Align Glucose/fructose transport protein (characterized, see rationale)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= uniprot:A0A0H3C6H3 (478 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 444 bits (1141), Expect = e-129 Identities = 220/455 (48%), Positives = 308/455 (67%), Gaps = 4/455 (0%) Query: 25 VAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAFAAGR 84 V I A A +GGF+FG+D+ VING + + +F L G V L+G A+GA+ AG Sbjct: 17 VVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGP 76 Query: 85 LADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYISEVT 144 LAD WGR M ++A+L ISA+G+G +++RL+GG+GVG ASV+ P YI+EV+ Sbjct: 77 LADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVS 136 Query: 145 PANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMFWMQIIPAG 204 PA +RGRL S+QQ+ I+ G+ A +++ LA TAG ++ + WLGL AWRWMF + ++PA Sbjct: 137 PARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPAL 196 Query: 205 VFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQG---AKKVEEIRASLSADHKPTF 261 ++ +LG+PESPR+LVAKG+ +A+ +L ++ K+ +I SL ++++P Sbjct: 197 IYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYRPGL 256 Query: 262 SDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILSGT 321 DL L V+ W G++L+VFQQ VGIN++FYY S LW SVGF+E D+ I++++ Sbjct: 257 RDLRGSMAGLLPVV-WVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSV 315 Query: 322 LSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGLTA 381 +++L L+AI L+D+IGRKPLL IGSAGM VTLG++ WCFS A AL+L G+ A Sbjct: 316 VNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVA 375 Query: 382 LIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPALAAA 441 L+AAN YV+FF LSWGP++WV+LGEMFPN++R ALAV AQW+ANF I+ SFPAL+ Sbjct: 376 LVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSFPALSEL 435 Query: 442 SLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAM 476 L YG YA A+VS V K V ET+G ELE M Sbjct: 436 GLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 Lambda K H 0.325 0.138 0.417 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: 751 Number of extensions: 43 Number of successful extensions: 2 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: 478 Length of database: 472 Length adjustment: 33 Effective length of query: 445 Effective length of database: 439 Effective search space: 195355 Effective search space used: 195355 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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