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 PP_0927 PP_0927 aromatic amino acid transport protein
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 293 bits (750), Expect = 8e-84 Identities = 162/438 (36%), Positives = 256/438 (58%), Gaps = 16/438 (3%) Query: 13 QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLY 72 QRGLKNRHIQLIA+ G IGTGLFLG ++I L GPS++ Y I G + ++++R +GEM+ Sbjct: 11 QRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMRQLGEMVV 70 Query: 73 QDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTE 132 ++P SF +F +Y E G+ W+Y +V V V MAEL A+G Y+ +W PD P W T Sbjct: 71 EEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWATA 130 Query: 133 VFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDTVSVTNI 192 V++ L+N K +GE EFWF ++K+VAI+ +I L+ S H G D SV N+ Sbjct: 131 AIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSG-HGGPD-ASVANL 188 Query: 193 TKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLFY 252 + FFPNG++ + ++MF+F +E +G+TAAE DNPR ++ KA NQ+ RI++FY Sbjct: 189 WQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILIFY 248 Query: 253 VGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFSITR 312 +GAL ++S+Y W+ + SPFV IF + A ++N VVLT+A S NS +++ +R Sbjct: 249 IGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYNSCVYANSR 308 Query: 313 NLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAISNSFVFITSVA 372 L+ L+ + + K S++GVP+ AL ++ I+ + +F + ++A Sbjct: 309 MLFGLASQGDAP--RQLLKVSRSGVPLTALAVSAFATGLCVLINYLMP-GGAFGLLMALA 365 Query: 373 TNLFLVVYLMTLITYLKYRK---SSDFDPKGFVLPAAH-IFIPLAIAGFVLIFISLFC-- 426 + ++ + IT+LK+RK ++ P F H + L +A VLI + ++ Sbjct: 366 VSALVINWASISITHLKFRKAKLAAGITP--FYKSLGHPLTNYLCLAFIVLILVVMYLTP 423 Query: 427 ---FKDTIVPAIGSVIWV 441 ++PA +V+WV Sbjct: 424 PIRISVMLIPAWIAVLWV 441 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: 501 Number of extensions: 29 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: 453 Length adjustment: 33 Effective length of query: 424 Effective length of database: 420 Effective search space: 178080 Effective search space used: 178080 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