Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 6936374 Sama_0562 glucose/galactose transporter (RefSeq)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__SB2B:6936374 Length = 413 Score = 380 bits (976), Expect = e-110 Identities = 209/438 (47%), Positives = 283/438 (64%), Gaps = 29/438 (6%) Query: 1 MAFAAPPAPSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLN 60 MAF + P G+A + + G +TS+FF+WGF+T LNDILIPHLK +F L+ Sbjct: 1 MAFVSSTTPQN----GSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLS 56 Query: 61 YAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPA 120 Y +AMLVQF FFGAYFL+S AG+L+AR+GY +GI+ GL+ G F+PA+++ Y Sbjct: 57 YTQAMLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYAL 116 Query: 121 FLGALFVLATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILS 180 FL ALFVLA+GIT+LQV+AN +VA LGPE++A+SRL LAQALNSLG L P FG LLI Sbjct: 117 FLLALFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFG 176 Query: 181 AAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAV-FVYLFRLPALTEKTE 239 AA + E VQ PYL LA V+ ++AV F++L K Sbjct: 177 AAAGTHE-------------------AVQLPYLLLAAVIGIIAVGFIFL----GGKVKHA 213 Query: 240 QASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWV 299 V S L H +L G LAIF YVG EV+IGSFLVNY + P IG + E++AA V Sbjct: 214 DMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELV 273 Query: 300 AYYWLGAMIGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFN 359 ++YW GAMIGRF G+AL + +P +LA A L++ T+++ G +A+ +V+++G FN Sbjct: 274 SWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFN 333 Query: 360 SIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCY 419 SIMFPTIF+L IE +G +T S LL AIVGGA++P +QG+ AD++GVQ +F +P CY Sbjct: 334 SIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCY 393 Query: 420 AYIVFYGLYG-SRIKSDT 436 YI +Y + +R+ +T Sbjct: 394 FYICWYAFFARNRMNGET 411 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: 543 Number of extensions: 24 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: 413 Length adjustment: 32 Effective length of query: 410 Effective length of database: 381 Effective search space: 156210 Effective search space used: 156210 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