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_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ25 (459 letters) >NCBI__GCF_001277995.1:WP_082353324.1 Length = 468 Score = 302 bits (773), Expect = 2e-86 Identities = 168/456 (36%), Positives = 251/456 (55%), Gaps = 16/456 (3%) Query: 2 ENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFF 61 +N RGL NRH+QLIAI G IGTGLF+G+GKTI + GPSVI Y +IG +FF Sbjct: 3 DNAAPDTHLHRGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFV 62 Query: 62 LRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWL 121 +R +GE+L + + S + V+ G G+ T W+YW + ++++ AI Y Q+W Sbjct: 63 MRAMGELLLANLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWW 122 Query: 122 PQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYS 181 P++PLWL ++ + +LF LN R FGE EFWFA+IK+ AI+ +I +V F Sbjct: 123 PEIPLWLPGVLTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAF--- 179 Query: 182 TVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKK 241 G +AS +N+ + FP+G F+ Q+ +FAF +E G AAET +P+ Sbjct: 180 ----GAPNGTTASFNNLIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPET 235 Query: 242 SLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVV 301 +LP+AIN IP+RI++FYV AL IM + W+ + D SPFV +F L GI AA +INFVV Sbjct: 236 TLPRAINSIPIRIVVFYVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVV 295 Query: 302 LTSAASALNSSLFSATRNMYSLAQQ---HDKGRLTPFTKLSKAGIPINALYMATALSLLA 358 +TSAAS+ NS +FS +R +Y L+ + + + ++ G+ + L + A+ LL Sbjct: 296 ITSAASSANSGIFSTSRMLYGLSLEGAAPKRWGVLSKRQVPARGLTFSVLCLIPAVGLLY 355 Query: 359 PVLTLIPQIKNAFDFAASCTTNLFLVV--YFITLYTYWQYRKSEDYNPKGFLTPKPQITV 416 T+I AF + ++ LF+VV Y + Y ++ R E + F P + Sbjct: 356 AGGTVI----EAFTLITTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMA 411 Query: 417 PFIVAIFAIVFASLFFNADTFYPALGAIVWTIFFGL 452 ++ F + L DT L VW I G+ Sbjct: 412 VVVLVFFVAMLGVLSLETDTRTALLATPVWFIILGV 447 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: 624 Number of extensions: 39 Number of successful extensions: 4 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: 468 Length adjustment: 33 Effective length of query: 426 Effective length of database: 435 Effective search space: 185310 Effective search space used: 185310 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