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 GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q9I403 (248 letters) >FitnessBrowser__psRCH2:GFF3102 Length = 365 Score = 107 bits (266), Expect = 4e-28 Identities = 75/225 (33%), Positives = 115/225 (51%), Gaps = 13/225 (5%) Query: 16 IGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRTVPNRLVSGIATAYVEIFRNV 75 +G +T GL T+ IA VG AL LG LL + R + + ++E +R V Sbjct: 145 LGLQTVPTSQWGGLMLTVVIAAVGIAGALPLGILLALGRRSDMPAIRVLCVTFIEFWRGV 204 Query: 76 PLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCLGLFTAARVCEQVRTGIQ 135 PL+ LF+ ++P LPEG+ +L+ A L VV F AA + E VR G+Q Sbjct: 205 PLITVLFMSSVMLPLFLPEGM------NLDKLLRAMLMVV----FFEAAYIAEVVRGGLQ 254 Query: 136 ALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLNIFKNSSVASLIGLMELL 195 A+P GQ AA AMG + V+LPQA +++IP + + F+ +FK++S+ +IGL + L Sbjct: 255 AIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDFL 314 Query: 196 AQTKQTAEFSANL---FEAFTLATLIYFTLNMSLMLIMRLVERKV 237 K+ A L E + A L+Y+ + +ERK+ Sbjct: 315 NSIKRATADPAWLGMSTEGYVFAALVYWMFCFGMSRYSMRLERKL 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: 270 Number of extensions: 19 Number of successful extensions: 3 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