Align LacI family transcriptional regulator (characterized, see rationale)
to candidate BPHYT_RS20680 BPHYT_RS20680 LacI family transcriptional regulator
Query= uniprot:A0A161ZH48 (318 letters) >FitnessBrowser__BFirm:BPHYT_RS20680 Length = 321 Score = 435 bits (1119), Expect = e-127 Identities = 223/316 (70%), Positives = 265/316 (83%) Query: 3 LPFAGRLLAVAMLAAASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQKD 62 LP R +A A + LP+ +AFA+ KPKVALVMKSLANEFFLTME GAK YQK Sbjct: 6 LPARRRAIAAGAAFLAVSILPMPAAFAQAAHKPKVALVMKSLANEFFLTMETGAKDYQKQ 65 Query: 63 HSGDFELISNGIKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGITV 122 + F+L++NGIKDETDTA Q RIVEQMI+SKV+ALVIAPADSKA+VPV+KKAVDAGI V Sbjct: 66 NPAKFDLVTNGIKDETDTANQIRIVEQMIVSKVDALVIAPADSKALVPVLKKAVDAGIIV 125 Query: 123 INIDNQLDPAVVKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTNAQ 182 +NIDN+LD V+KSK++ +PFVGPDN KGA+ VG+YLAK LK+GD VGIIEGV+TTTNAQ Sbjct: 126 VNIDNKLDNDVLKSKDLNIPFVGPDNAKGAQKVGDYLAKHLKSGDNVGIIEGVTTTTNAQ 185 Query: 183 QRTAGFKDAMEAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGAVS 242 QRTAGFK AM A +KVV+LQSG+WEIDKG VAS +L+ P++KALL GND+MA+GAVS Sbjct: 186 QRTAGFKQAMAAGGMKVVALQSGEWEIDKGNAVASQILNANPDVKALLCGNDNMAIGAVS 245 Query: 243 AVRAAGKAGKVQVVGYDNINAIKPMLKDGRVLATADQFAARQAVFGIETALKIIKGETVD 302 AVRAAGKAGKVQ+VGYD+INAIKPMLKDGRVLATA+Q+AA+QAVFGI+TALK + Sbjct: 246 AVRAAGKAGKVQIVGYDDINAIKPMLKDGRVLATANQYAAKQAVFGIDTALKALSEHKKQ 305 Query: 303 SGANGVIETPVELVTK 318 S +GV+ETPV+LVTK Sbjct: 306 SELSGVVETPVDLVTK 321 Lambda K H 0.314 0.130 0.348 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: 329 Number of extensions: 6 Number of successful extensions: 1 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: 318 Length of database: 321 Length adjustment: 28 Effective length of query: 290 Effective length of database: 293 Effective search space: 84970 Effective search space used: 84970 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