Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_084938021.1 HA51_RS24860 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_002095475.1:WP_084938021.1 Length = 341 Score = 353 bits (906), Expect = e-102 Identities = 176/341 (51%), Positives = 230/341 (67%), Gaps = 3/341 (0%) Query: 1 MKKSVFFGSVALAALVAGAASA---STLDDVKARGQLICGSNPGLTGFAAPDANGVYQGF 57 MKK + VA A+L+A A A +TLD +K +G + CG + GL GF+ DA+G + G Sbjct: 1 MKKMMLSTLVAAASLLAVAQQAHAGTTLDAIKKKGFVQCGISDGLPGFSYADASGKFTGI 60 Query: 58 DVAVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFV 117 DV VC+A AAAV GD KVKY PLT + RFTAL SGEVD+L RN+TWT SRD + F Sbjct: 61 DVDVCRAAAAAVFGDASKVKYTPLTAKERFTALQSGEVDILSRNTTWTSSRDGGMGFLFA 120 Query: 118 AVNYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADD 177 VNYYDG GF+ +K G+ SAKELDGAT+C+Q GT TE+N+AD+FKAN M YTPV Sbjct: 121 GVNYYDGIGFLTHKKAGLKSAKELDGATVCIQAGTDTELNVADYFKANKMQYTPVTFDRS 180 Query: 178 AEGQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGD 237 E + +G CD+ ++D S L + R L D ++LPE+ISKEPLGPVVR GD++W Sbjct: 181 DESAKALDSGRCDTLSSDQSQLYALRVKLGKPDDFIVLPEVISKEPLGPVVRRGDDDWFT 240 Query: 238 IVRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAIL 297 IV+WS +A++ AEE GI N++++AA P++ LLG EGD GK + LDN +A I Sbjct: 241 IVKWSLFAMLNAEEMGINSKNVDQMAAKPTTPDMAHLLGAEGDFGKDLKLDNKWAYNIIK 300 Query: 298 ASGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 GNY EVF+ N+G +++ +ARG NA W QGG+ YAPP R Sbjct: 301 QVGNYQEVFDRNVGKDSALKIARGQNALWNQGGIQYAPPVR 341 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: 340 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: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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