Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 377 bits (967), Expect = e-109 Identities = 214/515 (41%), Positives = 320/515 (62%), Gaps = 24/515 (4%) Query: 19 SVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGD 78 + P I++ + K F V AL + + GE+HAL+GENGAGKSTLMK+LSG+++ G Sbjct: 2 ATPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGT 61 Query: 79 ILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGRE-PRKAMGL-FIDEDE 136 I ++ + + A LGIGII+QEL++++ L+ +N++IGR +K G+ ID E Sbjct: 62 ITINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWRE 121 Query: 137 LNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEI 196 + +AA + R+ L +D V L+++ +QM+EIAK L D++V+IMDEPT++L N E+ Sbjct: 122 MRVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEV 181 Query: 197 AELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMM 256 LF I+ L+ +G IVYISHK+ E+R+I DR +VM+DG + + + + S D I+ +M Sbjct: 182 DYLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLM 241 Query: 257 VGRALDGEQRIPPDTSRN---DVVLEVRGLNRG--RAIRDVSFTLRKGEILGFAGLMGAG 311 VGR L + N + V EVR + + +RD+SF++ +GEILGFAGL+G+G Sbjct: 242 VGRELQNRFNAMKENVSNLAHETVFEVRNVTSRDRKKVRDISFSVCRGEILGFAGLVGSG 301 Query: 312 RTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQAN 371 RTE+ +FG D GEI ++G +SP DAV G+ Y++E R+ G + N Sbjct: 302 RTELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQN 361 Query: 372 IALS----------SMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQ 421 +A+S +MG F V +QR ++ LA+K SV Q LSGGNQ Sbjct: 362 MAISRSLKDGGYKGAMGLFHEVD--EQRTAENQREL----LALKCHSVNQNITELSGGNQ 415 Query: 422 QKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRM 481 QK++I+KWL +++ FDEPTRGIDVGAK+EIYK++ LA+ GK I+M+SSELPE++ + Sbjct: 416 QKVLISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITV 475 Query: 482 SHRVLVMCEGRITGELA-RADATQEKIMQLATQRE 515 R+ V CEGR+T L R D ++E+IM A +E Sbjct: 476 CDRIAVFCEGRLTQILTNRDDMSEEEIMAWALPQE 510 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: 609 Number of extensions: 22 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: 510 Length adjustment: 35 Effective length of query: 485 Effective length of database: 475 Effective search space: 230375 Effective search space used: 230375 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