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 PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 291 bits (746), Expect = 2e-83 Identities = 169/468 (36%), Positives = 258/468 (55%), Gaps = 33/468 (7%) Query: 2 ENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFF 61 + + + E +RGL+NRHIQLIA+ G IGTGLFLG+ ++ GPS+I Y + G F Sbjct: 3 DEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62 Query: 62 LRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWL 121 +R +GEM+ +P SF +F KY G G+ + W+YW++ V V ++ELTA+G Y+QFW Sbjct: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWW 122 Query: 122 PQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYS 181 P+VP W+ V L+ +N +N + FGE EFWFA+IKV AIIGMI + Sbjct: 123 PEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYM-------- 174 Query: 182 TVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKK 241 L T AS+SN++D FP+G + A+ +MF+F +E +G+TAAE P K Sbjct: 175 --LFSGTGGPQASVSNLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGK 232 Query: 242 SLPKAINQIPVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVMVFQLIGIKW 292 +PKAINQ+ R+L+FYVGAL +++++ W + SPFV +F LIG Sbjct: 233 VIPKAINQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDT 292 Query: 293 AAALINFVVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMAT 352 AA ++NFVVLT+A S NS ++ +R +Y LA+Q D + KL+K G+P+ AL ++ Sbjct: 293 AAHILNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPK--ALMKLNKQGVPLLALGVSA 350 Query: 353 ALSLLAPVLTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNP-----KGF 407 ++LL+ ++ + A + + ++ + + T+ ++RK K F Sbjct: 351 LITLLSVLVNYLAP-HEALELLFALVVASLMINWAMISLTHLKFRKIMSQQGIVPGFKSF 409 Query: 408 LTP-KPQITVPFIVAIFAIVFASLFFNADTFYPALGAIVWT-IFFGLY 453 P + + F+V I ++ A F VW I FG Y Sbjct: 410 WFPFSNYLCLAFMVMIVCVMLMIPGIRASVF----AIPVWVLIIFGFY 453 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: 603 Number of extensions: 39 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: 459 Length of database: 467 Length adjustment: 33 Effective length of query: 426 Effective length of database: 434 Effective search space: 184884 Effective search space used: 184884 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