Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate GFF3090 HP15_3033 amino acid ABC transporter, inner membrane subunit
Query= reanno::pseudo5_N2C3_1:AO356_05500 (242 letters) >lcl|FitnessBrowser__Marino:GFF3090 HP15_3033 amino acid ABC transporter, inner membrane subunit Length = 240 Score = 106 bits (264), Expect = 5e-28 Identities = 72/228 (31%), Positives = 111/228 (48%), Gaps = 6/228 (2%) Query: 3 EQLLQNLGLSAFSLQGFGPLLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSRVKLLRIP 62 E L QN +A ++ + G T+ L LSL++ +L+ + A + R + P Sbjct: 7 EWLNQNEIFTAMTIMEY----WDGMVTTVHLVFLSLVIGLLVAVPLAILRTVRNPFVSGP 62 Query: 63 AQLYTTLIRGVPDLVLMLLIFYSLQTWLTSFTDFMEWEYIEIDPFGAGVITLGFIYGAYF 122 LYT L RG P L+ + +I+Y L + + WE +PF ++ AY Sbjct: 63 VWLYTYLFRGTPLLIQLYIIYYGLAQ-IEGIQETFWWEIFR-EPFYPALLAFTLNTAAYT 120 Query: 123 TETFRGAILAVPRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALV 182 TE RGAI++ P G++EAA AYG+ R R +V P R A+ N + ML A+A+ Sbjct: 121 TEIIRGAIISTPNGEIEAAKAYGMNWFMRMRRIVLPSAARRAVQAYSNEVIFMLHASAIA 180 Query: 183 SIIGLADLVKAAQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLE 230 S++ + DL AA++ Y F + AL Y+ +T F R LE Sbjct: 181 SVVTIVDLTGAARNIYSRFYAPFDAFIFVALCYMALTFILVFAFRKLE 228 Lambda K H 0.329 0.142 0.423 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: 145 Number of extensions: 8 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: 242 Length of database: 240 Length adjustment: 23 Effective length of query: 219 Effective length of database: 217 Effective search space: 47523 Effective search space used: 47523 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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