Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate BPHYT_RS11220 BPHYT_RS11220 LacI family transcriptional regulator
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS11220 Length = 320 Score = 97.1 bits (240), Expect = 5e-25 Identities = 82/245 (33%), Positives = 120/245 (48%), Gaps = 18/245 (7%) Query: 66 NQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIK---VDDDSLFL 122 NQI+ V I VDAI++AP PV+K+A A I VV +D + + L + Sbjct: 84 NQIRIVEQMIVSKVDAIVLAPADSKALVPVVKKAVDAGIIVVNIDNRLDPEVLKSKDLNV 143 Query: 123 TRIASDFSEEGRKIGQWLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIV 182 + D + +K+G +L K + ++ ++G T A R AGF + AK+V Sbjct: 144 PFVGPDNRKGAQKVGDYLAKKLKAGDEVGIIEGVSTTTNAQQRTAGFKDAMQKV-GAKVV 202 Query: 183 RSQTGEFTRAKGKEVMEGFLKAQNGQP-LCAVWSHNDEMALGAVQAIKEAGLKPGKDILI 241 Q+GE+ KG V L N P L A+ + ND MA+GAV A++ AG K GK +L+ Sbjct: 203 SVQSGEWEIDKGNAVASAML---NEYPNLKALLAGNDNMAIGAVSAVRAAG-KQGK-VLV 257 Query: 242 VSVDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLK---GNKDQAKL---ISTTG 295 V D + + DG V AT + Y A ID LK G+K QA+L + T Sbjct: 258 VGYDNINAIKPMLKDGRVLATAD--QYAAKQAVFGIDTALKALSGHKKQAELSGVVETPC 315 Query: 296 DVFTQ 300 D+ T+ Sbjct: 316 DLVTK 320 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: 246 Number of extensions: 19 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: 313 Length of database: 320 Length adjustment: 27 Effective length of query: 286 Effective length of database: 293 Effective search space: 83798 Effective search space used: 83798 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