Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_068002934.1 PsAD2_RS04495 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >NCBI__GCF_001623255.1:WP_068002934.1 Length = 290 Score = 123 bits (308), Expect = 7e-33 Identities = 69/216 (31%), Positives = 118/216 (54%), Gaps = 6/216 (2%) Query: 164 GRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLL 223 GR+ NSL V + ST + + I AAYAL F GR + + + +VP + L+P+ Sbjct: 81 GRALNNSLIVGLLSTGLTLTIGCMAAYALVRFQFMGRGTVSMGTLLMRIVPPAVLLVPVF 140 Query: 224 QLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFD 283 G+ F +TY GI L +T LP I++L++++ +P ++ E+AR+DGA+ F Sbjct: 141 ----GIWTFQYGLDQTYAGIILIYTAMNLPFVIWILQSFIVQVPIQLEEAARMDGANPFQ 196 Query: 284 IFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNW 343 +F ++LP+ P LA+ AIF F WN+ L+A G +T +VN + +W Sbjct: 197 VFFLVVLPIIQPGLAAAAIFTFRIAWNEFLLANALSGRSTRTAPVT--IVNSITEYDIDW 254 Query: 344 EILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 ++ A+ + + P++ F + ++ G+ AG+VKG Sbjct: 255 GVIMATGMLLAIPPILFTFVASKQIITGMTAGAVKG 290 Lambda K H 0.324 0.139 0.418 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: 245 Number of extensions: 10 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: 380 Length of database: 290 Length adjustment: 28 Effective length of query: 352 Effective length of database: 262 Effective search space: 92224 Effective search space used: 92224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 49 (23.5 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