Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate 206676 DVU1237 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::Smeli:SMc02119 (397 letters) >MicrobesOnline__882:206676 Length = 256 Score = 88.2 bits (217), Expect = 2e-22 Identities = 47/134 (35%), Positives = 80/134 (59%) Query: 264 PEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRII 323 P+ ++ +ALS A++ E+ RAGI + KGQTEAA +LG T LVV+PQA R I Sbjct: 122 PDMLAAIIALSVCYGAYMGEVFRAGIEAIPKGQTEAARSLGFNRVETMFLVVLPQAWRTI 181 Query: 324 IPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSL 383 +PP+ ++++ + K++SL I AD++ G +++ Q E ++ +VYL ++L S Sbjct: 182 LPPVGNEFIAMLKDTSLVSIIAVADILRRGREFASESFQYFETYTMIALVYLLITLLLSK 241 Query: 384 FMNWYNARMALVER 397 ++ AR+ +R Sbjct: 242 GVSIMEARLNYYDR 255 Score = 45.8 bits (107), Expect = 1e-09 Identities = 25/58 (43%), Positives = 34/58 (58%) Query: 92 GFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWY 149 G + T V + II + IG I G+GRLS N I ++ YVEV R IP L+ +F+ Y Sbjct: 55 GILVTFQVTVFSIICSIPIGLITGLGRLSRNRGINLVASTYVEVVRGIPLLVQLFYIY 112 Lambda K H 0.327 0.141 0.412 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: 211 Number of extensions: 6 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: 2 Length of query: 397 Length of database: 256 Length adjustment: 27 Effective length of query: 370 Effective length of database: 229 Effective search space: 84730 Effective search space used: 84730 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 (21.7 bits) S2: 48 (23.1 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