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 Pf1N1B4_4976 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976 Length = 473 Score = 329 bits (843), Expect = 1e-94 Identities = 187/464 (40%), Positives = 280/464 (60%), Gaps = 23/464 (4%) Query: 2 NTNQNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMY 61 +T++ E QR L NRHIQL+A+ G IGTGLF+G+GK I L+G SII +Y+IIG +Y Sbjct: 4 DTHEITEQAVLQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVY 63 Query: 62 ILLRAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINF 121 ++RA+GE+L + N SF +F YLG + +F+ WSY L + + + +G + + Sbjct: 64 FVMRAMGELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQY 123 Query: 122 WLPDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYH 181 W PD+P W+ + +++ L LN L K FGE EFWF +IKI+A++ LI +++LI S + Sbjct: 124 WFPDVPAWIPAIGMMLTLFALNVLTVKLFGEVEFWFAIIKIIAVVALISVSVLLIASSFV 183 Query: 182 TGTD-TVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKA 240 + T T S+T++ FPNGL FF FQM +F+F E IG AAET +P TL KA Sbjct: 184 SPTGVTASLTHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPKA 243 Query: 241 INQIPIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAA 300 IN IP+RI+LFYV +L+ I+++ W+ + +KSPFV +F + G AA +VNFVVLTSAA Sbjct: 244 INSIPLRIILFYVLSLVCIIAVTSWQQVSPNKSPFVELFLIAGFPAAAGIVNFVVLTSAA 303 Query: 301 SALNSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTS-LLILFTPFISMIP 359 S+ NS +FS +R L+ L+ L N + F + SK VP+ +L FT+ L++L + +IP Sbjct: 304 SSANSGVFSSSRMLFGLADLGNAPGI--FRRLSKNSVPLISLAFTTFLMLLGVLLLFIIP 361 Query: 360 AISNSFVFITSVATNLFLVVYLMTLITYLKYRKS-------SDFDPKGFVLPAAHIFIPL 412 + +F +++V+ L + + L +Y+ YRK+ S + G V A + L Sbjct: 362 EVMTAFTIVSTVSAILVIFTWSTILASYIAYRKARPDLHAQSRYKMPGGVPMA---WFSL 418 Query: 413 AIAGFVLIFISLFCFKDT-----IVPAIGSVIWVLIFGLFTFFK 451 A FVL ++L DT ++PA IW+ I F+ FK Sbjct: 419 AFLAFVLCLLAL--RPDTRLALCVMPA--WFIWLAIAYQFSHFK 458 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: 594 Number of extensions: 33 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: 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