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_104484934.1 UN63_RS01070 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_002936955.1:WP_104484934.1 Length = 394 Score = 402 bits (1032), Expect = e-116 Identities = 202/378 (53%), Positives = 269/378 (71%), Gaps = 1/378 (0%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 DP R++ +QI+ + I+ GF+W++ +NT NL +GFGFL AGF I QSLI +S Sbjct: 17 DPAKRALLFQIILLAIVAGFIWFIVNNTLTNLETRGITTGFGFLDDPAGFAIAQSLIPYS 76 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 TY R +VG+LNTLLV+ GI ATI+GF++G+ RLS NWLIA+L + YVE+FRNIP Sbjct: 77 EVDTYGRTFVVGLLNTLLVSFLGIIGATILGFILGVARLSPNWLIARLASAYVELFRNIP 136 Query: 144 PLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203 LL +FFWY VL LP PR+S + S++LN RGL P+P+ G + +AL++AI Sbjct: 137 LLLQMFFWYFAVLRTLPSPRDSFNIGDSVFLNVRGLYLPEPLPSAGFHWIWVALLLAIAL 196 Query: 204 SIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGS 263 + + R+ H+RQ ATGQ W ++ LI+ LPLL FV+ G PL + P FN G Sbjct: 197 ATWLIRFNHRRQEATGQRLPVGWISLGLILVLPLLTFVMLGAPLDWQYPELRGFNFRDGM 256 Query: 264 VVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQAL 323 + PEF++L+L+L+ YTA+FIAEIVR GI+ V GQ+EAA ALG+ S RLV++PQA+ Sbjct: 257 TIIPEFLALWLSLTIYTAAFIAEIVRSGIQAVSHGQTEAAHALGIKDSLTLRLVIIPQAM 316 Query: 324 RIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLSLSI 382 R+IIPPLTSQYLNLTKNSSLA AIG+ DLV+V GT LNQ+GQAIE++ I +VYL++S+ Sbjct: 317 RVIIPPLTSQYLNLTKNSSLATAIGYPDLVSVFAGTTLNQTGQAIEVIAITMLVYLTISL 376 Query: 383 LTSLFMNWFNAKMALVER 400 S FMNWFN++MALVER Sbjct: 377 TVSFFMNWFNSRMALVER 394 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: 553 Number of extensions: 25 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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