Align Fructose import permease protein FruG (characterized)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 159 bits (402), Expect = 1e-43 Identities = 100/305 (32%), Positives = 166/305 (54%), Gaps = 5/305 (1%) Query: 26 LAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAI 85 L A +LMI+ ++ + + S+ A +LA+A T I+T GIDLSVG + Sbjct: 37 LLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTM 96 Query: 86 VAITAVV-GLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLAR 144 + AV+ G+ L N G+P L + + GA+ G ++G +I + + PFIATL M L + Sbjct: 97 MTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLK 156 Query: 145 GLASIIS-TDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLH 203 GL+ +IS T + F FS I+ I D + L V+I +V + + L+ Sbjct: 157 GLSLVISGTRPIYFNDTEGFSAIAQDSLIGD---LIPSLPIPNAVLILFLVAIGASIILN 213 Query: 204 HTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGV 263 T GR +A+G + + L G+ V + +Y S + +A ++ + + SA+ +G Sbjct: 214 KTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQ 273 Query: 264 GWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMIL 323 G+ELDA+A+VVIGGT ++GG G +LG+++G+ + S+L V EW T+V G++I+ Sbjct: 274 GYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIII 333 Query: 324 VFVVL 328 + V L Sbjct: 334 LAVYL 338 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: 250 Number of extensions: 11 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: 347 Length adjustment: 29 Effective length of query: 311 Effective length of database: 318 Effective search space: 98898 Effective search space used: 98898 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