Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >NCBI__GCF_900105005.1:WP_090275879.1 Length = 334 Score = 159 bits (403), Expect = 5e-44 Identities = 96/243 (39%), Positives = 142/243 (58%), Gaps = 8/243 (3%) Query: 1 MIELKNVNKYY--GTHHV--LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56 MIE + VNK Y G + L +L+++ G+ IIG SG+GKST +R +N LEE S+G Sbjct: 1 MIEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNG 60 Query: 57 EVVV---NNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113 ++V + LN + + R+ M+FQHFNL TV N+ L ++++ Sbjct: 61 RIMVAGEDTTALNAEG-LRRFRQRVGMIFQHFNLLSSATVADNVALPLRLAGSANRQQIA 119 Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173 L VGL D A+ YPA LSGGQ+QRV IAR+L T+ +L DE TSALDP T + Sbjct: 120 ARVASLLDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQ 179 Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERAR 233 VL ++ EI+ + N T+V++THEM + V D++ M+ G IVE+ ++ F +P+ R Sbjct: 180 VLQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTR 239 Query: 234 LFL 236 F+ Sbjct: 240 SFV 242 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: 157 Number of extensions: 8 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: 242 Length of database: 334 Length adjustment: 26 Effective length of query: 216 Effective length of database: 308 Effective search space: 66528 Effective search space used: 66528 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. 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