Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate BWI76_RS07235 BWI76_RS07235 hypothetical protein
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__Koxy:BWI76_RS07235 Length = 307 Score = 150 bits (379), Expect = 3e-41 Identities = 95/299 (31%), Positives = 166/299 (55%), Gaps = 8/299 (2%) Query: 1 MNMKKLATLVSAVALSATVSANAMAKD-TIALVVSTLNNPFFVSLKDGAQKEADKLGYNL 59 MN+KK V A ++ + A MAKD ++ + ++ ++ F L+ QKE K G Sbjct: 1 MNIKKT---VVASLIACMLPAVVMAKDISVGVSMALFDDNFLTILRTAMQKEMQKDGVKA 57 Query: 60 VVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDR--QA 117 V D++ + +++L VQ+ +G +++NP D++AV + A +A IP+I ++R QA Sbjct: 58 QVEDAKGDVSQQLQQVQNFIGQGVDAIIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQA 117 Query: 118 TKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAH 177 + ++++ SD+VL G++ + +AK V L G + R+R +G ++ VA + Sbjct: 118 QLTDKMAYVGSDSVLAGRLQMEALAKAMNGKGNVAILLGDLANESTRDRTKGVEEVVAKY 177 Query: 178 -KFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMV 236 ++ Q A F R ++V+ N +T+ D+QA+ + NDEMA+GAL+AL + +++ Sbjct: 178 PDIKIVQKQTAKFTRNDAVDVVSNWMTSGEDIQAIASNNDEMAIGALQAL-GKNPNHILI 236 Query: 237 VGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVK 295 G DGTPD + + +GK+ ATI Q G V+ A K+ GEKV+ V +L+ K Sbjct: 237 AGVDGTPDALQMLKNGKMIATIFQDAKGQGEGAVDAAIKLANGEKVEKVIDVPYQLITK 295 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: 259 Number of extensions: 16 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: 307 Length adjustment: 27 Effective length of query: 269 Effective length of database: 280 Effective search space: 75320 Effective search space used: 75320 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