Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate BPHYT_RS13585 BPHYT_RS13585 amino acid ABC transporter permease
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__BFirm:BPHYT_RS13585 Length = 218 Score = 128 bits (322), Expect = 8e-35 Identities = 76/221 (34%), Positives = 123/221 (55%), Gaps = 13/221 (5%) Query: 21 YLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNVPLLVQ 80 +L + G TI I ++++ LG LL +MR NR+VS A ++ + R +P++VQ Sbjct: 9 FLPILLKGAVVTIEITFCSFVLSTVLGLLLALMRVSDNRVVSNAAATFINVIRGLPIIVQ 68 Query: 81 LFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPYG 140 LF YF++PDL G+Q SA+ + + LG+ + E R GIQA+ +G Sbjct: 69 LFYIYFVLPDL---GVQL----------SAFQAGFIGLGIAYSVYQAENFRAGIQAIDHG 115 Query: 141 QTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELLAQTKQ 200 Q AA+++G R I R V+LPQAFRI +PP + + + K+SS+AS I + E+ + Sbjct: 116 QIEAAQSIGMRGAMIMRRVVLPQAFRIALPPYGNTLVMMLKDSSLASTITVAEMTRAGQL 175 Query: 201 TAEFSANLFEAFTLATLIYFTLNMSLMLIMRLVERKVAVPG 241 A + FTL L+Y L++ L+ +R +ER++ + G Sbjct: 176 IASSTFQNMTVFTLVALLYLGLSLPLVYGLRRLERRLGLKG 216 Lambda K H 0.327 0.141 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: 146 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: 218 Length adjustment: 23 Effective length of query: 225 Effective length of database: 195 Effective search space: 43875 Effective search space used: 43875 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