Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate 8500596 DvMF_1344 extracellular solute-binding protein family 3 (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_05495 (260 letters) >FitnessBrowser__Miya:8500596 Length = 272 Score = 117 bits (294), Expect = 2e-31 Identities = 87/256 (33%), Positives = 126/256 (49%), Gaps = 17/256 (6%) Query: 5 LLTLSALALCMAAGVATAKEYK--------ELRFGVDPSYAPFESKAADGSLVGFDIDLG 56 LL + A MAA + AK+ ELR G D Y PFE +G+ VGFDIDL Sbjct: 11 LLAVLVAAPAMAADIELAKKSTLNEIMARGELRVGFDAGYMPFEMTDKNGNYVGFDIDLA 70 Query: 57 NAICAELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKVIDFSSE-LFSGPTA 115 + + VK V +DFDGMIP L ++KFD +IS MTVT R I+F++ + G + Sbjct: 71 KELAKAMGVKFVPVNTDFDGMIPALLSDKFDIIISGMTVTQERNLRINFANPYIVVGQSV 130 Query: 116 YVFKKGSGLSEDVASLKGK--TIGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLT 173 V KK G + L T+ GT E AK +L KA K ++++ + ++ Sbjct: 131 IVSKKHEGKVKTWEDLNKPEYTVVSRLGTTGEEAAKRMLPKA--KYKSFEKEADGALEVI 188 Query: 174 SGRLDAAIQDMLQAELGFLKSPKGEGYEVSKPVDSELLPAKTAIGIKKGNSELKALLDKG 233 +G+ DA + DM + + KG+ + KP E L GIKKG+ + LD Sbjct: 189 NGKADAWVYDMPFNVVFMAEQGKGKAIHLDKPFTYEPL----GFGIKKGDPDFLNFLDNF 244 Query: 234 IKALHDDGKYAEIQKK 249 + + +DG+Y I K Sbjct: 245 LSQIKNDGRYDRIYNK 260 Lambda K H 0.314 0.133 0.370 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: 199 Number of extensions: 14 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: 260 Length of database: 272 Length adjustment: 25 Effective length of query: 235 Effective length of database: 247 Effective search space: 58045 Effective search space used: 58045 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