Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate 206398 DVU0966 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2958 (260 letters) >MicrobesOnline__882:206398 Length = 272 Score = 112 bits (280), Expect = 8e-30 Identities = 87/259 (33%), Positives = 127/259 (49%), Gaps = 19/259 (7%) Query: 4 ALLTLSAL--ALCMAAGVATAKEYK--------ELRFGVDPSYAPFESKAADGSLVGFDI 53 A + ++AL A MAA + AK+ ELR G D Y PFE +G+ VGFDI Sbjct: 8 AAMMMAALLAAPAMAADIELAKKSTLNEIMARGELRVGFDAGYLPFEMTDKNGNYVGFDI 67 Query: 54 DLGNAICAELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSE-LFSG 112 D+ + + VK V +DFDGMIP L ++KFD +IS MTVT R I+F+ + G Sbjct: 68 DIAKEMARAMGVKFVPVNTDFDGMIPALLSDKFDIIISGMTVTQERNLKINFADPYIVVG 127 Query: 113 PTAYVFKKGSGLSEDVASLKGK--TVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYA 170 T + KK G + L TV GT E AK +L KA K +++ + Sbjct: 128 QTVLLSKKLEGKVKSWKDLNSPEYTVVSRLGTTGEEAAKRMLPKA--KFKSFDKEADGAL 185 Query: 171 DLTSGRLDAAIQDMLQAELGFLKSPKGEGYEVSKPVDSELLPSKTAIGIRKGNSELKALL 230 ++ +GR DA + DM + + K + + KP E L GI+KG+ + L Sbjct: 186 EVVNGRADAWVYDMPFNVVFMAEQGKDKVVHLDKPFTYEPL----GFGIKKGDPDFLNFL 241 Query: 231 NKGIKALHDDGKYAEIQKK 249 N ++ + +DG+Y I K Sbjct: 242 NNFMRQIKNDGRYDRIYDK 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: 183 Number of extensions: 13 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: 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