Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate 18116 b4088 D-allose transporter subunit (NCBI)
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__Keio:18116 Length = 311 Score = 148 bits (373), Expect = 2e-40 Identities = 98/292 (33%), Positives = 155/292 (53%), Gaps = 12/292 (4%) Query: 3 MKKLATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVL 62 M K S + +S +A A A+V+ TL+NPF+V +K G + EA LG ++ + Sbjct: 1 MNKYLKYFSGTLVGLMLSTSAFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIF 60 Query: 63 --DSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATK- 119 S+ + +L +DL+ + K + P S + V A + I ++ LD + Sbjct: 61 ASPSEGDFQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKIDMD 120 Query: 120 ------GEVVSHIASDNVLGGKIAGDYIAKKAG-EGAKVIELQGIAGTSAARERGEGFQQ 172 G V + + +DNV G +I K G EG +V ++G AG ++ R G + Sbjct: 121 NLKKAGGNVEAFVTTDNVAVGAKGASFIIDKLGAEGGEVAIIEGKAGNASGEARRNGATE 180 Query: 173 AVA-AHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK 231 A A + ++ASQPAD+DRIK L+V N+L +P+++A++ ND MA+G +A+ AGK Sbjct: 181 AFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGK 240 Query: 232 S-DVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKV 282 + V+VVG DG P+ K V G++ AT+AQ P IGA G++ K KV Sbjct: 241 TGKVLVVGTDGIPEARKMVEAGQMTATVAQNPADIGATGLKLMVDAEKSGKV 292 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: 252 Number of extensions: 21 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