Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_068010715.1 PsAD2_RS22100 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_001623255.1:WP_068010715.1 Length = 450 Score = 217 bits (552), Expect = 7e-61 Identities = 144/438 (32%), Positives = 229/438 (52%), Gaps = 13/438 (2%) Query: 26 AAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADR 85 A A L G L+G++ AV+ GA L+ F G VA+ +G ++G+ + +D Sbjct: 6 ACVAVLCGFLYGYNEAVVGGAYDLLEAYFVFPPYWRGILVAALPLGGLVGAFLCAHLSDA 65 Query: 86 FGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARF 145 +GR+ ++ + +V+ SL +GLA +L R + G+AIG +S+ Y+AE+SP + Sbjct: 66 YGRRSALIISGLLFVLGSLLSGLALELYLLSCARLLVGIAIGISSLAALQYLAEISPPKA 125 Query: 146 RGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA---WRWMFGIVAVPSTIFLLVTLLL 202 RGRL+A QL + LGIL A+LS +I + W+ ++ + + + L +L Sbjct: 126 RGRLLAAFQLLVSLGILSAYLSEALINRVPLTGDPFNHWQLLYLMSGIAAVAMLAGSLAS 185 Query: 203 PESPRWLAIHGQADRARDVMQRL------GFADPRAELARIELAEAREEAAGKPRLFQRS 256 ESPRWLA+ G+A A +L +A + +L R + A A +E G L + Sbjct: 186 LESPRWLAMVGKAGHAEATFIKLEPTQTPDWAIRQVKLLRQD-AIATQEKRGWRELLSAN 244 Query: 257 HFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSA-LLQSIAVGGTNLVFTVAA 315 A+ + QLSG+ LL+YAP I E G S L ++ ++ + + Sbjct: 245 MRPITGFALMCFLLQQLSGVYVLLFYAPSILEEFGLPESSVHTLTTLGFAAALILGSALS 304 Query: 316 LFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLI-LFGLLGFIAAFAMSQGAV 374 +FLIDR GRRPL+ +G CAATLLL+ W ++ PDG I L G+ F+ FA S G + Sbjct: 305 VFLIDRIGRRPLMVMGYPCCAATLLLIIWGMDMPAPDGIWITLTGIFLFVVNFAFSIGPL 364 Query: 375 IWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQL 433 WV+++E+FPS +R KG AL + +W++ +AFP V + FF Sbjct: 365 PWVYMAELFPSHLRAKGMALAVSLNWILTFLAVFAFPKIYQFVSVNQILLFFVVTSFFGA 424 Query: 434 LWTWKFMPETNGIALEDM 451 ++ + PETN + LE++ Sbjct: 425 VYMVRKAPETNTLTLENI 442 Lambda K H 0.327 0.139 0.420 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: 541 Number of extensions: 30 Number of successful extensions: 6 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: 458 Length of database: 450 Length adjustment: 33 Effective length of query: 425 Effective length of database: 417 Effective search space: 177225 Effective search space used: 177225 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