSHDAYVY Sbjct: 121 KFGENPNRGFEFENGKPKANEGTSVEGKLLLEHAQLLIAASRDGILTCHEDVLSHDAYVY 180 Query: 181 SFEPSQVPGRFSLDLRDTLAGYFPIAVDGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV 240 SFEPSQVPGRFSLDLRDTLAGYFPIAVDGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV Sbjct: 181 SFEPSQVPGRFSLDLRDTLAGYFPIAVDGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV 240 Query: 241 GACTETPALQNFDQRVLANSAAMTHFLALCAPLCD 275 GACTETPALQNFDQRVLANSAAMTHFLALCAPLCD Sbjct: 241 GACTETPALQNFDQRVLANSAAMTHFLALCAPLCD 275 Lambda K H 0.320 0.137 0.418 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: 435 Number of extensions: 9 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: 275 Length of database: 275 Length adjustment: 25 Effective length of query: 250 Effective length of database: 250 Effective search space: 62500 Effective search space used: 62500 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: 47 (22.7 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