Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate RR42_RS36980 RR42_RS36980 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_16285 (248 letters) >FitnessBrowser__Cup4G11:RR42_RS36980 Length = 224 Score = 107 bits (268), Expect = 2e-28 Identities = 68/205 (33%), Positives = 104/205 (50%), Gaps = 11/205 (5%) Query: 32 TIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIWYFLVPDL 91 T+A+++ +++ + + V+ P + A V L R PLLVQLF WYF L Sbjct: 2 TVALSVAVFVLGCAIAAGWLVLARSPIMPLRLTARGAVGLLRRTPLLVQLFFWYFGAAQL 61 Query: 92 LPQN----LQDWYKQDLN------PTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQ 141 L + L DW + P+ A L+ + +GL+ +A ++ G+ +PRGQ Sbjct: 62 LGEGAIGALYDWQGWRIGGWHVPAPSLEA-LASLAGIGLYASAFYARELEAGLANVPRGQ 120 Query: 142 ESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQT 201 +AA A+GF +W V+LPQA RI P+ +F KN+S+A IG E+ +Q Sbjct: 121 GAAALALGFTPAAAFWRVVLPQALRIAARPMVGQFCQTIKNTSLAMAIGFAEMSYTARQV 180 Query: 202 AEFSANLFEAFTLATLIYFTLNMSL 226 S F+AF LATL+Y L + L Sbjct: 181 ETDSLMTFQAFGLATLLYVALILLL 205 Lambda K H 0.326 0.139 0.432 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: 151 Number of extensions: 10 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: 248 Length of database: 224 Length adjustment: 23 Effective length of query: 225 Effective length of database: 201 Effective search space: 45225 Effective search space used: 45225 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: 46 (22.3 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