Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate AO353_25190 AO353_25190 amino acid transporter
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25190 Length = 471 Score = 314 bits (804), Expect = 5e-90 Identities = 174/460 (37%), Positives = 266/460 (57%), Gaps = 15/460 (3%) Query: 6 EKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTI 65 E+ QR L NRHIQL+A+ G IGTGLF+G+GK I ++G S+I Y++IG+ ++F +R + Sbjct: 10 EQPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGMFVYFVMRAM 69 Query: 66 GEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVP 125 GE+L ++ + +F +F Y G R +F WSYWL + + +G + Q+W P VP Sbjct: 70 GELLLSNLNFKTFADFTGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQYWFPDVP 129 Query: 126 LWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLS 185 W+ + ML LF LN L R FGE EFWFA+IK+ A++ +I +++++A +F S Sbjct: 130 AWIPAVGMLMTLFALNVLTVRLFGEVEFWFAIIKIIAVVTLIGVSLVMIASSF---VSPS 186 Query: 186 GKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPK 245 G T ASL+++ D FP+G + F QM +F+F E IG AAET +P+K+LPK Sbjct: 187 GVT----ASLNHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTLPK 242 Query: 246 AINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSA 305 AIN IP+RI+LFYV AL I+A+ +W + +KSPFV +F + G AA ++NFVVLTSA Sbjct: 243 AINSIPLRIILFYVLALACIIAVTSWQQVSPNKSPFVELFLVAGFPAAAGIVNFVVLTSA 302 Query: 306 ASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLT-LI 364 AS+ NS +FS++R ++ LA + + F LS+ +P+ +L T L L+ +L ++ Sbjct: 303 ASSANSGVFSSSRMLFGLASHDNAPGI--FRHLSRNSVPLLSLAFTTLLMLVGVLLLFIV 360 Query: 365 PQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSE-DYNPKG-FLTPKPQITVPFIVAI 422 P++ AF ++ + L + + L +Y YRKS D + K + P F + Sbjct: 361 PEVMTAFTIVSTVSAILVIFTWSTILASYIAYRKSRPDLHAKSVYKMPGGVPMAWFSLTF 420 Query: 423 FAIVFASLFFNADTFYPAL---GAIVWTIFFGLYSHYKKI 459 V L DT L G +W +H +K+ Sbjct: 421 LGFVLCLLALRPDTRIALLVMPGWFIWLAIAYQLTHSRKL 460 Lambda K H 0.329 0.141 0.434 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: 617 Number of extensions: 30 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: 459 Length of database: 471 Length adjustment: 33 Effective length of query: 426 Effective length of database: 438 Effective search space: 186588 Effective search space used: 186588 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