Align D-fructose transporter, sugar porter family (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter
Query= reanno::Korea:Ga0059261_1777 (458 letters) >FitnessBrowser__Pedo557:CA265_RS23325 Length = 443 Score = 314 bits (804), Expect = 4e-90 Identities = 170/424 (40%), Positives = 252/424 (59%), Gaps = 6/424 (1%) Query: 29 AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88 AA GG LFGFD AVISG+ L+ QF LT GF S +G ++G LIAG +D +GR Sbjct: 18 AAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGAMVGCLIAGYVSDAYGR 77 Query: 89 KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148 K ++ A ++ SSL +AP+ + F+V RF G+ +G AS+++P+YIAE++P +FRGR Sbjct: 78 KPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASMLSPMYIAELAPPKFRGR 137 Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208 LVA+NQL IVLGILI L NY + + AWRWMFG+ A+PS IFL+ +LPESPRW Sbjct: 138 LVAINQLTIVLGILITNLINYTLRN--TGEDAWRWMFGLGAIPSGIFLIGISILPESPRW 195 Query: 209 LAIHGQADRARDVMQRLGFADPRAE-LARIELAEAREEAAGKPRLFQRSHFTPVACAIAI 267 L G+ ++A V+ ++G + A+ L IE R+ +F + +F V I + Sbjct: 196 LVQKGKNEKALKVLNKIGNHEFAADALKNIEQTLQRKSNVEHESIFNKMYFPAVMIGIGL 255 Query: 268 AMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRRPL 327 A+F Q GIN + YAP++FE G D LLQ++ +G N++FT++A+FL+D+ GR+PL Sbjct: 256 AIFQQFCGINTVFNYAPKLFESIGTSQDDQLLQTVFIGAVNVIFTISAMFLVDKIGRKPL 315 Query: 328 LFVGSVICAATLLLVGWQLESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPSAV 387 + +G+ A +L+ L S T++ + LL I +A+S V WV ISE+FP+ V Sbjct: 316 MLIGAGGLAVLYVLISQLLASG---STMVSWFLLSAIGVYAVSLAPVTWVLISEIFPNKV 372 Query: 388 RGKGQALGSTTHWVMAAAITWAFPVFAASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIA 447 R K W + + FP+ + +F + A+ L + WKF+ ET G Sbjct: 373 RVKATTWAILCLWGAYFVLVFTFPILFDWLKESIFYIYAAICTLGCIGIWKFVKETKGKT 432 Query: 448 LEDM 451 LE++ Sbjct: 433 LEEI 436 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: 508 Number of extensions: 23 Number of successful extensions: 4 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: 443 Length adjustment: 33 Effective length of query: 425 Effective length of database: 410 Effective search space: 174250 Effective search space used: 174250 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 17 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