Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate AO356_00470 AO356_00470 ABC transporter permease
Query= TCDB::A1VZQ3 (250 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00470 Length = 220 Score = 137 bits (345), Expect = 2e-37 Identities = 68/203 (33%), Positives = 118/203 (58%) Query: 41 KDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQI 100 +D GF+ +++ S+LA+++ T+ G + G++ T +RA R YV+L + P+ + + Sbjct: 15 RDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLV 74 Query: 101 FFLFYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQ 160 FY P LG ++ F GVLG+ + G++V+E+VR + A+PRGQ EAS + G T+ Q Sbjct: 75 LACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQAIGLTFYQ 134 Query: 161 QMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIF 220 + Y+++PQ +R ILP N ++K +++L ++G AEL+ S A Y+F Sbjct: 135 SLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFMTLEFYLF 194 Query: 221 AAVLYFIICYPLAYFAKAYENKL 243 A L+FII Y + + E ++ Sbjct: 195 AGFLFFIINYAIELLGRHIEKRV 217 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: 146 Number of extensions: 7 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: 250 Length of database: 220 Length adjustment: 23 Effective length of query: 227 Effective length of database: 197 Effective search space: 44719 Effective search space used: 44719 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