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_013644894.1 METBO_RS06515 sugar porter family MFS transporter
Query= TCDB::Q9XIH7 (511 letters) >NCBI__GCF_000191585.1:WP_013644894.1 Length = 453 Score = 283 bits (723), Expect = 1e-80 Identities = 164/466 (35%), Positives = 265/466 (56%), Gaps = 32/466 (6%) Query: 25 YAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAG 84 + A + S+ ++ GYD GV+SGA +FI++D LS E+ + + I +++G+ +G Sbjct: 13 FVILVAAITSIGGLLFGYDTGVISGAILFIREDFLLSTTAQEVTVSAVLIGAVIGASISG 72 Query: 85 RTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEV 144 +D GR+ IVLA F GA+ + N +++ R V GI +G A I P+Y AEV Sbjct: 73 ILADRYGRKIMIVLASIIFGIGAIFSSVSPNVNALIISRVVVGIAIGMASFIVPLYIAEV 132 Query: 145 APASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPEHLGWRFMLGVGAVPSVFLAIGVLA 204 AP + RG L S ++ I +GI++ Y+ + +F+ + WR+MLG+ +PS+ LA+G+ Sbjct: 133 APINIRGALVSLNQLAITLGIVISYMVDLYFA---PNGSWRWMLGLAVIPSLILALGMFF 189 Query: 205 MPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIVVPNKKS 264 MP SPRWL+ +G A VL K I +D++ + V + + +++ N Sbjct: 190 MPPSPRWLISKGFESKAVAVLKK--------IRGIDNVDKEV----NEIEQTLLLEN--- 234 Query: 265 AGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLL 324 +G W DLL P +R LI +G+ QQ +GI+ V+ Y+PTI AGL++ + Sbjct: 235 --EGKWSDLL---EPKIRSALIIGIGLAAFQQLTGINTVIYYAPTILEFAGLQTATVTIF 289 Query: 325 ATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNPGQT--L 382 ATV +GVV L VV ++DR GRR LLL + GM +SL +G + + PG T L Sbjct: 290 ATVGIGVVNVLLTVVSILLIDRLGRRPLLLAGITGMIVSLGIMGLAFII----PGLTSSL 345 Query: 383 KWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMT 442 W LAV +M +V +F+I GP+ W+ +EI+P+R+R + S+ M+N + ++ +T Sbjct: 346 GW---LAVICLMLYVGSFAISLGPIFWLMIAEIYPLRIRGRAMSIVTMINWATNLVVAIT 402 Query: 443 FLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETL 488 FL++ + L G F L+ +A + +F + +PET+G LEE+E L Sbjct: 403 FLTIIELLGASGTFWLYGVIAVLSLLFVYYRVPETKGKSLEEIERL 448 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: 649 Number of extensions: 41 Number of successful extensions: 6 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: 453 Length adjustment: 34 Effective length of query: 477 Effective length of database: 419 Effective search space: 199863 Effective search space used: 199863 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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