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 WP_012401946.1 BPHY_RS13050 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000020045.1:WP_012401946.1 Length = 246 Score = 90.5 bits (223), Expect = 5e-23 Identities = 66/213 (30%), Positives = 106/213 (49%), Gaps = 9/213 (4%) Query: 188 TGMIAVGIALVIAIVASI--IIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGF 245 T +++ ++ IV S+ ++ +K+ AA G + ++ I LIV + V+ Sbjct: 33 TVTVSLSAWVIALIVGSLFGVLRTVPNKKLAAIGTVYVAIFRNIPLIVQFFIWYLVI--- 89 Query: 246 PLTFDVPVAGKFN-LTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAG 304 P V + F L G+ F S + L +TA+ + E VR GI +P+GQ A Sbjct: 90 PELLPVSIGTWFKQLPPGAQF---FSSSIICLGLFTAARVCEQVRSGINALPRGQRGAGL 146 Query: 305 ALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSG 364 ALG R V++P A RII+PPLTS++LN+ KNS++A IG DL A +++ + Sbjct: 147 ALGFTQWQTYRYVLLPVAYRIIVPPLTSEFLNIFKNSAVASTIGLLDLSAQARQLVDYTA 206 Query: 365 QAIEIVCIWGIVYLSLSILTSLFMNWFNAKMAL 397 Q E + YL ++++ M AK L Sbjct: 207 QTYESFIAVTVAYLLINLIVMTLMRIVEAKSRL 239 Score = 57.8 bits (138), Expect = 3e-13 Identities = 31/83 (37%), Positives = 48/83 (57%) Query: 78 SLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVE 137 S ++ +TY LL G+ T+ V+++ A I+G L G+ R N +A + TVYV Sbjct: 12 SPVSTGEPTTYLGWLLSGLWVTVTVSLSAWVIALIVGSLFGVLRTVPNKKLAAIGTVYVA 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: 288 Number of extensions: 16 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 Apr 09 2024. 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