Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= reanno::pseudo1_N1B4:Pf1N1B4_772 (248 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 106 bits (265), Expect = 3e-28 Identities = 70/218 (32%), Positives = 116/218 (53%), Gaps = 13/218 (5%) Query: 22 FDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQL 81 F + LS + WT+A++ A+I +G ++ + RT + V AT Y++LF+ PLL+QL Sbjct: 9 FLFLLSAVQWTLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQGTPLLMQL 68 Query: 82 FIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQ 141 F+ +F + DLNP +A L L L +A + E R IQA+PRGQ Sbjct: 69 FLVFFGATVM---------GLDLNPWAAAALG----LTLNASAFLGEIWRGCIQAVPRGQ 115 Query: 142 EAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQT 201 AA A+G + P + V+LPQA ++ +PP + + K++S+A++IG EL + Sbjct: 116 WEAASALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQIV 175 Query: 202 AEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVAV 239 + F F + ++YF + L LL +E++ A+ Sbjct: 176 NNATFQPFLVFGIVAVLYFLMCWPLSLLSARLERRYAL 213 Lambda K H 0.326 0.140 0.433 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: 137 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: 248 Length of database: 216 Length adjustment: 23 Effective length of query: 225 Effective length of database: 193 Effective search space: 43425 Effective search space used: 43425 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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