Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_082008539.1 H744_RS06585 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q52663 (338 letters) >NCBI__GCF_000940995.1:WP_082008539.1 Length = 349 Score = 343 bits (881), Expect = 3e-99 Identities = 172/347 (49%), Positives = 241/347 (69%), Gaps = 10/347 (2%) Query: 1 MKKSVFFGSVAL---AALVAGAASAS------TLDDVKARGQLICGSNPGLTGFAAPDAN 51 MKK + S++L A +V+G+A A+ TL VK G L CG + GL GF++ DA Sbjct: 4 MKKVINSVSISLLVSALMVSGSAMATPDSAGATLKKVKEAGVLKCGVSTGLPGFSSTDAK 63 Query: 52 GVYQGFDVAVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTE 111 G ++G DV C+AVAAAVL D KV++VPLT + RFTAL SGE+D+L RN+TWT RD+ Sbjct: 64 GNWEGIDVEYCRAVAAAVLQDASKVQFVPLTAKERFTALQSGEIDILSRNTTWTMQRDSA 123 Query: 112 LALDFVAVNYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTP 171 L ++FV VNYYDGQGFMV+K LG++SAKELDGA++C+Q+GTTTE+NLAD+F+ + M++ P Sbjct: 124 LGINFVGVNYYDGQGFMVSKELGIASAKELDGASVCIQSGTTTELNLADYFRMHGMSFKP 183 Query: 172 VNIADDAEGQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHG 231 V + + F AG CD T+D S L + R L + + V+LPE+ISKEPLGPVV G Sbjct: 184 VVFDTSDQTVKGFEAGRCDVLTSDQSQLYALRIKLADPSSAVVLPEVISKEPLGPVVAQG 243 Query: 232 DNNWGDIVRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDF 291 D+ W +I +W+ +V AEEYGI + N++ + ST +P + RLLG++G G+ +GL +D+ Sbjct: 244 DDQWFNIAKWTLNVMVNAEEYGIDQTNVDSMKKST-DPNVLRLLGVDGPKGQGLGLADDW 302 Query: 292 AKRAILASGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338 + + + GNYG+ FE +G + + +ARGLNA W GG+MYAPP R Sbjct: 303 SYQVLKQVGNYGDSFERTVGTGSPLKIARGLNALWNDGGIMYAPPVR 349 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: 343 Number of extensions: 7 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: 349 Length adjustment: 29 Effective length of query: 309 Effective length of database: 320 Effective search space: 98880 Effective search space used: 98880 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