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 8502074 DvMF_2787 extracellular solute-binding protein family 3 (RefSeq)
Query= TCDB::Q9I402 (302 letters) >FitnessBrowser__Miya:8502074 Length = 275 Score = 118 bits (296), Expect = 1e-31 Identities = 85/277 (30%), Positives = 138/277 (49%), Gaps = 19/277 (6%) Query: 1 MRIAPSLLSTAIVAALLSAPVVADELTGTLKKIKETGTITLGHRDASIPFSYLGTEPGKP 60 MR+ L + + L+++ +A + ++K K+ I +G SIP ++ E G+ Sbjct: 1 MRLVKLLAMASALTVLMASVAMAGPVFDRIQKEKK---IRIGIMTDSIPGAFYN-EKGEW 56 Query: 61 IGYSHDLQLKVVEAVKKELNLPELKVRYNLVTSQTRIPLVQNGTVDIECGSTTNNEERQK 120 G+ +D+ +V + + E+ + V ++TRI LVQ+G +D+ + T+ ER K Sbjct: 57 GGFDYDMATEVAKRMGVEIERVQ-------VNNKTRIALVQSGQIDLSVSNMTHTRERDK 109 Query: 121 QVDFSVGIFEVGTRLLSKKTANIKDFDDLKGKNVVTTAGTTSE----RLLKAMNADKKMG 176 VDFS+ F G ++L+KK K D+ GK + T GTTSE R LK D Sbjct: 110 SVDFSLTYFFDGQKILAKK-GQFKSVKDMVGKKIATMQGTTSEVNVRRALKEA-GDPNAE 167 Query: 177 MNIISAKDHGESFMMLESGRAVAFMMDDALLYGEMAKAKKPDDWVVGGTPQSFEIYGCMV 236 N+IS + E F L++GR + D ++L G AK P + + G S E YG + Sbjct: 168 TNVISFQKESECFQALQNGRVAGWSTDASILVGYAAKT--PGQFELVGDFLSDEPYGMAM 225 Query: 237 RKGDAAFKKVVDKAITDTYASGEVNKIYDKWFTQPIP 273 + D+A + V+ AI D + G IY+KW+ P Sbjct: 226 PQDDSALRDAVNAAIQDMWKDGTYKSIYNKWYGPGTP 262 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: 194 Number of extensions: 15 Number of successful extensions: 4 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: 275 Length adjustment: 26 Effective length of query: 276 Effective length of database: 249 Effective search space: 68724 Effective search space used: 68724 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: 47 (22.7 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