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 AO356_27270 AO356_27270 MFS transporter
Query= TCDB::Q9XIH7 (511 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27270 Length = 472 Score = 229 bits (585), Expect = 1e-64 Identities = 150/488 (30%), Positives = 245/488 (50%), Gaps = 25/488 (5%) Query: 1 MNSSGVEQGVVIAESEPPRGNRSRYAFACAILASMTSIILGYDIGVMSGASIFIKDDLKL 60 +NS G P + RY +A+ ++ G+D GV++GA +++KDDL L Sbjct: 3 INSYGNTADTSATFVSPEKHQAQRYLQKITWIATFGGLLFGFDTGVINGALLYMKDDLGL 62 Query: 61 SDVQLEILMGILNIYSLVGSGAAGRTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIM 120 + ++ L I +++G+ +GR SD GRR I+ FF GAL A ++ Sbjct: 63 TPFTEGLVASALLIGAMMGALFSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLNVMV 122 Query: 121 VGRFVAGIGVGYAMMIAPVYTAEVAPASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPE 180 RF G+ VG A ++ P Y AE+AP+S RG + + E+ I G L + +N L Sbjct: 123 AARFTLGLAVGGASVVVPAYLAEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFS 182 Query: 181 HLG--WRFMLGVGAVPSVFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISR 238 L WR+ML + +P+V L +G+L MPESPRWL +GR + +VL K + A + Sbjct: 183 DLDGVWRWMLALATLPAVALWLGMLYMPESPRWLATKGRFREGLEVL-KLVREEYYAKAE 241 Query: 239 LDDIKRAVGIPDDMTDDVIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQAS 298 ++ I + + N++ KG W+DL + R I + +GI Q + Sbjct: 242 MEAITQQIS-------------NERFIKKGGWRDLSQK---GARRIFLIGIGIAVTSQLT 285 Query: 299 GIDAVVLYSPTIFSKAGLKSKNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMG 358 G+++++ + I ++AGL+ ++ L+A V GV+ VG ++DR GRR ++L Sbjct: 286 GVNSIMYFGTQILTEAGLEQRS-ALIANVVNGVISIGATFVGIALLDRVGRRPMMLLGFT 344 Query: 359 GMFLSLTALGTSLTVINRNPGQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPV 418 G LSL +G ++ + + + L + + F+A+ GP WV +EIFP+ Sbjct: 345 GTTLSLLLIGLVSVFVDPSVTRAM-----LILGAMAMFLASMQGLIGPAFWVLLAEIFPM 399 Query: 419 RLRAQGASLGVMLNRLMSGIIGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETR 478 R+R + + L + +IGM F SL + IG F +F G + F ++PETR Sbjct: 400 RIRGGCMGMAIAAFWLTNVMIGMFFPSLVATIGIGQTFFVFVGAGLLSLTFVAVWVPETR 459 Query: 479 GIPLEEME 486 G LEE+E Sbjct: 460 GSTLEEIE 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: 667 Number of extensions: 47 Number of successful extensions: 5 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: 472 Length adjustment: 34 Effective length of query: 477 Effective length of database: 438 Effective search space: 208926 Effective search space used: 208926 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