Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)
Query= TCDB::Q52663 (338 letters) >FitnessBrowser__Miya:8502446 Length = 271 Score = 105 bits (263), Expect = 1e-27 Identities = 79/253 (31%), Positives = 115/253 (45%), Gaps = 10/253 (3%) Query: 1 MKKSVFFGSVALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVY-QGFDV 59 MK+ V L A A ++D+KARG L+CG F D GFD+ Sbjct: 1 MKRLVLLAVALCVVLTGTMAHAGKIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDI 60 Query: 60 AVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAV 119 +CKAVA LG +++K V T TR L G VD++ T F RD +DF Sbjct: 61 DICKAVADK-LGVKLELKTV--TSATRIPMLTQGSVDMVAATMTHKFERDD--VIDFSIT 115 Query: 120 NYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAE 179 + DGQ +V K GV SA +L G + G+T+E N+ KA T V+ + + Sbjct: 116 YFMDGQKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNI----KAAQPEATVVSFDEYPQ 171 Query: 180 GQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIV 239 G ++ TTD++ L R + P I+ + IS EP G + D+ + D+V Sbjct: 172 AFLALKQGKAEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDLV 231 Query: 240 RWSFYALVAAEEY 252 + L + EY Sbjct: 232 NRTLVDLWNSGEY 244 Lambda K H 0.316 0.132 0.384 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: 188 Number of extensions: 9 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: 338 Length of database: 271 Length adjustment: 27 Effective length of query: 311 Effective length of database: 244 Effective search space: 75884 Effective search space used: 75884 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 (21.6 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