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 BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= TCDB::Q9XIH7 (511 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 228 bits (580), Expect = 5e-64 Identities = 142/468 (30%), Positives = 242/468 (51%), Gaps = 28/468 (5%) Query: 19 RGNRSRYAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLV 78 R N++ F C LA++ ++ G DIGV++GA FI ++ ++S E ++ + + V Sbjct: 9 RSNKTMTFFVC-FLAALAGLLFGLDIGVIAGALPFIANEFQISAHTQEWVVSSMMFGAAV 67 Query: 79 GSGAAGRTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAP 138 G+ +G S LGR+ ++++ F G+L A N +++ R + G+ VG A AP Sbjct: 68 GAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAP 127 Query: 139 VYTAEVAPASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPEHLGWRFMLGVGAVPSVFL 198 +Y +E+AP RG + S ++ I IGIL Y+S+ FS WR+MLGV +P+V L Sbjct: 128 LYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYSG---AWRWMLGVIIIPAVLL 184 Query: 199 AIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIV 258 IGV+ +P+SPRW + R DA +VL + +T EA LD+I+ ++ + Sbjct: 185 LIGVVFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLKV---------- 234 Query: 259 VPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKS 318 K +G ++K+ + R + + + QQ +G++ ++ Y+P IF AG + Sbjct: 235 ----KQSGWSLFKE-----NSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYAN 285 Query: 319 KNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNP 378 +Q+ TV VG+ L + +VDR+GR+ L+ M L + LG+ + + Sbjct: 286 TTEQMWGTVIVGLTNVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMHI----- 340 Query: 379 GQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGI 438 G A AV ++ F+ F++ AGP+ WV CSEI P++ R G + N + + I Sbjct: 341 GIHSATAQYFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMI 400 Query: 439 IGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEME 486 +G TFL++ L F ++ G+ +PET+ + LE +E Sbjct: 401 VGATFLTMLNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIE 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: 682 Number of extensions: 36 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: 464 Length adjustment: 34 Effective length of query: 477 Effective length of database: 430 Effective search space: 205110 Effective search space used: 205110 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 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