Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate WP_090448712.1 BLS63_RS26115 histidine/lysine/arginine/ornithine ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773 (244 letters) >NCBI__GCF_900100495.1:WP_090448712.1 Length = 254 Score = 218 bits (555), Expect = 9e-62 Identities = 120/255 (47%), Positives = 169/255 (66%), Gaps = 17/255 (6%) Query: 2 ISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVVD 61 + ++ ++K YG +VL S K G+VI + G SGSGKST ++C+N LE G I+++ Sbjct: 4 LEVQDLHKRYGSHEVLKGVSLAAKAGDVISIIGSSGSGKSTFLRCINLLEQPHGGKILLN 63 Query: 62 GTSI------------ADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRS 109 G + ADPK L ++RSR+ MVFQHF L+ H++ EN+ A + VLG S Sbjct: 64 GEELKLLANKDGALKAADPK-QLQRMRSRLAMVFQHFNLWSHMSALENVMEAPVHVLGVS 122 Query: 110 KEEATKKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDP 169 K+EA +K L +VG++ +P +SGG+QQRVAIARALAM+P VMLFDEPTSALDP Sbjct: 123 KKEALEKAEHYLNKVGVAHRKDAYPAHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 Query: 170 EMVNEVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIE-DCKKEEFFGDIN 228 E+V EVL VM LA EG TM+ VTHEMGFAR+V+++++F+ +G + E C KE +N Sbjct: 183 ELVGEVLKVMQDLAMEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEERGCPKEVL---VN 239 Query: 229 ARAERTQHFLNKILQ 243 ++ER + FL+ L+ Sbjct: 240 PQSERLKQFLSGSLK 254 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: 10 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: 254 Length adjustment: 24 Effective length of query: 220 Effective length of database: 230 Effective search space: 50600 Effective search space used: 50600 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 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