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_084932255.1 HA51_RS04135 sugar porter family MFS transporter
Query= TCDB::Q9XIH7 (511 letters) >NCBI__GCF_002095475.1:WP_084932255.1 Length = 474 Score = 237 bits (605), Expect = 6e-67 Identities = 143/474 (30%), Positives = 244/474 (51%), Gaps = 27/474 (5%) Query: 19 RGNRSRYAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLV 78 + RY ++A+ ++ GYD+GV++GA ++ L L+ + ++ L + ++ Sbjct: 4 QAEHKRYMRKIIVIATFGGLLFGYDVGVINGALPYMAKSLGLNSLSTGLITSALLMGAVF 63 Query: 79 GSGAAGRTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAP 138 G+ G+ SD +GRR I+ FF L A + +MV RFV G VG A + P Sbjct: 64 GAILGGKLSDLVGRRKNILFLALLFFVSTLGCSIAPDIQTMMVCRFVLGFAVGGASVTVP 123 Query: 139 VYTAEVAPASSRGFLTSFPEIFINIGILLGYVSNYFFSKL---PEHLGWRFMLGVGAVPS 195 Y AE+APA SRG + ++ E+ I G+L+ ++SN EH+ WR+ML + +P+ Sbjct: 124 TYLAEMAPAQSRGRMVTWNELMIVGGVLIAFISNAVLGITLGENEHV-WRYMLALAMIPA 182 Query: 196 VFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDD 255 V L G+L +PESPRWLV QGR +A VL++ + I L +IK A+ Sbjct: 183 VCLFFGMLTVPESPRWLVKQGREAEAKSVLERIRDEHTAGI-ELYNIKHAIS-------- 233 Query: 256 VIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAG 315 +++ GK +++L + P +R I++ + + Q +G+++++ + I AG Sbjct: 234 -----HEQQLGKVKFRELNI---PWIRRIMLIGIAVAVFSQTTGVNSIMYFGTEILRDAG 285 Query: 316 LKSKNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVIN 375 L++ + L+ A G++ L G ++DR GRR ++L + G + L + + +++ Sbjct: 286 LET-SAALIGNTAFGLISVLSTFAGIWLLDRAGRRPMMLVGLAGTTVILLVIAIATSMLA 344 Query: 376 RNPGQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLM 435 NP + +T + F+A GPV WV SEIFP+R+R G + V + Sbjct: 345 GNPAMPY-----VVLTLTVIFLAFMQGAIGPVLWVTLSEIFPLRIRGAGMGISVAFLWIT 399 Query: 436 SGIIGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETLF 489 + IG+TF + +G + G F FA + ++ F PET+G LEE+E F Sbjct: 400 NFFIGLTFPMMLEGFGLSGTFFAFAAIGVVGFIIMKMFFPETKGKSLEEIEESF 453 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: 653 Number of extensions: 43 Number of successful extensions: 4 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: 474 Length adjustment: 34 Effective length of query: 477 Effective length of database: 440 Effective search space: 209880 Effective search space used: 209880 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