Align Aromatic amino acid permease, AroP (characterized)
to candidate WP_017597638.1 D471_RS0105135 amino acid permease
Query= TCDB::Q46065 (463 letters) >NCBI__GCF_000341125.1:WP_017597638.1 Length = 452 Score = 317 bits (811), Expect = 7e-91 Identities = 166/444 (37%), Positives = 266/444 (59%), Gaps = 9/444 (2%) Query: 17 LTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMAAARPASGSF 76 + ++ +G ++GAGLF+G+G I AGPA + +Y +AGA+V L ++ LGEM + PA G+F Sbjct: 1 MALIAIGGSVGAGLFIGSGAVIHTAGPAAVFSYALAGALVFLTLRALGEMVVSVPAGGAF 60 Query: 77 SRYGEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWFGVEPWIPSLVCVVFFAV 136 S Y AFG AGF++GW+YW++ +++ AE A+I+G W + W+ +L+ ++ V Sbjct: 61 SDYARLAFGPRAGFTIGWIYWWLYAVLVAAESVAGASILGQWVNLPQWLLALLVLLSMTV 120 Query: 137 VNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTFVGTSNFIGDHGFMPNG 196 NL++VR F E E +F+ +KV I+AFL+IG G GS +N GF PNG Sbjct: 121 ANLISVRVFAETESFFSLVKVGTIVAFLLIGGLWALGLWSGSGGSHVANLWEHGGFAPNG 180 Query: 197 ISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAVIWRISVFYLGSVLVITFL 256 V A + V FAFGG+EI+TIAA ESD+P ++ A+ V+WRI +FYL S++V+ + Sbjct: 181 WVAVLAATVVVLFAFGGVEIITIAAGESDEPERGVASAITNVLWRIGLFYLASIVVVVMV 240 Query: 257 MPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALLSAFNAQIYATSRLVFSMA 316 +P+ + + SPF ++ +PG ME ++++A+LS NA +Y TSR++F+++ Sbjct: 241 VPWNTTD----LERSPFVVVMETVGVPGAAVIMEVVVLVAVLSVLNAAMYTTSRMLFALS 296 Query: 317 NRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAGLLDFLLNAVGGCLIVVWA 376 + DAPR S+ + VP A++L +V+V +Y P + FL+ ++G L+V++ Sbjct: 297 RQGDAPRALSRTTKRGVPARAIVLGTVVGYVAVVAEYLLPGKVFGFLVASIGAILLVLFV 356 Query: 377 MITLSQLKL-RKELQANDEISTVRMWAHPWLGILTLVLLAGLVALMLGDAASRSQVYSVA 435 I SQL + R+ + E T+RMW P+ LT V+LAGL+A+ + AA Q ++ Sbjct: 357 TICASQLVVGRRVRRRAPERLTLRMWGFPY---LTWVVLAGLIAIAVAMAAIPDQRQALF 413 Query: 436 IVYGFLVLLSFVTVNSPLRGGRTP 459 G V+++ V R G TP Sbjct: 414 ASLG-SVVVAVVAFEVRKRWGSTP 436 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: 554 Number of extensions: 26 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: 463 Length of database: 452 Length adjustment: 33 Effective length of query: 430 Effective length of database: 419 Effective search space: 180170 Effective search space used: 180170 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