HHomp--prediction and classification of outer membrane proteins.
HHomp--prediction and classification of outer membrane proteins.
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DOI：
10.1093/nar/gkp325
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Söding J
中科院分区：
文献类型：
--
作者：
Remmert M;Linke D;Lupas AN;Söding J
外膜蛋白（OMP）是在革兰氏阴性菌，线粒体和塑料的外膜中发现的跨膜蛋白。 β-桶OMP通过共同的血统相关。相似性。给定输入序列，HHOMP构建了一个概况范围的Markov模型（HMM），并通过成对的HMM比较将其与OMP数据库进行比较，从而通过PROFTMB整合了OMP预测。 000推定的OMP序列是用详尽的，及时的同源性检测方法HHSENSER收集的，从代表PDB的23数据库。在59个已知的OMP中识别57个，并将其正确分配给其功能子组。
Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. Most prediction methods have focused on analogous features, such as alternating hydrophobicity patterns. Here, we start from the observation that almost all β-barrel OMPs are related by common ancestry. We identify proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20 000 putative OMP sequences. These were collected with the exhaustive, transitive homology detection method HHsenser, starting from 23 representative OMPs in the PDB database. In a benchmark on TransportDB, HHomp detects 63.5% of the true positives before including the first false positive. This is 70% more than PROFtmb, four times more than BOMP and 10 times more than TMB-Hunt. In Escherichia coli, HHomp identifies 57 out of 59 known OMPs and correctly assigns them to their functional subgroups. HHomp can be accessed at http://toolkit.tuebingen.mpg.de/hhomp.
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