Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate GFF355 PS417_01810 ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__WCS417:GFF355 Length = 319 Score = 109 bits (273), Expect = 9e-29 Identities = 63/171 (36%), Positives = 99/171 (57%), Gaps = 5/171 (2%) Query: 149 AVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLIT 208 A+ WG L TL ++ V + L +G+ L R S+ P +R + ++E RG PL+ Sbjct: 113 ALGPLMWG-LWTTLWLSVVSGILGLIIGLATGLCRLSSNPTLRDLSTIYVELVRGTPLLV 171 Query: 209 VLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMG 268 +F+ F+ +N + + + LF AY+AE+VR G+Q+I +GQ EAA ++G Sbjct: 172 QIFI----FYFFIGTVLNLSREFAGIAALSLFTGAYVAEIVRAGVQSITRGQNEAARSLG 227 Query: 269 LGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQ 319 L +SM V+LPQA K V+P + FI+L KDTSLV +I + +LL S ++ Sbjct: 228 LSASQSMRHVVLPQAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGRE 278 Lambda K H 0.330 0.144 0.469 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: 315 Number of extensions: 24 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: 365 Length of database: 319 Length adjustment: 29 Effective length of query: 336 Effective length of database: 290 Effective search space: 97440 Effective search space used: 97440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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