Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 5208608 Shew_1119 glucose/galactose transporter (RefSeq)
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__PV4:5208608 Length = 418 Score = 196 bits (497), Expect = 2e-54 Identities = 140/426 (32%), Positives = 222/426 (52%), Gaps = 30/426 (7%) Query: 29 MGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVAR 88 M ++ +FF+ GF T LN L+P+LK + +L +A L+ F+F+ A +LP+ ++ + Sbjct: 1 MAIVAGLFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRK 60 Query: 89 LGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGP 148 +GYK G+ G+ + + F PAA + FL A V+ TG T+LQ A N YV +GP Sbjct: 61 VGYKTGMAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGP 120 Query: 149 EKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQE-AQT 207 E+SA++R+++ LN +AP L+ +A +L + E ++ E A Sbjct: 121 EESAAARVSVMGILNKGAGVIAP-----LVFTALIL--DSFKDRVGVELTQAQIDEMANG 173 Query: 208 VQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAIFFY 267 + PYLG+AI + +LA+ V LP L + EQ + L HP++ GV+A+FFY Sbjct: 174 LVFPYLGMAIFIGVLALLVKKSPLPELENEDEQEEGTKGHTREALSHPNLALGVVALFFY 233 Query: 268 VGGEV----AIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAM-IGRFIG-------SA 315 V EV IG+F ++ L + + G M+ V Y LG + I RFI SA Sbjct: 234 VAVEVIAGDTIGTFALS-LGVENYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISA 292 Query: 316 LLAKLSPRKLL----AIFAAINMALV-LTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLG 370 +L + +L +A N LV M T+ M + +GL N+I++P ++ L Sbjct: 293 ILGLMLTLGILFGDNESYAIANALLVPFGGAMLPDTLLM--IAFLGLANAIVWPAVWPLA 350 Query: 371 IERMGPMTGEASSLLIMAIVGGAIVPFVQGL--FADHIGVQHAFFLPLLCYAYIVFYGLY 428 + MG +T S+LL+M I GGA P GL A +G Q + + L CY +I+FY + Sbjct: 351 LSGMGKLTSTGSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYAVK 410 Query: 429 GSRIKS 434 G +++S Sbjct: 411 GYKMRS 416 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: 494 Number of extensions: 36 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: 418 Length adjustment: 32 Effective length of query: 410 Effective length of database: 386 Effective search space: 158260 Effective search space used: 158260 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