Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate BPHYT_RS16695 BPHYT_RS16695 glutamate/aspartate ABC transporter permease GltJ
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__BFirm:BPHYT_RS16695 Length = 246 Score = 91.7 bits (226), Expect = 2e-23 Identities = 49/129 (37%), Positives = 72/129 (55%) Query: 269 FMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIP 328 F S + L +TA+ + E VR GI +PKGQ A A+G R V++P A RII+P Sbjct: 111 FSSSIICLGLFTAARVCEQVRSGINALPKGQRAAGLAMGFTQWQTYRYVLLPVAYRIIVP 170 Query: 329 PLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSLFM 388 PLTS++LN+ KNS++A IG DL A +++ + Q E I Y+ ++++ M Sbjct: 171 PLTSEFLNIFKNSAVASTIGLLDLSAQARQLVDYTSQTYESFIAVTIAYMLINLVVMQLM 230 Query: 389 NWFNAKMAL 397 W AK L Sbjct: 231 RWVEAKTRL 239 Score = 53.5 bits (127), Expect = 6e-12 Identities = 29/83 (34%), Positives = 46/83 (55%) Query: 78 SLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVE 137 S ++ +TY LL G T+ V+++ A I+G L G+ R N + + T+YV Sbjct: 12 SPVSTGEPTTYLGWLLSGFWVTITVSLSAWVIALIVGSLFGVLRTVPNKWASGIGTLYVA 71 Query: 138 VFRNIPPLLVIFFWYLGVLSVLP 160 +FRNIP ++ F WYL + +LP Sbjct: 72 IFRNIPLIVQFFIWYLVIPELLP 94 Lambda K H 0.327 0.141 0.432 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: 292 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 246 Length adjustment: 27 Effective length of query: 373 Effective length of database: 219 Effective search space: 81687 Effective search space used: 81687 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 (21.7 bits) S2: 48 (23.1 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