Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate GFF2975 HP15_2919 amino acid ABC transporter, permease protein
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >FitnessBrowser__Marino:GFF2975 Length = 223 Score = 126 bits (317), Expect = 3e-34 Identities = 73/214 (34%), Positives = 116/214 (54%), Gaps = 1/214 (0%) Query: 3 YQLNFAAVWRDFDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVT 62 +Q ++ A L+ G+ L ++ + IG +G+ ++K LR A+ Y+ Sbjct: 5 FQFDWQAAIDSIPFLIKGIPYTLLISFGGLLIGFALGIFFGLLSINKKWFLRWPATAYIE 64 Query: 63 VIRNTPILVLILLIYFALPSL-GIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQR 121 + R TPILV +L I++ LP L G +D L + + ++L +GAY++EV RGG+ SI KGQ Sbjct: 65 IFRGTPILVQVLFIFYGLPDLIGGPIDPLTAGIAAIALNSGAYISEVVRGGVQSIDKGQT 124 Query: 122 EAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKIN 181 EAGL++GL Q V P R ++P L N I KDTSL + I V EL + Sbjct: 125 EAGLSLGLSRTQTFWSVVWPQAFRRMIPPLGNQAIVSIKDTSLFSVIGVGELVRQGQIYI 184 Query: 182 VESYRVIETWLVTTALYVAACYLIAMVLRYFEQR 215 ++ E + V LY+A ++++LR+ E+R Sbjct: 185 ANTFTAFEVYFVVAILYLAITLSLSIILRFVERR 218 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: 129 Number of extensions: 7 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