Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 149 bits (376), Expect = 7e-41 Identities = 90/247 (36%), Positives = 139/247 (56%), Gaps = 8/247 (3%) Query: 1 MIELKNVNKYYGTHH----VLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56 MI +V+K Y L+ +L + +GE IIG SG+GKST IR +N LE S G Sbjct: 1 MIRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGG 60 Query: 57 EVVVNNLVLNHKNK--IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKK-EAE 113 ++++ + + R+ M+FQHFNL TV N+ P++L ++ + + Sbjct: 61 SILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAF-PLRLAGETDAGKIK 119 Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173 + L+ VGL A+ YPA LSGGQ+QRV IAR+L + +L DE TSALDP+T Sbjct: 120 ARVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTAS 179 Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERAR 233 VL+++ EI+ + T+V++THEM + V DR+ ++ G IVE ++ F +P+ R Sbjct: 180 VLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTR 239 Query: 234 LFLGKIL 240 F+ + L Sbjct: 240 RFVNEAL 246 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: 155 Number of extensions: 9 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: 336 Length adjustment: 26 Effective length of query: 216 Effective length of database: 310 Effective search space: 66960 Effective search space used: 66960 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 17 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