Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate HSERO_RS05170 HSERO_RS05170 LacI family transcription regulator
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__HerbieS:HSERO_RS05170 Length = 324 Score = 326 bits (836), Expect = 4e-94 Identities = 167/292 (57%), Positives = 219/292 (75%), Gaps = 6/292 (2%) Query: 24 TVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQENQIKAVRSFIAQGVDAII 83 T+GFSQVG+ES WRT+ + ++K AKQ G++LKFADAQQKQENQ+KA+RSFIAQ VD I Sbjct: 34 TMGFSQVGAESEWRTANTVSIKDAAKQAGVNLKFADAQQKQENQVKAIRSFIAQKVDVIA 93 Query: 84 IAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLFLTRIASDFSEEGRKIGQWLMDK 143 +PVVE+GW+ VL+EAK AKIPV++ DR + V D SL++T I SDF EEGR+ G+WL++K Sbjct: 94 FSPVVESGWETVLREAKAAKIPVILTDRAVNVSDKSLYVTFIGSDFVEEGRRAGRWLLEK 153 Query: 144 TQ----GNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRSQTGEFTRAKGKEVME 199 + G+ +I ELQGTVG+ AIDR AGF +VI P KI+RSQTG+FTRAKGKEVME Sbjct: 154 AKSMPAGDINIVELQGTVGSAPAIDRKAGFEEVIKGEPRLKIIRSQTGDFTRAKGKEVME 213 Query: 200 GFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSVDGVPDYFKAMADGDV 259 FLKA+ G+ + +++HND+MA+GA+QAI+EAG+KPGKDI+I+S+DGV F+AM G + Sbjct: 214 AFLKAE-GKKINVLYAHNDDMAIGAIQAIEEAGMKPGKDIIIISIDGVKGAFEAMMAGKL 272 Query: 260 NATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVFTQETAAAEYEKRR 311 N TVE SP L GP I +K K+ K I+T +F E AA E+ R+ Sbjct: 273 NVTVECSPLL-GPQLMQIAKDIKAGKEVPKRITTEEGIFPAEVAAKEFPNRK 323 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: 318 Number of extensions: 10 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: 324 Length adjustment: 27 Effective length of query: 286 Effective length of database: 297 Effective search space: 84942 Effective search space used: 84942 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