Align Fructose import permease protein FruG (characterized)
to candidate H281DRAFT_05272 H281DRAFT_05272 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Burk376:H281DRAFT_05272 Length = 365 Score = 202 bits (515), Expect = 8e-57 Identities = 116/317 (36%), Positives = 185/317 (58%), Gaps = 9/317 (2%) Query: 18 LDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGG 77 +D + +P +++F + G ++ + + L +D+A+L+I+A+ MT I++GG Sbjct: 12 VDPRTLPIAVTILLFCALFGFGSVMYTGFFSWQVLLDLLVDNAFLLIVAIGMTFVIVSGG 71 Query: 78 IDLSVGAIVAITAVVGLKLANA-GVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIAT 136 IDLSVG++VA+T +V L+ + ++++ I+L++G VFG + G LI F +Q FI T Sbjct: 72 IDLSVGSVVALTTIVEAVLSERYHLSVWVIVPIVLVMGTVFGAVQGALIHFFRLQAFIVT 131 Query: 137 LSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVV 196 L+ MF ARGL +I+T S+T + + + I +N V+IA V ++ Sbjct: 132 LAGMFFARGLCFLITTQSITITDPTFHAISAFRLDIGIGSVTAN-------VLIAFVALL 184 Query: 197 FGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGS 256 H TR GR +YA+GG+ SA LMGLPV T+ +Y S +AL V+T + S Sbjct: 185 GAIYVAHFTRFGRNVYAVGGNARSALLMGLPVAHTRIGVYALSGFCSALGGAVFTFYVLS 244 Query: 257 AKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLG-SLVRSILDPLTSDFGVPAEWTT 315 G G ELDA+A+ VIGGT++TGG GYV+GS+ G ++ +I +T D + + WT Sbjct: 245 GYGLQGQGMELDAIAATVIGGTLLTGGVGYVVGSLFGVGILGTIQTLITFDGTLSSWWTR 304 Query: 316 IVIGLMILVFVVLQRAV 332 IVIG ++ F +LQR + Sbjct: 305 IVIGALLCAFCLLQRLI 321 Lambda K H 0.327 0.142 0.400 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: 331 Number of extensions: 17 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: 340 Length of database: 365 Length adjustment: 29 Effective length of query: 311 Effective length of database: 336 Effective search space: 104496 Effective search space used: 104496 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: 49 (23.5 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