Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate 8500830 DvMF_1571 extracellular solute-binding protein family 3 (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__Miya:8500830 Length = 249 Score = 134 bits (336), Expect = 2e-36 Identities = 92/248 (37%), Positives = 136/248 (54%), Gaps = 10/248 (4%) Query: 4 YKKFLLAAAVSLVFSANAMA-ADKLKM-GIEAAYPPFNNKDASGQVVGFDKDIGDALCAK 61 ++ L AA++LV + +A A+K + GI+A YPPF D SG+ GFD + D + K Sbjct: 2 FRMTTLVAALALVLALGGVAFAEKTYINGIDANYPPFAYVDKSGKPAGFDVESMDWIAKK 61 Query: 62 MKVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSA 121 M + DWDGIIP L AKK D + S +SITEER+Q V+F++PY++ K FIA K + Sbjct: 62 MGFKVTHQPMDWDGIIPNLLAKKIDMVCSGMSITEERRQKVNFSNPYWNVKQVFIAKKGS 121 Query: 122 EFKTDKDSLKGKV-IGAQRATLAGTWLE---DELGSDITTKLYDTQENAYLDLTSGRVDA 177 TD+ LKGKV +G QR T L+ + G + YD+ A D+ +GR+DA Sbjct: 122 TLNTDQ-ILKGKVKLGVQRGTSEAEALQKDKEAKGYGYDLRFYDSAPLAIEDVLNGRIDA 180 Query: 178 ILADKYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGT 237 D D G+A + G +S+ G+A RK D EL +N K ++AD Sbjct: 181 ATMDNLPADD--AAAKGKAIQVVG-VYGDSEDFGVATRKEDAELLKMINDGYKLLMADPY 237 Query: 238 YKKINDKY 245 ++++ K+ Sbjct: 238 WEQLKQKH 245 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: 174 Number of extensions: 11 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: 249 Length adjustment: 24 Effective length of query: 227 Effective length of database: 225 Effective search space: 51075 Effective search space used: 51075 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