Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate PP_5023 PP_5023 Amino acid ABC transporter, permease protein
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Putida:PP_5023 Length = 320 Score = 122 bits (306), Expect = 1e-32 Identities = 70/174 (40%), Positives = 103/174 (59%), Gaps = 6/174 (3%) Query: 160 GGWFGLT--YVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIE 217 G G+T + PL GL TL +S V A+ L +G+ L R SN P ++ L TV++E Sbjct: 104 GDQIGVTRHWAAGPLAWGLWTTLWISVVSGALGLVIGLFAGLCRLSNNPTLRDLSTVYVE 163 Query: 218 VIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKG 277 ++RG PL+ +F+ F+ + + + ++LF AY+AE+VR G+Q+I KG Sbjct: 164 LVRGTPLLVQIFI----FYFFIGTVLNLSREFAGVAALALFTGAYVAEIVRAGVQSIAKG 219 Query: 278 QYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDL 331 Q E A SLGL+ Q M ++LPQA K V+P + FI L KDTSLVS+I + +L Sbjct: 220 QNEAARSLGLNAGQSMRHVILPQAFKRVLPPLAGQFISLVKDTSLVSVIAITEL 273 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: 306 Number of extensions: 17 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: 320 Length adjustment: 29 Effective length of query: 355 Effective length of database: 291 Effective search space: 103305 Effective search space used: 103305 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: 49 (23.5 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