Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_058932055.1 AU252_RS18980 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_001484605.1:WP_058932055.1 Length = 459 Score = 363 bits (931), Expect = e-105 Identities = 198/435 (45%), Positives = 267/435 (61%), Gaps = 8/435 (1%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 LG ++ R LTMMGLGSAIGAGLFLG+G GI+AAGPAVL++Y++AG +++LVM LGEMA Sbjct: 14 LGHTMKPRQLTMMGLGSAIGAGLFLGSGAGIQAAGPAVLISYLVAGTLIILVMWALGEMA 73 Query: 68 AARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIM-GAWFGVEPWIP 126 AA P SG+FS Y E A G AG ++GWL+W L++V+ AE GAA ++ W + W Sbjct: 74 AANPTSGAFSVYAERALGKTAGATVGWLWWLQLVVVIAAEALGAAGLLFSVWPAIPVWAL 133 Query: 127 SLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNF 186 +L +V F +NL V+ FGEFE+WFA +KVA I+AFL +G AL+ G LP G +N Sbjct: 134 ALTFMVVFTAINLTGVKNFGEFEFWFAILKVAAIVAFLAVGAALLLGLLPDVASPGLANI 193 Query: 187 IGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFY 246 D F P G+ GVA L V FAFGG EIV +AAAE++ P ++ A+R V+WRI VFY Sbjct: 194 TTD--FAPAGLGGVATALFVVIFAFGGTEIVAVAAAETEDPEHSVGKAIRTVLWRILVFY 251 Query: 247 LGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIY 306 +GSV VI ++P S SPF +L A IPG + + V+ALLSA NA +Y Sbjct: 252 IGSVFVIAAVLPVSS-----EGLASPFAGVLDAARIPGAGTAITLVAVVALLSALNANLY 306 Query: 307 ATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNA 366 SR+V+S+A R +APR ++LS + VP AV +S+ F F + L+ P +L L Sbjct: 307 GASRMVYSLAERGEAPRFLARLSGASVPMLAVGVSVAFGFFATVLELLFPDRILPALFQL 366 Query: 367 VGGCLIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAA 426 VG +VVW +SQL LR+ +RM P L I LVLL + A+ + Sbjct: 367 VGSTCLVVWGTALVSQLILRRRADREGAELPLRMKGFPGLTICGLVLLGLIFAIGFSAES 426 Query: 427 SRSQVYSVAIVYGFL 441 SR Q+ S ++ L Sbjct: 427 SRGQLLSTFVLVACL 441 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: 607 Number of extensions: 37 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: 459 Length adjustment: 33 Effective length of query: 430 Effective length of database: 426 Effective search space: 183180 Effective search space used: 183180 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