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_013402767.1 CALHY_RS04220 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000166355.1:WP_013402767.1 Length = 220 Score = 85.1 bits (209), Expect = 2e-21 Identities = 65/213 (30%), Positives = 104/213 (48%), Gaps = 22/213 (10%) Query: 191 IAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLV---FVVSGFPL 247 IAV I LV +VA++ K + VW L G PLL+ F+ G P Sbjct: 26 IAVTIGLVFGLVAALFRIS---KIKVLNYIGSFYVW----LFRGTPLLLQIFFIYYGLPK 78 Query: 248 TFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALG 307 VP ++ P F++ +AL + ++ AEI+R I + KGQ EAA ALG Sbjct: 79 I--VP----------ALTLPAFLAGAIALIINSGAYTAEIIRAAILSIDKGQYEAAKALG 126 Query: 308 LHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAI 367 + R V+VPQ + +IPP+ ++++ L K+SSL IG +L+ + +G+ Sbjct: 127 MTYLQTMRYVIVPQTYKRLIPPIGNEFIALLKDSSLVSTIGMVELMRAAQLKASATGRDA 186 Query: 368 EIVCIWGIVYLSLSILTSLFMNWFNAKMALVER 400 EI ++YL+L+ + S NW ++ E+ Sbjct: 187 EIYIAALVIYLALTTVFSTIFNWLEKRLGKYEQ 219 Score = 37.0 bits (84), Expect = 5e-07 Identities = 20/73 (27%), Positives = 37/73 (50%) Query: 88 YARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLV 147 Y LL + T+ + + + G + + R+S+ ++ + + YV +FR P LL Sbjct: 9 YFPVLLKASVVTIELTAIAVTIGLVFGLVAALFRISKIKVLNYIGSFYVWLFRGTPLLLQ 68 Query: 148 IFFWYLGVLSVLP 160 IFF Y G+ ++P Sbjct: 69 IFFIYYGLPKIVP 81 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: 208 Number of extensions: 11 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: 220 Length adjustment: 26 Effective length of query: 374 Effective length of database: 194 Effective search space: 72556 Effective search space used: 72556 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 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