Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_012411414.1 NPUN_RS25940 ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000020025.1:WP_012411414.1 Length = 254 Score = 151 bits (382), Expect = 1e-41 Identities = 93/230 (40%), Positives = 137/230 (59%), Gaps = 11/230 (4%) Query: 1 MIELKNVNKYYGTHHV----LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56 +I L+N+ K YG+ L ++NL V++GE I+GPSGSGKST + + L+ ++G Sbjct: 21 IIRLENIFKIYGSGETEVRALNDVNLIVEQGEYCAIMGPSGSGKSTAMNIIGCLDRPTTG 80 Query: 57 EVVVNNL---VLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113 ++NL ++ ++ I K VFQ F+L P +T L+N+ L PM + KE Sbjct: 81 HYYLDNLDVAQMDDRSLAHIRNKKLGFVFQQFHLLPQLTALENVIL-PMLYAGVNPKERS 139 Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173 + A L VGL ++ N P LSGGQQQRVAIAR++ + +L DEPT ALD T QE Sbjct: 140 DRAIVALTRVGLANRLNNKPTQLSGGQQQRVAIARAIVNRPVVLLADEPTGALDSRTTQE 199 Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENI-PSE 222 VLD+ E+ + S T+V+VTHE A++ RI++ DG +V N+ PS+ Sbjct: 200 VLDIFSEL-NASGITVVMVTHEPEVARQ-TQRIVWFRDGQVVHSNLTPSD 247 Lambda K H 0.317 0.133 0.372 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: 145 Number of extensions: 11 Number of successful extensions: 4 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: 242 Length of database: 254 Length adjustment: 24 Effective length of query: 218 Effective length of database: 230 Effective search space: 50140 Effective search space used: 50140 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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