Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 117 bits (294), Expect = 2e-31 Identities = 61/208 (29%), Positives = 115/208 (55%), Gaps = 21/208 (10%) Query: 42 DAFINGFIY-------TLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNV 94 D F++ F Y T+ V++++ + I G G + S+ I+R YVE+ + + Sbjct: 47 DPFLDIFKYVWVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGI 106 Query: 95 PLVIQIFFLFYALPVL--------------GIRLDIFTIGVLGVGAYHGAYVSEVVRSGI 140 PL++Q+ + ++A PV+ + + + + G+ +GAY+SE+ R+GI Sbjct: 107 PLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGI 166 Query: 141 LAVPRGQFEASASQGFTYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAEL 200 ++P+GQ EA+ S G ++ Q MRY+I+PQ +R++LPPM N+ + L+K+TS++ V A++ Sbjct: 167 QSIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADM 226 Query: 201 MHSADSYAADYGNYAPAYIFAAVLYFII 228 + + A N + +LY I+ Sbjct: 227 VRLGREFTATNFNPIEVWTMIGLLYLIL 254 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: 180 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 250 Length of database: 273 Length adjustment: 25 Effective length of query: 225 Effective length of database: 248 Effective search space: 55800 Effective search space used: 55800 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: 47 (22.7 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