dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Abstract

BackgroundAnnotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies. The latter is either due to positional sequence conservation as a result of a very simple, physically induced pattern or integral sequence properties that are critical for function. Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations.ResultsBased on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. Subsequent statistical stratification of the fold-related hits into cohorts of functionally-related domains allows for the function postulation of the query sequence. Briefly, the technical problems as to how to recognize non-globular parts in the domain model, resolve contradictory HMMER2/HMMER3 results and evaluate fold-related domain hits for homology, are addressed in this work. The framework is benchmarked against a set of SCOP-to-Pfam domain models. Despite being a sequence-to-profile method, dissectHMMER performs favorably against a profile-to-profile based method-HHsuite/HHsearch. Examples of function annotation using dissectHMMER, including the function discovery of an uncharacterized membrane protein Q9K8K1_BACHD (WP_010899149.1) as a lactose/H+ symporter, are presented. Finally, dissectHMMER webserver is made publicly available at http://dissecthmmer.bii.a-star.edu.sg.ConclusionsThe proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. Overall, this translates into an opportunity for any novel protein sequence to be functionally characterized.ReviewersThis article was reviewed by Masanori Arita, Shamil Sunyaev and L. Aravind.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0068-3) contains supplementary material, which is available to authorized users.

xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

“…Briefly, it is the fold-critical parts (the supposedly 3D structural part) of a sequence-to-domain alignment that argues for a similar overall fold, hence similar function whereas the remnant part represents disordered, fibrillary or other non-globular regions that might be not obligatory for the domain fold [13, 14, 24]. As such, the E-values of the fold-critical contributions has to be more significant than the remnant parts to justify for annotation transfer.…”

“…8, the β glocal HMMER2 and γ local HMMER3 sequence-to-domain hits can be stratified into paired HMMER2/HMMER3 hits, HMMER2-only hits and HMMER3-only hits. More specifically, the paired hits are HMMER2 and HMMER3 hits where the domain model sequences overlap (see dissectHMMER for details [13, 14]). The orphaned HMMER2 and HMMER3 hits are those that are found only by the HMMER variant itself.…”

“…For the paired HMMER2/HMMER3 hits, each glocal-mode HMMER2 hit is reconstructed to reproduce the local alignment made by its HMMER3 counterpart. As a result, a new E-value for this reconstructed local-mode HMMER2 alignment is also derived following published procedures [9, 13, 14]. …”

The Novel Secreted Meloidogyne incognita Effector MiISE6 Targets the Host Nucleus and Facilitates Parasitism in Arabidopsis

“…The prediction of transmembrane domain and NLS were performed using TMHMM 5 and NucPred ( Brameier et al, 2007 ) based on a sequence score ≥ 0.5. Domains were predicted in local PuTTY based on HMMER 3.1b1 ( Wong et al, 2015 ) and the active conserved domains were blasted to the Pfam database ( Finn et al, 2014 ). A phylogenetic analysis of homologues was carried out using the maximum likelihood method with MEGA 5 ( Tamura et al, 2011 ).…”

Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z

“…Yet, proteins with many transmembrane helices (TMs), low complexity regions or other non-globular segments remain difficult sequence-analytic targets as significance criteria break down due to the amino acid compositional bias [ 4 ]. For some functionally uncharacterized sequences, focusing the analysis on fold-critical segments [ 5 , 6 ] or on complex TMs (that carry an evolutionary signature versus simple, merely hydrophobic TMs) [ 7 , 8 ] can expand the reach of sequence similarity searches to previously not seen functionally annotated homologues.…”