Align Ribose import permease protein RbsC (characterized)
to candidate PP_2760 PP_2760 putative ribose transport permease protein
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Putida:PP_2760 Length = 327 Score = 144 bits (363), Expect = 3e-39 Identities = 96/307 (31%), Positives = 157/307 (51%), Gaps = 14/307 (4%) Query: 16 WLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVIL------- 68 WL+ + +L+A ++ + +PNF T++NL N+L Q+++ +A G+T VI+ Sbjct: 17 WLLRRGALLAFAAILLAFALSAPNFLTLSNLVNVLAQSAILGSLAFGLTTVIIGGGSNVV 76 Query: 69 TSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFI 128 + G+DLS+ + L L+ AV AS+ +V++AA L G AIG + ++V R+ + Sbjct: 77 SGGLDLSLAANLGLSAAVYASLNNAGFGDVVSIAATLGTGLAIGTLNALVVVGFRLPPLL 136 Query: 129 ATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWY 188 ATL M L+ G+ +V T NT + L G +GVP W++ V Sbjct: 137 ATLATMNLVAGLELVLTE----NTVLPSTSPLLEGLAFGSWVGVPALAWVLLAVGGVLIV 192 Query: 189 MLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPT 248 + +T G +YA+G A +G++V Y + GL SLA A S + T Sbjct: 193 LTQYTPFGLRLYAIGEYPEAANAAGLSVRGYVFASYLISGLCGSLAAFCSAAWFSGS--T 250 Query: 249 AGTGYELDAIAAVVLGGTSLAGG-KGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKA 307 G+G L ++ A+ G + + I GTL+ L++G L NG LL +SS++ V+ Sbjct: 251 TGSGEMLLSVVAIAFLGVIFSQRLQPSIGGTLLATLLVGVLINGFQLLNISSFWVDGVQG 310 Query: 308 VVILLAV 314 V+ILL V Sbjct: 311 VLILLVV 317 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: 245 Number of extensions: 10 Number of successful extensions: 1 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: 327 Length adjustment: 28 Effective length of query: 293 Effective length of database: 299 Effective search space: 87607 Effective search space used: 87607 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: 48 (23.1 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