Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate 18252 b4227 predicted sugar transporter subunit: periplasmic-binding component of ABC superfamily (NCBI)
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__Keio:18252 Length = 318 Score = 129 bits (325), Expect = 7e-35 Identities = 88/276 (31%), Positives = 143/276 (51%), Gaps = 14/276 (5%) Query: 3 MKKLATLVSAVALSATVSANAMAKD-TIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVV 61 M K +VSAV SA +S+ A+A T+ + + + + A+ EA+K G L + Sbjct: 1 MWKRLLIVSAV--SAAMSSMALAAPLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKI 58 Query: 62 LDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQ---AT 118 D Q ++ V+ +G + I P + +K A A IPV LDR Sbjct: 59 ADGQQKQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKD 118 Query: 119 KGEVVSHIASDNVLGGKIAGDYIAKKA-GEGAKVIELQGIAGTSAARERGEGFQQAVA-A 176 K ++ + +DN+L GK+ GD++ K+ G+ V+ELQG G S A +R +GF +A+ A Sbjct: 119 KSLYMTTVTADNILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAIDRKKGFAEAIKNA 178 Query: 177 HKFNVLASQPADFDRIKGLNVMQNLLTAH---PDVQAVFAQNDEMALGALRALQTAG--- 230 ++ SQ DF R KG VM++ + A ++ V+A ND+M +GA++A++ AG Sbjct: 179 PNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKP 238 Query: 231 KSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIG 266 D++ DG PD KA+ DG+ A++ P+ G Sbjct: 239 GKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAG 274 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: 227 Number of extensions: 19 Number of successful extensions: 6 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: 318 Length adjustment: 27 Effective length of query: 269 Effective length of database: 291 Effective search space: 78279 Effective search space used: 78279 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