Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 437 bits (1123), Expect = e-127 Identities = 241/501 (48%), Positives = 332/501 (66%), Gaps = 10/501 (1%) Query: 13 EILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEIL 72 EIL+ KG+ KRFPGVVA+D +D ++ E+ ++ GENGAGKSTL+KI++G + D G + Sbjct: 22 EILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVR 81 Query: 73 VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132 G V+F S DA GI++IHQELNL +++VAENI+LA E RG VD Sbjct: 82 YRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPF------VDYRT 135 Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192 + + ++ L IG SP LV L+ AQ+QMVEI KAL + R++ MDEPTSSLT ET Sbjct: 136 LNSNAQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESET 195 Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252 +LF II L++ G++++++SHRLDE+ I DR+ V+RDG+ I V+ I+ M Sbjct: 196 VQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARM 255 Query: 253 VGREVE-FFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311 VGR ++ +P T +I L VR+L+ +SFE+RKGE+LGFAGL+GAGRTET Sbjct: 256 VGRPLDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETA 315 Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371 +FG + +SG I + V I +P +AI+ GI + EDRK GL L M V NI L + Sbjct: 316 RAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLAN 375 Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431 ++ IS G L +E I+E YV+ L I+TP++ QI NLSGGNQQK+V++KWL + Sbjct: 376 VRAISSRGF-LRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGSR 434 Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491 IL FDEPTRGIDVGAK I+ ++ LAA G V++ISSELPE+L ++DRI V EG ITA Sbjct: 435 ILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITA 494 Query: 492 VLDNREKRVTQEEIMYYASGQ 512 VL+ R+ +QEEI+++ASG+ Sbjct: 495 VLETRQ--TSQEEILHHASGR 513 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: 631 Number of extensions: 28 Number of successful extensions: 9 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: 516 Length adjustment: 35 Effective length of query: 485 Effective length of database: 481 Effective search space: 233285 Effective search space used: 233285 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