Align The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter
Query= TCDB::Q9XIH7 (511 letters) >NCBI__GCF_000226135.1:WP_010537714.1 Length = 309 Score = 143 bits (361), Expect = 8e-39 Identities = 97/321 (30%), Positives = 160/321 (49%), Gaps = 35/321 (10%) Query: 25 YAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAG 84 Y +++A++ + GYD V+SG + +L +Q +G I S+VG AG Sbjct: 9 YLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVLFAG 68 Query: 85 RTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEV 144 SD LGR+ T+V++ F AL + ++ +++ R + G+G+G +++P+Y +EV Sbjct: 69 ILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYISEV 128 Query: 145 APASSRGFLTSFPEIFINIGILLGYVSNY---------------FFSKLPEHLGWRFMLG 189 + A RG L S ++ + +G L Y+ NY + +K+ WR MLG Sbjct: 129 SVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRGMLG 188 Query: 190 VGAVPSVFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIP 249 + +P+V I + +PESPRWL+++G+ A +L+K N+ EA S+L++ K + Sbjct: 189 MEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNETKSVL--- 245 Query: 250 DDMTDDVIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPT 309 S K W LL++P I+ C+ I Q G++AV+ Y P+ Sbjct: 246 -------------TSETKSEWA-LLMKPGIFKAVIIGVCIAI--LGQFMGVNAVLYYGPS 289 Query: 310 IFSKAGLKSKNDQLLATVAVG 330 IF AGL S D L V VG Sbjct: 290 IFENAGL-SGGDSLFYQVLVG 309 Lambda K H 0.324 0.140 0.415 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: 388 Number of extensions: 25 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: 511 Length of database: 309 Length adjustment: 31 Effective length of query: 480 Effective length of database: 278 Effective search space: 133440 Effective search space used: 133440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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