Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Ga0059261_2650 Ga0059261_2650 glucose/galactose transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Korea:Ga0059261_2650 Length = 425 Score = 342 bits (878), Expect = 1e-98 Identities = 187/431 (43%), Positives = 275/431 (63%), Gaps = 17/431 (3%) Query: 2 AFAAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNY 61 A A P AP+ S Y A+ +L S+FFMWGF+T +N+ L+PHL++VF L+Y Sbjct: 7 AGAVPAAPAPES-----------YRRALALLASLFFMWGFITVINNTLLPHLRSVFDLDY 55 Query: 62 AEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAF 121 L++ +F AYF+ S+P+ L+ R+GY++ +VAGL V G+AG AA++ Y Sbjct: 56 TRTTLIESVWFIAYFVASIPSARLIERIGYQRSLVAGLLVMAAGSAGMMLAASIPSYGVT 115 Query: 122 LGALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSA 181 L LFV+A+GIT+LQVAAN YVA++G ++ASSRL L QA+NS GT LAP FG LIL Sbjct: 116 LAMLFVIASGITLLQVAANPYVAVVGRPETASSRLNLVQAMNSAGTMLAPAFGAWLILGR 175 Query: 182 AV-LSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQ 240 + ++E L+ AE+ A +AQ+V PY +A+ L +LA+ + F LPA+ T + Sbjct: 176 SKGGTSEAGTVLTQAERFA----DAQSVILPYGLVAVALVMLALVIACFPLPAMGAATRR 231 Query: 241 ASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVA 300 + ++ S +H +++FGV AIF Y+ E+ + + VN++S PDI N++ + A +++ Sbjct: 232 LAKEERRNHSLWKHRNLVFGVPAIFIYLIAEIGVANLFVNFVSQPDIANLTHEQAGHYLT 291 Query: 301 YYWLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNS 360 + W G M GRF GSAL+ + +LA+FA A++L G AM++++ +G F+S Sbjct: 292 FLWGGMMAGRFAGSALMQRFDAAHVLAVFAIGAFAVMLVATFATGPTAMWALILVGFFHS 351 Query: 361 IMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYA 420 IMFPTIF+LGI +GP+T E S LLIMAI GGA+V VQG AD G+Q +F L C Sbjct: 352 IMFPTIFTLGIRGLGPLTEEGSGLLIMAIAGGALV-IVQGWLADQWGLQLSFLLTAACEV 410 Query: 421 YIVFYGLYGSR 431 Y++FY L+GSR Sbjct: 411 YVLFYALWGSR 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: 459 Number of extensions: 17 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: 425 Length adjustment: 32 Effective length of query: 410 Effective length of database: 393 Effective search space: 161130 Effective search space used: 161130 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