Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= TCDB::Q88NY3 (248 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 135 bits (340), Expect = 9e-37 Identities = 80/248 (32%), Positives = 135/248 (54%), Gaps = 18/248 (7%) Query: 5 WDW---GVFFKSTGV---GSETYLD---WYITGLGWTIAIAITAWIIALLLGSLLGVMRT 55 W W GVF + G+ + +LD + G+G T+ +A+ ++ + L+LG + R Sbjct: 27 WWWLVAGVFVLTGGLMLFQPDPFLDIFKYVWVGIGITVLVAVVSYFLMLILGMFGALGRL 86 Query: 56 VPNRLVSGIATAYVELFRNVPLLVQLFIWYFLVPDLLP---EGLQ--EWFKQDLNPTTSA 110 N ++ G+AT YVE+ R +PLLVQL WYF P ++ +GL NP A Sbjct: 87 SKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMA 146 Query: 111 LISVVICLGLFTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIP 170 + + C G + + E R GIQ++PKGQ AAR++G S Q V+LPQA R+++P Sbjct: 147 IWGMTFCYGAYMS----EIYRAGIQSIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLP 202 Query: 171 PLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLM 230 P+ +EF+ + K++S+ S + + +++ ++ + N E +T+ L+Y L + L+ Sbjct: 203 PMGNEFIALLKDTSLVSTVAVADMVRLGREFTATNFNPIEVWTMIGLLYLILTLLSSRLI 262 Query: 231 RMVEKKVA 238 +EKK A Sbjct: 263 NYIEKKTA 270 Lambda K H 0.325 0.139 0.425 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: 175 Number of extensions: 8 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: 248 Length of database: 273 Length adjustment: 24 Effective length of query: 224 Effective length of database: 249 Effective search space: 55776 Effective search space used: 55776 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 47 (22.7 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