Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate PfGW456L13_3607 Amino acid ABC transporter, permease protein
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3607 Length = 281 Score = 97.8 bits (242), Expect = 3e-25 Identities = 62/203 (30%), Positives = 104/203 (51%), Gaps = 8/203 (3%) Query: 175 GLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVM 234 G +TL L F I +SL LG + AL R S V + + + RG PL+ + + + Sbjct: 77 GAALTLFLCFCSIWLSLLLGFVTALARLSRSAVAFGVASFYASFFRGTPLLIQILLIYLG 136 Query: 235 LPLFLPQGVTFDKFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMG 294 LP GV +I +SL AY++E+ R G+ A+ GQ E A +LGL Sbjct: 137 LPQL---GVVPGAISAGIIALSLNYGAYLSEIFRAGIMAVAPGQREAAMALGLGPVATFL 193 Query: 295 FIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTGL 354 IVLPQA++ +IP + FI + KD+SL+S++G+++++ + + + ++ + L Sbjct: 194 HIVLPQAMRTIIPPTTSQFISMLKDSSLISVMGVWEVMFL-----AQSYGRSSYRYIEML 248 Query: 355 IFAGFVFWLFCFGMSRYSGFMER 377 A ++WL G+ +ER Sbjct: 249 TTAAVIYWLLSIGLELIQNRLER 271 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: 274 Number of extensions: 12 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: 281 Length adjustment: 28 Effective length of query: 356 Effective length of database: 253 Effective search space: 90068 Effective search space used: 90068 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