Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= SwissProt::P39328 (341 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 142 bits (357), Expect = 2e-38 Identities = 101/310 (32%), Positives = 159/310 (51%), Gaps = 18/310 (5%) Query: 27 ALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLSV 86 +LLL++L S +P+F +V + + IL A +LAI T VI T GIDLSV Sbjct: 42 SLLLMILFFSFASPNFMEV--------DNLVSILQSTAVNGVLAIACTYVIITSGIDLSV 93 Query: 87 GAVMAIAGATTAA-MTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLILMV 145 G +M +T G LP+ + +A+ G L+G +G+++A LK+ PF+ATL +M+ Sbjct: 94 GTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMM 153 Query: 146 AGRGVAQLITAGQIVTFNSPD-LSWFGSGSL-------LFLPTPVIIAVLTLILFWLLTR 197 +G++ +I+ + + FN + S SL L +P V+I L I ++ Sbjct: 154 LLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILN 213 Query: 198 KTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAG 257 KT G + A+G N A + +GV + Y SG IAG+I+A+ + A G Sbjct: 214 KTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPA-LG 272 Query: 258 LWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVV 317 ELDAI AVVIGG SL GG +L +++GA I+ + G+ + E VV V++ Sbjct: 273 QGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVII 332 Query: 318 LCVLIVQSQR 327 + + + R Sbjct: 333 ILAVYLDILR 342 Lambda K H 0.327 0.142 0.416 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: 265 Number of extensions: 10 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: 341 Length of database: 347 Length adjustment: 29 Effective length of query: 312 Effective length of database: 318 Effective search space: 99216 Effective search space used: 99216 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