Align L-alanine and D-alanine permease (characterized)
to candidate Pf6N2E2_5633 Aromatic amino acid transport protein AroP
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Length = 472 Score = 409 bits (1050), Expect = e-118 Identities = 203/455 (44%), Positives = 288/455 (63%), Gaps = 12/455 (2%) Query: 10 GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVI 69 G+ + G LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y I G +I Sbjct: 3 GQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMI 62 Query: 70 MRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWF 129 MR LGEM V PVAGSFS +A Y G AGFL+GWN W L+++ ++E+TAV Y+ W Sbjct: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWA 122 Query: 130 PDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGND 189 PD+P W+ A A + + INL VK FGE EFWFA+IK+V I+ M+ G ++ G G Sbjct: 123 PDIPTWVSAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG-- 180 Query: 190 GVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGS 249 G ++NLW+HGGF PNGVSG++M++ ++MF++ G+EM+G TA EA P+ IP AI Sbjct: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 250 VFWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFV 300 V +RIL+FY+GAL V+LS+ PW+ + GSPFV F LG TAA I+NFV Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 Query: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLN 360 V+TAALS N G + RML +A+ G AP +K GVP R++L S A L+ VLLN Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKVLSKIDKRGVPVRSILASAAVTLVAVLLN 360 Query: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420 YL+P+ + S+ + W MI + KFR+ ++ + + L +W YP +Y+ L Sbjct: 361 YLIPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTHQTPLFKALW-YPYGNYICL 419 Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFY 455 AF+V ++G+M P +V++Y P ++V + V ++ Sbjct: 420 AFVVFILGVMLLIPGIQVSVYAIPVWVVFMAVCYW 454 Lambda K H 0.328 0.142 0.444 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: 642 Number of extensions: 29 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: 473 Length of database: 472 Length adjustment: 33 Effective length of query: 440 Effective length of database: 439 Effective search space: 193160 Effective search space used: 193160 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