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) >FitnessBrowser__Marino:GFF3090 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:
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