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 AO356_29455 AO356_29455 amino acid transporter
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29455 Length = 484 Score = 324 bits (830), Expect = 4e-93 Identities = 183/458 (39%), Positives = 270/458 (58%), Gaps = 13/458 (2%) Query: 8 ENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAI 67 E QR L NRHIQL+A+ G IGTGLF+G+GK I L+G SII +Y+IIG +Y ++RA+ Sbjct: 10 EQPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMRAM 69 Query: 68 GEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLP 127 GEML + N +F +F YLG + +F+ WSY L + + + +G + +W PD+P Sbjct: 70 GEMLLSNLNFKTFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPDVP 129 Query: 128 IWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTD-T 186 W+ + +L+ L LN L + FGE EFWF +IKI+A++ LI +++LI S + + + T Sbjct: 130 AWIPAIGMLMTLFALNVLTVRLFGEIEFWFAIIKIIAVVTLIGVSLVLIASSFVSPSGVT 189 Query: 187 VSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPI 246 S+ ++ FPNGL FF FQM +F+F E IG AAET NP TL KAIN IP+ Sbjct: 190 ASLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRNPEKTLPKAINSIPL 249 Query: 247 RIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSA 306 RI+LFYV AL I+++ W+ + KSPFV +F + G AA +VNFVVLTSAAS+ NS Sbjct: 250 RIILFYVLALACIIAVTSWQQVSPSKSPFVELFLVAGFPAAAGIVNFVVLTSAASSANSG 309 Query: 307 LFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILF-TPFISMIPAISNSF 365 +FS +R L+ L+ N D F + S VP+ +L FT+LL+L + ++P + +F Sbjct: 310 VFSSSRMLFGLA--NQDNAPGIFRRLSGNSVPLLSLAFTTLLMLVGVLLLFIVPEVMTAF 367 Query: 366 VFITSVATNLFLVVYLMTLITYLKYRKSSD--FDPKGFVLPAA--HIFIPLAIAGFVLIF 421 +++V+ L + + L +Y+ YRK + +P + LA GFVL Sbjct: 368 TIVSTVSAILVIFTWSTILASYIAYRKKRPELHAKSAYKMPGGVPMAWFSLAFLGFVLCL 427 Query: 422 ISLFCFKDTIVPAI---GSVIWVLIFGLFTFFKKIKTA 456 ++L DT + + G IW+ I T +K K+A Sbjct: 428 LAL--RPDTRIALLVMPGWFIWLAIAYQLTDARKPKSA 463 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: 603 Number of extensions: 37 Number of successful extensions: 4 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: 484 Length adjustment: 33 Effective length of query: 424 Effective length of database: 451 Effective search space: 191224 Effective search space used: 191224 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