Align Ribose import permease protein RbsC (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 287 bits (735), Expect = 2e-82 Identities = 145/298 (48%), Positives = 207/298 (69%), Gaps = 4/298 (1%) Query: 24 IALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALT 83 I LLV+ ++ S +F + N+ N+L+Q S+NAI+AVGMT VILT GIDLSVGS++AL Sbjct: 41 IGLLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALA 100 Query: 84 GAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMV 143 G +AA ++ +NA+ A+A +A+G GA G VA + I TL M + RG+ ++ Sbjct: 101 GTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALI 160 Query: 144 YTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALG 203 YT G P++ D +FG G+ LGV PV IM ++++ AW +L GRY+YA+G Sbjct: 161 YTGGYPIDG----LPDWVSFFGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYAIG 216 Query: 204 GNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVL 263 GNE ATRLSG+ V ++K+IVY++ GL ++ A I+ ARL S QP AG G+ELDAIAAVV+ Sbjct: 217 GNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGVGFELDAIAAVVM 276 Query: 264 GGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDNKKQ 321 GGTS++GG+G I+GTLIGAL+LG LNNGLN++GV+ Y Q ++K +ILLA+ + ++ Sbjct: 277 GGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDRR 334 Lambda K H 0.324 0.139 0.393 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: 326 Number of extensions: 21 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: 321 Length of database: 335 Length adjustment: 28 Effective length of query: 293 Effective length of database: 307 Effective search space: 89951 Effective search space used: 89951 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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