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 Pf6N2E2_5404 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5404 Length = 365 Score = 107 bits (268), Expect = 3e-28 Identities = 74/233 (31%), Positives = 121/233 (51%), Gaps = 19/233 (8%) Query: 8 GVFFKSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATA 67 GVF G+ + W GL T+ IA VG + AL LG +L + R + + Sbjct: 143 GVF----GLDAVATSQW--GGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVT 196 Query: 68 YVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVC 127 ++E +R VPL+ LF+ ++P LPEG+ + + A + V+ LF +A + Sbjct: 197 FIEFWRGVPLITVLFMSSVMLPLFLPEGM------NFDKLLRALIGVI----LFQSAYIA 246 Query: 128 EQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVAS 187 E VR G+QA+P GQ AA AMG + V+LPQA +++IP + + F+ +FK++S+ Sbjct: 247 EVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVI 306 Query: 188 LIGLMELLAQTKQTA---EFSANLFEAFTLATLIYFTLNMSLMLIMRLVERKV 237 +IGL +LL KQ A ++ E + A L+++ + +ERK+ Sbjct: 307 IIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKL 359 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: 243 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: 365 Length adjustment: 27 Effective length of query: 221 Effective length of database: 338 Effective search space: 74698 Effective search space used: 74698 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: 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