Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 420 bits (1079), Expect = e-122 Identities = 231/499 (46%), Positives = 328/499 (65%), Gaps = 11/499 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L A+G+ K FPGVVA+D+V+F++ + +L+GENGAGKSTL+KIL G+ PD GE+ + Sbjct: 23 LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKL 82 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G + SP+DA + GI++IHQELNL MTVAENI+ +R + + VD M Sbjct: 83 RGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIW-----IRREPKNRFGFVDHGEM 137 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + +L + + P+ VR+L+ A RQMVEI KA+ E ++ MDEPTS+LT E Sbjct: 138 RRMTAKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVA 197 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LFEII L+S+GI +V+++H+++E+ I+D V RDGK IG E D II+MMV Sbjct: 198 HLFEIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMV 257 Query: 254 GREV-EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 GRE+ + FP E G++ L V+NL ++VSF+VR GE+LG AGLVG+GR+ Sbjct: 258 GREITQMFPKE-EVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAE 316 Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372 +FGV SG I ++G++V I + AI+ + + EDRK G +L + + +N+ + L Sbjct: 317 TLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVL 376 Query: 373 K-KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431 + K + G V ER+ E+ ++L +KTP++ + ENLSGGNQQKV++ +WL TN Sbjct: 377 QDKFVKRGFV-SEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPR 435 Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491 ILI DEPTRGIDVGAKAEIHR++ ELA G AVIMISSE+PE+L +SDRI+VM EG +T Sbjct: 436 ILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTG 495 Query: 492 VLDNREKRVTQEEIMYYAS 510 +LD E TQ ++M A+ Sbjct: 496 ILDRAE--ATQIKVMELAA 512 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: 699 Number of extensions: 30 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: 513 Length adjustment: 35 Effective length of query: 485 Effective length of database: 478 Effective search space: 231830 Effective search space used: 231830 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