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 WP_009122015.1 BUB52_RS10060 sugar porter family MFS transporter
Query= TCDB::AIU41385.1 (509 letters) >NCBI__GCF_900129655.1:WP_009122015.1 Length = 479 Score = 268 bits (684), Expect = 4e-76 Identities = 155/479 (32%), Positives = 255/479 (53%), Gaps = 41/479 (8%) Query: 31 AILASMTSILLGYDIGVMSGASIYIQEDLKISDVEVEILIGILNLYSLIGSAAAGRTSDW 90 AI+A+ +L G+D GV+SGA ++Q+D I D +E++ + ++ G+ G+ +D+ Sbjct: 17 AIIAATGGLLFGFDTGVISGAIPFLQKDFGIDDGVIELITTAGLVGAIAGALFCGKVTDY 76 Query: 91 IGRRYTIVFAGAIFFTGALLMGFATNYAFLMVGRFVAGIGVGYALMIAPVYNAEVSPASS 150 +GR+ I+ + IF GA+ G A + L++ R GI +G + P+Y AE+SP + Sbjct: 77 LGRKKVILASAVIFAIGAVWSGIAPDSTNLILARLFLGIAIGVSSFAVPLYIAEISPTNI 136 Query: 151 RGALTSFPEVFVNIGILLGYVANYAFSGLPINLGWRLMLGVGVFPSVILAVGVLTMPESP 210 RG L S ++ V +G+L+ Y+++ F+ WR M G+ P++IL +G+ MPESP Sbjct: 137 RGTLVSMFQLMVTLGVLVSYLSDLFFADEVDVTCWRPMFYAGILPALILLIGMFCMPESP 196 Query: 211 RWLVMQGRLGDAKHVLDKTSDSLEEAQLRLADIKEAAGIPEHCTEDV-VQVPKHSHGEEV 269 RWL+ +GR A +L+K E G E + ++ K + Sbjct: 197 RWLMSKGRKQKAMLILNKI---------------EGHGAAEEVAHSINEEIEKSKNEISK 241 Query: 270 WKELLLHPTPPVRHILIAAVGFHFFQQMSGIDALVLYSPRIFRASGITDSSTLLLATVAV 329 W EL+ P +R L A+G FFQQ GI+ ++ YSP+IF +G + + + A V V Sbjct: 242 WSELI---KPTLRTPLFIAIGIMFFQQFVGINTVIYYSPKIFFMAGFDGAVSAIWAAVGV 298 Query: 330 GFSKTIFTLIAIGFLDRVGRRPLLLTSVAGMIASLLCLGTSLTIVDHEKEKMMWASVVCL 389 G + TL++I F+DR+GRR L T + G+I SL+ L S V+ W +V+ Sbjct: 299 GVVNVVATLVSIYFVDRLGRRKLYFTGLTGIILSLITLSLSFVFVNELGNAGQWLTVI-- 356 Query: 390 TMVLAYVGFFSIGMGPIAWVYSSEIFPLKLRAQGCSMGTAVNRIMSGVLTMTFITLYKAI 449 + YV FF+I +GP+ W+ SE+FP K+R G S+G+ + + +++ TF + A+ Sbjct: 357 -FMFLYVAFFAISIGPLGWLIISEVFPQKVRGLGASVGSLSVWVFNSIVSFTFFKIVNAL 415 Query: 450 TMGGT---------------FFLYGAIATVGWVFFYTMLPETQGRTLEDMEVLFGKFWR 493 T+ GT F YG IA + ++ Y +PET+G +LE +E +WR Sbjct: 416 TIPGTEIMVDGEQVGNPAGAFGFYGLIALLALIWGYFYVPETKGISLEKIE----DYWR 470 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: 718 Number of extensions: 49 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: 479 Length adjustment: 34 Effective length of query: 475 Effective length of database: 445 Effective search space: 211375 Effective search space used: 211375 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 24 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