Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_008991179.1 I215_RS06545 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_000300875.1:WP_008991179.1 Length = 444 Score = 366 bits (939), Expect = e-106 Identities = 198/428 (46%), Positives = 278/428 (64%), Gaps = 10/428 (2%) Query: 29 AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTV-ASALIGTVLGSLIAGAPADRFG 87 AAL G LFGFDT VISGA + LQ +G TDA G V A AL GTV+G++ G P ++FG Sbjct: 11 AALAGFLFGFDTVVISGADKQLQELWGTTDAFHGSVVMAMALWGTVVGAIFGGIPTNKFG 70 Query: 88 RKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRG 147 R+ + + Y+VS++G+ L D +F FRF+GGL +GA+++ P YI+E++P + RG Sbjct: 71 RRNTLFFIGALYLVSAIGSALVNDPVSFAAFRFIGGLGVGASTIAAPTYISEIAPPKNRG 130 Query: 148 RLVAMNQLNIVLGILIAFLSNYII--AGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPES 205 RLV+M Q NIVLGIL+AFLSNY++ AG + WRWM G+ A+P+ I++L L +P+S Sbjct: 131 RLVSMYQFNIVLGILMAFLSNYLLRDAG----NQPWRWMLGVEAIPAFIYMLFVLFIPKS 186 Query: 206 PRWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTPVACAI 265 PRWL + A+ V+Q++ +L+ + +++ + +F + + P+ A Sbjct: 187 PRWLLSKSKIAEAKQVLQKMNIGMDIDQLSE-NIQQSKGDRTTAESIFLKRYRFPLMLAF 245 Query: 266 AIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRR 325 +A FNQ+SGINA LYYAPRIFE+AG DS+LL SI +G NL+FT+ +FLID+ GR+ Sbjct: 246 LVAFFNQMSGINAFLYYAPRIFEIAGLEQDSSLLSSIGIGVVNLIFTLIGVFLIDKAGRK 305 Query: 326 PLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPS 385 L+ VGS+ +LLLV + G + L FIA+ A+ QGAVIWVFISE+FP+ Sbjct: 306 QLMLVGSIGYIISLLLVACAF-FFQWGGLWVPIFLFIFIASHAVGQGAVIWVFISEIFPN 364 Query: 386 AVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTWKFMPETN 444 +R GQA GS+ HWV+AA I PV S+G G+VF FF MM QLL+ MPET Sbjct: 365 HLRASGQAFGSSVHWVLAAIIPSFVPVLFTSIGAGYVFLFFAIMMFFQLLFVLFMMPETK 424 Query: 445 GIALEDMN 452 G +LED++ Sbjct: 425 GKSLEDLS 432 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: 592 Number of extensions: 29 Number of successful extensions: 7 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: 444 Length adjustment: 33 Effective length of query: 425 Effective length of database: 411 Effective search space: 174675 Effective search space used: 174675 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