Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate 8501185 DvMF_1919 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Miya:8501185 Length = 223 Score = 147 bits (370), Expect = 2e-40 Identities = 77/213 (36%), Positives = 121/213 (56%), Gaps = 1/213 (0%) Query: 8 AAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNT 67 + +W LL G+ L + + L +AIG ++G A A ++ ++ R LA +YV IR T Sbjct: 8 SVMWESVPLLLGGVHLTIIITLGGLAIGFLLGTATGLAKTARGKLPRALADIYVEAIRGT 67 Query: 68 PILVLILLIYFALP-SLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLA 126 P++V ++ +YF +P + G+R+ + + +I +++ +GAY+ E+ RG + SI GQ EAG + Sbjct: 68 PLIVQVMFLYFGVPLATGMRIPPVTAGIIAIAVNSGAYIAEIVRGAVESIDVGQTEAGRS 127 Query: 127 IGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYR 186 IGL Q YV P R ++P L N FI KDTSL I V ELT ++I ++R Sbjct: 128 IGLTRMQTLLYVVWPQAFRRMIPPLGNQFIISLKDTSLLVVIGVGELTRQGQEIIAVNFR 187 Query: 187 VIETWLVTTALYVAACYLIAMVLRYFEQRLAIR 219 E WL +Y+ IA LR +E++L R Sbjct: 188 AFEVWLTVAVMYLVMTLSIARALRVYERKLNAR 220 Lambda K H 0.329 0.142 0.414 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: 120 Number of extensions: 5 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: 223 Length adjustment: 22 Effective length of query: 198 Effective length of database: 201 Effective search space: 39798 Effective search space used: 39798 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