Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Keio:17809 Length = 501 Score = 440 bits (1132), Expect = e-128 Identities = 239/498 (47%), Positives = 337/498 (67%), Gaps = 4/498 (0%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 ++ L+ + K FPGV AL + G V AL+GENGAGKST+MK+L+G+Y RD+G +L Sbjct: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 GK T P+ +Q GIGIIHQELNL+ L+ A+NIF+GRE G ID + +A Sbjct: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGK-IDWKTMYAEA 122 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 + A++ L VG+L++ QQMVEIAK LSF+S+V+IMDEPT AL + E LFR Sbjct: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 +IR+L++QG GIVYISH+M E+ +I D V+V RDG++IA + + D++I MMVGR L Sbjct: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242 Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321 + +Q D + D+ L+V L G + DVSFTLRKGEILG +GLMGAGRTE+ + ++G Sbjct: 243 E-DQYPHLDKAPGDIRLKVDNLC-GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300 Query: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381 A P +G + + G + V +SP D +A+GI Y+SEDRK GL +GM V+ N++L+++ F+ Sbjct: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360 Query: 382 RVGFMDQRAI-REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440 R G + A ++A ++R +KTPS+EQ LLSGGNQQK+ IA+ L+ +L D Sbjct: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420 Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500 EPTRG+DVGAK EIY+L++ G +I+++SSE+PEVL MS R++VM EG ++GE R Sbjct: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480 Query: 501 DATQEKIMQLATQRESAV 518 ATQE +M A + + V Sbjct: 481 QATQEVLMAAAVGKLNRV 498 Lambda K H 0.320 0.135 0.372 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: 624 Number of extensions: 29 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: 501 Length adjustment: 34 Effective length of query: 486 Effective length of database: 467 Effective search space: 226962 Effective search space used: 226962 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 (21.8 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