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 WP_041096193.1 SUTH_RS00310 transporter substrate-binding domain-containing protein
Query= TCDB::Q9I402 (302 letters) >NCBI__GCF_000828635.1:WP_041096193.1 Length = 300 Score = 277 bits (708), Expect = 2e-79 Identities = 145/293 (49%), Positives = 200/293 (68%), Gaps = 4/293 (1%) Query: 10 TAIVAALL--SAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKPIGYSHDL 67 TA++ A++ +AP +A E TGTLKK+K+ G+ITLG R++S P SYL + +P+GY D+ Sbjct: 5 TALLVAIVIAAAPALAQE-TGTLKKVKDNGSITLGIRESSYPLSYLDDKQ-QPVGYHIDV 62 Query: 68 QLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQKQVDFSVG 127 ++V+AVK +L LP LK+++ VTSQ RIPLV NGTVD+ECGSTTNNE RQKQV F+ Sbjct: 63 CNRIVDAVKAQLKLPALKLQHQAVTSQNRIPLVANGTVDLECGSTTNNEARQKQVAFAPT 122 Query: 128 IFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSERLLKAMNADKKMGMNIISAKDHGE 187 F R+ KK + I L GK V TT GTTS +L++A K + + KDH + Sbjct: 123 TFVTNVRMAVKKASGITGLAQLGGKPVATTTGTTSVQLMRAHEKGKGIDFKEVYGKDHAD 182 Query: 188 SFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMVRKGDAAFKKVV 247 +F+MLE+ RAVAF+MDD LL G + +K P D+ + G + E M+R+ D AFKK+V Sbjct: 183 AFLMLETDRAVAFVMDDNLLAGLIVSSKSPADYAIVGEVLNVEPIAIMLRRDDPAFKKLV 242 Query: 248 DKAITDTYASGEVNKIYDKWFTQPIPPKGLNLNFPMSEELKKLIASPTDKAAE 300 D A+ SGE++K+Y +WF PIPPK +++NFPMSE+LKKLI +P+D AE Sbjct: 243 DAAVIGLMKSGELDKLYTRWFLSPIPPKNVSMNFPMSEQLKKLIKAPSDAPAE 295 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: 296 Number of extensions: 9 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: 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 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