Align Fructose import permease protein FruG (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 150 bits (379), Expect = 5e-41 Identities = 94/314 (29%), Positives = 167/314 (53%), Gaps = 16/314 (5%) Query: 26 LAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAI 85 L V+ +L+ I G L + + ++ A++ I+AV M I++GGIDLSVG++ Sbjct: 41 LGPVIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSM 100 Query: 86 VAITAVVGLKLANA-----GVPAFLVMIIMLL---IGAVFGLLAGTLIEEFNMQPFIATL 137 A+ A + NA G P V++ MLL +GAVFGL+ G LI + ++PFI TL Sbjct: 101 AALIAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTL 160 Query: 138 STMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVF 197 T+ + R + F G + +++ I +N L + V I L+V + Sbjct: 161 GTLGIFRAYLTY-------FSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIV 213 Query: 198 GYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSA 257 G V L+ T GR + AIG + A+ + V + + + Y+ +A+++Y +GSA Sbjct: 214 GGVILNRTAYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSA 273 Query: 258 KNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIV 317 T G+ WEL+A+A+V++GGT++ GG G + G+V+G+++ S++ + + + + + Sbjct: 274 SPTTGLLWELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAA 333 Query: 318 I-GLMILVFVVLQR 330 + G +I+ +QR Sbjct: 334 VQGFVIIAVAFMQR 347 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: 301 Number of extensions: 22 Number of successful extensions: 3 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: 350 Length adjustment: 29 Effective length of query: 311 Effective length of database: 321 Effective search space: 99831 Effective search space used: 99831 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