Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_008483730.1 B3C1_RS06620 sugar MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >NCBI__GCF_000299915.1:WP_008483730.1 Length = 438 Score = 218 bits (555), Expect = 3e-61 Identities = 140/443 (31%), Positives = 239/443 (53%), Gaps = 34/443 (7%) Query: 12 TSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTF 71 T++ + ++R + PMA ++ ++FF++GF+T LN LIP L+ V L +A+ V F+F Sbjct: 3 TTMSASQQQRSSLMPMA--IIGTLFFIFGFVTWLNGALIPFLQIVCDLTSTQALFVAFSF 60 Query: 72 FGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATG 131 + AY + +LP ++ R GYKKG+ GL + +G GF PAA + FL + FV+ TG Sbjct: 61 YIAYTVTALPMAWIMERTGYKKGMALGLGLIALGCLGFIPAAMSQTFAIFLVSQFVVGTG 120 Query: 132 ITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAP-KFGGLLILSAAVLSAEQIA 190 +T+LQ A+N Y+ +GP++SA+ R+++ LN +AP F L++ ++A+ +A Sbjct: 121 LTILQTASNPYIVHIGPQESAAVRISIMGLLNKGAGVVAPLVFTALVLGDFEGITAKTVA 180 Query: 191 KLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVS 250 L+PAE+ A Q A + PYLG+A+ + LL + + LP L T+ A + S Sbjct: 181 TLAPAERAAQVEQLAHGLILPYLGMALAMVLLTIAMVFSPLPELALDTD-ADDTEDDKRS 239 Query: 251 PLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGR 310 L+ P ++ G + IF YVG EV + + S + N A + +Y +IG Sbjct: 240 VLQFPQLVLGAVGIFCYVGVEVIAADTIGLFGSELGVAN-----ATSLTSYTMAFMVIGY 294 Query: 311 FIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKG----------------------TVA 348 +G L+ ++ + L +A+ + LVL+ + G TVA Sbjct: 295 LLGLVLIPRVLKQSLALTLSAV-LGLVLSLAVVLGSPEQHWLSDTLWGWLGLPTVPNTVA 353 Query: 349 MYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGV 408 + V +G N++++P I+ L ++ +G T + S+LLIM I GGA++P + G +D Sbjct: 354 L--VALLGFANAMVWPAIWPLALDGLGKFTAKGSALLIMGIAGGALLPLLYGYLSDVADH 411 Query: 409 QHAFFLPLLCYAYIVFYGLYGSR 431 Q A+ + L CY +I+++ L G + Sbjct: 412 QQAYLMMLPCYLFILYFALAGHK 434 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: 498 Number of extensions: 20 Number of successful extensions: 3 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: 438 Length adjustment: 32 Effective length of query: 410 Effective length of database: 406 Effective search space: 166460 Effective search space used: 166460 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