Align L-alanine and D-alanine permease (characterized)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter
Query= reanno::pseudo5_N2C3_1:AO356_17670 (473 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 394 bits (1013), Expect = e-114 Identities = 197/451 (43%), Positives = 283/451 (62%), Gaps = 12/451 (2%) Query: 13 AQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRA 72 + G LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y I G +IMR Sbjct: 6 SSSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQ 65 Query: 73 LGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDV 132 LGEM V PVAGSFS +A Y G AGFL+GWN W L+++ ++E+TAV Y+ W+P++ Sbjct: 66 LGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEI 125 Query: 133 PRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVA 192 P W+ A A V + INL VK FGE EFWFA+IK+V I+ M+ G ++ G G G Sbjct: 126 PTWVSAAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTG--GPQ 183 Query: 193 LGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFW 252 ++NLW HGGF P+GV G++M++ ++MF++ G+EM+G TA EA P+ IP AI V + Sbjct: 184 ASVTNLWEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIY 243 Query: 253 RILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVVIT 303 RIL+FY+GAL V+LS+ PW+ + GSPFV F LG TAA I+NFVV+T Sbjct: 244 RILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLT 303 Query: 304 AALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLV 363 AALS N G + RML +A+ G AP AK GVP R++L S A L+ VL+NYL+ Sbjct: 304 AALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLI 363 Query: 364 PEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFL 423 P+ + S+ + W MI + KFR+ ++ + + L +W YP +Y+ LAF+ Sbjct: 364 PQHALELLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPLFKALW-YPYGNYVCLAFV 422 Query: 424 VLVVGLMAYFPDTRVALYVGPAFLVLLTVLF 454 V ++ +M P +V+++ P +++ + V + Sbjct: 423 VFILVIMLMIPGIQVSVFAIPVWVMFMAVCY 453 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: 629 Number of extensions: 30 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: 473 Length adjustment: 33 Effective length of query: 440 Effective length of database: 440 Effective search space: 193600 Effective search space used: 193600 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