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 Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= TCDB::Q9XIH7 (511 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 200 bits (508), Expect = 1e-55 Identities = 135/458 (29%), Positives = 229/458 (50%), Gaps = 40/458 (8%) Query: 33 ASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAGRTSDWLGR 92 A++ ++ G+D V+SGA+ ++ L+D L + I +++GS AG +D GR Sbjct: 29 AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88 Query: 93 RYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEVAPASSRGF 152 + ++ + +L G A + +V RF+ G+ +G A ++ P+Y AEV+PA RG Sbjct: 89 KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148 Query: 153 LTSFPEIFINIGILLGYVSNYFFSKLPEH-LGWRFMLGVGAVPSVFLAIGVLAMPESPRW 211 L + ++ I +GIL+ ++SNY + L ++ + WR+M G+ AVPS + L +PESPRW Sbjct: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208 Query: 212 LVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPD---DMTDDVIVVPNKKSAGKG 268 L + G+ R D+ + +G D ++ + +++AGK Sbjct: 209 LAIHGQ------------------ADRARDVMQRLGFADPRAELARIELAEAREEAAGK- 249 Query: 269 VWKDLLVRPTPSVRHILIAC-LGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLLATV 327 R +AC + I Q SGI+A++ Y+P IF AG + LL ++ Sbjct: 250 ------PRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAG-AGADSALLQSI 302 Query: 328 AVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNPGQTLKWAIG 387 AVG +F V ++DRFGRR LL +G + + T L + + P T Sbjct: 303 AVGGTNLVFTVAALFLIDRFGRRPLLF--VGSVICAATLLLVGWQLESAKPDGT------ 354 Query: 388 LAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMTFLSLS 447 L + ++ F+A F++ G V WV+ SE+FP +R +G +LG + +M+ I F + Sbjct: 355 LILFGLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFA 414 Query: 448 KGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEM 485 + G F F + ++ + F+PET GI LE+M Sbjct: 415 ASVG-GWVFAFFGAMMLLQLLWTWKFMPETNGIALEDM 451 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: 602 Number of extensions: 38 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 511 Length of database: 458 Length adjustment: 34 Effective length of query: 477 Effective length of database: 424 Effective search space: 202248 Effective search space used: 202248 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 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