Align Ribose import permease protein RbsC (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 290 bits (743), Expect = 3e-83 Identities = 155/299 (51%), Positives = 207/299 (69%), Gaps = 4/299 (1%) Query: 23 LIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 LI LLVL+ ++ST +PNF ++NL NI + SVNAI+A GMT VILTSGIDLSVGS++A+ Sbjct: 28 LIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSIVAV 87 Query: 83 TGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTM 142 +G V+ + A +A+ A + +GA G + GV+ A + FI TL M LRG+ Sbjct: 88 SGVVSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRGMAY 147 Query: 143 VYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYAL 202 T G P+ + +L G G +G+P PV IM +V+L AW++L TR GR+IYA+ Sbjct: 148 TITEGQPIVSSSLSFREL----GNGYLIGIPIPVIIMLVVYLLAWFILERTRFGRHIYAV 203 Query: 203 GGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVV 262 GGN A RL+G+ V ++ VY + G+ A LAGII AR+ SAQPTAGTGYELDAIAAVV Sbjct: 204 GGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYELDAIAAVV 263 Query: 263 LGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDNKKQ 321 LGGTSLAGG+GRI+GTLIG++ILG L+ GL LL V + Q+++K +VI+LAV +D KQ Sbjct: 264 LGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIVIILAVAIDGLKQ 322 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: 297 Number of extensions: 11 Number of successful extensions: 2 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: 339 Length adjustment: 28 Effective length of query: 293 Effective length of database: 311 Effective search space: 91123 Effective search space used: 91123 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 Apr 09 2024. 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