Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_074882195.1 PsAD2_RS21425 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_001623255.1:WP_074882195.1 Length = 448 Score = 239 bits (610), Expect = 1e-67 Identities = 154/437 (35%), Positives = 236/437 (54%), Gaps = 21/437 (4%) Query: 31 LGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASAL-IGTVLGSLIAGAPADRFGRK 89 L G L G++ V+SGA L QF T LG VASAL +G +LGS+ A +D GR+ Sbjct: 11 LCGFLSGYNGGVVSGAYSLLVQQFHFTP-FLGGVVASALPLGGLLGSIFASYSSDHMGRR 69 Query: 90 GVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGRL 149 +L A +VV +L +G + ++ RF+ G A G + + P Y++E++P RGR+ Sbjct: 70 TSILISASLFVVGALMSGTTNHVETLIIARFLVGFATGIVTPIGPQYLSEIAPPLVRGRM 129 Query: 150 VAMNQLNIVLGILIAFLSNYIIAGL-VQYDVAWRW--MFGIVAVPSTIFLLVTLLLPESP 206 + Q+ G+L A+++N II+G+ +DV RW MF + +P+ + L+ L P SP Sbjct: 130 IGAYQMMTSGGVLSAYVANQIISGISADFDVINRWQLMFALSGIPAVVLLVGMLFAPRSP 189 Query: 207 RWLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTP-----V 261 RWL + G+ AR+V LG + EE + + R P Sbjct: 190 RWLLLRGRNQDAREVFYMLGSKGAEDWGEKAVNTAINEERSTRGTCRWRDLIGPELRSIT 249 Query: 262 ACAIAIAMFNQLSGINALLYYAPRIF-ELAGAGADSALLQSIAVGGTNLVFTVAALFLID 320 AIAI + QLSGIN ++YYAP+I +L A +++LL + ++G + ++ ALFL D Sbjct: 250 IFAIAIFVIQQLSGINVVIYYAPQILSQLGFALHETSLLATTSLGVVMFLTSIPALFLFD 309 Query: 321 RFGRRPLLFVGSVIC--AATLLLVGWQLESAKPDGTLILFGLLG---FIAAFAMSQGAVI 375 +FGRR LL +G +C A L +V LE +G L G LG ++AAFA+S G + Sbjct: 310 KFGRRSLLIIGLPLCGFAEILAMVPVYLE----NGELAWLGALGLCLYMAAFALSIGPLP 365 Query: 376 WVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLL 434 W++I+E+FP R KG +G T+W+ + FPV AS G W+FA F L + Sbjct: 366 WIYIAEIFPVQARAKGMVIGVMTNWIFNFGVVLMFPVLIASFGIFWMFAMFITTCFLGMC 425 Query: 435 WTWKFMPETNGIALEDM 451 + ++ PET G+ +E + Sbjct: 426 YAVRYAPETKGVPIEQI 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: 590 Number of extensions: 33 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: 448 Length adjustment: 33 Effective length of query: 425 Effective length of database: 415 Effective search space: 176375 Effective search space used: 176375 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