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 N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 292 bits (748), Expect = 1e-83 Identities = 158/395 (40%), Positives = 229/395 (57%), Gaps = 11/395 (2%) Query: 4 LQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLR 63 +Q QRGLQ RHI+L+A+ IG GLFLG+ I++ GP+++ +Y+L G+A+F +R Sbjct: 1 MQTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMR 60 Query: 64 TIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQ 123 +GEM +P SF + Y G GY T W+YW + + CI+E+TA+G Y+ W P Sbjct: 61 ALGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPD 120 Query: 124 VPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTV 183 VP W+ + L + +N + +GE EFWFAMIKV I+ MIV ++ V Sbjct: 121 VPQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGV 180 Query: 184 LSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSL 243 +G +SN++ P+GA + ALQMVMFA+ +E IG+TA E NPKKS+ Sbjct: 181 PTG--------ISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSI 232 Query: 244 PKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLT 303 P AIN + RIL+FYVGAL IM+I+ W+ + SPFVM F+ +GIK AA +INFVVLT Sbjct: 233 PDAINSVFWRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLT 292 Query: 304 SAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLTL 363 +A S+ N ++S R +++LAQQ R F S +GIP A+ ++ L +L Sbjct: 293 AALSSCNGGIYSTGRMLFNLAQQGQAPR--TFAVTSPSGIPNRAVLVSLVALLFGVLLNY 350 Query: 364 IPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRK 398 + K F + S T + + I L T +YR+ Sbjct: 351 LVPAK-VFVWVTSAATFGAIWTWGIVLITQMKYRR 384 Score = 24.3 bits (51), Expect = 0.009 Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 18/147 (12%) Query: 3 NLQEKHEAQR--------GLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILI 54 NL ++ +A R G+ NR + + +A L G + P+ +F ++ Sbjct: 311 NLAQQGQAPRTFAVTSPSGIPNRAVLVSLVA--------LLFGVLLNYLVPAKVFVWVT- 361 Query: 55 GIAMFFFLRTIGEMLYNDPSQHSFLNFVTKYSGV-RTGYFTQWSYWLVIVFVCISELTAI 113 A F + T G +L L+ + V R +F SY + V + L Sbjct: 362 SAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGY 421 Query: 114 GTYIQFWLPQVPLWLIEIVMLALLFGL 140 + L PLWL+ + +L +FGL Sbjct: 422 FPDTRVALIVGPLWLVLLTVLYYVFGL 448 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: 632 Number of extensions: 31 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 459 Length of database: 454 Length adjustment: 33 Effective length of query: 426 Effective length of database: 421 Effective search space: 179346 Effective search space used: 179346 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