Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Ac3H11_1958 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
Query= TCDB::A3ZI83 (242 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1958 Length = 245 Score = 214 bits (545), Expect = 1e-60 Identities = 118/244 (48%), Positives = 166/244 (68%), Gaps = 5/244 (2%) Query: 1 MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60 MIELKNV+K+YG VL + ++ +GE +V+ GPSGSGKST I+ +N LE GE+ V Sbjct: 1 MIELKNVSKWYGPVQVLNECSATINKGEVVVVCGPSGSGKSTLIKTINALEPFQKGEITV 60 Query: 61 NNLVLNHKN-KIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119 + + L+ + + R MVFQHF L+PH++V NLT+A +K+ +S EA++ K Sbjct: 61 DGVKLHDPSTNLPKLRSRVGMVFQHFELFPHLSVTDNLTIAQIKVLGRSADEAKKRGLKM 120 Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179 L+ VGL+ + +P LSGGQQQRVAIAR+L +LFDEPTSALDPE + EVLDVM Sbjct: 121 LERVGLIAHKDKFPGQLSGGQQQRVAIARALSMDPIVMLFDEPTSALDPEMVGEVLDVMV 180 Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFME-DGAIVEENIPSEFFSNP--KTERARLFL 236 ++++ TM+ VTHEMGFA++V++R+IFM+ G I+E+ EFF+NP + R + FL Sbjct: 181 GLANE-GMTMMCVTHEMGFARKVSNRVIFMDVGGKILEDCSKDEFFNNPDARQPRTKDFL 239 Query: 237 GKIL 240 KIL Sbjct: 240 NKIL 243 Lambda K H 0.317 0.133 0.372 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: 158 Number of extensions: 7 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: 242 Length of database: 245 Length adjustment: 24 Effective length of query: 218 Effective length of database: 221 Effective search space: 48178 Effective search space used: 48178 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: 41 (21.7 bits) S2: 46 (22.3 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