Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate GFF3088 HP15_3031 extracellular solute-binding protein, family 3
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__Marino:GFF3088 Length = 250 Score = 173 bits (439), Expect = 3e-48 Identities = 89/249 (35%), Positives = 146/249 (58%), Gaps = 5/249 (2%) Query: 5 KKFLLAAAVSLVFSANAMAADK--LKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKM 62 KK + AA+ +L A A + L++ + Y PF KD +G++ GF+ ++ +A+C +M Sbjct: 2 KKMIFAASCALALIAGGAQAQERDLRIAFDVPYEPFEYKDENGELTGFEVELAEAMCEEM 61 Query: 63 KVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAE 122 CE V WDG+IP L A+KFD ++SS+SIT ER + V F++PYY+ + P+S Sbjct: 62 NANCEFVIQAWDGMIPGLLARKFDLIMSSMSITPERAERVLFSEPYYNTPGGWFGPESFN 121 Query: 123 FK-TDKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILAD 181 TD +++GK +G QR T T++ + +G +T K Y T ++ LDL R+D + D Sbjct: 122 TDVTDMSAMEGKTVGVQRGTTMDTYVTENMGGIVTIKRYTTADDMVLDLEGQRLDVVFVD 181 Query: 182 KYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKI 241 V + T+ G ++ G+ V + +G+A+R+ D +L ++NAAL+ + DGTY I Sbjct: 182 YPVGEQTVLTKEG--FKEVGEAVKLGEGVGVAMRQRDTDLAEEVNAALRTLKEDGTYDTI 239 Query: 242 NDKYFPFNI 250 KYF ++I Sbjct: 240 MQKYFAYDI 248 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: 153 Number of extensions: 9 Number of successful extensions: 3 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: 250 Length adjustment: 24 Effective length of query: 227 Effective length of database: 226 Effective search space: 51302 Effective search space used: 51302 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: 46 (22.3 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