Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate AO356_27120 AO356_27120 ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2958 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27120 Length = 260 Score = 385 bits (988), Expect = e-112 Identities = 195/258 (75%), Positives = 221/258 (85%), Gaps = 2/258 (0%) Query: 3 KALLTLSALALCMAAGVATAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAICAE 62 K L + LALC +A +AKEY LRFGVD +YAPFESKAADGSL GFDIDLGNAICA+ Sbjct: 5 KKLYLVMGLALCTSA--VSAKEYSTLRFGVDANYAPFESKAADGSLKGFDIDLGNAICAK 62 Query: 63 LKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKKGS 122 L VKC WVESDFDG+IPGL+A KFDG++SSMTVT REKAIDFS+ELFSG T+YVFKKGS Sbjct: 63 LSVKCIWVESDFDGLIPGLRAGKFDGILSSMTVTATREKAIDFSNELFSGFTSYVFKKGS 122 Query: 123 GLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAAIQ 182 GL+ DVASLKGKTVGY QG+IQEAYAKAVLDKAGVK Q+YQNQDQVY DL +GRLDA++Q Sbjct: 123 GLNTDVASLKGKTVGYFQGSIQEAYAKAVLDKAGVKIQSYQNQDQVYYDLVAGRLDASLQ 182 Query: 183 DMLQAELGFLKSPKGEGYEVSKPVDSELLPSKTAIGIRKGNSELKALLNKGIKALHDDGK 242 D LQA+LGF+ SP+G YE+S V+S LPSKTAIGI KGN+ELKALL+K I+ALHDDG Sbjct: 183 DTLQAQLGFITSPQGAEYEMSPSVESPYLPSKTAIGIAKGNTELKALLDKAIQALHDDGT 242 Query: 243 YAEIQKKHFGDLNLYSGK 260 Y IQK+HFGDLNLYSGK Sbjct: 243 YDSIQKQHFGDLNLYSGK 260 Lambda K H 0.313 0.132 0.368 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: 295 Number of extensions: 6 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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