Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Burk376:H281DRAFT_01057 Length = 517 Score = 432 bits (1110), Expect = e-125 Identities = 231/506 (45%), Positives = 334/506 (66%), Gaps = 5/506 (0%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL++ I K F +L + L +R GEIHAL+GENGAGKSTL K+++GV+APD GEI Sbjct: 12 LLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDSGEIRF 71 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G+P+ + ++ GI++I+QEL + P +VA N+F G+E RTR+G++DH M Sbjct: 72 AGQPLQWKSAADAKRHGIHVIHQELVLFPQSTVAENIFAGAEPRTRIGVLDHGRMNRDAQ 131 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 A+L +LG + + G LS+A+QQ VEIA+A+ +R++I+DEPTA ++ +E + LF Sbjct: 132 ALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQLLFAR 191 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245 VR LR +G+AI+YISHR+ E++ L DRVTV++DG V +++V++MVGR + Sbjct: 192 VRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRDQLVRLMVGREMK 251 Query: 246 EFYQHQRIAPADAAQLPTVMQVRAL-AGGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304 + Y + P A +P V++V L G ++ AS VRAGE++G AG+VG+GRTELA Sbjct: 252 DIYPDK---PILAPGVPNVLEVNGLCVGNRVVDASLTVRAGEIVGIAGMVGSGRTELAAG 308 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364 +FGA G + + G PR A+R G+ +V EDRK QGL + + VA N T + Sbjct: 309 IFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLMLLDVAQNVTATTLA 368 Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424 + +R GL+R A+AAI + AHP V LSGGNQQKVL++RW+ + +VLI Sbjct: 369 QVSRFGLMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVLISRWVRVCKRVLI 428 Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484 LDEPTRGVD+ AK+EIY+++ L S+G+ +++ISSEL EVIG+ DRVLVMREG I GE++ Sbjct: 429 LDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRVLVMREGRINGEVS 488 Query: 485 GAAITQENIMRLATDTNVPRTAPASH 510 G +T+ +IMRLAT T +T +H Sbjct: 489 GEQMTEHDIMRLAT-TETSQTTGDAH 513 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: 748 Number of extensions: 48 Number of successful extensions: 6 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: 517 Length adjustment: 35 Effective length of query: 486 Effective length of database: 482 Effective search space: 234252 Effective search space used: 234252 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