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 BWI76_RS07360 BWI76_RS07360 phenylalanine transporter
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Koxy:BWI76_RS07360 Length = 458 Score = 297 bits (761), Expect = 4e-85 Identities = 162/455 (35%), Positives = 266/455 (58%), Gaps = 18/455 (3%) Query: 7 EENKPS-QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLR 65 EE+ P+ RGL+NRHIQLIA+ G IGTGLFLG G +I + GP+++ Y + G + ++++R Sbjct: 12 EESGPTLHRGLQNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYAVAGIVAFLIMR 71 Query: 66 AIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPD 125 +GEM+ ++P SF +F +Y G G+ W+Y ++ V V MAEL A G Y+ +WLPD Sbjct: 72 QLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWLPD 131 Query: 126 LPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTD 185 +P W+ +++ +N +N + +GE EFWF +IK++AIIG+I + ++F + G Sbjct: 132 VPTWIWAAAFFLIINAVNLVNVRLYGEAEFWFALIKVLAIIGMIGFGLWMLFGGH--GGS 189 Query: 186 TVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIP 245 + N+ K FF G S ++MF+F +E IG+TAAE NP ++ KA+NQ+ Sbjct: 190 KAGIDNLWKHGGFFATGWHGLIMSLAVIMFSFGGLELIGITAAEAQNPEKSIPKAVNQVV 249 Query: 246 IRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNS 305 RI+LFY+G+L+ ++++Y W +I +D SPFV IF + A+ +NFV+L ++ S NS Sbjct: 250 YRILLFYIGSLVVLLALYPWVEIQSDSSPFVMIFHNLDSNVVASALNFVILVASLSVYNS 309 Query: 306 ALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFIS-MIPAISNS 364 ++S +R L+ LS N K + SK GVPVN+LL + ++ ++ ++P + Sbjct: 310 GVYSNSRMLFGLSVQGNAP--KFLARVSKRGVPVNSLLLSGIITSLVVVLNYLLPQKALG 367 Query: 365 FVFITSVATNLFLVVYLMTLITYLKY-----RKSSDFDPKGFVLPAAHIFIPLAIAGFVL 419 + VAT L+ ++M + +LK+ RK + K + PA++ + IA L Sbjct: 368 LLMALVVAT--LLLNWIMICLAHLKFRAAQRRKGREPKFKALLSPASNY---ICIAFLAL 422 Query: 420 IFISLFCFKDTIVPAIGSVIWVLIFGLFTFFKKIK 454 I + + + AI +W+L LF FK ++ Sbjct: 423 ILVLMCTIDGMRLSAILLPVWILF--LFAAFKTLR 455 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: 516 Number of extensions: 31 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: 458 Length adjustment: 33 Effective length of query: 424 Effective length of database: 425 Effective search space: 180200 Effective search space used: 180200 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