Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 283 bits (725), Expect = 6e-81 Identities = 160/458 (34%), Positives = 255/458 (55%), Gaps = 24/458 (5%) Query: 1 MENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFF 60 M++ QRGL+NRHIQLIA+ G IGTGLFLG +TIQ+ GPSV+ Y + G+ F Sbjct: 1 MQDQSTPERLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFL 60 Query: 61 FLRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFW 120 +R +GEM+ +P SF +F +Y G+ + W+YW+V V V ++ELTA+G Y+Q+W Sbjct: 61 IMRQLGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYW 120 Query: 121 LPQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHY 180 P P W + ++ +N + +GE EFWFA++KV AI+ MI L+ G+ H Sbjct: 121 WPDFPTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLL-GSGHG 179 Query: 181 STVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPK 240 AS++N++ FP+G V AL ++MF+F +E +G+TAAE NP+ Sbjct: 180 G---------PDASVANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPR 230 Query: 241 KSLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFV 300 +S+PKA NQ+ RIL+FY+GAL +++++ W + SPFVM+F + A ++N V Sbjct: 231 ESIPKATNQVVYRILIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIV 290 Query: 301 VLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYM-ATALSLLAP 359 VLT+A S NS +++ +R ++ LA Q D R K+S++G+P+ AL + A A L Sbjct: 291 VLTAALSVYNSCVYANSRMLFGLASQGDAPR--QLLKVSRSGVPLTALAVSAFATGLCVL 348 Query: 360 VLTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSE-------DYNPKGFLTPKP 412 + L+P AF + + ++ + T+ ++RK++ Y G Sbjct: 349 INYLMP--GGAFGLLMALAVSALVINWASISITHLKFRKAKLAAGITPFYKSLGHPLTN- 405 Query: 413 QITVPFIVAIFAIVFASLFFNADT-FYPALGAIVWTIF 449 + + FIV I +++ + PA A++W F Sbjct: 406 YLCLAFIVLILVVMYLTPPIRISVMLIPAWIAVLWVAF 443 Lambda K H 0.329 0.141 0.434 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: 32 Number of successful extensions: 2 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: 459 Length of database: 453 Length adjustment: 33 Effective length of query: 426 Effective length of database: 420 Effective search space: 178920 Effective search space used: 178920 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 (21.8 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