Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 145 bits (366), Expect = 7e-40 Identities = 85/222 (38%), Positives = 130/222 (58%), Gaps = 22/222 (9%) Query: 5 FSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIR 64 F VW G+ +TV + S L ++G+ +GRL+ K ++ L T YV +R Sbjct: 53 FKYVWVGIG-------ITVLVAVVSYFLMLILGMFGALGRLS-KNTILRGLATFYVEIVR 104 Query: 65 GTPLLVQLFILFFGLP----------QFGILLP----AFVCGVIGLGIYSGAYVSEVVRG 110 G PLLVQL +F P FG ++ V + G+ GAY+SE+ R Sbjct: 105 GIPLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRA 164 Query: 111 AIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIH 170 IQSI KGQMEAARS+GMS AMR V+LPQA+ ++PP+GNEFIAL+K+++LVS + + Sbjct: 165 GIQSIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVA 224 Query: 171 DLMHEGQKIISVSYRSLEVYLAIAVVYFILTGATTLVLRRIE 212 D++ G++ + ++ +EV+ I ++Y ILT ++ ++ IE Sbjct: 225 DMVRLGREFTATNFNPIEVWTMIGLLYLILTLLSSRLINYIE 266 Lambda K H 0.328 0.143 0.412 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: 161 Number of extensions: 5 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: 222 Length of database: 273 Length adjustment: 24 Effective length of query: 198 Effective length of database: 249 Effective search space: 49302 Effective search space used: 49302 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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