Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_058858199.1 AS188_RS06680 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_001482365.1:WP_058858199.1 Length = 482 Score = 211 bits (537), Expect = 4e-59 Identities = 133/432 (30%), Positives = 219/432 (50%), Gaps = 11/432 (2%) Query: 29 AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88 A GGLLFG+DT VI+GA + + + GLT G +S + +G+L G +D +GR Sbjct: 33 ACFGGLLFGYDTGVINGALRPMTEELGLTPFTEGVVTSSLVFAAAVGALSGGRISDAWGR 92 Query: 89 KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148 + +L +A+ + V ++ P+ + R GLA+G AS V P+++AE++P RG Sbjct: 93 RRTILLLAVLFFVGTMIVVFTPNYEVLVAGRVCLGLAVGGASAVVPVFLAELAPYEIRGS 152 Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGL-VQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPR 207 + N++ IV+G L AF+ N +I + + + WR+MF I A+P+ + L +PESPR Sbjct: 153 IAGRNEVAIVIGQLSAFVINAVIGNVFIDHPSVWRYMFAISALPAVALFVGMLRMPESPR 212 Query: 208 WLAIHGQADRARDVMQRLGFADPR-AELARIELAEAREEAAGK----PRLFQRSHFTPVA 262 WL G+ + A +V++ + + AEL +E E A + L + + Sbjct: 213 WLVEKGRHEEALEVLRSVRSEERAVAELGEVEHVAEEESAENRIGLGAVLRNKWLIRIML 272 Query: 263 CAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRF 322 I + + QL+GIN+++YY + +G A +AL+ +IA G +V AL ++DR Sbjct: 273 VGIGLGIAQQLTGINSIMYYGQIVLIESGFSASAALIANIAPGVIAVVGGFIALAMMDRL 332 Query: 323 GRRPLLFVGSVICAATLLLVGWQ---LESAKPDGTLILFGL-LGFIAAFAMSQGAVIWVF 378 RR +G + LL+G LE P ++ L + F+ + +WV+ Sbjct: 333 DRRKTFVIGFSLTTTCHLLIGIASVVLEEGNPLRPFVILALVVAFVGSMQTFLNVAVWVY 392 Query: 379 ISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVG-GWVFAFFGAMMLLQLLWTW 437 +SEVFP +RG G + WV ++ FP +VG F F + +L L++ Sbjct: 393 LSEVFPLHMRGFGIGVSIFALWVANGVLSLYFPSLVDAVGITGTFFLFAGVGVLALVFVA 452 Query: 438 KFMPETNGIALE 449 +PET G LE Sbjct: 453 TQVPETRGRTLE 464 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: 546 Number of extensions: 37 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: 482 Length adjustment: 33 Effective length of query: 425 Effective length of database: 449 Effective search space: 190825 Effective search space used: 190825 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