Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate BPHYT_RS23870 BPHYT_RS23870 LacI family transcription regulator
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS23870 Length = 328 Score = 285 bits (728), Expect = 1e-81 Identities = 158/313 (50%), Positives = 205/313 (65%), Gaps = 9/313 (2%) Query: 6 IITALGLWAVSATCAYAT----TVGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQ 61 + G ++ AYA T+GF+QVG+ES WRT+ +E++K+ A I LKF+DAQ Sbjct: 17 LCAGFGALTLATPGAYAQDKQITLGFAQVGAESAWRTANTESIKSAAADAKIKLKFSDAQ 76 Query: 62 QKQENQIKAVRSFIAQGVDAIIIAPVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSLF 121 QKQENQIKA+RS+IAQ VD I +PVVE+GW+PVL+EAK AKIPV++ DRNI D SL+ Sbjct: 77 QKQENQIKAIRSYIAQKVDVIAFSPVVESGWEPVLREAKAAKIPVILTDRNIDTKDTSLY 136 Query: 122 LTRIASDFSEEGRKIGQWLMD---KTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPN 178 +T I SDF EEGR+ G WL D QG +IAELQGTVG+ A DR +G +VI + P Sbjct: 137 VTMIGSDFLEEGRRGGHWLEDHFKNDQGPINIAELQGTVGSAPANDRHSGLVEVIKSDPK 196 Query: 179 AKIVRSQTGEFTRAKGKEVMEGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKD 238 KI+ SQ+G+FT A GK+VME F+K G + V++HND+MALGA+QA++EAG+ PGKD Sbjct: 197 FKIIASQSGDFTLAGGKQVMEAFIKTY-GNKINVVYAHNDDMALGAIQAMEEAGMHPGKD 255 Query: 239 ILIVSVDGVPDYFKAMADGDVNATVELSPYLGGPAFDAIDAYLKGNKDQAKLISTTGDVF 298 I +VS D F+AMA G +N VE SP LG A+ + G K K I T VF Sbjct: 256 ITVVSFDATKGGFQAMAAGKMNVDVECSPLLGPQLMSAVKDVVAG-KSLPKRILTEETVF 314 Query: 299 TQETAAAEYEKRR 311 AA R+ Sbjct: 315 PMSVAAQTLPTRK 327 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: 270 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: 328 Length adjustment: 28 Effective length of query: 285 Effective length of database: 300 Effective search space: 85500 Effective search space used: 85500 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