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 BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter
Query= TCDB::F2HQ24 (457 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS15500 BPHYT_RS15500 aromatic amino acid transporter Length = 461 Score = 295 bits (755), Expect = 2e-84 Identities = 166/449 (36%), Positives = 265/449 (59%), Gaps = 18/449 (4%) Query: 1 MNTNQNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALM 60 MN+ Q ++ +RGLKNRHIQLIA+ G IGTGLFLG+ + GPS+I Y I G + Sbjct: 1 MNSAQQQDGL--KRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGIIA 58 Query: 61 YILLRAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYIN 120 ++++R +GEM+ Q+P SF +F +Y G+ PG+ W+Y ++ V V+MAEL A+GTYI+ Sbjct: 59 FMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYIH 118 Query: 121 FWLPDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHY 180 +W P +P W++ + L+ +N N K +GETEFWF +IK+VA+IG+I+ L+ S + Sbjct: 119 YWWPGVPTWVSALVCFALINAINLANVKAYGETEFWFAIIKVVAVIGMIVFGGYLLISGH 178 Query: 181 HTGTDTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKA 240 G S+TN+ FFP+G F ++MF+F +E IG+TAAE D P+ ++ KA Sbjct: 179 --GGPQASITNLWSHGGFFPHGFHGLFMMLAVIMFSFGGLELIGITAAEADQPQKSIPKA 236 Query: 241 INQIPIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAA 300 +NQ+ RI++FY+ +L ++S+Y W ++ A SPFV IF IG A ++N VVLT+A Sbjct: 237 VNQVIYRILIFYICSLTVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAAL 296 Query: 301 SALNSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFIS-MIP 359 S NS +++ +R LY L++ N + K + GVP A+ ++L ++ +IP Sbjct: 297 SVYNSGVYANSRMLYGLAEQGNAP--RALMKVDRRGVPYMAIGLSALATFTCVIVNYLIP 354 Query: 360 AISNSFVFITSVATNLFLVVYLMTLITYLKYRKS-----SDFDPKGFVLPAAHIFIPLAI 414 A + + VA ++ + + +T+LK RK+ K F P ++ +I LA Sbjct: 355 AEALGLLMALVVAA--LVLNWALISLTHLKSRKAMVAAGETLVFKSFWFPVSN-WICLAF 411 Query: 415 AGFVLIFISL---FCFKDTIVPAIGSVIW 440 +L+ +++ +VPA V+W Sbjct: 412 MALILVILAMTPGLSVSVWLVPAWLVVMW 440 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: 31 Number of successful extensions: 2 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: 461 Length adjustment: 33 Effective length of query: 424 Effective length of database: 428 Effective search space: 181472 Effective search space used: 181472 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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