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 WP_082353324.1 CDES_RS02405 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ24 (457 letters) >NCBI__GCF_001277995.1:WP_082353324.1 Length = 468 Score = 325 bits (832), Expect = 3e-93 Identities = 178/443 (40%), Positives = 263/443 (59%), Gaps = 12/443 (2%) Query: 14 RGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLYQ 73 RGL NRH+QLIAI G IGTGLF+G+GK+I + GPS+I VY IIG +++ ++RA+GE+L Sbjct: 13 RGLSNRHLQLIAIGGAIGTGLFMGSGKTISVAGPSVILVYAIIGFMLFFVMRAMGELLLA 72 Query: 74 DPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTEV 133 + N S + VS LG G+ W+Y + MA+++AI Y +W P++P+W+ V Sbjct: 73 NLNYKSLRDAVSDILGPGAGFVTGWTYWFCWIATGMADIVAITGYTQYWWPEIPLWLPGV 132 Query: 134 FVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHY--HTGTDTVSVTN 191 +++L LN + FGE EFWF +IKIVAI+ LI ++ + + GT T S N Sbjct: 133 LTIIVLFALNLAAVRLFGEMEFWFAIIKIVAIVALIAVGFFMVITAFGAPNGT-TASFNN 191 Query: 192 ITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLF 251 + + FFPNG++ F FQ+ +FAFV +E G AAET +P TL +AIN IPIRIV+F Sbjct: 192 LIEHGGFFPNGITGFLAGFQIAIFAFVGIELAGTAAAETKDPETTLPRAINSIPIRIVVF 251 Query: 252 YVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFSIT 311 YV AL IM + W ++ D SPFV +F L GI AA ++NFVV+TSAAS+ NS +FS + Sbjct: 252 YVLALAVIMMVTPWNEVSPDNSPFVQMFALAGIPAAAGIINFVVITSAASSANSGIFSTS 311 Query: 312 RNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPA---ISNSFVFI 368 R LY LS K + SK VP L F+ L ++ P + ++ A + +F I Sbjct: 312 RMLYGLSL--EGAAPKRWGVLSKRQVPARGLTFSVLCLI--PAVGLLYAGGTVIEAFTLI 367 Query: 369 TSVATNLFLVVYLMTLITYLKYRKSSD--FDPKGFVLPAAHIFIPLAIAGFVLIFISLFC 426 T+V++ LF+VV+ L+ Y+ YR+ + + F +P + + + FV + L Sbjct: 368 TTVSSVLFMVVWSYILVAYIVYRRRNPELHEKSVFKMPGGVVMAVVVLVFFVAMLGVLSL 427 Query: 427 FKDTIVPAIGSVIWVLIFGLFTF 449 DT + + +W +I G+ F Sbjct: 428 ETDTRTALLATPVWFIILGVGWF 450 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: 548 Number of extensions: 30 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: 468 Length adjustment: 33 Effective length of query: 424 Effective length of database: 435 Effective search space: 184440 Effective search space used: 184440 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 24 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