Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >FitnessBrowser__psRCH2:GFF4241 Length = 335 Score = 169 bits (428), Expect = 6e-47 Identities = 102/245 (41%), Positives = 144/245 (58%), Gaps = 10/245 (4%) Query: 1 MISIKSINKWYG----DFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56 MI ++K Y D L E+ GEV + G SG+GKSTL++ +N LE G Sbjct: 1 MIEFHQVHKTYRTGGRDVPALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGG 60 Query: 57 DIVVDGTSI-ADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLG-RSKEEAT 114 I+V+G + A L + R RVGM+FQHF L T+ +N+ + +++ G RS+ E Sbjct: 61 RILVNGEDVTALDADGLRRFRQRVGMIFQHFNLLMSKTVADNVAMP-LRLAGIRSRREID 119 Query: 115 KKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174 + LLERVGL HA K+P QLSGGQ+QRV IARALA +P ++L DE TSALDP+ Sbjct: 120 ARVAALLERVGLKEHARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTAS 179 Query: 175 VLDVMVQLAHE-GMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAER 233 VL ++ ++ E +T++ +THEM R+V DRV MD G I+E E F ++ + Sbjct: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDRVAVMDAGAIVEQGPVTEVF--LHPKHPT 237 Query: 234 TQHFL 238 TQ F+ Sbjct: 238 TQRFV 242 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: 219 Number of extensions: 9 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: 335 Length adjustment: 26 Effective length of query: 218 Effective length of database: 309 Effective search space: 67362 Effective search space used: 67362 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