Align Acetylornithine deacetylase (EC:3.5.1.16) (characterized)
to candidate 5211139 Shew_3555 hypothetical protein (RefSeq)
Query= reanno::MR1:202842 (275 letters) >FitnessBrowser__PV4:5211139 Length = 274 Score = 372 bits (956), Expect = e-108 Identities = 175/269 (65%), Positives = 216/269 (80%) Query: 1 MVSRSPFESFQWKSDIFNCESTDIDNFYLQLEQEMSRLGMVEKKLGEVGKYSVSLYQSPA 60 M SR PF+SF W SDIF+C+S DI +FY +LE++ SRLG+ +KLG+ G + + LYQSPA Sbjct: 1 MSSRDPFQSFTWHSDIFSCQSNDISSFYARLEEQASRLGLQARKLGDAGPHPLELYQSPA 60 Query: 61 AKSGLPSLLICAGFHGEESAGPWGLLHFLSEASVELFERVNLSILPLVNPTGFKRGHRFN 120 K+ PS+LI AGFHGEE+AGPWGLL+FL+E ELF ++NLS+LPLVNPTGFKRGHRFN Sbjct: 61 QKADQPSILISAGFHGEEAAGPWGLLYFLNELEPELFGQINLSLLPLVNPTGFKRGHRFN 120 Query: 121 KFGENPNRGFEFENGKPKANEGTSVEGKLLLEHAQLLIAASRDGILTCHEDVLSHDAYVY 180 K G+NPNRGF ENG+ ++N+ TS EG++LL H+QLL AAS+DGILTCHEDVL D Y+Y Sbjct: 121 KLGQNPNRGFVLENGRGRSNQDTSSEGEILLAHSQLLAAASKDGILTCHEDVLLTDTYIY 180 Query: 181 SFEPSQVPGRFSLDLRDTLAGYFPIAVDGEIDGCPVKDGLIFNHFDTSFEACLVRSGARV 240 SFE +Q PG+FS +LRD L YFPIA DG ID CPV+DG+IFNHFD SFEA LVR GA V Sbjct: 181 SFEANQHPGQFSRELRDALGHYFPIAQDGLIDDCPVQDGIIFNHFDLSFEAFLVRLGASV 240 Query: 241 GACTETPALQNFDQRVLANSAAMTHFLAL 269 G C+ETP Q+FDQR+LAN+A + F+ L Sbjct: 241 GVCSETPGQQSFDQRILANAAIIKRFVEL 269 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: 296 Number of extensions: 14 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: 274 Length adjustment: 25 Effective length of query: 250 Effective length of database: 249 Effective search space: 62250 Effective search space used: 62250 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