Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 433 bits (1114), Expect = e-126 Identities = 236/506 (46%), Positives = 329/506 (65%), Gaps = 13/506 (2%) Query: 1 MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60 +T P L+MR I ++F AL ++L IR GE+ AL GENGAGKSTLMK+L+G++APD Sbjct: 4 VTGVPFLEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDP 63 Query: 61 G-EILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAA 119 G IL++G+ VAL D +R G+N+IYQELAV N++V N+F+ E RTRLGLID Sbjct: 64 GGTILVEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPR 123 Query: 120 MRSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 179 M VL + + LS+ +QQ +EIA+AL RS+ +IMDEPTA+LS ET Sbjct: 124 MYREAREVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHET 183 Query: 180 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMM 239 L +V+RLR+ +A++YISHR+ E++ LADRVTVLRDG VG ++ E +V++M Sbjct: 184 SVLLGIVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLM 243 Query: 240 VGRSLSEFYQHQRIAPADAAQLPTVMQVRAL-------AGGKIRPASFDVRAGEVLGFAG 292 V R LSE Y P A V++VRAL A +IR SF + GEVLG AG Sbjct: 244 VARELSELYGE----PQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAG 299 Query: 293 LVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQM 352 LVG+GRTE+ ++FG + G + +EG+PV I P A+R+GI +V EDRK QGL L M Sbjct: 300 LVGSGRTEIMEMIFGMRACT-GSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGM 358 Query: 353 AVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLL 412 V N ++ R++ V+ R ++ L +K E V LSGGNQQK+++ Sbjct: 359 TVRENFSLTHLERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVI 418 Query: 413 ARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVL 472 A+W+ +PKVLI+DEPTRG+D+ AK+E++ L+ RLA++G+ V+VISS+L EV+ + DR+L Sbjct: 419 AKWVARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRIL 478 Query: 473 VMREGMITGELAGAAITQENIMRLAT 498 +REG I+GEL+ A +QE +M LAT Sbjct: 479 TVREGRISGELSRAQASQEKVMALAT 504 Lambda K H 0.320 0.135 0.378 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: 750 Number of extensions: 37 Number of successful extensions: 11 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: 521 Length of database: 505 Length adjustment: 35 Effective length of query: 486 Effective length of database: 470 Effective search space: 228420 Effective search space used: 228420 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 (21.8 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