Align Ribose ABC transporter ATPase; SubName: Full=Sugar ABC transporter ATP-binding protein; SubName: Full=Sugar ABC transporter ATPase (characterized, see rationale)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:A0A1N7TZ92 (517 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 344 bits (883), Expect = 4e-99 Identities = 204/505 (40%), Positives = 308/505 (60%), Gaps = 21/505 (4%) Query: 10 LSVSGIGKTYAQPV--LSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTPTTGHMQF 67 +S++GIGK++ PV L + LT+ GE+ AL GENGAGKSTL K++ G+ PT G + Sbjct: 6 ISMAGIGKSFG-PVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITI 64 Query: 68 NGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDN--LPSHCGW--ISRKQLRK 123 N + A +LG+ ++ QEL+++ LTV ENL++ CG I +++R Sbjct: 65 NNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRV 124 Query: 124 AAIEAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEM 183 A + +VGL +D D V +L I H+QM+EIA+ L+ D V+I+DEPT+ LT +EV+ Sbjct: 125 RAAMMLLRVGLK-VDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDY 183 Query: 184 LFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLVTLMVG 243 LF + +L+ G AI+YISH+L E+ R+ R V++DG VC +++ +++ +V LMVG Sbjct: 184 LFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMVG 243 Query: 244 RELGEHIDLGPRTIGGPA----LTVKGLTRSD--KVRDVSFEVRAGEIYGISGLIGAGRT 297 REL + + A V+ +T D KVRD+SF V GEI G +GL+G+GRT Sbjct: 244 RELQNRFNAMKENVSNLAHETVFEVRNVTSRDRKKVRDISFSVCRGEILGFAGLVGSGRT 303 Query: 298 ELLRLIFGADLADSGTVALGSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISAN 357 EL+ +FG D G + L + +S RSP+DAV G+A ITE R+ G SI+ N Sbjct: 304 ELMNCLFGVDKRAGGEIRLNG--KDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQN 361 Query: 358 IALGNMPEISGG----GVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIG 413 +A+ + G G+ + DE A+ Q + + ++ S Q ++ELSGGNQQKV+I Sbjct: 362 MAISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNITELSGGNQQKVLIS 421 Query: 414 RWLERDCSVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGV 473 +WL V++FDEPTRGIDVGAK +IY ++ +L GK +++VSS+L E++ +CDRI V Sbjct: 422 KWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRIAV 481 Query: 474 LSAGRLIETF-ERDSWTQDELLAAA 497 GRL + RD +++E++A A Sbjct: 482 FCEGRLTQILTNRDDMSEEEIMAWA 506 Lambda K H 0.319 0.136 0.382 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: 598 Number of extensions: 34 Number of successful extensions: 9 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: 517 Length of database: 510 Length adjustment: 35 Effective length of query: 482 Effective length of database: 475 Effective search space: 228950 Effective search space used: 228950 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