Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_143690237.1 BW971_RS07675 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_900156495.1:WP_143690237.1 Length = 480 Score = 333 bits (855), Expect = 6e-96 Identities = 174/432 (40%), Positives = 259/432 (59%), Gaps = 7/432 (1%) Query: 1 MAKSNEGLGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVM 60 +A S+ LG GLR RH+ ++ LG IGAGLF+G+GV I AGPA +++++I G I +L+M Sbjct: 6 VAASDAELGKGLRRRHMNLIALGGVIGAGLFVGSGVVIADAGPAAVVSFLIGGLITMLIM 65 Query: 61 QMLGEMAAARPASGSFSRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFG 120 +ML EMA A+P GSF Y A G GF GWLYW+ ++V+ E I+ W Sbjct: 66 RMLAEMAVAQPVVGSFYVYARRALGRRGGFVTGWLYWYFFVVVVAVEAVAGGRIVQLWLP 125 Query: 121 VEP-WIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGST 179 P W+ SLV ++ NLV+ R FGEFEYWF+ IKV I+ FL +GI I G P ST Sbjct: 126 EVPLWVLSLVLMLTLTATNLVSARSFGEFEYWFSSIKVVAIVVFLFVGILWITGLWPDST 185 Query: 180 FVGTSNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVI 239 G SN + GF P+G V A ++ + G EIVTIAAAESD+P +A+S A+R++I Sbjct: 186 -PGLSNLVDHGGFTPSGWGAVLAAVVPCVAFYTGAEIVTIAAAESDEPEQAVSRAMRSII 244 Query: 240 WRISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLS 299 RI +FY+GS+LV+ + P+ + + SP+ +L++ IP M I++ A+LS Sbjct: 245 LRIILFYVGSILVVVTVQPWNT----KSVGVSPYASVLSVLGIPAVSTIMNLIVLTAVLS 300 Query: 300 AFNAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGL 359 N+ +Y TSR+VF++ D PR F++LS + VP A+LL +VSV Y + Sbjct: 301 CLNSALYTTSRMVFALTTHGDGPRFFTRLSANGVPRRAILLGTVVGYVSVAATYIWGDVV 360 Query: 360 LDFLLNAVGGCLIVVWAMITLSQLKLRKELQANDEIS-TVRMWAHPWLGILTLVLLAGLV 418 DFL+N+ G + V+ +I +SQ+ LR+ ++ D + ++MW PWL T+ ++ ++ Sbjct: 361 FDFLVNSYGAVALFVYLIIAVSQVVLRRRVERQDPTALRLKMWLFPWLSYATIAVMVAVI 420 Query: 419 ALMLGDAASRSQ 430 M ++RSQ Sbjct: 421 LAMAFLPSTRSQ 432 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: 533 Number of extensions: 31 Number of successful extensions: 6 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: 480 Length adjustment: 33 Effective length of query: 430 Effective length of database: 447 Effective search space: 192210 Effective search space used: 192210 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