Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_011188233.1 DP_RS04975 amino acid ABC transporter permease
Query= TCDB::Q8YSA2 (501 letters) >NCBI__GCF_000025945.1:WP_011188233.1 Length = 336 Score = 150 bits (378), Expect = 9e-41 Identities = 87/207 (42%), Positives = 127/207 (61%), Gaps = 5/207 (2%) Query: 283 LLQGALVTIQLTILSTVLGLICGTLIALTRLSQFTPARLFARAYVDFFRGTPLLVQIFMI 342 LL +T++++ + ++G+ G L L+R+S+ + F+ Y++ RGTPL+VQIF+ Sbjct: 126 LLISLWITLKVSFFAIIIGITLGILTGLSRVSENPLLKWFSIIYIELIRGTPLMVQIFLW 185 Query: 343 YFG----IPALAQQLGFTFNFDRWVAGVIALSVNAAAYIAEIVRAGIQSIETGQTEAAKS 398 YF I A Q+G W GVIAL+ AY AEIVRAGIQS+ GQ EAA+S Sbjct: 186 YFVVGNLINAFLTQIGIGGVPPLWF-GVIALATFTGAYTAEIVRAGIQSVHRGQMEAARS 244 Query: 399 LGLNPWLTMRLVIFPQAFRRMLPPLGNEFISLLKDTSLVAVIGFEELFRKGQLIVADNYR 458 LGL +MR VI PQA RR++PPL +FISL+KD+SL+ VI E+ + + IV+ + Sbjct: 245 LGLTYAESMRKVILPQALRRIMPPLAGQFISLIKDSSLLGVIAIREVTKATREIVSSSLM 304 Query: 459 AFEIYAAVAIVYLCLTLLASQVLSRLE 485 +E++ A++YL LT S + LE Sbjct: 305 PYEMWITCALLYLVLTFALSLCVQHLE 331 Lambda K H 0.323 0.137 0.394 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: 362 Number of extensions: 16 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: 501 Length of database: 336 Length adjustment: 31 Effective length of query: 470 Effective length of database: 305 Effective search space: 143350 Effective search space used: 143350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 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