Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate SM_b21137 SM_b21137 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__Smeli:SM_b21137 Length = 219 Score = 258 bits (658), Expect = 8e-74 Identities = 128/215 (59%), Positives = 166/215 (77%) Query: 6 SWLHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLI 65 S+L +LW+AR L G SV SLL+IV+GT++G+ GL L YG ++ R Y D I Sbjct: 4 SFLDQLWLARIPLLKGLGVSVSISLLSIVVGTVLGVFVGLALVYGFRPVKWIVRGYTDFI 63 Query: 66 RGTPVFVLVLACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEAS 125 RGTPV VLVLA +Y+ +G +G FQAGVL L +FC SHV E+VRGALQ++P+GQ EA+ Sbjct: 64 RGTPVLVLVLASYYVLSTIGIDLGPFQAGVLALAVFCSSHVGELVRGALQSIPKGQTEAA 123 Query: 126 QAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIART 185 +AIGLTF Q+ YVL PQALRQ LP WVN++ E+VKASTLLS+IGV+ELLL TQ++I+RT Sbjct: 124 KAIGLTFAQTFTYVLGPQALRQALPAWVNTAAEMVKASTLLSIIGVSELLLRTQELISRT 183 Query: 186 FMTLEFYLFAGFLFFIINYAIELLGRHIEKRVALP 220 FM+LEFY FAGFL+F+INY IE GR++E++ A+P Sbjct: 184 FMSLEFYFFAGFLYFVINYGIERFGRYVERKTAVP 218 Lambda K H 0.330 0.142 0.443 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: 224 Number of extensions: 10 Number of successful extensions: 1 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: 219 Length adjustment: 22 Effective length of query: 198 Effective length of database: 197 Effective search space: 39006 Effective search space used: 39006 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