Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate RR42_RS31740 RR42_RS31740 ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >FitnessBrowser__Cup4G11:RR42_RS31740 Length = 222 Score = 144 bits (363), Expect = 1e-39 Identities = 73/214 (34%), Positives = 125/214 (58%), Gaps = 1/214 (0%) Query: 4 QLNFAAVWRDFDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLS-KHRALRVLASVYVT 62 +L+F+ VW + L+ G G+ +E+ ++ +GCV+GLL+ L + R + L + YVT Sbjct: 2 ELDFSPVWAGWPDLVRGAGVTVEVTACALVLGCVMGLLVGIGRLDPRRRVVYGLCTAYVT 61 Query: 63 VIRNTPILVLILLIYFALPSLGIRLDKLPSFIITLSLYAGAYLTEVFRGGLLSIPKGLRE 122 IR TP+LV + L++F LP I L +I L +Y+GAY++E+ RG + S+ KG E Sbjct: 62 AIRGTPLLVQLFLLFFGLPQFDILLPAFVCGVIGLGIYSGAYVSEIVRGAIQSVDKGQME 121 Query: 123 AGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINV 182 A +IG+ Q V +P + ++P L N FI+L K+++L + + + ++ + +KI Sbjct: 122 AARSIGMSSGQAMRAVILPQAIVRMIPPLGNEFIALIKNSALVSLLTIHDVMHEGQKIIS 181 Query: 183 ESYRVIETWLVTTALYVAACYLIAMLLRYLEQRL 216 SYR +E +L +Y+ + LR++EQRL Sbjct: 182 VSYRSLEVYLAIALVYLLLTSAAGLFLRHMEQRL 215 Lambda K H 0.329 0.143 0.416 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: 125 Number of extensions: 8 Number of successful extensions: 2 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: 220 Length of database: 222 Length adjustment: 22 Effective length of query: 198 Effective length of database: 200 Effective search space: 39600 Effective search space used: 39600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 45 (21.9 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