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 AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__azobra:AZOBR_RS08660 Length = 399 Score = 381 bits (978), Expect = e-110 Identities = 191/380 (50%), Positives = 260/380 (68%) Query: 21 AMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLI 80 ++ DP R++FYQ+L + I++ W++ HNT NL++ + A+GFGFL A F IG+SLI Sbjct: 20 SLSDPTVRAVFYQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLI 79 Query: 81 TFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFR 140 + +Y RA LVG+LNTL V++ G+ AT++G LIG+ RLS NWLIAKL + YVE+ R Sbjct: 80 DYHPRDSYGRAFLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVR 139 Query: 141 NIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIA 200 NIPPLL +FFWY V +P R+++ ++L+ RGL P P D +G AL IA Sbjct: 140 NIPPLLQLFFWYALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIA 199 Query: 201 IVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLT 260 ++ I + RWA RQ TGQPF +++L++GLPL+ ++ G P DVP FN Sbjct: 200 VIGVIFLRRWAKARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPKLQGFNFV 259 Query: 261 GGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVP 320 GG V+ PEF ++ + L YTA+FIAE+VR GI V GQ+EAA ALG+ RLVV+P Sbjct: 260 GGVVLTPEFFAILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLP 319 Query: 321 QALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSL 380 QALR+I+PPLTSQYLNLTKNSSLA+AIG+ DLV++ T LNQ+GQAIE V + YL + Sbjct: 320 QALRVIVPPLTSQYLNLTKNSSLALAIGYPDLVSIANTTLNQTGQAIEGVAMIMGTYLVI 379 Query: 381 SILTSLFMNWFNAKMALVER 400 S+ S+FMNW+N ++ALVER Sbjct: 380 SLGISIFMNWYNKRIALVER 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: 581 Number of extensions: 20 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 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