Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate WP_009133853.1 HMPREF9450_RS05320 sugar MFS transporter
Query= uniprot:A0A1I2JXG1 (442 letters) >NCBI__GCF_000231275.1:WP_009133853.1 Length = 445 Score = 201 bits (511), Expect = 4e-56 Identities = 138/447 (30%), Positives = 223/447 (49%), Gaps = 31/447 (6%) Query: 10 SKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQF 69 S +LP AA R T AM +L +FF++GF + +N IL+P+ K +LN+ ++ L+ F Sbjct: 2 STGNLPAAAPARKTSVA-AMAILGLMFFIFGFTSWVNSILVPYFKIGCELNHFQSYLIVF 60 Query: 70 TFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLA 129 + AY +M++P+ ++ R+G+K+GI+ G +GA F PAA YP FL FV+ Sbjct: 61 ALYSAYLIMAIPSSAILKRVGFKRGIMYGFFCTALGALIFIPAAWWRSYPVFLAGSFVIG 120 Query: 130 TGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAE-- 187 G +LQ AAN YV ++GP + R+ + N +AP LI +A VL Sbjct: 121 AGSAMLQAAANPYVTMIGPINTTVKRMAIMGICNKFAGLVAP-----LIFAAVVLKVTDS 175 Query: 188 ------QIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALT--EKTE 239 + A L PA + A V PY A L ++ VF+ LP L EK + Sbjct: 176 DLFVQLESATLDPAARSAMLDSLVHRVMVPYAIFAAFLIVIGVFIRFSMLPELNLEEKNK 235 Query: 240 Q-ASVKQHSLVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANW 298 Q + S + P+++ GV+A+F ++G +V +++Y M A + Sbjct: 236 QEVAPGGEGKTSVFQFPYLILGVVAMFLHIGTQVVTIDTIISYAQTM---GMDLLEAKTF 292 Query: 299 VAYYWLGAMIGRFIGSALLAK-LSPRKLLAIFAAINMALVLTTMMTK---------GTVA 348 +Y ++G +G L+ K +S ++ I + L L + ++ Sbjct: 293 PSYTLSLVILGNVLGVLLIPKIISQTRVFQICCTLGFLLSLGVVWGNTQVDFLGHHANIS 352 Query: 349 MYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGV 408 ++ +V IGL NS+++ I+ L I +G T SS+LIMA+ G A+VP + G AD + Sbjct: 353 IWFLVGIGLANSLVYGGIWPLAIRGLGRFTKTGSSMLIMALFGNAVVPLIYGYIADTASL 412 Query: 409 QHAFFLPLL-CYAYIVFYGLYGSRIKS 434 + A+F LL +AY++FY G RI S Sbjct: 413 RIAYFWILLPGFAYLMFYAFCGYRITS 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: 501 Number of extensions: 22 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: 445 Length adjustment: 32 Effective length of query: 410 Effective length of database: 413 Effective search space: 169330 Effective search space used: 169330 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 24 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