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 H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Burk376:H281DRAFT_04042 Length = 506 Score = 290 bits (743), Expect = 6e-83 Identities = 151/365 (41%), Positives = 227/365 (62%), Gaps = 18/365 (4%) Query: 1 MENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFF 60 ++N ++ +RGL+NRHIQLIA+ G IGTGLFLG+ +Q GPS+I Y + G+ F Sbjct: 46 LDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFM 105 Query: 61 FLRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFW 120 +R +GEM+ +P SF +F KY G G+ + W+YW++ V V ++ELTA+GTY+ +W Sbjct: 106 IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYW 165 Query: 121 LPQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIV-TAIILVAGNFH 179 P VP W+ +V A + +N N + +GETEFWFA+IKV A+IGMI+ +LV+G+ Sbjct: 166 WPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGH-- 223 Query: 180 YSTVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNP 239 AS+SN++ FPHG L ++MF+F +E IG+TAAE P Sbjct: 224 ---------GGPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEP 274 Query: 240 KKSLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINF 299 +KS+PKA+NQ+ RIL+FY+ +L +++++ W+ + A SPFVM+F IG A ++N Sbjct: 275 QKSIPKAVNQVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNV 334 Query: 300 VVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAP 359 VVLT+A S NS +++ +R +Y LA+Q + R K+ + G+P YMA LS LA Sbjct: 335 VVLTAALSVYNSGVYANSRMLYGLAEQGNAPR--ALMKVDRRGVP----YMAIGLSALAT 388 Query: 360 VLTLI 364 +I Sbjct: 389 FTCVI 393 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: 618 Number of extensions: 34 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: 506 Length adjustment: 34 Effective length of query: 425 Effective length of database: 472 Effective search space: 200600 Effective search space used: 200600 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: 52 (24.6 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