Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_069956932.1 BEN30_RS03095 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_001746755.1:WP_069956932.1 Length = 327 Score = 368 bits (944), Expect = e-106 Identities = 179/326 (54%), Positives = 231/326 (70%), Gaps = 1/326 (0%) Query: 13 AALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVLGD 72 A ++A +A A TL+DV ARG L CG N GL GF+ D G + G DV VC+AVAAAVLGD Sbjct: 3 ATMIATSAFAGTLEDVTARGTLSCGVNTGLPGFSLQDDKGNWTGIDVDVCRAVAAAVLGD 62 Query: 73 PMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVNKS 132 KV++VPLT + RFTAL SGE+D+L RN+TWT +RDT L L+F VNYYDGQGF+V K+ Sbjct: 63 ATKVRFVPLTAKERFTALQSGEIDMLSRNTTWTHTRDTSLGLNFAGVNYYDGQGFLVQKA 122 Query: 133 LGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACDSY 192 LGV SAKELDGA++C+Q GTTTE+NLAD+F+ N M Y+ V + ++ F A CD Sbjct: 123 LGVKSAKELDGASVCIQAGTTTELNLADYFRLNGMKYSAVVYDTSDQTREGFEAARCDIL 182 Query: 193 TTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAEEY 252 T+D S L + R+ + + V+LPE+ISKEPLGPVVR GD+ W +IV+W+ YA V AEE Sbjct: 183 TSDQSQLYAIRSKMADPTSAVVLPEVISKEPLGPVVRQGDDAWFNIVKWTLYAQVNAEEM 242 Query: 253 GITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANIGA 312 G+T AN E+ + +P ++RLLG EGD G K+G+ D+A + GNYGE+FE N+G Sbjct: 243 GVTSANAMEMKTAA-DPNVKRLLGTEGDAGAKLGISADWAYNVVSQVGNYGEMFERNVGL 301 Query: 313 STSIGLARGLNAQWTQGGLMYAPPFR 338 T + +ARGLNA W GGL YAPP R Sbjct: 302 KTPLAIARGLNALWNNGGLQYAPPIR 327 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: 334 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: 338 Length of database: 327 Length adjustment: 28 Effective length of query: 310 Effective length of database: 299 Effective search space: 92690 Effective search space used: 92690 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: 49 (23.5 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