Align Fructose:H+ symporter, Frt1 (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter
Query= TCDB::Q8NJ22 (566 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 164 bits (414), Expect = 9e-45 Identities = 137/460 (29%), Positives = 215/460 (46%), Gaps = 37/460 (8%) Query: 89 TYMVIMLGFFASFAGILSGVDQSTISGASYGMKASLKLTSDEDSLISSLMPLGAVGGSIL 148 T + + A+ G L G D + ISG+ ++ +LT + + + LGA+ G ++ Sbjct: 8 TAYITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGAMVGCLI 67 Query: 149 LTPLSEYFGRKVALVISCIFYTIGGILCAAAQDVHTMYAGRFLIGVGVGIEGGGVGVYIA 208 +S+ +GRK L+I+ + + A A + RF G+GVG+ +YIA Sbjct: 68 AGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASMLSPMYIA 127 Query: 209 ESVPSTVRGSLVSLYQFNIALGELVGYVIGVIFFDV-KGGWRYMLGSSLVFSTILFVGLF 267 E P RG LV++ Q I LG L+ +I + + WR+M G + S I +G+ Sbjct: 128 ELAPPKFRGRLVAINQLTIVLGILITNLINYTLRNTGEDAWRWMFGLGAIPSGIFLIGIS 187 Query: 268 FLPESPRWLIHKGYDVEAYKVWRRLRDTSDLGNKREFLEMKHAAEQDRQLKEQESRFKSM 327 LPESPRWL+ KG + +A KV + +GN + EQ Q K +S+ Sbjct: 188 ILPESPRWLVQKGKNEKALKVLNK------IGNHEFAADALKNIEQTLQRKSNVEH-ESI 240 Query: 328 FDLILIPRNRRALLYSIMMVSLGQLTGINAIMYYMSTLMGQIGFSPKQAVAMSMVGGAAL 387 F+ + P A++ I + Q GIN + Y L IG S + ++ GA Sbjct: 241 FNKMYFP----AVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDDQLLQTVFIGAVN 296 Query: 388 LIGTIPAILYMDKFGRRPWSMTIIGFSVGLVLVGVGYQIDLNTNLAAAEGVYLTGQIL-- 445 +I TI A+ +DK GR+P + +IG + GL ++ V L + L A+ ++ +L Sbjct: 297 VIFTISAMFLVDKIGRKP--LMLIG-AGGLAVLYV-----LISQLLASGSTMVSWFLLSA 348 Query: 446 YNIFFGTYATLTWVVPSESFSLATRSIGMTICSAFLYLW------AFTVTYNFNKMKDAF 499 ++ + A +TWV+ SE F R T A L LW FT F+ +K++ Sbjct: 349 IGVYAVSLAPVTWVLISEIFPNKVRVKATT--WAILCLWGAYFVLVFTFPILFDWLKESI 406 Query: 500 TYTGLTLGFYGGIAIVIGIPYQLLFMPETKDKTLEEIDDI 539 Y + G I I F+ ETK KTLEEI+DI Sbjct: 407 FYIYAAICTLGCIGI-------WKFVKETKGKTLEEIEDI 439 Lambda K H 0.323 0.139 0.404 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: 560 Number of extensions: 30 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: 566 Length of database: 443 Length adjustment: 34 Effective length of query: 532 Effective length of database: 409 Effective search space: 217588 Effective search space used: 217588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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