Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_057509309.1 ABB28_RS14540 glucose/galactose MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >NCBI__GCF_001431535.1:WP_057509309.1 Length = 429 Score = 213 bits (543), Expect = 7e-60 Identities = 136/415 (32%), Positives = 212/415 (51%), Gaps = 10/415 (2%) Query: 23 TDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPA 82 T ++ ++ +FF+ GF T LN LI +K F+L+ A LV F+ +YF ++LP+ Sbjct: 11 TSVTTSIAIVGVLFFLIGFFTWLNGPLITFVKLAFELDEVGAFLVLMVFYLSYFFLALPS 70 Query: 83 GLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAY 142 ++ R G KKG+ L V GAA F A +YP LG LF++ +G+ +LQ A N Y Sbjct: 71 SWILRRTGMKKGLSLSLLVMAAGAATFGEFATQRWYPGALGGLFIIGSGLALLQTAINPY 130 Query: 143 VALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRV 202 +++LGP ++A+ R+ L N + LAP G L+L + + + A + A Sbjct: 131 ISILGPIETAARRIALMGICNKVAGMLAPVLIGTLVLHGVGDLSTAVEQADVATRAALLN 190 Query: 203 QEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLV---SPLRHPHVLF 259 A + PYLG+A +L +L+V V LP L A+ + S + PH+ Sbjct: 191 DFAAKIHAPYLGMAALLVVLSVAVLFSPLPELKSSEANAAPAGKGGIERSSIFQFPHLWL 250 Query: 260 GVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAM-IGRFIGSALLA 318 GVL +F YVG EV G + Y D+ + + LGAM +G +G L+ Sbjct: 251 GVLCLFVYVGVEVMAGDAIGTYGHGFDLPLDQTKMFTSLT----LGAMLVGYVVGLLLIP 306 Query: 319 K-LSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPM 377 + +S + L+I A++ + + T G V++ V +G N++M+P IF L I +G Sbjct: 307 RFVSQSRYLSISASLGVLFCVGAYFTHGYVSVAFVALLGFANAMMWPAIFPLAIRGLGRF 366 Query: 378 TGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLL-CYAYIVFYGLYGSR 431 T S+LL+M I GGAI+P + H+ Q F L ++ CY YI+FY G R Sbjct: 367 TETGSALLVMGIAGGAIIPQAFAVLKQHVDFQLVFLLLMVPCYLYILFYSTIGHR 421 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: 514 Number of extensions: 34 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: 429 Length adjustment: 32 Effective length of query: 410 Effective length of database: 397 Effective search space: 162770 Effective search space used: 162770 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