Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 390 bits (1003), Expect = e-113 Identities = 209/500 (41%), Positives = 321/500 (64%), Gaps = 12/500 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L+ GI K FPGV A+DNV+ +V + I +L+GENGAGKSTL+K L G+ + D+G IL Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G+ ++FHS +A + GIS++HQELNL +V +N++L G+ T VD++ M Sbjct: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWL------GRYPTKGMFVDQDKM 126 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 Y +K + D + P A V L+ +Q QM+EI KA +I+ MDEPTSSLT +E Sbjct: 127 YRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LF II LK RG +V++SH+++E+ ++ D + V+RDG+ I +D II MMV Sbjct: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMV 246 Query: 254 GREV-EFFPHGIETRPGEIALEVRNLKW--KDKVKNVSFEVRKGEVLGFAGLVGAGRTET 310 GR + + FP E +PGE+ LEVRNL + +++VSF++ KGE+LG AGLVGA RT+ Sbjct: 247 GRSLNQRFPDK-ENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDI 305 Query: 311 MLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLP 370 + +FG+ +K +G I ++G+++ N +AI G L+ E+R+ G+ + + N ++ Sbjct: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365 Query: 371 SLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430 +++ +LD + + ++ + + +KTP +LSGGNQQKV++ +WL T Sbjct: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425 Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490 +IL+ DEPTRGIDVGAK EI+++I ELA +GK +I+ISSE+PE+L ++DRI+VM G ++ Sbjct: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485 Query: 491 AVLDNREKRVTQEEIMYYAS 510 ++D K TQ EI+ AS Sbjct: 486 GIVDT--KTTTQNEILRLAS 503 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: 694 Number of extensions: 44 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