Align D-fructose transporter, sugar porter family (characterized)
to candidate WP_089216652.1 CHB69_RS14085 sugar porter family MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >NCBI__GCF_900188185.1:WP_089216652.1 Length = 455 Score = 372 bits (955), Expect = e-107 Identities = 214/445 (48%), Positives = 277/445 (62%), Gaps = 10/445 (2%) Query: 9 AGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASA 68 AG+P + R T+A + A AL GLLFGFDTAVI+G T L F LT LG TV++A Sbjct: 12 AGSP-QGGRITLAAAIGTA--ALAGLLFGFDTAVIAGVTHDLTRLFALTPETLGLTVSAA 68 Query: 69 LIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGA 128 L GT+ G+L AG P D FG + + +A Y V+ LG LAP FL FRF+ GLAIG Sbjct: 69 LWGTLAGALFAGKPGDAFGSRDSLRVLAAFYFVAGLGCALAPSWTLFLFFRFLCGLAIGG 128 Query: 129 ASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIV 188 +SV+ P+YIAE++P R RG LV + QL IV+GIL A+LSN +IAGLV WRW GI Sbjct: 129 SSVLAPVYIAEIAPPRRRGLLVGLFQLMIVIGILTAYLSNAVIAGLVDGGAGWRWKLGIT 188 Query: 189 AVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFAD--PRAELARIELAEAREEA 246 A P+ +F ++ +P SPRWL + G+A AR+ + R+G A AELAR+E A R+ Sbjct: 189 AAPALLFFILLFAIPHSPRWLVVKGRASEAREALARIGMAPDAAAAELARVEQALMRDPP 248 Query: 247 AGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGG 306 +L R H P+ AI +AMFNQL+GINA+LYY IF A AG+ S Q++ +G Sbjct: 249 --NEKLSWRRHRRPMTLAILVAMFNQLAGINAVLYYLNDIF--ARAGSLSPDRQAVLIGL 304 Query: 307 TNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAA 366 NL+FT+ + LIDR GR+ LL G+ A L + L A L+L L+GFIA Sbjct: 305 ANLIFTLVGMALIDRIGRKTLLLAGAAGMALCLSIAAGVLFGAL-GNALMLPALVGFIAF 363 Query: 367 FAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGWVFAFFG 426 FA SQGAVIWV+ISEVFP+ VR +G ALG++THW+M A I FP+ A G FA F Sbjct: 364 FATSQGAVIWVYISEVFPTPVRARGSALGASTHWLMNALIAGVFPILVAWSPGAPFAIFA 423 Query: 427 AMMLLQLLWTWKFMPETNGIALEDM 451 A M+LQ + PET G+ L+ M Sbjct: 424 AAMVLQFVVVAAIFPETRGVDLDAM 448 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: 619 Number of extensions: 24 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: 458 Length of database: 455 Length adjustment: 33 Effective length of query: 425 Effective length of database: 422 Effective search space: 179350 Effective search space used: 179350 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