Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate SMc03893 SMc03893 amino-acid transport system permease ABC transporter protein
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >FitnessBrowser__Smeli:SMc03893 Length = 226 Score = 135 bits (341), Expect = 5e-37 Identities = 69/201 (34%), Positives = 122/201 (60%) Query: 18 LWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLAC 77 LW+G + ++ ++L+ LG +G+V +V + A RFYV +IRGTP+ V + Sbjct: 16 LWAGLIFTIPLTLLSFTLGLALGLVTAVVRLFAPAPFAAVARFYVWVIRGTPLLVQLFVI 75 Query: 78 FYMAPALGWQIDAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALA 137 FY P++G +DAF A ++G TL G++ +EI+R + ++PRGQ EA+ +IG+++ QA+ Sbjct: 76 FYGLPSMGILLDAFPAALIGFTLNIGAYSSEIIRAVISSVPRGQWEAAYSIGMSWSQAMR 135 Query: 138 YVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLFAGF 197 +LPQA R +P N+ +VK ++L + I V EL + Q+I+A ++ L Y+ A Sbjct: 136 RTILPQAGRVAVPPLSNTFISLVKDTSLAAAITVPELFQTAQRIVATSYEPLILYIEAAL 195 Query: 198 LFFIINYAIELLGRHIEKRVA 218 ++ +++ + L +E+R A Sbjct: 196 IYLVMSSVLSALQGKLEQRFA 216 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: 165 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 220 Length of database: 226 Length adjustment: 22 Effective length of query: 198 Effective length of database: 204 Effective search space: 40392 Effective search space used: 40392 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 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