Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate RR42_RS16450 RR42_RS16450 hypothetical protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS16450 Length = 211 Score = 95.9 bits (237), Expect = 9e-25 Identities = 49/120 (40%), Positives = 86/120 (71%), Gaps = 1/120 (0%) Query: 243 LLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIP 302 L A +AL++ +AA+ AEI+R+GI++V GQ EAA+++G+ N LR VI+PQA R+++P Sbjct: 88 LPAAIIALSMSSAAYNAEIIRAGIRAVHRGQREAAQAVGMTNPRILRHVILPQATRIVLP 147 Query: 303 PLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLL 362 P +++ K++SLA+ I PE++ L A T+ + T +A+EV+ I ++YLA++ ++L+ Sbjct: 148 PYMGNFISHTKSTSLASVITVPELM-LSAQTIYSSTYRAVEVLTIAGAIYLALTTVLTLV 206 Score = 47.4 bits (111), Expect = 4e-10 Identities = 21/75 (28%), Positives = 41/75 (54%) Query: 54 IDYTEADSYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVF 113 ID+ + Y + L L T+L+ + + T+ G ++ + R S++ ++ A +Y+ +F Sbjct: 3 IDFVQVLPYLPILLKAALLTILLAVVTQVCGTVFGLLLALGRDSRHAVLRGAAFIYIWIF 62 Query: 114 RNIPPLLQILFWYFA 128 R P LL + F Y+A Sbjct: 63 RGTPVLLHLFFVYYA 77 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: 145 Number of extensions: 6 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: 211 Length adjustment: 26 Effective length of query: 349 Effective length of database: 185 Effective search space: 64565 Effective search space used: 64565 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: 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