Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_04149 H281DRAFT_04149 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Burk376:H281DRAFT_04149 Length = 506 Score = 398 bits (1022), Expect = e-115 Identities = 210/499 (42%), Positives = 312/499 (62%), Gaps = 9/499 (1%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 ILK I K FPGV A+ + E+ EI +L+GENGAGKSTL+KIL G+ +PD G I + Sbjct: 4 ILKLDNITKSFPGVKALQGIHLEIARGEIHALLGENGAGKSTLMKILCGIYQPDEGTITI 63 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 GE F + DA G+ ++ QE +L + EN+FL E G ++ M Sbjct: 64 EGEPRHFANYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGREMKNGL-----GLLNRGGM 118 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + E+ +G +R L+ AQ+Q VEI KAL E RI+ +DEPT++LT E E Sbjct: 119 RRVAAEIFGRLGVSIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAE 178 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LF I+ LK +G++++F+SH L+E+ + DRI V+RDG+ +G + + DV +++MMV Sbjct: 179 HLFAIMRDLKKQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSDVGRLVEMMV 238 Query: 254 GREVEF-FPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311 GR +E FP RP ++ L+V+ L+ + F +R+GE+LGFAGLVG+GRTET Sbjct: 239 GRRIESSFPPKPPLRPDAKVVLDVQKLQLLKDSPMLQFTLREGEILGFAGLVGSGRTETA 298 Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371 L V G + +I +NG + +P DA++ G+G++PE RK +GL+ ++K NI + + Sbjct: 299 LAVIGADPAHVKEIRINGEAANLSDPADALRAGVGILPESRKTEGLITDFSIKQNISINN 358 Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431 L K +D+R E + D +KR+ +K P+++ LSGGNQQKVV+A+WL + + Sbjct: 359 LGKYRSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVATLSGGNQQKVVIARWLNHHTN 418 Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491 ILIFDEPTRGIDVGAKAEI+ ++REL A+G ++IMISSELPEI+ + DR+ V +G I A Sbjct: 419 ILIFDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVAVFRQGRIEA 478 Query: 492 VLDNREKRVTQEEIMYYAS 510 +L+ ++ +M YA+ Sbjct: 479 LLEG--DQIDSNAVMTYAT 495 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: 660 Number of extensions: 31 Number of successful extensions: 7 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: 506 Length adjustment: 35 Effective length of query: 485 Effective length of database: 471 Effective search space: 228435 Effective search space used: 228435 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