Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >MicrobesOnline__882:206399 Length = 337 Score = 98.6 bits (244), Expect = 2e-25 Identities = 54/134 (40%), Positives = 83/134 (61%), Gaps = 1/134 (0%) Query: 236 GWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQ 295 G IP L +AL ++T A++AEIVR+GI+SV GQ EAARSLG+ ++RKVI+PQ Sbjct: 202 GLSAIPPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQMEAARSLGMSYAQSMRKVILPQ 261 Query: 296 ALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAI 355 A R I+PPL Q+++L K+SSL I E+ V+ + Q E+ + +YL + Sbjct: 262 AFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKA-TREVVTTSLQPFELWIVCALLYLVL 320 Query: 356 SISISLLMNWYNKR 369 + ++SL + + +R Sbjct: 321 TFTLSLCVQYLERR 334 Score = 57.0 bits (136), Expect = 7e-13 Identities = 26/65 (40%), Positives = 40/65 (61%) Query: 65 VFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILF 124 + L GL TL V+ + +I+ +LG + G+AR+S N + LA Y+E+ R P L+Q+ Sbjct: 126 ILLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFL 185 Query: 125 WYFAV 129 WYF V Sbjct: 186 WYFVV 190 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: 313 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 337 Length adjustment: 29 Effective length of query: 346 Effective length of database: 308 Effective search space: 106568 Effective search space used: 106568 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: 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