Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate BPHYT_RS13585 BPHYT_RS13585 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09905 (231 letters) >FitnessBrowser__BFirm:BPHYT_RS13585 Length = 218 Score = 129 bits (325), Expect = 3e-35 Identities = 76/216 (35%), Positives = 121/216 (56%), Gaps = 15/216 (6%) Query: 8 FGPALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPELLW 67 F P L GA++T+++ + L VLGLL AL + S + + T+ ++RG+P ++ Sbjct: 9 FLPILLKGAVVTIEITFCSFVLSTVLGLLLALMRVSDNRVVSNAAATFINVIRGLPIIVQ 68 Query: 68 VLLIYFGTVNLMRALGEYLGMPDLA--LNAFAAGVIALGLCFGAYATEVFRGAILAIPKG 125 + IYF +PDL L+AF AG I LG+ + Y E FR I AI G Sbjct: 69 LFYIYFV-------------LPDLGVQLSAFQAGFIGLGIAYSVYQAENFRAGIQAIDHG 115 Query: 126 HREAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAQI 185 EA ++G+ I R+++PQ +RIALP GN ++++KD++L S I + E+ R Q+ Sbjct: 116 QIEAAQSIGMRGAMIMRRVVLPQAFRIALPPYGNTLVMMLKDSSLASTITVAEMTRAGQL 175 Query: 186 GVTVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERR 221 + + Q T + + AL+YLGL++ + G+ LERR Sbjct: 176 IASSTFQNMTVFTLVALLYLGLSLPLVYGLRRLERR 211 Lambda K H 0.329 0.143 0.435 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: 152 Number of extensions: 12 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: 231 Length of database: 218 Length adjustment: 22 Effective length of query: 209 Effective length of database: 196 Effective search space: 40964 Effective search space used: 40964 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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