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 AO356_18220 AO356_18220 amino acid ABC transporter permease
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18220 Length = 223 Score = 128 bits (322), Expect = 8e-35 Identities = 71/212 (33%), Positives = 124/212 (58%), Gaps = 6/212 (2%) Query: 28 GLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNVPLLVQLFIWYFL 87 G+ T+ + +G + + LG++L +MR N+L+S IA AYV FR++PLL+ + +Y Sbjct: 18 GMVMTLKLMAMGVVGGIILGTILALMRLSHNKLISNIAGAYVNYFRSIPLLLVITWFYLA 77 Query: 88 VPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAARA 147 VP +L W + P A+ S VV +F AA CE VR G+Q++P GQ AA+A Sbjct: 78 VPFVL-----RWITGEDTPI-GAFGSCVVAFMMFEAAYFCEIVRAGVQSIPKGQMGAAQA 131 Query: 148 MGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELLAQTKQTAEFSAN 207 +G Q R ++LPQAFR + P L + + +F+++S+ +GL++ L ++ + Sbjct: 132 LGMNYGQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNASRANGDIIGR 191 Query: 208 LFEAFTLATLIYFTLNMSLMLIMRLVERKVAV 239 E +A L+YFT++ + L+++ ++++ AV Sbjct: 192 SNEFLIVAGLVYFTISFAASLLVKRLQKRFAV 223 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: 158 Number of extensions: 4 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: 223 Length adjustment: 23 Effective length of query: 225 Effective length of database: 200 Effective search space: 45000 Effective search space used: 45000 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 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