Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease
Query= TCDB::Q8XEV7 (438 letters) >FitnessBrowser__Dyella79:N515DRAFT_1918 Length = 442 Score = 208 bits (529), Expect = 3e-58 Identities = 124/411 (30%), Positives = 224/411 (54%), Gaps = 9/411 (2%) Query: 24 LLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIPASLVIKKTS 83 +L+ +F +WG LNDILI K+VF L+ + LVQ F+G YFL+++PA L++ + Sbjct: 31 VLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGLLVARLG 90 Query: 84 YKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANTYSSMIGPKA 143 YK I+ GL + VG F+PA+ M Y FL A+F +A G++ L+ AAN Y +++GP+ Sbjct: 91 YKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVALLGPEK 150 Query: 144 YATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHNFKVLMLENTLE 203 A+ RL ++Q +G G L+ S +Q+A ++ + ++V + Sbjct: 151 SASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQEAQTVQG 210 Query: 204 PYKYMIMVLVVVMVLFLLTRFPT-CKVAQTASHKRPSALDTLRYLASNARFRRGIVAQFL 262 PY + +VL ++ V L R P + + AS K+ S + LR+ G++A F Sbjct: 211 PYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRH----PHVLFGVLAIFF 266 Query: 263 YVGMQVAVWSFTIRLAL--ELGDINERDASTFMVYSFACFFIGKFIANILMTRFNPEKVL 320 YVG +VA+ SF + ++G+++E+ A+ ++ Y + IG+FI + L+ + +P K+L Sbjct: 267 YVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRKLL 326 Query: 321 ILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVDNEHTEMAGAVI 380 +++ I + + A+Y V + + + TI++ ++ + T A +++ Sbjct: 327 AIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERM-GPMTGEASSLL 385 Query: 381 VMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVYFWRESKVRGN 431 +MAIVG A+VP +QG AD +Q +F + +LC+ Y+ Y S+++ + Sbjct: 386 IMAIVGGAIVPFVQGLFADHI-GVQHAFFLPLLCYAYIVFYGLYGSRIKSD 435 Lambda K H 0.329 0.139 0.412 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: 414 Number of extensions: 12 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: 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:
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