Align Probable binding protein component of ABC transporter, 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 PfGW456L13_1042 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1042 Length = 300 Score = 353 bits (905), Expect = e-102 Identities = 181/289 (62%), Positives = 216/289 (74%), Gaps = 2/289 (0%) Query: 8 LSTAIVAALLSAPVVADE--LTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKPIGYSH 65 L + LL + V A+E LTGTL KI +ITLG+RDAS+PFSY+G GKP+GYS Sbjct: 6 LLACTLGLLLGSQVQANEAPLTGTLSKIASANSITLGYRDASVPFSYVGDHSGKPMGYSV 65 Query: 66 DLQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDFS 125 DL K+VE ++++L LP+LKV+YNLVTSQTRIPLVQNGTVD+ECGST ERQKQV FS Sbjct: 66 DLAGKIVERIQQQLALPDLKVKYNLVTSQTRIPLVQNGTVDLECGSTGVTAERQKQVAFS 125 Query: 126 VGIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKDH 185 G V +LL+ K + IK+F DL+GKNVVTTAGTT+ER LK+ N D K+ M +ISAKDH Sbjct: 126 YGFIYVKGQLLTAKDSGIKNFADLRGKNVVTTAGTTNERFLKSYNVDHKIDMFVISAKDH 185 Query: 186 GESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFKK 245 GE+F ML+SGRA AF MDDALLYGE AKA P WVV G QS EIY CMVRK D F Sbjct: 186 GEAFQMLQSGRAAAFYMDDALLYGERAKANDPHKWVVVGEEQSREIYSCMVRKDDPQFLA 245 Query: 246 VVDKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASP 294 +V+ A+ D Y+SGE+N IY +WF QPIPPKGLNL FPM+ ELK +IA P Sbjct: 246 LVNGALADLYSSGEINGIYKRWFEQPIPPKGLNLEFPMTSELKAIIAKP 294 Lambda K H 0.314 0.132 0.370 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: 279 Number of extensions: 4 Number of successful extensions: 1 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: 302 Length of database: 300 Length adjustment: 27 Effective length of query: 275 Effective length of database: 273 Effective search space: 75075 Effective search space used: 75075 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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