The phrase "alignment of loop" is correct and usable in written English.
It can be used in contexts related to programming, engineering, or any field where loops are relevant, particularly when discussing the arrangement or configuration of loops.
Example: "The alignment of loop in the code was crucial for ensuring the program executed correctly."
Alternatives: "loop configuration" or "loop arrangement".
(B) Alignment of Loop 1 and Loop 2 between PolB and homologous ThyXs from Streptomyces.
Structure-based sequence alignment of loop 2 residues of characterized class Ia, class Ib, and class II RNRs, with asterisk denoting RNRs for which structures are available.
The alignment of loop A across the Cys-loop family is challenging (e.g., see ref (19)), but we considered Phe138 to align with the aromatic in loop A. The data indicate that an aromatic is important but not critical at this location.
(H ) Sequence alignment of pore loop region in PCH-2 orthologs, and equivalent region of human p97 and NSF, and E. coli ClpX.
The glycine-rich loop between β2 and β3, from Gly Thr, has the consensus sequence GXGGXGT which is highly conserved throughout the Bet v 1 superfamily (rmsd of 0.35 Å for the alignment of all loop atoms, Figure 4, inset).
Alignment of these loops with the corresponding loops of HAdV-C5 (species C, CAR interacting), HAdV-B35 (species B, CD46 interacting), Ad11 (species B, CD46 interacting), and Ad37 (species D, CAR and Sialic acid/GD1a glycan interacting) reveals different topologies in these critical receptor interacting regions (Fig. 3a 35,36,37,38.
Some rafts were associated with dislocation lines while some form as a result of alignment of dislocation loops.
The alignment of H3 loops was done according to (Chailyan et al., 2012; Lefranc et al., 2003; Morea et al., 1998) where insertions were introduced in the middle of the region comprised between the conserved residues Cys92 and Gly104.
Phosphorylation at these sites causes a re-alignment of the loop that coordinates Mg2+ -positioning that is essential for ATP-binding and catalysis.
In contrast to the peptide alignment, the SH3 domain alignment is highly reliable, mainly the alignment of n-SRC-loop and RT-loop in SH3 domains.
Figure S2B, Supporting Information, shows sequence alignment of the activation loop of various STE20 protein kinases.
