Align Fructose import permease protein FruG (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 169 bits (427), Expect = 1e-46 Identities = 103/328 (31%), Positives = 180/328 (54%), Gaps = 12/328 (3%) Query: 1 MTTATANKVKAPKKGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHA 60 MTT T + + K + ++++ +++ +++I + L + + + ++ + Sbjct: 1 MTTQTVSGRRYFTKAWLMEQK------SLIALLVLIAIVSTLSPNFFTINNLFNILQQTS 54 Query: 61 YLIILAVAMTLPILTGGIDLSVGAIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLL 120 I+AV MTL ILT GIDLSVG+++A+T V + V A + + L +GA G + Sbjct: 55 VNAIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAV 114 Query: 121 AGTLIEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISN 180 G ++ + +Q FIATL M L RG+ + + S P F+ +++ I Sbjct: 115 TGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGS---PVNTGFTENADLFGWFG---IGR 168 Query: 181 DLSFNVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSA 240 L V I +V + + LHHTR GR IYA+GG+ ++ L G+ V + + I+Y Sbjct: 169 PLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCG 228 Query: 241 TLAALASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSIL 300 LA+LA I+ A + SA+ T G G+ELDA+A+VV+GGT + GG G ++G+++G+L+ L Sbjct: 229 LLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFL 288 Query: 301 DPLTSDFGVPAEWTTIVIGLMILVFVVL 328 + + GV + + IV ++IL+ V++ Sbjct: 289 NNGLNLLGVSSYYQMIVKAVVILLAVLV 316 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: 264 Number of extensions: 13 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: 321 Length adjustment: 28 Effective length of query: 312 Effective length of database: 293 Effective search space: 91416 Effective search space used: 91416 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