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:D8IZC7 (521 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 371 bits (953), Expect = e-107 Identities = 205/505 (40%), Positives = 312/505 (61%), Gaps = 12/505 (2%) Query: 4 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63 TP + M GI KSFG AL ++LT+ PGEIHAL+GENGAGKSTLMKVLSG+H P +G I Sbjct: 3 TPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTI 62 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRL---GLIDHAAM 120 ++ D + GI +IYQEL+V ++V N+++G L ++ +ID M Sbjct: 63 TINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREM 122 Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180 R R +L ++G + LSI+ +Q +EIA+ L+ ++++IMDEPT++L+ +E + Sbjct: 123 RVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVD 182 Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240 LF ++ +LR EG AI+YISH++AE+ + DR TV++DGS V + ++ ++ IV++MV Sbjct: 183 YLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMV 242 Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAG---GKIRPASFDVRAGEVLGFAGLVGAG 297 GR L + + ++ A TV +VR + K+R SF V GE+LGFAGLVG+G Sbjct: 243 GRELQNRFNAMKENVSNLAH-ETVFEVRNVTSRDRKKVRDISFSVCRGEILGFAGLVGSG 301 Query: 298 RTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAAN 357 RTEL LFG D R+GG+I L G+ + P A++ G+AY+ E R+ G F ++A N Sbjct: 302 RTELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQN 361 Query: 358 ATMNVASR----HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLA 413 ++ + + +GL A + L +K + +LSGGNQQKVL++ Sbjct: 362 MAISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNITELSGGNQQKVLIS 421 Query: 414 RWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLV 473 +WL P+V+I DEPTRG+D+ AK+EIY+++ +LA G ++++SSELPE+I +CDR+ V Sbjct: 422 KWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRIAV 481 Query: 474 MREGMITGELAGA-AITQENIMRLA 497 EG +T L +++E IM A Sbjct: 482 FCEGRLTQILTNRDDMSEEEIMAWA 506 Lambda K H 0.320 0.135 0.378 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: 632 Number of extensions: 27 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: 521 Length of database: 510 Length adjustment: 35 Effective length of query: 486 Effective length of database: 475 Effective search space: 230850 Effective search space used: 230850 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