Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate BWI76_RS18355 BWI76_RS18355 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Koxy:BWI76_RS18355 Length = 222 Score = 118 bits (296), Expect = 1e-31 Identities = 73/204 (35%), Positives = 118/204 (57%), Gaps = 6/204 (2%) Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216 G + TL ++ G+ L LG +LAL R S + I+ + +I +RG PLI LFM Sbjct: 18 GAVFTLQLSIGGMFFGLVLGFILALMRMSPVWPIKWLARMYISIFRGTPLIAQLFMIYYG 77 Query: 217 LPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMG 276 LP F G+ D + A+IG+ L +AY AE +R + +I KGQ+EAAA++G+ W++M Sbjct: 78 LPQF---GIELDPIPAAMIGLSLNTAAYAAETLRAAIASIDKGQWEAAASIGMTRWQAMR 134 Query: 277 LVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVF 336 ILPQA ++ +P + N+FI+L KDTSL I + +L + + + L + T Y+ Sbjct: 135 RAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLITS--RTLEVFTM-YLA 191 Query: 337 AALVFWIFCFGMSRYSMHLERKLD 360 A+L++W+ +S + E +L+ Sbjct: 192 ASLIYWVMATVLSTLQNYFENQLN 215 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: 254 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: 365 Length of database: 222 Length adjustment: 26 Effective length of query: 339 Effective length of database: 196 Effective search space: 66444 Effective search space used: 66444 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: 47 (22.7 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