Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >NCBI__GCF_000015985.1:WP_172599875.1 Length = 249 Score = 300 bits (769), Expect = 1e-86 Identities = 151/243 (62%), Positives = 183/243 (75%), Gaps = 2/243 (0%) Query: 2 ISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 61 I I +NKWYG F VL D + V KGE IV+CGPSGSGKSTLI+C+N LE Q G IVVD Sbjct: 9 IQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEHQSGQIVVD 68 Query: 62 GTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQLL 121 G + N+ K+RS VGMVFQHF LFPHLTI EN T+A I V K+EA + + L Sbjct: 69 GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENCTLAPIWVRKTPKKEAEEVAMHYL 128 Query: 122 ERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMVQ 181 ++V + AHK+PGQLSGGQQQRVAIAR+L M P +MLFDEPTSALDPEM+ EVLD M++ Sbjct: 129 KKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDEPTSALDPEMIKEVLDTMIE 188 Query: 182 LAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLNKI 241 LA EGMTM+CVTHEMGFA+ VA+RVIFMDQG+I+E + EFF N ++ERT+ FL++I Sbjct: 189 LAEEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGEFFR--NPKSERTKLFLSQI 246 Query: 242 LQH 244 L H Sbjct: 247 LGH 249 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: 214 Number of extensions: 4 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: 244 Length of database: 249 Length adjustment: 24 Effective length of query: 220 Effective length of database: 225 Effective search space: 49500 Effective search space used: 49500 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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