Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_012278756.1 SHAL_RS19120 phospholipid ABC transporter ATP-binding protein MlaF
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000019185.1:WP_012278756.1 Length = 270 Score = 99.8 bits (247), Expect = 6e-26 Identities = 80/267 (29%), Positives = 127/267 (47%), Gaps = 22/267 (8%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 L+ + +T G V DVS S G++TAI+GP+G GKTTL I G P G + Sbjct: 8 LVETQGMTFSRGERVIFQDVSLSIPQGKVTAIMGPSGIGKTTLLKLIGGQLIPDSGSVKF 67 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 D + R + + ++ S+ FQ+ LF M+V +N+ F++ Sbjct: 68 DGVDVHK--CSRSELFALRKRMSML--FQSGALFTDMNVFDNV------------AFALR 111 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 GLP E + L+ V L A L G QRR +ARA+ EP M+ Sbjct: 112 EHSGLP-----EDIIRRIVLMKLEAVGLRGAAQLMPTELSGGMQRRAALARAIALEPEMI 166 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 DEP AG +P G L L+ + D + +++ HD++ V+ I+D+V VL R I+ Sbjct: 167 LYDEPFAGQDPISMGVLVKLIRELSDALNLTSVVVSHDVAEVLGIADYVYVLADKRIIAH 226 Query: 251 GDPAFVK-NDPAVIRAYLGEEEDEELP 276 G P ++ ++ ++ ++G E D +P Sbjct: 227 GTPEELRLSEDPKLKQFIGGEPDGPVP 253 Lambda K H 0.319 0.137 0.397 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: 162 Number of extensions: 11 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: 294 Length of database: 270 Length adjustment: 26 Effective length of query: 268 Effective length of database: 244 Effective search space: 65392 Effective search space used: 65392 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 (21.8 bits) S2: 47 (22.7 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