Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate SMa0079 SMa0079 ABC transporter permease
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Smeli:SMa0079 Length = 222 Score = 110 bits (274), Expect = 3e-29 Identities = 67/213 (31%), Positives = 112/213 (52%), Gaps = 13/213 (6%) Query: 23 DWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLF 82 D + G T+ ++ A +I L++ +T ++ + Y+E+ RN P LVQ+F Sbjct: 14 DQLLVGAWLTVRLSCAAMLIGLVVSVFCAWGKTAGPAILRHVIDGYIEIIRNTPFLVQIF 73 Query: 83 IWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPKGQE 142 +F +P L GL+ L+P ++AL+++V+ G + E +R GI+++ KGQ Sbjct: 74 FIFFGMPSL---GLR------LSPNSAALLALVVNFGAYGT----EIIRAGIESIHKGQV 120 Query: 143 AAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA 202 A A+G S PQI+ V++ A R + P LTS+F+ + N+SV S+I +L A Sbjct: 121 EAGWALGLSRPQIFRYVVMKPALRTVYPALTSQFIYLMLNTSVVSVISADDLAAAGNDLQ 180 Query: 203 EFSANLFEAFTLATLIYFTLNMGLMLLMRMVEK 235 + FE + TLIY L++G L +EK Sbjct: 181 SATFASFEVYIAVTLIYLALSVGFSALFYALEK 213 Lambda K H 0.325 0.139 0.425 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: 109 Number of extensions: 6 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: 248 Length of database: 222 Length adjustment: 23 Effective length of query: 225 Effective length of database: 199 Effective search space: 44775 Effective search space used: 44775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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