Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease
Query= SwissProt::P11551 (438 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease Length = 442 Score = 271 bits (694), Expect = 2e-77 Identities = 158/413 (38%), Positives = 237/413 (57%), Gaps = 8/413 (1%) Query: 24 YIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGI 83 Y + +L S+FF+W LNDIL+P + F L +A L+Q F+ YF++ +PAG+ Sbjct: 25 YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84 Query: 84 LMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVT 143 L+ +L YK GI+ GL + +GAA FWPAA + Y FL LF++A G+ L+ AAN +V Sbjct: 85 LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144 Query: 144 VLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHS 203 +LGPE S RL LAQ NS G +A FG LILS ++ + K+SP + AY+ Sbjct: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIA-KLSPAEQVAYRVQ 203 Query: 204 LVLSVQTPYMIIVAIVLLVALLIMLTKFPAL-QSDNHSDAKQGSFSASLSRLARIRHWRW 262 +VQ PY+ + ++ L+A+ + L + PAL + + KQ S + L R H + Sbjct: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPL----RHPHVLF 259 Query: 263 AVLAQFCYVGAQTACWSYLIRY-AVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISR 321 VLA F YVG + A S+L+ Y ++ +I M+ AAN++ + IGRF G+ L+++ Sbjct: 260 GVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAK 319 Query: 322 FAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTK 381 +P K+LA +A I MAL L + G V + ++ F SI +PTIFSLGI+ +G T Sbjct: 320 LSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTG 379 Query: 382 YGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFARFRSQ 434 SS ++M I+GG IV V G +D G + A +P LC+A I + + S+ Sbjct: 380 EASSLLIMAIVGGAIVPFVQGLFADHIG-VQHAFFLPLLCYAYIVFYGLYGSR 431 Lambda K H 0.329 0.140 0.425 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: 475 Number of extensions: 29 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: 438 Length of database: 442 Length adjustment: 32 Effective length of query: 406 Effective length of database: 410 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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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