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 GFF2849 PS417_14545 amino acid transporter
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__WCS417:GFF2849 Length = 465 Score = 321 bits (823), Expect = 3e-92 Identities = 177/436 (40%), Positives = 258/436 (59%), Gaps = 12/436 (2%) Query: 4 LQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLR 63 L EK QR L NRHIQL+A+ G IGTGLF+G+GK I ++G S+I Y++IG+ ++F +R Sbjct: 8 LYEKPALQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMR 67 Query: 64 TIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQ 123 +GE+L ++ + SF +F Y G R +F WSYWL I + +G + Q+W P Sbjct: 68 AMGELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVIGDAVVVGGFFQYWFPH 127 Query: 124 VPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTV 183 VP W+ + ML LF LN L R FGE EFWFA+IK+ A++ +I + +L+A +F T Sbjct: 128 VPAWMPAVGMLLTLFALNVLTVRLFGEVEFWFAIIKLIAVLTLIGVSGVLIASSFVSPTG 187 Query: 184 LSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSL 243 + +AS +++ D FP+G + F QM +F+F E IG AAET P+K+L Sbjct: 188 V-------TASFTHLLDPQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRAPEKTL 240 Query: 244 PKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLT 303 PKAIN IP+RI+LFYV AL I+A+ +W ++ KSPFV +F + G AA ++NFVVLT Sbjct: 241 PKAINSIPLRIILFYVLALACIIAVTSWQHVSPSKSPFVELFLVAGFPAAAGIVNFVVLT 300 Query: 304 SAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLT- 362 SAAS+ NS +FSA+R ++ LA D + F +LSK+ +P +L T L LL VL Sbjct: 301 SAASSANSGVFSASRMLFGLADLGDAPGI--FRRLSKSSVPFISLAFTTLLMLLGLVLLF 358 Query: 363 LIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSE-DYNPKG-FLTPKPQITVPFIV 420 ++P++ AF ++ + L + + L +Y YRK D + K + P + F + Sbjct: 359 VVPEVMTAFTIVSTVSAILVIFTWSTILASYIAYRKKRPDLHAKSLYKMPGGVLMAWFSL 418 Query: 421 AIFAIVFASLFFNADT 436 A A V L DT Sbjct: 419 AFLAFVLGLLALRPDT 434 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: 639 Number of extensions: 29 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: 465 Length adjustment: 33 Effective length of query: 426 Effective length of database: 432 Effective search space: 184032 Effective search space used: 184032 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