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) >FitnessBrowser__BFirm:BPHYT_RS15500 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:
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