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 RR42_RS28305 RR42_RS28305 proline-specific permease
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 286 bits (732), Expect = 1e-81 Identities = 169/460 (36%), Positives = 251/460 (54%), Gaps = 14/460 (3%) Query: 2 ENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFF 61 E + E+ + RGL++RHIQ+IAI G IG GLFLGAG+ I + GP ++ +Y + G+A+FF Sbjct: 11 ERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFI 70 Query: 62 LRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWL 121 +R +GE+L P SF + ++ G G+ T WSYW + V ++E+TA+ Y+ +W Sbjct: 71 MRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWF 130 Query: 122 PQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYS 181 P VP W+ + LA+L+ +N + FGE EFWFA+IKV I+ MIV + ++ F Sbjct: 131 PDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAII---FFGV 187 Query: 182 TVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKK 241 T L +AS SN++ P G V LQ+VMFA+ +E IG+TA E NP+K Sbjct: 188 TPLG-----PTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEK 242 Query: 242 SLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVV 301 LP A N + RIL+FYVGAL+ +MA+ W+ + SPFV VF+ IG+ AAA++N VV Sbjct: 243 VLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVV 302 Query: 302 LTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVL 361 +T+AAS+ NS +FS R +Y+LAQ R F ++S +P A+ + AL + +L Sbjct: 303 ITAAASSCNSGIFSTGRMLYTLAQFGQAPR--AFGRVSSKHVPSIAITFSAALMGIGVLL 360 Query: 362 TLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRK---SEDYNPKGFLTPKPQITVPF 418 I + F + S + L + I + + YRK + F P Sbjct: 361 NYIVP-EQVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWL 419 Query: 419 IVAIFAIVFASLFFNADTFYPALGAIVWTIFFGLYSHYKK 458 +VA V L + T A VW G+ + K Sbjct: 420 VVAFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGYRFTK 459 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: 666 Number of extensions: 35 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: 472 Length adjustment: 33 Effective length of query: 426 Effective length of database: 439 Effective search space: 187014 Effective search space used: 187014 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