Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate RR42_RS09485 RR42_RS09485 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS09485 Length = 216 Score = 90.1 bits (222), Expect = 5e-23 Identities = 52/134 (38%), Positives = 78/134 (58%), Gaps = 1/134 (0%) Query: 238 GLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQ 297 GL+LS TA +L + Y A++ EI RG I +VP GQWEA+ AL LTR Q L +V+PQ Sbjct: 80 GLKLS-PMTAAMLAMSIYASAYLGEIWRGCIEAVPQGQWEASEALALTRWQQLRHVVLPQ 138 Query: 298 ALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAIN 357 A+R+ +P V KN+S+ +G +L Q N T +P VF+++ L Y A+ Sbjct: 139 AVRLALPPTVGFSVQLVKNTSITSIIGVIELTRAGQLINNATFQPFAVFVVVALIYFALC 198 Query: 358 AVISAGMNGLQQRL 371 +S+ +++RL Sbjct: 199 FPLSSAARRMERRL 212 Score = 33.9 bits (76), Expect = 4e-06 Identities = 18/55 (32%), Positives = 31/55 (56%) Query: 89 SLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWYF 143 +L V + + T+ G L +A S + LLR S Y+ +V+ TP+L+ L + Y+ Sbjct: 20 TLWVTLLAFVGGTLAGFLVALARTSRSALLRLASTVYIQIVQGTPVLIVLFLSYY 74 Lambda K H 0.326 0.140 0.445 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: 186 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: 377 Length of database: 216 Length adjustment: 26 Effective length of query: 351 Effective length of database: 190 Effective search space: 66690 Effective search space used: 66690 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: 47 (22.7 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