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 N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 300 bits (769), Expect = 5e-86 Identities = 167/442 (37%), Positives = 261/442 (59%), Gaps = 10/442 (2%) Query: 7 EENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRA 66 + N QRGL+ RHI+L+A+ IG GLFLG+ +I L GP+I+ YL+ G ++I++RA Sbjct: 2 QTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRA 61 Query: 67 IGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDL 126 +GEM Q+P SF + YLG PGY W+Y + + +AE+ A+G Y+ W PD+ Sbjct: 62 LGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDV 121 Query: 127 PIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLIL-TAIILIFSHYHTGTD 185 P W+ + LV + +N K +GE EFWF MIK+V I+ +I+ +++F + G Sbjct: 122 PQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVP 181 Query: 186 TVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIP 245 T ++N+ F PNG + QMVMFA++ +E IG+TA E DNP+ ++ AIN + Sbjct: 182 T-GISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVF 240 Query: 246 IRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNS 305 RI++FYVGAL IMSIY W ++ SPFV F+ +GIK AA ++NFVVLT+A S+ N Sbjct: 241 WRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNG 300 Query: 306 ALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFIS-MIPAISNS 364 ++S R L++L++ + + F S +G+P A+L + + +LF ++ ++PA Sbjct: 301 GIYSTGRMLFNLAQ--QGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPA--KV 356 Query: 365 FVFITSVATNLFLVVYLMTLITYLKYRKSSDFDPKG---FVLPAAHIFIPLAIAGFVLIF 421 FV++TS AT + + + LIT +KYR+ + F +P LA+A VL+ Sbjct: 357 FVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVV 416 Query: 422 ISLFCFKDTIVPAIGSVIWVLI 443 + F DT V I +W+++ Sbjct: 417 GLMGYFPDTRVALIVGPLWLVL 438 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: 556 Number of extensions: 27 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: 454 Length adjustment: 33 Effective length of query: 424 Effective length of database: 421 Effective search space: 178504 Effective search space used: 178504 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