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 AO353_25190 AO353_25190 amino acid transporter
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25190 Length = 471 Score = 323 bits (828), Expect = 7e-93 Identities = 181/462 (39%), Positives = 277/462 (59%), Gaps = 13/462 (2%) Query: 4 NQNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYIL 63 ++ E QR L NRHIQL+A+ G IGTGLF+G+GK I L+G SII +Y+IIG +Y + Sbjct: 6 SERVEQPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGMFVYFV 65 Query: 64 LRAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWL 123 +RA+GE+L + N +F +F YLG + +F+ WSY L + + + +G + +W Sbjct: 66 MRAMGELLLSNLNFKTFADFTGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQYWF 125 Query: 124 PDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTG 183 PD+P W+ V +L+ L LN L + FGE EFWF +IKI+A++ LI ++++I S + + Sbjct: 126 PDVPAWIPAVGMLMTLFALNVLTVRLFGEVEFWFAIIKIIAVVTLIGVSLVMIASSFVSP 185 Query: 184 TD-TVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAIN 242 + T S+ ++ FPNGL FF FQM +F+F E IG AAET +P TL KAIN Sbjct: 186 SGVTASLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPKAIN 245 Query: 243 QIPIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASA 302 IP+RI+LFYV AL I+++ W+ + +KSPFV +F + G AA +VNFVVLTSAAS+ Sbjct: 246 SIPLRIILFYVLALACIIAVTSWQQVSPNKSPFVELFLVAGFPAAAGIVNFVVLTSAASS 305 Query: 303 LNSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILF-TPFISMIPAI 361 NS +FS +R L+ L+ ++D F S+ VP+ +L FT+LL+L + ++P + Sbjct: 306 ANSGVFSSSRMLFGLA--SHDNAPGIFRHLSRNSVPLLSLAFTTLLMLVGVLLLFIVPEV 363 Query: 362 SNSFVFITSVATNLFLVVYLMTLITYLKYRKS-SDFDPKG-FVLPAA--HIFIPLAIAGF 417 +F +++V+ L + + L +Y+ YRKS D K + +P + L GF Sbjct: 364 MTAFTIVSTVSAILVIFTWSTILASYIAYRKSRPDLHAKSVYKMPGGVPMAWFSLTFLGF 423 Query: 418 VLIFISLFCFKDTIVPAI---GSVIWVLIFGLFTFFKKIKTA 456 VL ++L DT + + G IW+ I T +K+++A Sbjct: 424 VLCLLAL--RPDTRIALLVMPGWFIWLAIAYQLTHSRKLRSA 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: 591 Number of extensions: 36 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: 471 Length adjustment: 33 Effective length of query: 424 Effective length of database: 438 Effective search space: 185712 Effective search space used: 185712 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