Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 384 bits (985), Expect = e-111 Identities = 221/508 (43%), Positives = 323/508 (63%), Gaps = 14/508 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L K I K F GV A+D+V E+ + +++GENGAGKSTL+KIL+GV G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 NG+ V+F + DA +KGI++IHQELNL +++ ENIFL E T +D M Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREP-----ETPMGLLDVAKM 115 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + + +LL + P+ V L Q+Q+VEI KAL E ++I MDEPTS+++ +E E Sbjct: 116 HKEAAQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVE 175 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LF II L++ G ++ ++SH+LDE+ I+DR VV+RDGK I + + +I+ MV Sbjct: 176 ILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235 Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWK-----DK--VKNVSFEVRKGEVLGFAGLVGAG 306 GRE+ + E L V++L K DK +++++FE+ KGEVLG GL+GAG Sbjct: 236 GREIVIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAG 295 Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366 RTE M +FGV + +I + G+ E + P++A+ G+ L+PEDRK GLVL M + N Sbjct: 296 RTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTN 355 Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426 L + I GL LD++KE+ +++ Y+ L IK S Q+ E LSGGNQQKVVLAKWL Sbjct: 356 SSLTVVDSILSGGL-LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWL 414 Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486 AT +L+ DEPTRGID+ AK EI+++IR+LA +G +I++SSELPEIL +SDR++VM E Sbjct: 415 ATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAE 474 Query: 487 GEITAVLDNREKRVTQEEIMYYASGQKK 514 G +TA + + + +++EI+ A +KK Sbjct: 475 GRLTANIP-IDAQTSEDEILQAAIPKKK 501 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: 686 Number of extensions: 37 Number of successful extensions: 8 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: 502 Length adjustment: 35 Effective length of query: 485 Effective length of database: 467 Effective search space: 226495 Effective search space used: 226495 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