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 18233 b4208 D-alanine/D-serine/glycine transporter (NCBI)
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Keio:18233 Length = 470 Score = 328 bits (842), Expect = 2e-94 Identities = 181/446 (40%), Positives = 263/446 (58%), Gaps = 14/446 (3%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 +R L NRHIQLIAI G IGTGLF+G+GKTI + GPS+IF Y++IG +FF +R +GE+L Sbjct: 20 RRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELLL 79 Query: 71 NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130 ++ SF +F + G GYFT W+YW V ++++ AI Y QFW P + W+ Sbjct: 80 SNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVAS 139 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190 + ++ LL LN + FGE EFWFAMIK+ AI+ +IV +++VA +F T + Sbjct: 140 LAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGV------ 193 Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 AS +++++ FP G F Q+ +FAF +E +G TAAET +P+KSLP+AIN I Sbjct: 194 -EASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSI 252 Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310 P+RI++FYV AL+ IM++ W + +KSPFV +F L+G+ AA++INFVVLTSAAS+ N Sbjct: 253 PIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSAN 312 Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLTLI--PQIK 368 S +FS +R ++ LAQ+ + F KLSK +P L + + LL V+ L P + Sbjct: 313 SGVFSTSRMLFGLAQEGVAPK--AFAKLSKRAVPAKGLTF-SCICLLGGVVMLYVNPSVI 369 Query: 369 NAFDFAASCTTNLFLVVYFITLYTYWQYRKSED--YNPKGFLTPKPQITVPFIVAIFAIV 426 AF + + LF+ V+ I L +Y YRK + + P ++ +A F V Sbjct: 370 GAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFV 429 Query: 427 FASLFFNADTFYPALGAIVWTIFFGL 452 L DT L +W I GL Sbjct: 430 VVLLTLEDDTRQALLVTPLWFIALGL 455 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: 637 Number of extensions: 32 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: 470 Length adjustment: 33 Effective length of query: 426 Effective length of database: 437 Effective search space: 186162 Effective search space used: 186162 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