Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_089136613.1 CES79_RS06000 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >NCBI__GCF_002217945.1:WP_089136613.1 Length = 229 Score = 112 bits (279), Expect = 7e-30 Identities = 62/205 (30%), Positives = 118/205 (57%), Gaps = 6/205 (2%) Query: 18 LWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLAC 77 L+ G T+V+ + +A++LG ++G++ G++ T+ +R R Y++ R P VL+ Sbjct: 18 LFGGLWTTVEIAAVALVLGLILGVILGVLRTFPNRLLRLVLRLYLEFFRIVPTVVLLFLF 77 Query: 78 FYMAPA-LGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQAL 136 +Y+ P LG + A Q L L+ + +++IVRGAL ++P+ Q E+ AIGL Q Sbjct: 78 YYILPKQLGVNLPANQVATLVFALWTAAEMSDIVRGALISVPKHQRESGMAIGLNRLQLY 137 Query: 137 AYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIA---RTFMTLEFYL 193 YVL+PQA+ LP +N T ++K ++LL +I V +++ QQ++ + + T F++ Sbjct: 138 RYVLIPQAVSLELPATINLVTRVIKTTSLLMLISVMDVINVGQQVVEANNQKYPTGVFWV 197 Query: 194 FA--GFLFFIINYAIELLGRHIEKR 216 + ++F I+Y + + ++K+ Sbjct: 198 YGIIFVMYFAIDYPLSWWAKRMDKK 222 Lambda K H 0.330 0.142 0.440 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: 151 Number of extensions: 12 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: 220 Length of database: 229 Length adjustment: 22 Effective length of query: 198 Effective length of database: 207 Effective search space: 40986 Effective search space used: 40986 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 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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