Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 402 bits (1033), Expect = e-116 Identities = 224/504 (44%), Positives = 322/504 (63%), Gaps = 17/504 (3%) Query: 15 LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPD-AGEILV 73 L+ + I + FPGV A+D V+ E+ E+++L GENGAGKSTL+KILTG+ PD G ILV Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G+ V A G+++I+QEL + N+TV ENIFLA E RT +D M Sbjct: 70 EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREP-----RTRLGLIDRPRM 124 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 Y ++E+L I P V L+ Q+QM+EI KAL + I MDEPT+SL+ ET Sbjct: 125 YREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETS 184 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 L I++ L+ R I+VV++SHRL+E+ ++DR+ V+RDG+ +G + +T++++MV Sbjct: 185 VLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMV 244 Query: 254 GREV-EFFPHGIETRPGEIALEVRNLKWKD------KVKNVSFEVRKGEVLGFAGLVGAG 306 RE+ E + + LEVR L K +++++SF + +GEVLG AGLVG+G Sbjct: 245 ARELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSG 304 Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366 RTE M ++FG+ +G + + G+ V I+NP DAI+ GIG + EDRK QGL+L MTV++N Sbjct: 305 RTEIMEMIFGMRAC-TGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVREN 363 Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426 L L++ S + V R E E +V+ L IKTP + Q NLSGGNQQK+V+AKW+ Sbjct: 364 FSLTHLERYSPFQFVQHAR-ERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWV 422 Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486 A + +LI DEPTRGIDVGAKAE+H +I LAA+G VI+ISS+L E+L +SDRI+ + E Sbjct: 423 ARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVRE 482 Query: 487 GEITAVLDNREKRVTQEEIMYYAS 510 G I+ L + +QE++M A+ Sbjct: 483 GRISGELSRAQ--ASQEKVMALAT 504 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: 659 Number of extensions: 31 Number of successful extensions: 9 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: 520 Length of database: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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: 52 (24.6 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