Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_082060698.1 H744_RS20715 transporter substrate-binding domain-containing protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_000940995.1:WP_082060698.1 Length = 377 Score = 356 bits (914), Expect = e-103 Identities = 170/319 (53%), Positives = 228/319 (71%), Gaps = 1/319 (0%) Query: 20 ASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVLGDPMKVKYV 79 AS+ TL V+ +G L CG GL GF+ P+ G ++G DV C+AVAAA+LGD KVKY+ Sbjct: 60 ASSETLAKVQKQGYLQCGVTTGLPGFSNPNEKGEWEGLDVEFCQAVAAAILGDKTKVKYI 119 Query: 80 PLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVNKSLGVSSAK 139 PLT + RFTAL SGE+D+L RN+TWT RDT L ++F VNYYDGQGFM+NK+L + SA Sbjct: 120 PLTAKERFTALQSGEIDLLSRNTTWTLHRDTALGINFAGVNYYDGQGFMINKALEIESAA 179 Query: 140 ELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACDSYTTDASGL 199 ELDGA +CVQ+GTTTE+NLAD+F+ M YTPV A+ + F AG CD+ TTD SGL Sbjct: 180 ELDGAAVCVQSGTTTELNLADYFRHREMKYTPVVFDTAAQTVKGFEAGRCDALTTDQSGL 239 Query: 200 ASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAEEYGITKANL 259 + R LP+ + V+LP+IISKEPLGP VR GD+ W +IV+W+ A++ AEE G++ N+ Sbjct: 240 YALRLNLPDPSSAVVLPDIISKEPLGPAVRQGDDQWFNIVKWTLNAMITAEELGVSSHNV 299 Query: 260 EEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANIGASTSIGLA 319 +++ S +P IRRL+G +G GK +GL++D+A + I GNYGE FE +G S+ + + Sbjct: 300 DDMKMS-NDPNIRRLIGADGPKGKGLGLNDDWAYQVIKQVGNYGESFERTVGMSSPLEIK 358 Query: 320 RGLNAQWTQGGLMYAPPFR 338 RG+NA W GGL+YAPP R Sbjct: 359 RGINALWNDGGLLYAPPMR 377 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: 347 Number of extensions: 10 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: 377 Length adjustment: 29 Effective length of query: 309 Effective length of database: 348 Effective search space: 107532 Effective search space used: 107532 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