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 Pf6N2E2_5459 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459 Length = 473 Score = 282 bits (722), Expect = 1e-80 Identities = 156/430 (36%), Positives = 243/430 (56%), Gaps = 15/430 (3%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 +R L RHI+L+A+ IG GLFLG+ K I+M GP+++ +YI+ G+A+ +R +GEM Sbjct: 19 KRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMAV 78 Query: 71 NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130 ++P SF + Y G G+ T W+YW + + C++E+TA+ Y+ W P VP W+ Sbjct: 79 HNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIWA 138 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190 + L + +N + + FGE EFWFA+IK+ II M++ + ++A F V G Sbjct: 139 LAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALG---- 194 Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 +SN++ P+G + +LQMVMFA+ +E IG+TA E NP+K++P AI + Sbjct: 195 ----ISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250 Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310 RILLFYVGAL I++I+ W+ I SPFVM F+ +GIK AA +INFVV+T+A S+ N Sbjct: 251 FWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCN 310 Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLT-LIPQIKN 369 +FS R +YSLAQ F S G+P AL ++ A LL +L L+P+ Sbjct: 311 GGIFSTGRMLYSLAQNGQAP--AGFATTSANGVPRRALLLSIAALLLGVLLNYLVPE--K 366 Query: 370 AFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPKGFLTPKPQITVPFIVAIFAIVFAS 429 F + S T + + + L ++RKS + + L K ++ + + + A+ F Sbjct: 367 VFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAAL--KYRMWLYPVSSYLALAFLV 424 Query: 430 LFFNADTFYP 439 L ++P Sbjct: 425 LVVGLMAYFP 434 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: 648 Number of extensions: 32 Number of successful extensions: 2 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: 473 Length adjustment: 33 Effective length of query: 426 Effective length of database: 440 Effective search space: 187440 Effective search space used: 187440 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