Align Ribose import permease protein RbsC (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 240 bits (613), Expect = 3e-68 Identities = 140/305 (45%), Positives = 197/305 (64%), Gaps = 10/305 (3%) Query: 23 LIALLVLIAI-VSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLA 81 L A LV+I I +S SP F T + L NI+ Q SV I AVG T VI+TSGIDLSVGSL+A Sbjct: 29 LFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVA 88 Query: 82 LTGAVAASIV-----GIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLL 136 LTG VAA+++ G + + AALA+GAA GA+ G+ VA R+ FI TL MM + Sbjct: 89 LTGMVAATVMAGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMMAM 148 Query: 137 LRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLG 196 RG+T+ ++G T F + + F FG G+P P+ +M ++F+ +L T G Sbjct: 149 ARGLTLAISDG---RTKF-DFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFG 204 Query: 197 RYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELD 256 ++A+GGN+ A RL+GI V+++ + Y L G+ A++AGI+ RL+SA P+A G EL Sbjct: 205 HQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQ 264 Query: 257 AIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLV 316 IAAVV+GGTSLAGG+G IVGT IG +++G +N GL+LLGV+ ++ ++ VI AVL+ Sbjct: 265 VIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLL 324 Query: 317 DNKKQ 321 D Q Sbjct: 325 DALSQ 329 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: 257 Number of extensions: 14 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: 333 Length adjustment: 28 Effective length of query: 293 Effective length of database: 305 Effective search space: 89365 Effective search space used: 89365 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