Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS21615 HSERO_RS21615 ABC transporter substrate-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__HerbieS:HSERO_RS21615 Length = 271 Score = 128 bits (322), Expect = 1e-34 Identities = 80/220 (36%), Positives = 125/220 (56%), Gaps = 3/220 (1%) Query: 29 MGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKVECEVVTSDWDGIIPALNAKKFDFL 88 +G+E+AY PF++++ VVGFD DI AL K+ +E + V + ++G L D L Sbjct: 51 VGVESAYAPFSSENEQKDVVGFDIDIMKALAKKIGIEVKFVPTPFEGFFNFLAQGDRDLL 110 Query: 89 ISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFKTDK-DSLKGKVIGAQRATLAGTWL 147 IS+++IT+ERK++V F++PY+ Q IA +A+ K K + LK +G Q AT + Sbjct: 111 ISAITITDERKKSVAFSEPYFV-ATQTIALPAADTKVSKMEDLKPLTVGTQSATSGDELV 169 Query: 148 EDELG-SDITTKLYDTQENAYLDLTSGRVDAILADKYVNYDWLKTEAGRAYEFKGDPVVE 206 + LG + K +D+ A +L SG VDA++AD+ V +++ DP Sbjct: 170 QQVLGKNSAKIKRFDSTPLALKELESGGVDAVVADEPVVKNYIANNPNSKLRTVTDPSFP 229 Query: 207 SDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKINDKYF 246 + GIAVRK D EL K+N L E+ ADG++ I+ +YF Sbjct: 230 KEDYGIAVRKDDPELLAKINKGLAEMKADGSFAAISAQYF 269 Lambda K H 0.316 0.133 0.381 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: 165 Number of extensions: 10 Number of successful extensions: 2 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: 251 Length of database: 271 Length adjustment: 25 Effective length of query: 226 Effective length of database: 246 Effective search space: 55596 Effective search space used: 55596 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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