Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 7025545 Shewana3_2696 major facilitator transporter (RefSeq)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__ANA3:7025545 Length = 452 Score = 215 bits (547), Expect = 3e-60 Identities = 144/418 (34%), Positives = 220/418 (52%), Gaps = 25/418 (5%) Query: 35 IFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVARLGYKKG 94 +FF++GF+T LN LIP LK +LN EA LV F F+ AYF+M+LP ++ RLGYK G Sbjct: 27 LFFVFGFVTWLNGALIPFLKIACQLNEFEAYLVTFVFYIAYFVMALPTSSILTRLGYKMG 86 Query: 95 IVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGPEKSASS 154 + GL + GA F AA + + FL ALFVL TG+T+LQ AAN Y+ +GP +SA+ Sbjct: 87 MTLGLGIMAAGAGLFIVAALVGHFATFLLALFVLGTGLTLLQTAANPYIVCIGPRESAAM 146 Query: 155 RLTLAQALNSLGTFLAP-KFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTVQGPYL 213 R++L +N F+ P F ++ S +A LS A++ + A + PYL Sbjct: 147 RISLMGIVNKGAGFIVPIIFTAWILTGMEPYSETALASLSEAQRQLALTELANRLVHPYL 206 Query: 214 GLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVA 273 + +VL L FV+ LP E E+ Q + L++P V+ G L +F YVG EV Sbjct: 207 MMMLVLLGLMAFVWFSPLPE-PELGERVERTQTDWKAILQYPQVILGALTLFCYVGAEVI 265 Query: 274 IGSFLVNY---LSMPDIGNMSEQAAANWVAYYWLGAMI--------GRFIGSALLAKLSP 322 G + + L + G M+ V Y LG ++ +GSA+ L Sbjct: 266 AGDSIGLFSQGLGVAHFGMMTSYTMGFMVLGYVLGILLIPRWISQQTALVGSAIAGLLF- 324 Query: 323 RKLLAIFAAINMALVLTTMMTKGTVAMYSV-------VSIGLFNSIMFPTIFSLGIERMG 375 L + + + + L+ ++ G + + V +GL N++++P ++ L +E +G Sbjct: 325 --TLGVLLSDSQSQALSELLL-GWLGVLPVPDPVLYLALLGLANALVWPAVWPLALEGLG 381 Query: 376 PMTGEASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFYGLYGSRI 432 +T AS+LLIM I GGAI+P + G A G Q A+FL L CY I +Y ++G ++ Sbjct: 382 RLTATASALLIMGIAGGAILPLLYGYIAHSQGDSQMAYFLLLPCYGLIFYYAIWGHKL 439 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: 521 Number of extensions: 27 Number of successful extensions: 5 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: 452 Length adjustment: 33 Effective length of query: 409 Effective length of database: 419 Effective search space: 171371 Effective search space used: 171371 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