Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate Synpcc7942_0248 Synpcc7942_0248 Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__SynE:Synpcc7942_0248 Length = 396 Score = 114 bits (286), Expect = 2e-30 Identities = 77/242 (31%), Positives = 128/242 (52%), Gaps = 23/242 (9%) Query: 7 WGVFFK--------STGVGSETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPN 58 WGV F G+ + DW +GL T+A A+ + + +L LG LL + R Sbjct: 163 WGVLFLVGLWLLQGGLGLRPVSSNDW--SGLLLTLATALISMVCSLPLGILLALGRQSSL 220 Query: 59 RLVSGIATAYVELFRNVPLLVQLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICL 118 + ++ Y+ELFR +PL+ LF +VP +L EW ++ ++ L Sbjct: 221 PAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDS---EW-------RIDRILRAIVGL 270 Query: 119 GLFTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLN 178 +F +A + E VR G+QA+P+GQ AA A+G +L Q Y ++LPQA RI IP + FLN Sbjct: 271 TIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLN 330 Query: 179 VFKNSSVASLIGLMELLAQTKQTAEFSANL---FEAFTLATLIYFTLNMGLMLLMRMVEK 235 + +++++ S++GL+ELL ++ A L E + ++Y+ GL L R +E+ Sbjct: 331 LLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQ 390 Query: 236 KV 237 ++ Sbjct: 391 RL 392 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: 303 Number of extensions: 15 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: 396 Length adjustment: 27 Effective length of query: 221 Effective length of database: 369 Effective search space: 81549 Effective search space used: 81549 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: 48 (23.1 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