Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_012404721.1 BPHY_RS27410 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >NCBI__GCF_000020045.1:WP_012404721.1 Length = 219 Score = 139 bits (349), Expect = 6e-38 Identities = 69/202 (34%), Positives = 123/202 (60%) Query: 47 GFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYA 106 G + TL+ ++ + ++ + G I +M S II R YV L + PL++QIF ++Y Sbjct: 17 GAMVTLKFALASAVLGLLVGFIVAIMGISGQPIIAGIARAYVSLMRGTPLLVQIFVVYYG 76 Query: 107 LPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYII 166 LP LGI LD + G+L + A GAY+SE +R IL + +GQ+ A+ S G T++Q +RY+I Sbjct: 77 LPDLGISLDPTSAGILALTANAGAYLSESMRGAILGISQGQWGAAHSLGLTHMQTLRYVI 136 Query: 167 VPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVLYF 226 PQ +R+ +P + N +++LIK+TS++ ++ E++ +A A P Y+ AA +Y+ Sbjct: 137 CPQALRMAVPSLGNTLISLIKDTSLVSVITVTEMLRAAQEVIASTFQPLPLYLAAAAIYW 196 Query: 227 IICYPLAYFAKAYENKLKKAHL 248 ++ +++ + E +L +AH+ Sbjct: 197 LLSTGMSWVQRHVEVRLARAHV 218 Lambda K H 0.328 0.143 0.422 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: 135 Number of extensions: 7 Number of successful extensions: 1 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: 250 Length of database: 219 Length adjustment: 23 Effective length of query: 227 Effective length of database: 196 Effective search space: 44492 Effective search space used: 44492 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: 46 (22.3 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