Align Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized)
to candidate WP_008625717.1 C943_RS06720 sugar porter family MFS transporter
Query= TCDB::AGG19156.1 (491 letters) >NCBI__GCF_000330725.2:WP_008625717.1 Length = 469 Score = 195 bits (495), Expect = 3e-54 Identities = 137/475 (28%), Positives = 236/475 (49%), Gaps = 55/475 (11%) Query: 5 LLGYDIGVMSGAAIYIEKDLKVTDTQIE------ILLGILNLYSLIGSAMAGRTSDWVGR 58 L GYD V+ GA + E +T + L+G + +G+ SD GR Sbjct: 25 LFGYDWVVVGGAKPFYEPFFNLTSPSEQGWGTSSALVGCM-----VGAIACIFLSDQFGR 79 Query: 59 RYTIVISGAIFFTGAILMGLSTNYTFLMCGRFVAGLGVGYALTIAPVYAAEVSPASSRGF 118 + ++I+G +F AI L+ + + R V G+ +G AL ++P+Y AE+SPA RG Sbjct: 80 KKLLIIAGLLFSISAIGTALAPTFWWFNFYRIVGGIAMGIALNLSPLYIAEISPAHKRGT 139 Query: 119 LTSFPEVFVNVGILLGYISNYAFSFCALDL-----------------GWRLMLGVGAIPS 161 L + ++ + +G+LL + N+ S ++L GWR M GV AIP+ Sbjct: 140 LVTINQLLIMIGVLLAQLINWRISLLDIELPEDAGFQMIAASWSGTFGWRWMFGVEAIPA 199 Query: 162 VILAIGVLAMPESPRWLVMQGRLGDARQVLDKTSDSKEESMLRLADIKEAAGIPEDCNDD 221 + + + +PESPRWLV R+ +A+++L K + + LA+I++ + ED N+ Sbjct: 200 FVFFLSMFWVPESPRWLVKADRMDEAKKILGKIG-GPQYTESALAEIQQNLTL-EDPNNS 257 Query: 222 IVQVTGHSHGEGVWKELFVHPTPTVLHILIAALGFHFFQQASGIDALVLYSPRVFEKAGI 281 G GVW + +L ++ + F QQ SG++ ++ Y+ +F+ AG Sbjct: 258 ---------GIGVWLK------APILKVVAIGIFLSFLQQWSGVNVIIYYAADIFQAAGF 302 Query: 282 TSSDQLLLCTVGVGLSKTVFTLVATFFLDRVGRRPLLLTSMAGMVVSLVCLGTSLTIVDQ 341 + Q++L V +G + + + +DR GR+ LLL + M + + +G S + Sbjct: 303 -NLKQMMLNIVVIGGVMVLSVFITIYTVDRFGRKVLLLIGTSSMAILYLLIGYS--FFAE 359 Query: 342 HEGARMTWAVVLCLFCVLAFVGFFSTGIGPIAWVYSSEIFPLRLRAQGCGMGVAVNRVMS 401 +GA + VVL VL VG +S + P+ WV SEIFP+++R + + V + Sbjct: 360 QDGASL---VVL----VLVNVGVYSFTLAPLLWVVLSEIFPIKIRGAAMSIAALAHWVGN 412 Query: 402 GILSMTFISLYKAITMGGAFFLYAAIGAVGWIFFFTMLPETQGRTLEDMEVLFGK 456 L+ F + + + F+LY AI A G+ +LPET+G++LE +E+ F + Sbjct: 413 FTLTYFFPVIKENLGWANNFWLYGAICAFGFFVILFVLPETKGKSLEQIELDFAR 467 Lambda K H 0.326 0.141 0.428 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: 626 Number of extensions: 39 Number of successful extensions: 7 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: 491 Length of database: 469 Length adjustment: 34 Effective length of query: 457 Effective length of database: 435 Effective search space: 198795 Effective search space used: 198795 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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