Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate GFF137 Psest_0137 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__psRCH2:GFF137 Length = 231 Score = 92.0 bits (227), Expect = 1e-23 Identities = 60/198 (30%), Positives = 100/198 (50%), Gaps = 13/198 (6%) Query: 172 LWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVP---LITVL 228 L G +T+ L+ +A+ L LG+L AL + S ++ L + ++RGVP + ++ Sbjct: 12 LIAGTWMTIQLALASLALGLVLGLLGALAKTSPYSALRWLGGTYSTIVRGVPELLWVLLI 71 Query: 229 FMASVML-----PLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGAD 283 + ++ + LF + + F I + L AY EV RG L AIPKG E Sbjct: 72 YFGTISMIRGIGELFGIENLALSPFAAGTIALGLCFGAYATEVFRGALLAIPKGHREAGL 131 Query: 284 SLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTN 343 +LGL + ++LPQ +L +PG+ N F+ L KDT+LVS+IG+ ++ + S Sbjct: 132 ALGLGKRRIFTRLILPQMWRLALPGLGNLFMILMKDTALVSVIGLEEI-----MRRSQIA 186 Query: 344 WATAVTPLTGLIFAGFVF 361 + P T + A F++ Sbjct: 187 VTASKEPFTFFLVAAFIY 204 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: 259 Number of extensions: 15 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: 231 Length adjustment: 26 Effective length of query: 358 Effective length of database: 205 Effective search space: 73390 Effective search space used: 73390 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 Apr 09 2024. 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