Align L-tyrosine transporter (characterized)
to candidate PfGW456L13_4790 D-serine/D-alanine/glycine transporter
Query= reanno::pseudo5_N2C3_1:AO356_18530 (471 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4790 Length = 473 Score = 405 bits (1040), Expect = e-117 Identities = 200/456 (43%), Positives = 287/456 (62%), Gaps = 12/456 (2%) Query: 3 GQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMI 62 G+ + G LKR L RHI+L+ALG IG GLFLGSA ++ AGP+++L Y I G +I Sbjct: 10 GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVI 69 Query: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWA 122 MR LGEM V PVAGSFS +A Y G AGFL+GWN W L+++ ++E+TAV Y+ W Sbjct: 70 MRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWF 129 Query: 123 PDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG-- 180 PD+P W+ A A I + +INL VK FGE EFWFA+IK+V I+ M+ G ++ G G Sbjct: 130 PDVPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGND 189 Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 G ++NLW+HGGF PNGV G++M++ ++MF++ G+EM+G TA EA P+ IP AI Sbjct: 190 GVALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGS 249 Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300 V +RIL+FY+GAL V+LS+ PW+ + GSPFV F LG TAA I+NFV Sbjct: 250 VFWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFV 300 Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360 V+TAALS N G + RML +A+ G AP ++ GVP R++L S L+ VLLN Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLN 360 Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALW-YPYGNYICL 419 YLVP+ + ++ + W MI + KFR+ ++ ++ L +W YP +Y+ L Sbjct: 361 YLVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSASEAAGLKYRMWLYPVSSYLAL 420 Query: 420 AFVVFILGVMLLIPGIQISVYAIPVWVVFMWVCYVI 455 AF+V ++G+M P ++++Y P ++V + V + + Sbjct: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYV 456 Lambda K H 0.327 0.139 0.432 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: 670 Number of extensions: 32 Number of successful extensions: 4 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: 471 Length of database: 473 Length adjustment: 33 Effective length of query: 438 Effective length of database: 440 Effective search space: 192720 Effective search space used: 192720 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