Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_084005156.1 BEN30_RS06480 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_001746755.1:WP_084005156.1 Length = 340 Score = 233 bits (594), Expect = 5e-66 Identities = 128/323 (39%), Positives = 184/323 (56%), Gaps = 9/323 (2%) Query: 21 SASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVLGDPMKVKYVP 80 +AST++ VK RG ++CG + GF+ +A+G + GF V C+A AAVLG+ V+ Sbjct: 22 AASTIETVKNRGFVLCGVTDRVPGFSLHEADGSWSGFFVDFCRAAGAAVLGNADAVQIES 81 Query: 81 LTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVNKSLGVSSAKE 140 AL EVD+L STWT RDT +DF + +YDGQGF+++ +LGV S K+ Sbjct: 82 YW----LDALEGREVDILHAGSTWTLVRDTTRMIDFPGIYFYDGQGFILHSNLGVKSLKD 137 Query: 141 L----DGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACDSYTTDA 196 D + +T NL +F +T+T V I + F G CD D Sbjct: 138 AMTTKDLKVCAIGPSSTARANLEEFIANTGVTWTLVPIQTMDGMWRAFFGGRCDMAIHDR 197 Query: 197 SGLASSRA-TLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAEEYGIT 255 S L + A L ++ D V+LPE+ISKEPL P VR D W D++ W A +AAE+ G+ Sbjct: 198 SALVAVHAGRLDDSDDYVVLPEVISKEPLAPAVRSDDVQWRDLIFWVTMATIAAEDLGVN 257 Query: 256 KANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANIGASTS 315 + N++++ A + +PE+RRLLG + +G GL +D+A + I GNYGE+F N+G T Sbjct: 258 QDNVDDMLAHSTSPEVRRLLGADPGIGVGFGLSDDWAYQVIKQLGNYGEIFARNLGPKTQ 317 Query: 316 IGLARGLNAQWTQGGLMYAPPFR 338 ++RGLN W GGL+YAPP R Sbjct: 318 FKMSRGLNQLWRDGGLLYAPPVR 340 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: 314 Number of extensions: 15 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: 340 Length adjustment: 28 Effective length of query: 310 Effective length of database: 312 Effective search space: 96720 Effective search space used: 96720 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