Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate BWI76_RS08100 BWI76_RS08100 glutamate/aspartate transporter permease GltK
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Koxy:BWI76_RS08100 Length = 224 Score = 86.3 bits (212), Expect = 7e-22 Identities = 44/127 (34%), Positives = 81/127 (63%), Gaps = 1/127 (0%) Query: 243 LLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIP 302 L++ +A +++ AA+ +EI+R+GI+S+S GQ+ AA +LG+ + +++ VI+PQA R ++P Sbjct: 97 LISAMIAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLVILPQAFRAMVP 156 Query: 303 PLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLL 362 L +Q + L +++SL + + A T+ + G +E+I +VY S+S SLL Sbjct: 157 LLLTQGIVLFQDTSLVYVLSLADFFRT-ASTIGERDGTQVEMILFAGAVYFVFSLSASLL 215 Query: 363 MNWYNKR 369 ++W KR Sbjct: 216 VSWLKKR 222 Score = 47.0 bits (110), Expect = 5e-10 Identities = 23/63 (36%), Positives = 38/63 (60%), Gaps = 1/63 (1%) Query: 67 LIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILFWY 126 L GL+ TL +T +++ + G I+ V RLS ++ A YV VFR+I PL+ +L W+ Sbjct: 17 LAGLVITLKITVTAIVIGIVWGTILAVMRLSSFLPLAWFAKTYVNVFRSI-PLVMVLLWF 75 Query: 127 FAV 129 + + Sbjct: 76 YLI 78 Lambda K H 0.328 0.141 0.430 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: 180 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 224 Length adjustment: 26 Effective length of query: 349 Effective length of database: 198 Effective search space: 69102 Effective search space used: 69102 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 (21.8 bits) S2: 48 (23.1 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