Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Miya:8500595 Length = 337 Score = 95.1 bits (235), Expect = 2e-24 Identities = 50/122 (40%), Positives = 78/122 (63%), Gaps = 1/122 (0%) Query: 248 LALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQ 307 +AL ++T A++AEIVR+GI+SV GQ EAARSLG+ +RKVI+PQA R I+PPL Q Sbjct: 214 MALALFTGAYVAEIVRAGIQSVHRGQMEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQ 273 Query: 308 YLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLMNWYN 367 +++L K+SSL I E+ V+ + Q E+ + +YL ++ ++SL + + Sbjct: 274 FISLIKDSSLLGVIAIRELTKA-TREVVTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLE 332 Query: 368 KR 369 +R Sbjct: 333 RR 334 Score = 49.7 bits (117), Expect = 1e-10 Identities = 24/65 (36%), Positives = 38/65 (58%) Query: 65 VFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQILF 124 + L GL TL V+ + +I ++G + G+ R+S N ++ A Y+E+ R P L+QI Sbjct: 126 ILLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFL 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: 320 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