Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate BPHYT_RS01825 BPHYT_RS01825 sugar ABC transporter substrate-binding protein
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__BFirm:BPHYT_RS01825 Length = 339 Score = 162 bits (411), Expect = 8e-45 Identities = 93/256 (36%), Positives = 147/256 (57%), Gaps = 11/256 (4%) Query: 37 NNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAV 96 NNP+ ++ + A K G+ LV+ D+ ++ +K+++++Q++ + +L+ P + + Sbjct: 61 NNPWRLAETKSFKDIAAKCGWQLVMTDANSSNSKQVSDIQNMIAQHVDLLVFPPREEKPL 120 Query: 97 GNAVKMANQANIPVITLDRQATKG------EVVSHIASDNVLGGKIAGDYIAKKAGEGAK 150 V A +A IPVI +DR + + ++ I SD + G A D++ K G AK Sbjct: 121 APVVLQAKKAGIPVILVDRDVDQSVAKAGRDYITFIGSDFIDQGHRAADWLVKATGGKAK 180 Query: 151 VIELQGIAGTSAARERGEGFQQAVAAHK-FNVLASQPADFDRIKGLNVMQNLLTAHPDVQ 209 +IEL+G G SAA +R +GF + +A + ++ASQ DF R KG VM+ LL AHPDV Sbjct: 181 IIELEGTTGASAANDRKKGFDEIIAKNPGMTIIASQSGDFARDKGRQVMETLLQAHPDVT 240 Query: 210 AVFAQNDEMALGALRALQTAGK---SDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIG 266 AV+A NDEMALGA+ A++ AGK D+ +V DGT G A+ G+L A++ P G Sbjct: 241 AVYAHNDEMALGAIAAIKAAGKQPGKDIQIVTIDGTKGGMDAIAAGELGASVQSSP-FFG 299 Query: 267 AKGVETADKVLKGEKV 282 + A + KGEK+ Sbjct: 300 PLACDVAQRYAKGEKI 315 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: 232 Number of extensions: 13 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: 339 Length adjustment: 27 Effective length of query: 269 Effective length of database: 312 Effective search space: 83928 Effective search space used: 83928 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