Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 167 bits (422), Expect = 3e-46 Identities = 101/249 (40%), Positives = 147/249 (59%), Gaps = 10/249 (4%) Query: 1 MISIKSINKWYG----DFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56 MI ++K Y D L S ++ GEV + G SG+GKSTLI+ +N LE G Sbjct: 1 MIRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGG 60 Query: 57 DIVVDGTSI-ADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATK 115 I++DGT + A L R R+GM+FQHF L T+ +N+ +++ G + K Sbjct: 61 SILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFP-LRLAGETDAGKIK 119 Query: 116 KGL-QLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174 + +LL RVGL AHA K+P QLSGGQ+QRV IARALA P ++L DE TSALDP+ Sbjct: 120 ARVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTAS 179 Query: 175 VLDVMVQLAHE-GMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAER 233 VL+++ ++ E +T++ +THEM R+V DRV +D G+I+E + F ++ R Sbjct: 180 VLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVF--LHPRHPT 237 Query: 234 TQHFLNKIL 242 T+ F+N+ L Sbjct: 238 TRRFVNEAL 246 Lambda K H 0.321 0.136 0.394 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: 209 Number of extensions: 7 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: 244 Length of database: 336 Length adjustment: 26 Effective length of query: 218 Effective length of database: 310 Effective search space: 67580 Effective search space used: 67580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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