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_084057088.1 B9A12_RS06590 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_900176285.1:WP_084057088.1 Length = 399 Score = 362 bits (929), Expect = e-104 Identities = 192/398 (48%), Positives = 254/398 (63%), Gaps = 2/398 (0%) Query: 5 AVDTTPLHGTGWSFRSAMY--DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTAS 62 A+DTT H + + DPK R+IF+QIL + + W++ NT NL R A+ Sbjct: 2 ALDTTQTHDGVLREKPEPFWLDPKKRAIFFQILVVGAVALLAWYLISNTVANLQRQKIAT 61 Query: 63 GFGFLRGRAGFEIGQSLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRL 122 GFGFL A FEIG+S+I + + +TYARAL+VG LNT+ V+ GI +G IGI RL Sbjct: 62 GFGFLGKEASFEIGESVIAYDASNTYARALVVGALNTIKVSFIGIVITVFLGTFIGIARL 121 Query: 123 SRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFP 182 S NWLI++L +Y+E +++P LL +FFWY LP PR+++ ++L NRGL P Sbjct: 122 SSNWLISRLAAIYIEGMQDVPVLLQLFFWYAIFYETLPSPRQALKPMHGVFLCNRGLVMP 181 Query: 183 KPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVV 242 P + V +A A + + RWA KRQ TG+ F ++AL++GLPL V+ Sbjct: 182 VPEWHPAYGYVFLAFAAACLMVWGLRRWARKRQDETGKTFPVFRVSLALVLGLPLGVWAA 241 Query: 243 SGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEA 302 G P VP FN GG+ PEFM+L L L YTA+F+AE VR GI+ V KGQ EA Sbjct: 242 LGAPFAMSVPELRGFNFRGGTTWSPEFMALLLGLILYTAAFVAEAVRAGIQSVSKGQREA 301 Query: 303 AGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQ 362 A ALGL P+ V RLV++PQALR+IIPPLTSQ LNLTKNSSLA+AIG+ D V+V T +NQ Sbjct: 302 AMALGLRPAQVLRLVILPQALRVIIPPLTSQMLNLTKNSSLAVAIGYPDFVSVANTTINQ 361 Query: 363 SGQAIEIVCIWGIVYLSLSILTSLFMNWFNAKMALVER 400 +GQ+IE V + +VYL S+ TS FMNW+N K+ LVER Sbjct: 362 TGQSIEGVALIMLVYLIFSLSTSAFMNWYNKKVKLVER 399 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: 498 Number of extensions: 16 Number of successful extensions: 1 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: 400 Length of database: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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