Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_083529221.1 AS188_RS03395 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_001482365.1:WP_083529221.1 Length = 496 Score = 374 bits (960), Expect = e-108 Identities = 198/434 (45%), Positives = 283/434 (65%), Gaps = 10/434 (2%) Query: 12 LRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMAAARP 71 L+ RHL MM LGSAIG GLF+GTG I AGPAVL+++++A ++VLVM+ +GEMAAA P Sbjct: 32 LKPRHLVMMALGSAIGTGLFVGTGSAIALAGPAVLISFLVACVVLVLVMRAMGEMAAADP 91 Query: 72 ASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEP-WIPSLVC 130 A G+FS Y E A G AG +LGWL+W L++V+ AE T AA I+ + V P W +L Sbjct: 92 ARGAFSVYAEKALGRTAGQTLGWLWWAQLVVVIAAEATAAAQILSELWPVLPQWSLALAF 151 Query: 131 VVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFIGDH 190 +V F +NLV+VR GE E+WFA +KV ++AFL++G AL+ G LP S G +N Sbjct: 152 MVVFTALNLVSVRALGESEFWFALLKVGAVVAFLLVGAALLLGLLP-SPSPGLANLTAHG 210 Query: 191 GFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYLGSV 250 GFMP G++GVAA LL V FAFGG E+VT+AAAE+ P+ ++ A+R ++ R+ VFY+GSV Sbjct: 211 GFMPTGVTGVAAALLVVVFAFGGTELVTVAAAETRDPQRNVARAIRTIVVRVLVFYVGSV 270 Query: 251 LVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYATSR 310 ++ ++P+ + ++ + SPF +L++A +PG M +I LALLSA NA +Y SR Sbjct: 271 ALMVLILPWNT----ESLSSSPFVAVLSVAGLPGAQAVMAVVIALALLSALNANLYGASR 326 Query: 311 LVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAVGGC 370 ++ S+++R APR F +LS S VP AV+ S+ F FV+V L Y P +L FLLN +G Sbjct: 327 MLHSLSDRGCAPRRFVRLSGSGVPVPAVVASVLFGFVAVVLNYLWPEAVLGFLLNTIGST 386 Query: 371 LIVVWAMITLSQLKLRKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAASRSQ 430 ++VVWA+ +SQ+ LR+ +RMW P+L L L L+ G++ L D R+Q Sbjct: 387 VLVVWALSLVSQIVLRRRADREGRELPLRMWGFPYLSWLALALVGGILVLGWFDPVVRTQ 446 Query: 431 VYSVAIVYGFLVLL 444 + ++ G LV L Sbjct: 447 L----VLTGGLVAL 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: 631 Number of extensions: 32 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: 496 Length adjustment: 34 Effective length of query: 429 Effective length of database: 462 Effective search space: 198198 Effective search space used: 198198 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 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