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_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ24 (457 letters) >NCBI__GCF_002095475.1:WP_084934657.1 Length = 463 Score = 345 bits (886), Expect = 1e-99 Identities = 190/453 (41%), Positives = 272/453 (60%), Gaps = 8/453 (1%) Query: 7 EENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRA 66 E+ + +R L NRHIQLIAI G IGTGLF+G+GK+I L GPSIIFVY+IIG +++ ++RA Sbjct: 13 EQPEKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRA 72 Query: 67 IGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDL 126 +GE+L + SF +F + LG GYF W+Y V +A+++AI Y W P Sbjct: 73 MGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGF 132 Query: 127 PIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHT--GT 184 IWM+ + + LN K FGE EFWF +IKIVAI+ LI+T I+L+ HY + GT Sbjct: 133 SIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYPSPNGT 192 Query: 185 DTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQI 244 T S++NI FP GLS FF FQ+ +FAFV +E +G AAET +P L +AIN I Sbjct: 193 -TASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINAI 251 Query: 245 PIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALN 304 P+RI++FYV ALL IM++ W + ++SPFV +F LIG+ AA++VNFVVLTSAAS+ N Sbjct: 252 PVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAASSAN 311 Query: 305 SALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSL-LILFTPFISMIPAISN 363 S +FS +R L+ L++L K F + S VP L F+ L L++ I +IP + Sbjct: 312 SGIFSTSRMLFGLAELG--VAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDVMT 369 Query: 364 SFVFITSVATNLFLVVYLMTLITYLKYRKS--SDFDPKGFVLPAAHIFIPLAIAGFVLIF 421 F +T+V+ LF+ V+ + L +YL YRK F +P + +A F + Sbjct: 370 VFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAFVL 429 Query: 422 ISLFCFKDTIVPAIGSVIWVLIFGLFTFFKKIK 454 + L +DT + + +W +I L ++ K Sbjct: 430 VLLTLQEDTRQALMVTPLWFVILTLGWLLRRRK 462 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: 599 Number of extensions: 28 Number of successful extensions: 3 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: 463 Length adjustment: 33 Effective length of query: 424 Effective length of database: 430 Effective search space: 182320 Effective search space used: 182320 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