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 BPHYT_RS21680 BPHYT_RS21680 amino acid permease-associated protein
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__BFirm:BPHYT_RS21680 Length = 476 Score = 212 bits (539), Expect = 2e-59 Identities = 134/442 (30%), Positives = 222/442 (50%), Gaps = 23/442 (5%) Query: 1 MENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFF 60 M+ + E + GL+ RH+ +IA+ G IG GLF+G+G +Q GP+ + ++++ G + Sbjct: 1 MQRSTDTTELKAGLKQRHMTMIALGGVIGAGLFVGSGVVVQQAGPAAVLSFLITGALVVL 60 Query: 61 FLRTIGEMLYNDPSQHSFLNFVT------KYSGVRTGYFTQWSYWLVIVFVCISELTAIG 114 +R +GEM P+ SF + + SG G+ T W YW V V E A Sbjct: 61 VMRMLGEMACAMPAVGSFYEYARLAFGGKRASGNLAGFLTGWMYWYFWVIVVAVEAVAGA 120 Query: 115 TYIQFWLPQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILV 174 +QFWLP VP W I +V+L L N ++ +GE EFWFA IKVAAI+ + + V Sbjct: 121 KLVQFWLPDVPAWAISLVLLVTLTATNLVSVGSYGEFEFWFASIKVAAIMVFLFLGGMYV 180 Query: 175 AGNFHYSTVLSGKTVHDSASLSNIFDGFQLFPHGAWNFV-GALQMVMFAFTSMEFIGMTA 233 G L H +A L + L P G + GA+ F F E + + A Sbjct: 181 LG-------LWPAAKHVTAVLPTLLSHGGLMPKGIGPVLSGAVAATGFYF-GAEIVTIAA 232 Query: 234 AETVNPKKSLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWA 293 AE P K++ KA N + R+L+FYVG++L ++A+ W+ P +P+V +GI A Sbjct: 233 AEAQEPAKAVAKATNSVITRVLVFYVGSILLVVALVPWN-SPKMATPYVSALDAMGIPAA 291 Query: 294 AALINFVVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATA 353 A+++N +VLT+ SALNS L++A+R +++L + D K+++ G+P+ A+ + T Sbjct: 292 ASVMNAIVLTAVLSALNSGLYAASRMIFALTRHGDAP--AALAKVNRRGVPVRAILIGTV 349 Query: 354 LSLLAPVLTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPKGFLTPK-- 411 + V++ + F F + + + VY + + + R + + L + Sbjct: 350 FGYASVVMSYVSP-DTVFAFLVNSYGTVAIFVYVLIAISQLKLRARIERDAPEKLRVRMW 408 Query: 412 --PQITVPFIVAIFAIVFASLF 431 P +T I+ + I+ A F Sbjct: 409 CYPYLTWVAIIGMVGILVAMAF 430 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: 577 Number of extensions: 33 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: 476 Length adjustment: 33 Effective length of query: 426 Effective length of database: 443 Effective search space: 188718 Effective search space used: 188718 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