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 Pf1N1B4_4976 D-serine/D-alanine/glycine transporter
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4976 Length = 473 Score = 321 bits (822), Expect = 4e-92 Identities = 174/460 (37%), Positives = 269/460 (58%), Gaps = 15/460 (3%) Query: 4 LQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLR 63 + E+ QR L NRHIQL+A+ G IGTGLF+G+GK I ++G S+I Y++IG+ ++F +R Sbjct: 8 ITEQAVLQRTLSNRHIQLMAMGGAIGTGLFMGSGKIIALSGTSIILIYMIIGLFVYFVMR 67 Query: 64 TIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQ 123 +GE+L ++ + SF +F Y G R +F WSYWL + + +G + Q+W P Sbjct: 68 AMGELLLSNLNFKSFADFAGAYLGPRAAFFLGWSYWLSWSVAVVGDAVVVGGFFQYWFPD 127 Query: 124 VPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTV 183 VP W+ I M+ LF LN L + FGE EFWFA+IK+ A++ +I +++L+A +F T Sbjct: 128 VPAWIPAIGMMLTLFALNVLTVKLFGEVEFWFAIIKIIAVVALISVSVLLIASSFVSPTG 187 Query: 184 LSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSL 243 + +ASL+++ D FP+G + F QM +F+F E IG AAET +P+K+L Sbjct: 188 V-------TASLTHLLDKQAAFPNGLFGFFAGFQMAIFSFAGTELIGTAAAETRSPEKTL 240 Query: 244 PKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLT 303 PKAIN IP+RI+LFYV +L+ I+A+ +W + +KSPFV +F + G AA ++NFVVLT Sbjct: 241 PKAINSIPLRIILFYVLSLVCIIAVTSWQQVSPNKSPFVELFLIAGFPAAAGIVNFVVLT 300 Query: 304 SAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLT- 362 SAAS+ NS +FS++R ++ LA + + F +LSK +P+ +L T L LL +L Sbjct: 301 SAASSANSGVFSSSRMLFGLADLGNAPGI--FRRLSKNSVPLISLAFTTFLMLLGVLLLF 358 Query: 363 LIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSED--YNPKGFLTPKPQITVPFIV 420 +IP++ AF ++ + L + + L +Y YRK+ + + P F + Sbjct: 359 IIPEVMTAFTIVSTVSAILVIFTWSTILASYIAYRKARPDLHAQSRYKMPGGVPMAWFSL 418 Query: 421 AIFAIVFASLFFNADTFYPALGAIVWTIFFGL---YSHYK 457 A A V L DT W I+ + +SH+K Sbjct: 419 AFLAFVLCLLALRPDTRLALCVMPAWFIWLAIAYQFSHFK 458 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: 596 Number of extensions: 26 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: 459 Length of database: 473 Length adjustment: 33 Effective length of query: 426 Effective length of database: 440 Effective search space: 187440 Effective search space used: 187440 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