Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 390 bits (1001), Expect = e-113 Identities = 224/518 (43%), Positives = 325/518 (62%), Gaps = 20/518 (3%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 IL A+ I K F GV A+ +V FE+ EI +L+GENGAGKSTL+K+L+GV G + V Sbjct: 18 ILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAVRV 77 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSR-VDENY 132 +GE V F + DA GI++IHQELNL + VA+NIFL G++R ++ VD Sbjct: 78 DGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFL------GRERVIAGLFVDRKA 131 Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192 ++ LL+ +G + P+A V L ++Q+VEI KAL E RI+ MDEPTS+L+ E Sbjct: 132 SLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGEC 191 Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252 RLF+I+ L + G+ ++++SHR+DEVM++SDR+ V RDG+ + D +TII M Sbjct: 192 RRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTIIAAM 251 Query: 253 VGRE-VEFFPHGIETRPGEIALEVRNLK--------WKDKVKNVSFEVRKGEVLGFAGLV 303 VGR ++ GE L VR+L W+D +K VSF+VR GE+LG GL+ Sbjct: 252 VGRNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLL 311 Query: 304 GAGRTETMLLVFGVNQ-KESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMT 362 GAGRTE + +F N+ G+I ++G V I++P DA ++G L+ EDRK +GL L + Sbjct: 312 GAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHES 371 Query: 363 VKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVL 422 ++DN+ LP + +++R+GL E E +++ V L ++ Q LSGGNQQKVV+ Sbjct: 372 IRDNVALPLVGRLARFGLRSFE-GERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVI 430 Query: 423 AKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIV 482 KWLAT +L+ DEPTRGIDVGAK EI+ +I +LA G A++++SSELPE+L L+DRI+ Sbjct: 431 GKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRIL 490 Query: 483 VMWEGEITAVLDNREKRVTQEEIMYYASGQKKQNGRVA 520 VM EG T ++ E ++E IM A+ + + VA Sbjct: 491 VMAEGRQTGLISREE--ASEERIMQLAAPRSARGRAVA 526 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: 700 Number of extensions: 40 Number of successful extensions: 10 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: 526 Length adjustment: 35 Effective length of query: 485 Effective length of database: 491 Effective search space: 238135 Effective search space used: 238135 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