Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate 207827 DVU2340 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::Smeli:SMc02120 (384 letters) >MicrobesOnline__882:207827 Length = 230 Score = 123 bits (309), Expect = 4e-33 Identities = 77/218 (35%), Positives = 122/218 (55%), Gaps = 7/218 (3%) Query: 166 TYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLI 225 +Y + PL GG+ ++++L+ GI + LG+ L R S ++ V++EVIRG+PL+ Sbjct: 17 SYPDGPL-GGMAMSILLAIGGIFGAFWLGLAFGLMRLSEKWWVRAPAIVYVEVIRGIPLL 75 Query: 226 TVLFMASVMLPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSL 285 ++F + P+ L G T + ALI +F AY+AE+VR G+ A+P GQ E A Sbjct: 76 MLIFWFYFLAPIAL--GHTLPEAESALIAFIVFTGAYIAEIVRAGVLALPAGQMEAARGT 133 Query: 286 GLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWA 345 GLS Q M F++LPQAL+ +IP VN F+ L KDTSL IIG+ +L + N Sbjct: 134 GLSKTQAMLFVILPQALRNMIPSFVNQFVSLTKDTSLAYIIGVSELTRTA----TQVNNR 189 Query: 346 TAVTPLTGLIFAGFVFWLFCFGMSRYSGFMERLLDRSQ 383 T P + ++++ C+ ++ S +E+ + R Q Sbjct: 190 TLTAPTEIFLTIALMYFVICWVLTATSRRLEKQMARYQ 227 Lambda K H 0.329 0.144 0.454 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: 268 Number of extensions: 13 Number of successful extensions: 2 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: 384 Length of database: 230 Length adjustment: 26 Effective length of query: 358 Effective length of database: 204 Effective search space: 73032 Effective search space used: 73032 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: 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