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 CA265_RS01275 CA265_RS01275 hypothetical protein
Query= TCDB::Q9XIH7 (511 letters) >FitnessBrowser__Pedo557:CA265_RS01275 Length = 462 Score = 194 bits (493), Expect = 6e-54 Identities = 143/482 (29%), Positives = 227/482 (47%), Gaps = 46/482 (9%) Query: 25 YAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAG 84 + F ++A++ + G+D+ V+SG +K LS Q + + + +VG +G Sbjct: 9 FIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSG 68 Query: 85 RTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEV 144 SD +GRR + LA F A+ F+ YP ++ R +AG+GVG A ++P+Y +EV Sbjct: 69 YLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEV 128 Query: 145 APASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPE-HLG--------------WRFMLG 189 AP+ RG L F ++ I IGIL Y+SN F + H G WR M Sbjct: 129 APSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFI 188 Query: 190 VGAVPSVFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIP 249 VG VP+ + +L +PESPRWLV GR +A L K N E LD IK Sbjct: 189 VGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKI-NGAETGRLELDSIKE----- 242 Query: 250 DDMTDDVIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPT 309 + ++KS G +K+L+ P + +L + Q SGI+ V+ Y PT Sbjct: 243 ---------MASQKSGG---YKELMRLP---LSKLLALATILTALSQFSGINGVIFYGPT 287 Query: 310 IFSKAGLKSKNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGT 369 I AG+ + +D L V +G LF + VD +GRR L + +G + + T Sbjct: 288 ILKSAGIVT-SDALFYQVILGSANVLFTFIAISKVDTWGRRPLYI--IGSLCAAGALALT 344 Query: 370 SLTVINRNPGQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGV 429 + G W + +++ F+ F+ GP+ +V +EIFP +R S+ + Sbjct: 345 GFCFLMDITG----W---FMLFSIILFLLFFAFSLGPLKFVISTEIFPTHIRGTALSMCI 397 Query: 430 MLNRLMSGIIGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETLF 489 M + ++ M F + GL I F +F+ ++++ L ET+G LEE+E + Sbjct: 398 MTMWVSDWVVNMLFPIMRDGLGIATTFFIFSFFCILSFLYAKKKLFETKGKSLEEIEKAW 457 Query: 490 GS 491 S Sbjct: 458 NS 459 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: 592 Number of extensions: 33 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: 462 Length adjustment: 34 Effective length of query: 477 Effective length of database: 428 Effective search space: 204156 Effective search space used: 204156 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