Align Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= TCDB::AIU41385.1 (509 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 242 bits (617), Expect = 2e-68 Identities = 148/455 (32%), Positives = 242/455 (53%), Gaps = 28/455 (6%) Query: 32 ILASMTSILLGYDIGVMSGASIYIQEDLKISDVEVEILIGILNLYSLIGSAAAGRTSDWI 91 +LA++ ++ G DIGV+SGAS +I+ + ISD +E ++ + + +G+ AG S + Sbjct: 22 VLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEWIVSSMMFGAAVGALGAGWLSSHL 81 Query: 92 GRRYTIVFAGAIFFTGALLMGFATNYAFLMVGRFVAGIGVGYALMIAPVYNAEVSPASSR 151 GR+ +++ +F G+LL G A + L+ R + G+ +G A AP+Y AEV+P R Sbjct: 82 GRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLAEVAPEHIR 141 Query: 152 GALTSFPEVFVNIGILLGYVANYAFSGLPINLGWRLMLGVGVFPSVILAVGVLTMPESPR 211 GA+ S ++ + IGIL+ ++++ A S + WR MLGV P + +GVL +P+SPR Sbjct: 142 GAMISTYQLMITIGILVAFLSDTALS---YHGAWRWMLGVIAIPGALFLLGVLGLPDSPR 198 Query: 212 WLVMQGRLGDAKHVLDKTSDSLEEAQLRLADIKEAAGIPEHCTEDVVQVPKHSHGEEVWK 271 WL+M+GR +A VL + ADI+E P+ G +++ Sbjct: 199 WLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQ-------------RGWDLFA 245 Query: 272 ELLLHPTPPVRHILIAAVGFHFFQQMSGIDALVLYSPRIFRASGITDSSTLLLATVAVGF 331 E P R + QQ +G++ ++ Y+PRIF+ G D++ + T VG Sbjct: 246 E-----NPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGY-DTAAQMWFTALVGL 299 Query: 332 SKTIFTLIAIGFLDRVGRRPLLLTSVAGMIASLLCLGTSLT-IVDHEKEKMMWASVVCLT 390 + + T IAI +DR GR+P+L T A M L +G + ++ + E+ C+ Sbjct: 300 TNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTEQ-----YTCVA 354 Query: 391 MVLAYVGFFSIGMGPIAWVYSSEIFPLKLRAQGCSMGTAVNRIMSGVLTMTFITLYKAIT 450 M+L ++ F++ GP+ W SEI PLK R G + T N I + V+ TF++L I Sbjct: 355 MLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIG 414 Query: 451 MGGTFFLYGAIATVGWVFFYTMLPETQGRTLEDME 485 TF+LY A+ V V + ++PET+G TLE +E Sbjct: 415 NASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIE 449 Lambda K H 0.326 0.140 0.424 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: 688 Number of extensions: 42 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: 509 Length of database: 463 Length adjustment: 34 Effective length of query: 475 Effective length of database: 429 Effective search space: 203775 Effective search space used: 203775 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