Evolutionarily consistent families in SCOP: sequence, structure and function.
Evolutionarily consistent families in SCOP: sequence, structure and function.
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DOI：
10.1186/1472-6807-12-27
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发表时间：
2012-10-18
影响因子：
--
通讯作者：
Gough J
中科院分区：
文献类型：
--
作者：
Pethica RB;Levitt M;Gough J
SCOP是一种针对已知结构的蛋白质的层次化结构域分类系统。超家族水平有一个明确的定义：如果有共同进化祖先的结构、功能和序列证据，蛋白质结构域属于同一超家族。超级家庭被细分为家庭，然而，对于家庭层面的分组，没有这样明确的基础。SCOP家族是否将具有序列相似性的结构域分组在一起，它们是将结构相似的结构域分组还是按共同功能分组？我们回答的正是这些问题，但最重要的是，每个家族是否代表着一个超级家族中的一个不同的系统发育群。为每个超家族生成了几个系统发育树：一个来自多序列比对，一个基于结构距离，最后两个来自GO项或分配给结构域的EC编号的存在/不存在。将得到的树的拓扑和置信值与SCOP家族分类进行比较。我们表明，SCOP家族分组在进化上与经典的序列系统发育学有很高的一致性。根据(自动生成的)结构距离构建的树具有很好的相关性，但并不总是与SCOP(手动注释)分组一致。来自功能数据的树与家族水平的一致性不如来自结构或序列的树，尽管大多数人仍然同意这一点。GO和EC的大部分注释直接应用于一个族或族的子集；相对较少的术语适用于超家族级别。一个家族内的最大序列多样性平均为22%，但对于超家族来说接近于零。
SCOP is a hierarchical domain classification system for proteins of known structure. The superfamily level has a clear definition: Protein domains belong to the same superfamily if there is structural, functional and sequence evidence for a common evolutionary ancestor. Superfamilies are sub-classified into families, however, there is not such a clear basis for the family level groupings. Do SCOP families group together domains with sequence similarity, do they group domains with similar structure or by common function? It is these questions we answer, but most importantly, whether each family represents a distinct phylogenetic group within a superfamily. Several phylogenetic trees were generated for each superfamily: one derived from a multiple sequence alignment, one based on structural distances, and the final two from presence/absence of GO terms or EC numbers assigned to domains. The topologies of the resulting trees and confidence values were compared to the SCOP family classification. We show that SCOP family groupings are evolutionarily consistent to a very high degree with respect to classical sequence phylogenetics. The trees built from (automatically generated) structural distances correlate well, but are not always consistent with SCOP (hand annotated) groupings. Trees derived from functional data are less consistent with the family level than those from structure or sequence, though the majority still agree. Much of GO and EC annotation applies directly to one family or subset of the family; relatively few terms apply at the superfamily level. Maximum sequence diversity within a family is on average 22% but close to zero for superfamilies.
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影响因子：
3.7
作者：
Pethica R;Barker G;Kovacs T;Gough J
通讯作者：
Gough J
影响因子：
14.9
作者：
Gough, J;Chothia, C
通讯作者：
Chothia, C
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
14.9
作者：
Andreeva, A;Howorth, D;Murzin, AG
通讯作者：
Murzin, AG
影响因子：
64.8
作者：
Rokas, A;Williams, BL;Carroll, SB
通讯作者：
Carroll, SB