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 AO353_05965 AO353_05965 aromatic amino acid transporter
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 293 bits (750), Expect = 8e-84 Identities = 155/399 (38%), Positives = 239/399 (59%), Gaps = 24/399 (6%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 +RGL+NRHIQLIA+ G IGTGLFLG+ ++ GPS+I Y + G F +R +GEM+ Sbjct: 12 KRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMIV 71 Query: 71 NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130 +P SF +F Y G G+ + W+YW++ V V ++ELTA+G Y+QFW P+VP W+ Sbjct: 72 EEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWVSA 131 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMI-VTAIILVAGNFHYSTVLSGKTV 189 V L+ +NT+N + FGE EFWFA+IKV AIIGMI + +LV+G T Sbjct: 132 AVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSG-----------TG 180 Query: 190 HDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQ 249 AS+SN++ FP+G + A+ +MF+F +E +G+TAAE P+K +PKAINQ Sbjct: 181 GPQASVSNLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQ 240 Query: 250 IPVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVMVFQLIGIKWAAALINFV 300 + R+L+FYVGAL +++++ W + SPFV +F LIG AA ++NFV Sbjct: 241 VVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFV 300 Query: 301 VLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPV 360 VLT+A S NS ++ +R +Y LA+Q D + KL+K G+P+ AL ++ +++L V Sbjct: 301 VLTAALSVYNSGVYCNSRMLYGLAEQGDAPK--SLMKLNKQGVPLRALGISALITMLCVV 358 Query: 361 LTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKS 399 + + A + + ++ + + T+ ++RK+ Sbjct: 359 VNYVAP-NEALELLFALVVASLMINWAMISLTHLKFRKA 396 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: 574 Number of extensions: 34 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: 466 Length adjustment: 33 Effective length of query: 426 Effective length of database: 433 Effective search space: 184458 Effective search space used: 184458 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