Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459 Length = 473 Score = 293 bits (750), Expect = 8e-84 Identities = 169/458 (36%), Positives = 258/458 (56%), Gaps = 9/458 (1%) Query: 5 QNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILL 64 + + P +R L RHI+L+A+ IG GLFLG+ K+I + GP+I+ Y+I G + +++ Sbjct: 11 ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70 Query: 65 RAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLP 124 RA+GEM +P SF + YLG G+ W+Y + + +AE+ A+ Y+ W P Sbjct: 71 RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFP 130 Query: 125 DLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGT 184 D+P W+ + LV + +N + K FGE EFWF +IKIV II +++ + +I + Sbjct: 131 DVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDG 190 Query: 185 DTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQI 244 + ++N+ F PNG+ S QMVMFA++ +E IG+TA E NP+ T+ AI + Sbjct: 191 VALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSV 250 Query: 245 PIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALN 304 RI+LFYVGAL I+SIY W +I SPFV F+ +GIK AA ++NFVV+T+A S+ N Sbjct: 251 FWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCN 310 Query: 305 SALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFIS-MIPAISN 363 +FS R LYSL++ N + F S GVP ALL + +L ++ ++P Sbjct: 311 GGIFSTGRMLYSLAQ--NGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLVP--EK 366 Query: 364 SFVFITSVATNLFLVVYLMTLITYLKYRKSSDFDPKGFVLPAAHIF---IPLAIAGFVLI 420 FV++TS+AT + ++M L+ LK+RKS + + ++ LA+A VL+ Sbjct: 367 VFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLV 426 Query: 421 FISLFCFKDTIVPA-IGSVIWVLIFGLFTFFKKIKTAE 457 + F DT V +G VL+ LF FK T E Sbjct: 427 VGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGE 464 Lambda K H 0.330 0.144 0.431 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: 545 Number of extensions: 28 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: 457 Length of database: 473 Length adjustment: 33 Effective length of query: 424 Effective length of database: 440 Effective search space: 186560 Effective search space used: 186560 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