Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate RR42_RS09485 RR42_RS09485 amino acid ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS09485 Length = 216 Score = 122 bits (306), Expect = 9e-33 Identities = 69/203 (33%), Positives = 123/203 (60%), Gaps = 6/203 (2%) Query: 194 TLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLM 253 TL L++ V G L+AL R S +R S YI++ +G P++ +LF + ++ Sbjct: 20 TLWVTLLAFVGGTLAGFLVALARTSRSALLRLASTVYIQIVQGTPVLIVLFLSYYGLSVL 79 Query: 254 LDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVL 313 ++ + A++ ++I+ SAYL E RG ++A+PQGQ+EA+ AL L +Q R +VL Sbjct: 80 ---GLKLSPMTAAMLAMSIYASAYLGEIWRGCIEAVPQGQWEASEALALTRWQQLRHVVL 136 Query: 314 PQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLFLGVL 373 PQA+R+++P VG + L+++T++ SI+G++EL + L N A +A V++ + ++ Sbjct: 137 PQAVRLALPPTVGFSVQLVKNTSITSIIGVIELTRAGQ--LINNATFQPFA-VFVVVALI 193 Query: 374 YWLCCYGLAQLSRRLEQRLTPQR 396 Y+ C+ L+ +RR+E+RL R Sbjct: 194 YFALCFPLSSAARRMERRLHAHR 216 Lambda K H 0.329 0.142 0.471 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: 192 Number of extensions: 10 Number of successful extensions: 3 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: 396 Length of database: 216 Length adjustment: 26 Effective length of query: 370 Effective length of database: 190 Effective search space: 70300 Effective search space used: 70300 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