Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_000015985.1:WP_172599875.1 Length = 249 Score = 280 bits (715), Expect = 2e-80 Identities = 141/240 (58%), Positives = 185/240 (77%), Gaps = 2/240 (0%) Query: 2 IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61 I++ +NK+YG+ HVL+++N++V +GE++VI GPSGSGKST IRC+N LEE SG++VV+ Sbjct: 9 IQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEHQSGQIVVD 68 Query: 62 NLVLNHKNK-IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKYL 120 + L K I+ R MVFQHFNL+PH+T+L+N TLAP+ ++K KKEAEE A YL Sbjct: 69 GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENCTLAPIWVRKTPKKEAEEVAMHYL 128 Query: 121 KVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMKE 180 K V + ++A+ YP LSGGQQQRVAIARSLC K +LFDEPTSALDPE I+EVLD M E Sbjct: 129 KKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDEPTSALDPEMIKEVLDTMIE 188 Query: 181 ISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKIL 240 ++ + TM+ VTHEMGFA+ VA+R+IFM+ G IVE+N P EFF NPK+ER +LFL +IL Sbjct: 189 LA-EEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGEFFRNPKSERTKLFLSQIL 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: 202 Number of extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 218 Effective length of database: 225 Effective search space: 49050 Effective search space used: 49050 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