Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate WP_109940760.1 DLD82_RS08835 ATP-binding cassette domain-containing protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >NCBI__GCF_003173335.1:WP_109940760.1 Length = 348 Score = 135 bits (339), Expect = 1e-36 Identities = 76/226 (33%), Positives = 132/226 (58%), Gaps = 9/226 (3%) Query: 1 MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60 M+ ++++K G+F +L + + ++ GE +V+ GP+G+GK+ L++ + P G I++ Sbjct: 1 MLHTENLSKDMGEF-ILRNVTLDITPGEYLVIIGPTGAGKTILLETIAGFYPPDSGKIIM 59 Query: 61 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120 DG I TN+P + MV+Q + LFPHLT+ EN+ +K + E KK +++ Sbjct: 60 DGRDI----TNIPPKDRNICMVYQDYMLFPHLTVEENIGFG-LKTRKKDPEYIRKKTVEM 114 Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180 + + H+ P LSGG+QQR AIAR+L M+P ++L DEP SALD + + L + Sbjct: 115 ARLLSIDHLLHRKPETLSGGEQQRAAIARSLVMEPNLLLLDEPLSALDGQ-TRDKLRTEL 173 Query: 181 QLAHE--GMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFF 224 + H+ +T++ +TH +ADRV M++G+I++ +E F Sbjct: 174 RRIHDITNVTVVHITHNFEEVFSLADRVAIMNKGEIVQIGNPDEVF 219 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: 187 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: 348 Length adjustment: 26 Effective length of query: 218 Effective length of database: 322 Effective search space: 70196 Effective search space used: 70196 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: 48 (23.1 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