Align Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale)
to candidate Dsui_0637 Dsui_0637 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:A0A0H3PA28 (219 letters) >FitnessBrowser__PS:Dsui_0637 Length = 224 Score = 115 bits (288), Expect = 7e-31 Identities = 66/208 (31%), Positives = 117/208 (56%), Gaps = 10/208 (4%) Query: 10 IEFLMQGLFLTLKIALATCIISIVFGTFLAITKNYGDRLSKFLAACYIDIFRNTPLLLWM 69 + L +GL +TL++ L ++ I +GT LA+ + +RL FLAA Y+++FR+ PL++ + Sbjct: 13 LPLLGKGLLVTLEVTLTAIVVGIGWGTLLAVARLSSNRLLSFLAAGYVNLFRSVPLVMVI 72 Query: 70 LAACFVLP-VFFGQFPQAFW------GTIGFSLYTSSVMAEIIRGGLNSIPKGQFEAAYS 122 L ++P G F Q + F+L+ ++ +EIIR G+ S+PKGQ A + Sbjct: 73 LWFYLIVPQALKGLFGQDIGDIRLVSALVAFALFEAAYYSEIIRAGIQSVPKGQVAAGLA 132 Query: 123 QGFGKFFTLFYIILPQTFRKIIPALLSQIVTTVKDTAYLAGLGIAELTYNSKTILAKLTS 182 G T+ ++LPQ FR +IP LL+Q + +DT+ + +G+++ + + + Sbjct: 133 LGLTPGQTMRLVVLPQAFRNMIPLLLTQAIILFQDTSLVYVIGLSDFFGTAYKVGDRDGR 192 Query: 183 FEEILAMIGVVAGIYFIICFSLSMLVRY 210 E+L G YF+ICF++S LV++ Sbjct: 193 LVELLLFAGAA---YFVICFTVSRLVKH 217 Lambda K H 0.331 0.144 0.428 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: 152 Number of extensions: 7 Number of successful extensions: 3 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: 219 Length of database: 224 Length adjustment: 22 Effective length of query: 197 Effective length of database: 202 Effective search space: 39794 Effective search space used: 39794 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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