Align sugar transport protein 6 (characterized)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_091493 (507 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 203 bits (517), Expect = 9e-57 Identities = 142/476 (29%), Positives = 219/476 (46%), Gaps = 39/476 (8%) Query: 21 VFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCKYDNQFLQ 80 + V +A +GGL+FGYD SG V+ D LK F L Sbjct: 12 IMAIVAVATIGGLLFGYD---SGAVNGTQDGLKSAFAL----------------SEGGLG 52 Query: 81 LFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNLVMLIIGRLFL 140 SL + + +F+A +GRR M ++ FLIG + + + + R+ Sbjct: 53 FTVGSLLIGCFIGAFLAGRLADLIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAG 112 Query: 141 GFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTATVHPYGWRIA 200 G VG + P ++SE+APA +RG + + Q+M+ G+ A +VNY+ A + Sbjct: 113 GMAVGAASVLSPAYISEVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLF 172 Query: 201 LGG----------AGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKIRGVDDINDE 250 GG IPA + L I E+P L+ + +N E L + G ++ Sbjct: 173 WGGYEAWRWMYWMQAIPATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNK 232 Query: 251 YESIVHACDIASQVKDPYRKLLKPAS---RPPFIIGMLLQLFQQFTGINAIMFYAPVLFQ 307 I + S + R +L P RP G+LL +FQQ GIN I +Y L+Q Sbjct: 233 LTEIQASF---SDHRPTLRDILDPVKGGVRPIVWAGLLLAVFQQLVGINVIFYYGATLWQ 289 Query: 308 TVGFGSDAALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLIIGIILAK 367 GF + ALL +++G +++ A FV + LVDR GR+ LLL S M + + ++ Sbjct: 290 LAGFTENDALLINIVSGFVSIAACFVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSR 349 Query: 368 -DLGVTGTLGRPQAL--VVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAVAVS 424 L G L Q L + VI +YV+ F SWGP+ W++ E FP + R + AV Sbjct: 350 GSLDAQGKLVLSQQLGIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGF 409 Query: 425 CNMFFTFVIAQAFLSMLCGMRSGIFFFFSGWIIVMGLFAFF-FIPETKGIAIDDMR 479 F ++IAQ+F M G+ + + F V+ F FI ETKG+ ++DM+ Sbjct: 410 AQWFSNYLIAQSFPIMAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDMQ 465 Lambda K H 0.329 0.144 0.446 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: 576 Number of extensions: 30 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: 507 Length of database: 466 Length adjustment: 34 Effective length of query: 473 Effective length of database: 432 Effective search space: 204336 Effective search space used: 204336 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 (21.8 bits) S2: 52 (24.6 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