Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_074201578.1 BUQ81_RS06435 phosphate ABC transporter ATP-binding protein PstB
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_900141795.1:WP_074201578.1 Length = 262 Score = 107 bits (268), Expect = 2e-28 Identities = 83/256 (32%), Positives = 130/256 (50%), Gaps = 24/256 (9%) Query: 1 MIELKNVNKYY--GTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG-- 56 M+E+K+ + Y LK+INL V + +IGPSG GKST +R MN + ++ G Sbjct: 6 MMEVKDFSFTYPNAPKPSLKHINLRVVKNRITALIGPSGCGKSTLLRAMNRIHDLYPGCK 65 Query: 57 -----------EVVVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQ 105 V N L +N + R+ M+FQ +P M++ N+ +KLQ Sbjct: 66 YEGAINLQCVDGSVKNILEWTKENDLIRLRQKVGMIFQKPTPFP-MSIYDNIAYG-LKLQ 123 Query: 106 K-KSKKEAEETAFKYLKVVGLL----DKANVYPATLSGGQQQRVAIARSLCTKKPYILFD 160 +SK E ++ + L+ L D+ LSGGQQQR+ IARS+ + ILFD Sbjct: 124 GIRSKSELDDRVEEALRDGALWNEVKDRLKDDARGLSGGQQQRLCIARSVALRPDVILFD 183 Query: 161 EPTSALDPETIQEVLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIP 220 EPTSALDP + + +++ E+ Q T+ +VTH M A ++D FM G ++E + Sbjct: 184 EPTSALDPISTVAIEEMIMELREQ--YTICIVTHNMQQAARISDYTAFMYLGELIEYDET 241 Query: 221 SEFFSNPKTERARLFL 236 F+NP ++ ++ Sbjct: 242 DTIFTNPSQKQTEDYI 257 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: 136 Number of extensions: 4 Number of successful extensions: 3 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: 262 Length adjustment: 24 Effective length of query: 218 Effective length of database: 238 Effective search space: 51884 Effective search space used: 51884 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