Align LacI family transcriptional regulator (characterized, see rationale)
to candidate PfGW456L13_3912 Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
Query= uniprot:A0A161ZH48 (318 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3912 Length = 305 Score = 553 bits (1424), Expect = e-162 Identities = 288/305 (94%), Positives = 298/305 (97%) Query: 14 MLAAASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQKDHSGDFELISNG 73 MLAAASAALPVSSAFAET EKPKVALVMKSLANEFFLTMEDGAKAYQKDHSG+F+LISNG Sbjct: 1 MLAAASAALPVSSAFAETTEKPKVALVMKSLANEFFLTMEDGAKAYQKDHSGEFDLISNG 60 Query: 74 IKDETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGITVINIDNQLDPAV 133 IKDETDTAGQTRIVEQMIL+KVNALVIAPADSKAMVPVIKKA+DAGITVINIDNQLDPAV Sbjct: 61 IKDETDTAGQTRIVEQMILAKVNALVIAPADSKAMVPVIKKAIDAGITVINIDNQLDPAV 120 Query: 134 VKSKNITVPFVGPDNRKGARLVGEYLAKQLKAGDEVGIIEGVSTTTNAQQRTAGFKDAME 193 VKSKNI VPFVGPDNRKGARLVG+YLAKQLKAGDEVGIIEGVSTTTNAQQRTAGFKDAME Sbjct: 121 VKSKNINVPFVGPDNRKGARLVGDYLAKQLKAGDEVGIIEGVSTTTNAQQRTAGFKDAME 180 Query: 194 AAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGAVSAVRAAGKAGKV 253 AAQIKVVSLQSGDWEIDKG KVA+S+LSEYP KALLAGNDSMAVGAVSAVRAAGKAGKV Sbjct: 181 AAQIKVVSLQSGDWEIDKGNKVAASILSEYPQTKALLAGNDSMAVGAVSAVRAAGKAGKV 240 Query: 254 QVVGYDNINAIKPMLKDGRVLATADQFAARQAVFGIETALKIIKGETVDSGANGVIETPV 313 QVVGYDNINAI+PMLKDGRVLATADQFAA+QAVFGIETALKI+KGE VD GANGVIETPV Sbjct: 241 QVVGYDNINAIQPMLKDGRVLATADQFAAKQAVFGIETALKILKGEKVDGGANGVIETPV 300 Query: 314 ELVTK 318 ELVTK Sbjct: 301 ELVTK 305 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: 385 Number of extensions: 8 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: 305 Length adjustment: 27 Effective length of query: 291 Effective length of database: 278 Effective search space: 80898 Effective search space used: 80898 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