Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate WP_086509151.1 BZY95_RS06455 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5405 (254 letters) >NCBI__GCF_002151265.1:WP_086509151.1 Length = 167 Score = 276 bits (707), Expect = 1e-79 Identities = 129/167 (77%), Positives = 149/167 (89%) Query: 14 IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73 +++M+GVNKWYG FHVL+DI+L VK+GERIV+CGPSGSGKST IRC+N LEEHQ G IVV Sbjct: 1 MVEMRGVNKWYGDFHVLRDIDLEVKRGERIVICGPSGSGKSTLIRCINHLEEHQAGEIVV 60 Query: 74 DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133 G+ LT D+K+IE IRR VGMVFQHFNLFPHLT+L+NC LAPMWV+K P+R+AEE AM Y Sbjct: 61 GGIPLTQDVKRIEQIRRNVGMVFQHFNLFPHLTVLENCCLAPMWVQKKPRREAEEQAMRY 120 Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSAL 180 LERVRI EQA KYPGQLSGGQQQRVAIAR+LCM P++MLFDEPTSAL Sbjct: 121 LERVRIAEQARKYPGQLSGGQQQRVAIARSLCMHPEVMLFDEPTSAL 167 Lambda K H 0.322 0.137 0.407 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: 170 Number of extensions: 2 Number of successful extensions: 1 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: 254 Length of database: 167 Length adjustment: 21 Effective length of query: 233 Effective length of database: 146 Effective search space: 34018 Effective search space used: 34018 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 (21.9 bits) S2: 45 (21.9 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