Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate RR42_RS02585 RR42_RS02585 amino acid ABC transporter permease
Query= TCDB::Q88NY3 (248 letters) >FitnessBrowser__Cup4G11:RR42_RS02585 Length = 227 Score = 118 bits (296), Expect = 9e-32 Identities = 70/220 (31%), Positives = 121/220 (55%), Gaps = 5/220 (2%) Query: 20 TYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLV 79 T LD G+ ++ I +TA ++ ++ G++L +MR +L++ A YV +FR++PL++ Sbjct: 13 TTLDVLGEGMLVSLKITVTAVVVGIVWGTILAMMRLSSVKLLNWFAQGYVTIFRSIPLVM 72 Query: 80 QLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTGIQALPK 139 L ++ ++P LL + DL T S +I LF AA E +R GIQ++ + Sbjct: 73 VLLWFFLIIPQLLQKAFNLSQASDLRMT-----SALIAFALFEAAYYSEIIRAGIQSVSR 127 Query: 140 GQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTK 199 GQ AA+AMG + Q V+LPQA+R ++P L ++ + +F+++S+ + L + Q Sbjct: 128 GQMFAAQAMGMTYGQSMRLVILPQAFRNMVPLLLTQGIILFQDTSLVYVSALADFFGQAY 187 Query: 200 QTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAV 239 E + E A L+YF + LL++ +KKVAV Sbjct: 188 GIGERDGRIVEMLLFAGLVYFIICFSASLLVKRYQKKVAV 227 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: 150 Number of extensions: 6 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: 227 Length adjustment: 23 Effective length of query: 225 Effective length of database: 204 Effective search space: 45900 Effective search space used: 45900 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: 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