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 14712 b0576 phenylalanine transporter (NCBI)
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Keio:14712 Length = 458 Score = 290 bits (743), Expect = 5e-83 Identities = 158/463 (34%), Positives = 272/463 (58%), Gaps = 26/463 (5%) Query: 2 NTNQNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMY 61 +T N+E RGL NRHIQLIA+ G IGTGLFLG G +I + GP+++ Y + G + + Sbjct: 10 DTASNQE-PTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAF 68 Query: 62 ILLRAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINF 121 +++R +GEM+ ++P SF +F +Y G G+ W+Y ++ V V MAEL A G Y+ + Sbjct: 69 LIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQY 128 Query: 122 WLPDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYH 181 W PD+P W+ +++ +N +N + +GETEFWF +IK++AIIG+I + L+FS + Sbjct: 129 WFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGH- 187 Query: 182 TGTDTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAI 241 G + S+ N+ + FF G + S ++MF+F +E IG+TAAE +P ++ KA+ Sbjct: 188 -GGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAV 246 Query: 242 NQIPIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAAS 301 NQ+ RI+LFY+G+L+ ++++Y W ++ ++ SPFV IF + A+ +NFV+L ++ S Sbjct: 247 NQVVYRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLS 306 Query: 302 ALNSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALL----FTSLLILFTPFISM 357 NS ++S +R L+ LS N K T+ S+ GVP+N+L+ TSL++L + Sbjct: 307 VYNSGVYSNSRMLFGLSVQGNAP--KFLTRVSRRGVPINSLMLSGAITSLVVLINYLLP- 363 Query: 358 IPAISNSFVFITSVATNLFLVVYLMTLITYLKY-----RKSSDFDPKGFVLPAAHIFIPL 412 +F + ++ L+ ++M + +L++ R+ + K + P + ++ + Sbjct: 364 ----QKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGN-YLCI 418 Query: 413 AIAGFVLIFISLFCFKDTI-VPAIGSVIWVLIFGLFTFFKKIK 454 A G +L+ L C D + + AI +W++ LF FK ++ Sbjct: 419 AFLGMILL---LMCTMDDMRLSAILLPVWIVF--LFMAFKTLR 456 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: 534 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: 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