Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate BWI76_RS02165 BWI76_RS02165 D-allose transporter subunit
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__Koxy:BWI76_RS02165 Length = 311 Score = 152 bits (384), Expect = 9e-42 Identities = 107/311 (34%), Positives = 165/311 (53%), Gaps = 18/311 (5%) Query: 3 MKKLATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVL 62 M K + S + +S +A A A+V+ TL+NPF+V +K G + EA LG ++ + Sbjct: 1 MNKYLKIFSGTLMGVMLSTSAFAAADYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIF 60 Query: 63 --DSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATK- 119 S+ + +L +DL+ + K + P S + V A + I ++ LD + Sbjct: 61 ASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVAKAWKKGIYLVNLDEKIDMD 120 Query: 120 ------GEVVSHIASDNV-LGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQ 172 G V + + +DNV +G K A I K EG +V ++G AG ++ R G + Sbjct: 121 NLKKAGGNVEAFVTTDNVAVGAKGAAFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATE 180 Query: 173 AVA-AHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK 231 A A + ++ASQPAD+DRIK L+V N+L +P+V+A++ ND MA+G +A+ AGK Sbjct: 181 AFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNVKAIYCANDTMAMGVAQAVANAGK 240 Query: 232 S-DVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGV------ETADKVLKGEKVQA 284 + V+VVG DG P+ K V G++ ATIAQ P IGA G+ E + KV+ +K Sbjct: 241 TGKVLVVGTDGIPEARKMVEAGQMTATIAQNPADIGATGLKLMVDAEKSGKVIPLDKAPQ 300 Query: 285 KYPVDLKLVVK 295 VD LV K Sbjct: 301 FTLVDSILVTK 311 Lambda K H 0.313 0.129 0.344 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: 255 Number of extensions: 20 Number of successful extensions: 4 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: 296 Length of database: 311 Length adjustment: 27 Effective length of query: 269 Effective length of database: 284 Effective search space: 76396 Effective search space used: 76396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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