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_058858199.1 AS188_RS06680 sugar porter family MFS transporter
Query= TCDB::Q9XIH7 (511 letters) >NCBI__GCF_001482365.1:WP_058858199.1 Length = 482 Score = 219 bits (559), Expect = 1e-61 Identities = 143/459 (31%), Positives = 238/459 (51%), Gaps = 23/459 (5%) Query: 30 AILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAGRTSDW 89 +I+A ++ GYD GV++GA + ++L L+ ++ L + VG+ + GR SD Sbjct: 30 SIVACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRISDA 89 Query: 90 LGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEVAPASS 149 GRR TI+L FF G +++ F NY ++ GR G+ VG A + PV+ AE+AP Sbjct: 90 WGRRRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAPYEI 149 Query: 150 RGFLTSFPEIFINIGILLGYVSNYFFSK--LPEHLGWRFMLGVGAVPSVFLAIGVLAMPE 207 RG + E+ I IG L +V N + WR+M + A+P+V L +G+L MPE Sbjct: 150 RGSIAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLRMPE 209 Query: 208 SPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIVVPNKKSAGK 267 SPRWLV +GR +A +VL ++ ++E A++ L +++ V ++SA Sbjct: 210 SPRWLVEKGRHEEALEVL-RSVRSEERAVAELGEVEH--------------VAEEESAEN 254 Query: 268 GVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLLATV 327 + ++R +R I++ +G+ AQQ +GI++++ Y + ++G S + L+A + Sbjct: 255 RIGLGAVLRNKWLIR-IMLVGIGLGIAQQLTGINSIMYYGQIVLIESGF-SASAALIANI 312 Query: 328 AVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNPGQTLKWAIG 387 A GV+ + + ++DR RR + +G + V+ G L+ + Sbjct: 313 APGVIAVVGGFIALAMMDRLDRRKTFVIGFSLTTTCHLLIGIASVVLEE--GNPLRPFVI 370 Query: 388 LAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMTFLSLS 447 LA+ V+ FV + WVY SE+FP+ +R G + + + +G++ + F SL Sbjct: 371 LAL--VVAFVGSMQTFLNVAVWVYLSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLV 428 Query: 448 KGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEME 486 + I G F LFAGV A VF T +PETRG LE +E Sbjct: 429 DAVGITGTFFLFAGVGVLALVFVATQVPETRGRTLEALE 467 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: 657 Number of extensions: 40 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: 482 Length adjustment: 34 Effective length of query: 477 Effective length of database: 448 Effective search space: 213696 Effective search space used: 213696 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: 52 (24.6 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