Align Amino acid ABC transporter ATP binding 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 WP_053938866.1 WG78_RS16145 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q9I405 (244 letters) >NCBI__GCF_001294205.1:WP_053938866.1 Length = 242 Score = 417 bits (1071), Expect = e-121 Identities = 208/244 (85%), Positives = 225/244 (92%), Gaps = 2/244 (0%) Query: 1 MISIKNVSKWYGDFQVLTDCSTEVAKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60 MISIKN+SKWYGDFQVLTDCSTEV KGEVVVVCGPSGSGKSTLIKCVN LE FQKGDI+V Sbjct: 1 MISIKNISKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNGLEAFQKGDIIV 60 Query: 61 DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLSITENLTIAQIKVLGRSKEEATKKGLAL 120 DGTS+ DPKTNLPKLRSRVGMVFQ+FELFPHLSIT+NLT+AQ++VLGR+++EAT GL L Sbjct: 61 DGTSVGDPKTNLPKLRSRVGMVFQNFELFPHLSITQNLTLAQMQVLGRNRDEATVNGLRL 120 Query: 121 LERVGLKEHAHKHPGQLSGGQQQRVAIARALAMDPVVMLFDEPTSALDPEMVNEVLDVMV 180 L+RVGLK HA KHPGQLSGGQQQRVAIARALAMDP+ MLFDEPTSALDPEMVNEVLDVMV Sbjct: 121 LDRVGLKAHADKHPGQLSGGQQQRVAIARALAMDPIAMLFDEPTSALDPEMVNEVLDVMV 180 Query: 181 QLAHEGMTMMCVTHEMGFARKVANRVIFMDRGQIVEDCEKEEFFGDVSARSERAQQFLAK 240 +LA EGMTMMCVTHEMGFARKVANRVIFMD+G IVED KE+FFG S RSERAQ FL+K Sbjct: 181 ELAQEGMTMMCVTHEMGFARKVANRVIFMDKGAIVEDATKEDFFG--SPRSERAQVFLSK 238 Query: 241 ILPH 244 IL H Sbjct: 239 ILHH 242 Lambda K H 0.320 0.135 0.389 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: 282 Number of extensions: 7 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: 244 Length of database: 242 Length adjustment: 23 Effective length of query: 221 Effective length of database: 219 Effective search space: 48399 Effective search space used: 48399 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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