Align Aromatic amino acid permease, AroP (characterized)
to candidate BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= TCDB::Q46065 (463 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 325 bits (832), Expect = 3e-93 Identities = 181/465 (38%), Positives = 268/465 (57%), Gaps = 15/465 (3%) Query: 8 LGTGLRTRHLTMMGLGSAIGAGLFLGTGVGIRAAGPAVLLAYIIAGAIVVLVMQMLGEMA 67 L GL+ RH+TM+ LG IGAGLF+G+GV ++ AGPA +L+++I GA+VVLVM+MLGEMA Sbjct: 10 LKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVLVMRMLGEMA 69 Query: 68 AARPASGSFSRY------GEDAFGHWAGFSLGWLYWFMLIMVMGAEMTGAAAIMGAWF-G 120 A PA GSF Y G+ A G+ AGF GW+YW+ ++V+ E A ++ W Sbjct: 70 CAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGAKLVQFWLPD 129 Query: 121 VEPWIPSLVCVVFFAVVNLVAVRGFGEFEYWFAFIKVAVIIAFLIIGIALIFGWLPGSTF 180 V W SLV +V NLV+V +GEFE+WFA IKVA I+ FL +G + G P + Sbjct: 130 VPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYVLGLWPAAKH 189 Query: 181 VGT--SNFIGDHGFMPNGISGVAAGLLAVAFAFGGIEIVTIAAAESDKPREAISLAVRAV 238 V + G MP GI V +G +A + G EIVTIAAAE+ +P +A++ A +V Sbjct: 190 VTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYFGAEIVTIAAAEAQEPAKAVAKATNSV 249 Query: 239 IWRISVFYLGSVLVITFLMPYESINGADTAAESPFTQILAMANIPGTVGFMEAIIVLALL 298 I R+ VFY+GS+L++ L+P+ S A +P+ L IP M AI++ A+L Sbjct: 250 ITRVLVFYVGSILLVVALVPWNSPKMA-----TPYVSALDAMGIPAAASVMNAIVLTAVL 304 Query: 299 SAFNAQIYATSRLVFSMANRQDAPRVFSKLSTSHVPTNAVLLSMFFAFVSVGLQYWNPAG 358 SA N+ +YA SR++F++ DAP +K++ VP A+L+ F + SV + Y +P Sbjct: 305 SALNSGLYAASRMIFALTRHGDAPAALAKVNRRGVPVRAILIGTVFGYASVVMSYVSPDT 364 Query: 359 LLDFLLNAVGGCLIVVWAMITLSQLKLRKELQAN-DEISTVRMWAHPWLGILTLVLLAGL 417 + FL+N+ G I V+ +I +SQLKLR ++ + E VRMW +P+L + ++ + G+ Sbjct: 365 VFAFLVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMWCYPYLTWVAIIGMVGI 424 Query: 418 VALMLGDAASRSQVYSVAIVYGFLVLLSFVTVNSPLRGGRTPSDL 462 + M R ++ G L+L + V P G P L Sbjct: 425 LVAMAFIPEQRQPLWFGVASLGVLLLAYLLRVRKPDAGFGEPDTL 469 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: 589 Number of extensions: 33 Number of successful extensions: 7 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: 476 Length adjustment: 33 Effective length of query: 430 Effective length of database: 443 Effective search space: 190490 Effective search space used: 190490 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 17 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