Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_053938866.1 WG78_RS16145 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q52666 (263 letters) >NCBI__GCF_001294205.1:WP_053938866.1 Length = 242 Score = 283 bits (724), Expect = 2e-81 Identities = 143/241 (59%), Positives = 176/241 (73%) Query: 23 IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82 I I ++KWYG F VL D + V +GE +V+ GPSGSGKST+I+C+N LE Q G IIVD Sbjct: 2 ISIKNISKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNGLEAFQKGDIIVD 61 Query: 83 GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYL 142 G + N+ K+RS VGMVFQ+F LFPHL+I +NLTLA + V + EA + L Sbjct: 62 GTSVGDPKTNLPKLRSRVGMVFQNFELFPHLSITQNLTLAQMQVLGRNRDEATVNGLRLL 121 Query: 143 EKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQ 202 ++V + A K+PGQLSGGQQQRVAIAR+L M P MLFDEPTSALDPEM+ EVLD M++ Sbjct: 122 DRVGLKAHADKHPGQLSGGQQQRVAIARALAMDPIAMLFDEPTSALDPEMVNEVLDVMVE 181 Query: 203 LAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQILG 262 LA+EGMTM+CVTHEMGFA+ VANRVIFM G IVE DFF +P+SER + FLS+IL Sbjct: 182 LAQEGMTMMCVTHEMGFARKVANRVIFMDKGAIVEDATKEDFFGSPRSERAQVFLSKILH 241 Query: 263 H 263 H Sbjct: 242 H 242 Lambda K H 0.320 0.134 0.391 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: 178 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: 263 Length of database: 242 Length adjustment: 24 Effective length of query: 239 Effective length of database: 218 Effective search space: 52102 Effective search space used: 52102 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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