Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Dsui_0627 Dsui_0627 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__PS:Dsui_0627 Length = 267 Score = 131 bits (329), Expect = 3e-35 Identities = 83/267 (31%), Positives = 138/267 (51%), Gaps = 9/267 (3%) Query: 10 DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69 +R +L+A + K F GV A+ V + E EI LIG NGAGK+T LTG+ P+ G Sbjct: 3 ERPILLEASDVAKHFGGVKALRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGG 62 Query: 70 EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLA-YEAVRGQK-----RT 123 I+ G ++ +P +GI+ Q + L +MT EN+ + ++ R RT Sbjct: 63 RIVFAGAELDTSAPHKVAARGIARTFQNIRLFAHMTALENVMVGRHQRTRAGVFGAIFRT 122 Query: 124 LSSRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEP 183 +R +E + R++ELL +G L ++L+ ++ +EI +AL EP+++ +DEP Sbjct: 123 PGTRAEEAAIQRRAEELLHYVGIADRAHDLAKHLSYGDQRRLEIARALATEPKLLALDEP 182 Query: 184 TSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEF 243 + + ET L +IE ++ GI+V+ + H + VM + DR+ V+ G++I E Sbjct: 183 AAGMNASETGELRTLIEGIRKDGITVLLIEHDVKLVMGLCDRVAVLDYGEKICEDVPAVV 242 Query: 244 DVD-TIIKMMVGREVEFFPHGIETRPG 269 D +I +G E + P G E G Sbjct: 243 QKDPRVITAYLGAEAQ--PAGSEVAHG 267 Score = 72.0 bits (175), Expect = 2e-17 Identities = 50/214 (23%), Positives = 101/214 (47%), Gaps = 13/214 (6%) Query: 284 VKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKM 343 ++ VS +R+GE+ G G GAG+T + G+ G I G +++ P Sbjct: 23 LRGVSLTIREGEIYGLIGPNGAGKTTFFNCLTGLYVPNGGRIVFAGAELDTSAPHKVAAR 82 Query: 344 GIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRW---------GLVLDERKEEEISEDY 394 GI ++ +L MT +N+++ ++ G +E + +E+ Sbjct: 83 GIARTFQNIRL---FAHMTALENVMVGRHQRTRAGVFGAIFRTPGTRAEEAAIQRRAEEL 139 Query: 395 VKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMI 454 + + I + + + ++LS G+Q+++ +A+ LAT +L DEP G++ E+ +I Sbjct: 140 LHYVGIADRA-HDLAKHLSYGDQRRLEIARALATEPKLLALDEPAAGMNASETGELRTLI 198 Query: 455 RELAAQGKAVIMISSELPEILNLSDRIVVMWEGE 488 + G V++I ++ ++ L DR+ V+ GE Sbjct: 199 EGIRKDGITVLLIEHDVKLVMGLCDRVAVLDYGE 232 Lambda K H 0.319 0.138 0.381 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: 300 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 520 Length of database: 267 Length adjustment: 30 Effective length of query: 490 Effective length of database: 237 Effective search space: 116130 Effective search space used: 116130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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