Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_058929813.1 AU252_RS05225 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_001484605.1:WP_058929813.1 Length = 470 Score = 385 bits (990), Expect = e-111 Identities = 204/455 (44%), Positives = 285/455 (62%), Gaps = 7/455 (1%) Query: 4 SNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQML 63 S LG L+ R LTMMGLGSAIGAGLF+G+G GI+AAGPAVL++Y++AG +++LVM L Sbjct: 8 SGRALGAALKPRQLTMMGLGSAIGAGLFIGSGAGIQAAGPAVLISYLVAGTLIILVMWAL 67 Query: 64 GEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEP 123 GEMAAA P SG+FS Y A+G AG ++GWL+W L++V+ AE GAA ++ F P Sbjct: 68 GEMAAANPDSGAFSVYTAKAYGPVAGATVGWLWWLQLVVVIAAEALGAAGLLSTIFPALP 127 Query: 124 -WIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVG 182 W+ + V +V VNL +V+ FGEFE+WFA +KVA I+ FL++G AL+FGWLPG G Sbjct: 128 VWLMAFVFIVVLTAVNLTSVKNFGEFEFWFALLKVAAIVGFLLVGAALLFGWLPGVQSPG 187 Query: 183 TSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRI 242 +NF GD GF P+G +G+A L VAFAFGG EIV++AAAE+ +P ++ AVR V+WRI Sbjct: 188 LANFTGD-GFAPDGFAGIATALFVVAFAFGGTEIVSVAAAETAEPARSVRTAVRTVLWRI 246 Query: 243 SVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFN 302 VFY+G++ VI ++P S +SPF +L A +PG + + V ALLSA N Sbjct: 247 LVFYIGAIFVIAAVVPVGS-----AGLKSPFAAVLEAAGMPGAATAITLVAVAALLSALN 301 Query: 303 AQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDF 362 A +Y SR+ +S+A+R +APR+ + +S + VP AVL S+ F V+V L+ P +L Sbjct: 302 ANLYGASRMAYSLADRGEAPRLLASVSKARVPVVAVLASVAFGVVTVVLELAFPEKVLPV 361 Query: 363 LLNAVGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALML 422 LLN VG ++VW L+QL LR +RM PWL L++LA + + Sbjct: 362 LLNIVGSTCLLVWTSALLAQLALRLRANREGTELPLRMPGFPWLTCFGLLILAAIFTVGF 421 Query: 423 GDAASRSQVYSVAIVYGFLVLLSFVTVNSPLRGGR 457 SR Q+ S + L + +++ S GR Sbjct: 422 IGEDSRPQLLSTFALVALLAVANWLHHRSGKVAGR 456 Lambda K H 0.327 0.140 0.428 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: 612 Number of extensions: 48 Number of successful extensions: 4 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: 463 Length of database: 470 Length adjustment: 33 Effective length of query: 430 Effective length of database: 437 Effective search space: 187910 Effective search space used: 187910 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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