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_086509148.1 BZY95_RS06445 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_002151265.1:WP_086509148.1 Length = 396 Score = 411 bits (1057), Expect = e-119 Identities = 212/378 (56%), Positives = 272/378 (71%), Gaps = 1/378 (0%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 D R++ +Q+L I + F+ ++ NT NLA +GFGFL AGF IGQSLI +S Sbjct: 19 DRAKRALLFQVLLIAAVAAFLLYIIGNTQDNLAARGITTGFGFLDRTAGFGIGQSLIEYS 78 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 S STY R +VG+LNTLLV+ G+ ATIIGF++GI RLS NWLIA+L + Y+E+FRNIP Sbjct: 79 SQSTYGRTFVVGLLNTLLVSALGVIAATIIGFIVGIARLSPNWLIARLASGYIEIFRNIP 138 Query: 144 PLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203 LL IFFWY VL +P R+S L ++LN RGL P+P+F++G + + V+AIVA Sbjct: 139 LLLQIFFWYFAVLRAMPAARDSYSLGEVIFLNVRGLYLPEPLFESGFGLIPLTFVVAIVA 198 Query: 204 SIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGS 263 SI + W +R ATG+ W ++ALI+GLP+LV V +G P+T+DVP FN GG Sbjct: 199 SIALVIWNKRRHEATGKRLPAGWISLALILGLPMLVLVATGVPVTWDVPELRGFNFRGGI 258 Query: 264 VVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQAL 323 + PEF++L+LALS YTASFIAEIVR GI+ +P GQ+EAA AL L V RLVVVPQAL Sbjct: 259 TIIPEFLALWLALSIYTASFIAEIVRSGIQAIPHGQTEAAQALSLPQKLVLRLVVVPQAL 318 Query: 324 RIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSI 382 R+IIPPLTSQYLNL KNSSLA AIG+ DLV+V GT LNQ+GQAIE++ + VYL +S+ Sbjct: 319 RVIIPPLTSQYLNLIKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVISMTMAVYLIISL 378 Query: 383 LTSLFMNWFNAKMALVER 400 L S+FMNWFNA++ALVER Sbjct: 379 LVSMFMNWFNARVALVER 396 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: 571 Number of extensions: 27 Number of successful extensions: 2 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: 396 Length adjustment: 31 Effective length of query: 369 Effective length of database: 365 Effective search space: 134685 Effective search space used: 134685 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