Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate N515DRAFT_2412 N515DRAFT_2412 simple sugar transport system substrate-binding protein
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__Dyella79:N515DRAFT_2412 Length = 319 Score = 301 bits (770), Expect = 2e-86 Identities = 162/291 (55%), Positives = 206/291 (70%), Gaps = 5/291 (1%) Query: 24 TVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQENQIKAVRSFIAQGVDAII 83 TVGFSQVG+ES WRT+ + +VK+ G DLKF+DAQQKQENQIKA+RSFIAQ VD I Sbjct: 30 TVGFSQVGAESEWRTANTASVKSALVAPGFDLKFSDAQQKQENQIKALRSFIAQRVDVIA 89 Query: 84 IAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLFLTRIASDFSEEGRKIGQWLMDK 143 +PVVE+GW+PVL+EAK A IPVV+ DR +KV D SL+ + I SDF EEGRK G+WL+ Sbjct: 90 FSPVVESGWEPVLREAKAAGIPVVLTDRAVKVSDASLYASLIGSDFIEEGRKAGRWLLQD 149 Query: 144 TQGN---CDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRSQTGEFTRAKGKEVMEG 200 + G + ELQGTVG+ AIDR GF++VI P K+VRSQ+G+FTRAKGKEVME Sbjct: 150 STGKPGPIRVVELQGTVGSAPAIDRMKGFHEVIDTDPRFKLVRSQSGDFTRAKGKEVMEA 209 Query: 201 FLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSVDGVPDYFKAMADGDVN 260 FLKA+ G + +++HND+MA+GA+QAI+EAGL PGKDI IVS+DGV F+AM G +N Sbjct: 210 FLKAEGGH-IDVLFAHNDDMAIGAIQAIEEAGLTPGKDIRIVSIDGVRGAFEAMKAGKLN 268 Query: 261 ATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVFTQETAAAEYEKRR 311 AT+E +P G I G +++ G VFTQ+ AAA R+ Sbjct: 269 ATIECNPLFGAQLAQLIRDVHAGKPVPKRIVVEEG-VFTQDQAAAALPGRK 318 Lambda K H 0.316 0.131 0.376 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: 304 Number of extensions: 6 Number of successful extensions: 3 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: 313 Length of database: 319 Length adjustment: 27 Effective length of query: 286 Effective length of database: 292 Effective search space: 83512 Effective search space used: 83512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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