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 GFF4632 PS417_23700 aromatic amino acid transporter
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 300 bits (768), Expect = 7e-86 Identities = 165/433 (38%), Positives = 254/433 (58%), Gaps = 28/433 (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 KY G G+ W+YW++ V V ++ELTA+G YIQFW P +P W+ Sbjct: 72 EEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVSA 131 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190 +V + +NTLN +FFGETEFWFA+IKV AI+GMIV L L T Sbjct: 132 LVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYL----------LFSGTGG 181 Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 AS+SN++ FP+G + ++ +MF+F +E +G+TAAE P+K +PKAINQ+ Sbjct: 182 PQASVSNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQV 241 Query: 251 PVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVMVFQLIGIKWAAALINFVV 301 RIL+FYVGAL +++++ W + SPFV +F LIG AA ++NFVV Sbjct: 242 VYRILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVV 301 Query: 302 LTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVL 361 LT+A S NS ++ +R ++ LA+Q D + KL+K G+PI AL ++ +++L V+ Sbjct: 302 LTAALSVYNSGVYCNSRMLFGLAEQGDAPK--SLMKLNKQGVPIRALAISALVTMLCVVV 359 Query: 362 TLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKS---EDYNP--KGFLTP-KPQIT 415 + ++A + + ++ + + T+ ++RK+ + P K F P + Sbjct: 360 NYVAP-QSALELLFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLC 418 Query: 416 VPFIVAIFAIVFA 428 + F+V I +++ A Sbjct: 419 LAFMVMIISVMLA 431 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: 594 Number of extensions: 33 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