Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate CA265_RS08675 CA265_RS08675 glucose/galactose MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Pedo557:CA265_RS08675 Length = 428 Score = 213 bits (542), Expect = 9e-60 Identities = 131/416 (31%), Positives = 215/416 (51%), Gaps = 10/416 (2%) Query: 23 TDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPA 82 T P + ++ ++FF++GF+T N LIP K F L+ +A V F + AYF ++LP+ Sbjct: 10 TQGPKPLIIICALFFIFGFVTWANGTLIPFFKLSFGLSNLQAFFVTFASYMAYFFLALPS 69 Query: 83 GLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAY 142 ++ ++G+K GIV GL + G+G+ F PAA + FL +FV + +LQ A+N Y Sbjct: 70 SWILKKVGFKNGIVLGLVILGLGSLIFIPAAQTRTFGLFLTGIFVQGAALALLQTASNPY 129 Query: 143 VALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRV 202 + ++GP +SA+ R+++A N + P G L L A +QI + A Sbjct: 130 LTIIGPIESAAKRISIAGICNKFAGMIVPLIMGSLFLKNASEVEKQIKAATGAVHEQLLN 189 Query: 203 QEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLV---SPLRHPHVLF 259 V PY+ LAIV L A+F+ LP + + + + +V S + PH+ Sbjct: 190 DVLGRVNMPYIVLAIVFCLFAIFIKFTNLPEVEVEEDVIDESKGEVVKHKSIFQFPHLFL 249 Query: 260 GVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAK 319 G L IF YVG EV G + Y ++G +S + + + +IG IG + K Sbjct: 250 GALCIFVYVGAEVMAGDIIGIY--GRELG-ISPEISGKLTSITLFSMLIGYIIGIVTIPK 306 Query: 320 -LSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMT 378 +S +K L I A + + + + + A+ V +GL NS+M+P IF LGI +G T Sbjct: 307 YISQQKALRICAILGIIFTILSFVISSWFAVIFVALLGLANSLMWPAIFPLGISHLGKFT 366 Query: 379 GEASSLLIMAIVGGAIVPFVQGLFAD--HIGVQHAFFLPLL-CYAYIVFYGLYGSR 431 S+++IM I GGA++P + + H+ Q A+ L +L CY YI+++ + G + Sbjct: 367 KIGSAIMIMGIAGGALMPLLYAFLNEKLHVNFQLAYLLTVLPCYLYILYFAIKGHK 422 Lambda K H 0.327 0.140 0.414 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: 459 Number of extensions: 23 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: 442 Length of database: 428 Length adjustment: 32 Effective length of query: 410 Effective length of database: 396 Effective search space: 162360 Effective search space used: 162360 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 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