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 WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ25 (459 letters) >NCBI__GCF_002095475.1:WP_084934657.1 Length = 463 Score = 328 bits (842), Expect = 2e-94 Identities = 181/451 (40%), Positives = 262/451 (58%), Gaps = 12/451 (2%) Query: 5 QEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRT 64 ++ + +R L NRHIQLIAI G IGTGLF+G+GKTI + GPS+IF Y++IG +FF +R Sbjct: 13 EQPEKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRA 72 Query: 65 IGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQV 124 +GE+L ++ SF +F G GYFT W+YW V I+++ AI Y Q W P Sbjct: 73 MGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGF 132 Query: 125 PLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVL 184 +W+ ++ + LN + FGE EFWFA+IK+ AI+ +I+T I+LV + HY + Sbjct: 133 SIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLV--SMHYPSP- 189 Query: 185 SGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLP 244 +G T ASLSNI+D +FP G F Q+ +FAF +E +G AAET +P K LP Sbjct: 190 NGTT----ASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLP 245 Query: 245 KAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTS 304 +AIN IPVRI++FYV ALL IMA+ W+ + ++SPFV +F LIG+ AA+++NFVVLTS Sbjct: 246 RAINAIPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTS 305 Query: 305 AASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLT-L 363 AAS+ NS +FS +R ++ LA+ + F +LS +P L+ + L+ L L Sbjct: 306 AASSANSGIFSTSRMLFGLAELGVAHK--AFGRLSARAVPTTGLFFSCLCLLVGVALIYL 363 Query: 364 IPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKS--EDYNPKGFLTPKPQITVPFIVA 421 IP + F + + LF+ V+ I L +Y YRK + + F P + +A Sbjct: 364 IPDVMTVFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMA 423 Query: 422 IFAIVFASLFFNADTFYPALGAIVWTIFFGL 452 FA V L DT + +W + L Sbjct: 424 FFAFVLVLLTLQEDTRQALMVTPLWFVILTL 454 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: 642 Number of extensions: 26 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: 463 Length adjustment: 33 Effective length of query: 426 Effective length of database: 430 Effective search space: 183180 Effective search space used: 183180 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 24 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