Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_009563564.1 RSPH17029_RS18145 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_000015985.1:WP_009563564.1 Length = 345 Score = 285 bits (729), Expect = 1e-81 Identities = 151/335 (45%), Positives = 209/335 (62%), Gaps = 8/335 (2%) Query: 9 SVALAALVAGAASAS------TLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVC 62 SV A L+AGA +A+ TL VK RG+++CG +P GFAAPD+ G + GF+V C Sbjct: 10 SVLAALLLAGAGTAAFAQSGDTLAAVKERGEVLCGVHPARHGFAAPDSQGKWSGFEVDFC 69 Query: 63 KAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYY 122 A+AAAV GD KV++V L+ + RF A+ SGEVDVL RN T T SRDT L L+F +Y Sbjct: 70 HAIAAAVFGDANKVRFVALSSQQRFPAIQSGEVDVLARNVTATLSRDTALGLNFAPPIFY 129 Query: 123 DGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQ 182 G GF+V + G+ ++LDGA IC+ G+TTE N+A F A ++YTPV I ++ + Sbjct: 130 TGTGFLVRAADGIEKVEDLDGAAICMAPGSTTERNVAQIFAARGLSYTPVVIENNKQLVD 189 Query: 183 KFAAGACDSYTTDASGLASSRA-TLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRW 241 + G CD+ T D + L RA D V+LP I SKEPL VR GD+ W D+V+W Sbjct: 190 AYVTGRCDALTKDKAALPGVRAFDTEVPGDHVLLPGIYSKEPLAMAVRQGDDKWYDLVKW 249 Query: 242 SFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGN 301 YA AEE G+T+AN++E+ AS +P+I+ LLG+ GD G K+G+ ND+A + GN Sbjct: 250 VTYATFNAEELGVTQANVDEMKAS-DDPDIQTLLGVIGDNGTKLGVPNDWAYAIVKQVGN 308 Query: 302 YGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPP 336 Y +++ + G T + L R N WT+GGL+Y P Sbjct: 309 YEDIYMRHFGPDTPVALDRDQNQLWTEGGLLYGFP 343 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: 336 Number of extensions: 17 Number of successful extensions: 3 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: 345 Length adjustment: 29 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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 Apr 10 2024. 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