Align LacI family transcriptional regulator (characterized, see rationale)
to candidate HSERO_RS22225 HSERO_RS22225 ABC transporter substrate-binding protein
Query= uniprot:A0A161ZH48 (318 letters) >FitnessBrowser__HerbieS:HSERO_RS22225 Length = 325 Score = 101 bits (252), Expect = 2e-26 Identities = 92/311 (29%), Positives = 148/311 (47%), Gaps = 31/311 (9%) Query: 17 AASAALPVSSAFAETPEKPKVALVMKSLANEFFLTMEDGAKAYQKDHSGDFELISNGIKD 76 AA A +++A A EK ++A+V+KSL N FF +GAK ++ GD E+I G Sbjct: 2 AAGAIGLIAAAPAHAAEKVRIAMVVKSLGNGFFDAAHEGAKEAARE-LGDVEVIYTGPTT 60 Query: 77 ETDTAGQTRIVEQMILSKVNALVIAPADSKAMVPVIKKAVDAGITVINIDNQLDPAVVKS 136 T GQ IV +I KV+A+VI+ D+ A+VP+ K+A+ G+ V++ D+ + + Sbjct: 61 PT-AEGQIEIVNSLISQKVDAIVISANDANALVPITKRAMQRGVKVLSFDSGI------A 113 Query: 137 KNITVPFVGPDNRKGARLVG----EYLAKQLKAGDEVGIIEGVSTTTNAQQRTAGFKDAM 192 K + + P N A L+G + A+ + +V I+ + TN K A+ Sbjct: 114 KGGRLMQLNPSN---AELIGLKQIQMAAEAIGGAGDVAILSATAQATNQNIWIGEMKKAL 170 Query: 193 ---EAAQIKVVSLQSGDWEIDKGGKVASSMLSEYPNIKALLAGNDSMAVGAVSAVRAAGK 249 E +++K+V+ GD + DK + A +L +P +KA++A A AV Sbjct: 171 ARPEFSRMKLVATVYGDDQSDKSYREAIGLLRSHPGLKAIIAPTTVGINAAGKAVVDEKL 230 Query: 250 AGKVQVVGYDNINAIKPMLKDGRV----------LATADQFAARQAVFGIETALKIIKGE 299 GKV V G + + +K G V L A +AA Q V G +GE Sbjct: 231 VGKVYVTGLGLPSEMAGHVKSGAVKSFAIWNPIDLGYAATYAAYQFVKGKAQGK---EGE 287 Query: 300 TVDSGANGVIE 310 ++ G G I+ Sbjct: 288 SIAVGRMGSIK 298 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: 188 Number of extensions: 14 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: 318 Length of database: 325 Length adjustment: 28 Effective length of query: 290 Effective length of database: 297 Effective search space: 86130 Effective search space used: 86130 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