LOMETS results

LOMETS (LOcal MEta-Threading-Server) results

> T0292 ,277 residues, "easy" target

Your submitted sequence and predicted secondary structure (by PSI-PRED):

Seq:	SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLREL
SS :	CCCCCEEEEEEECCCCCEEEEEEEECCCCCEEEEEEEEHHHCCHHHHHHHHHHHHHHHHC
Pos:	123456789012345678901234567890123456789012345678901234567890

Seq:	KHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTL
SS :	CCCCCCEEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Pos:	123456789012345678901234567890123456789012345678901234567890

Seq:	ALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYY
SS :	HHHHHHCCCCCCCCEECCCCCHHHEEECCCCCEEECCCHHHHHCCCCHHHHHCCCCCHHH
Pos:	123456789012345678901234567890123456789012345678901234567890

Seq:	MSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSD
SS :	CCHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCHHHCH
Pos:	123456789012345678901234567890123456789012345678901234567890

Seq:	ELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
SS :	HHHHHHHHHCCCCCHHCCCHHHHHCCHHHHHHHHHCC
Pos:	1234567890123456789012345678901234567

For detailed information about output, please see readme file.

Prediction results by LOMETS consensus method

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Program	Target-template alignments	3-D models from threading alignments	Full-length models by MODELLER
1	2ou7a	265	0.956	16.919	0.260	High	SPARKS2	alignment_1	threading_1	model_1
2	2ou7A	265	0.956	16.652	0.264	High	PPA-II	alignment_2	threading_2	model_2
3	2ou7a	265	0.956	16.872	0.260	High	SP3	alignment_3	threading_3	model_3
4	2v5qa	265	0.956	16.917	0.260	High	SPARKS2	alignment_4	threading_4	model_4
5	2rkua	265	0.956	16.828	0.260	High	SPARKS2	alignment_5	threading_5	model_5
6	2v5qa	265	0.956	17.000	0.260	High	SP3	alignment_6	threading_6	model_6
7	2rkua	265	0.956	16.936	0.260	High	SP3	alignment_7	threading_7	model_7
8	2ou7A	259	0.935	18.065	0.270	High	SAM-T02	alignment_8	threading_8	model_8
9	2bfxA	262	0.945	20.360	0.279	High	PPA-I	alignment_9	threading_9	model_9
10	2bfxA	261	0.942	17.055	0.284	High	PPA-II	alignment_10	threading_10	model_10

Restraint files by LOMETS consensus method

Sidechain contacts

C alpha atom contacts

Short-range C alpha atom distances

Large-range C alpha atom distances

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The followings are the results of component servers of LOMETS

1.Models generated by PPA-I
PPA-I is a profile-profile alignment approach. It considers query and template profiles and predicted secondary structure information.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2bfxA	262	0.945	20.360	0.279	High	alignment_1	threading_1
2	1ia8a	262	0.945	18.878	0.240	High	alignment_2	threading_2
3	2cl1A	250	0.902	18.599	0.992	High	alignment_3	threading_3
4	1phk_	260	0.938	18.538	0.288	High	alignment_4	threading_4
5	1x8bA	254	0.916	18.120	0.260	High	alignment_5	threading_5
6	2eueA	233	0.841	17.719	0.300	High	alignment_6	threading_6
7	2a19B	252	0.909	17.658	0.306	High	alignment_7	threading_7
8	1o6ya	251	0.906	17.588	0.271	High	alignment_8	threading_8
9	2bujA	267	0.963	17.509	0.213	High	alignment_9	threading_9
10	1xqzA	257	0.927	17.178	0.280	High	alignment_10	threading_10

2.Models generated by SP3
SP3 uses sequence-derived and structure-derived profile-profile alignment. Secondary structure information is also considered in SP3.
The optimized threading is found by local dynamic programming.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2cl1a	250	0.902	17.129	0.988	High	alignment_1	threading_1
2	2v5qa	265	0.956	17.000	0.260	High	alignment_2	threading_2
3	2rkua	265	0.956	16.936	0.260	High	alignment_3	threading_3
4	2ou7a	265	0.956	16.872	0.260	High	alignment_4	threading_4
5	1phk_	260	0.938	16.046	0.292	High	alignment_5	threading_5
6	1koba	264	0.953	15.852	0.261	High	alignment_6	threading_6
7	1ia8a	262	0.945	15.766	0.252	High	alignment_7	threading_7
8	3c0ga	268	0.967	15.763	0.302	High	alignment_8	threading_8
9	1tkia	262	0.945	15.752	0.221	High	alignment_9	threading_9
10	1jksa	262	0.945	15.745	0.248	High	alignment_10	threading_10

3.Models generated by PPA-II
PPA-II is a profile-profile alignment approach. The only difference from PPA-I is that PPA-II uses sequence from SAM-T99.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2cl1A	249	0.898	18.336	0.996	High	alignment_1	threading_1
2	2h6dA	251	0.906	17.080	0.299	High	alignment_2	threading_2
3	2bfxA	261	0.942	17.055	0.284	High	alignment_3	threading_3
4	1ia8a	262	0.945	16.673	0.240	High	alignment_4	threading_4
5	2ou7A	265	0.956	16.652	0.264	High	alignment_5	threading_5
6	1phk_	260	0.938	15.795	0.285	High	alignment_6	threading_6
7	2iwiA	241	0.870	15.777	0.290	High	alignment_7	threading_7
8	2eueA	233	0.841	15.705	0.305	High	alignment_8	threading_8
9	1x8bA	254	0.916	15.687	0.260	High	alignment_9	threading_9
10	3cekA	246	0.888	15.610	0.280	High	alignment_10	threading_10

4.Models generated by SPARKS2
SPARKS2 is a threading algorithm considering knowledge-based structure score, mutation score and secondary structure derived score.
It is optimized by global-local dynamic programming.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2cl1a	250	0.902	17.096	0.992	High	alignment_1	threading_1
2	2ou7a	265	0.956	16.919	0.260	High	alignment_2	threading_2
3	2v5qa	265	0.956	16.917	0.260	High	alignment_3	threading_3
4	2rkua	265	0.956	16.828	0.260	High	alignment_4	threading_4
5	1jksa	262	0.945	16.128	0.248	High	alignment_5	threading_5
6	1phk_	260	0.938	16.050	0.292	High	alignment_6	threading_6
7	1xqza	257	0.927	15.972	0.280	High	alignment_7	threading_7
8	2qg5a	257	0.927	15.950	0.319	High	alignment_8	threading_8
9	1ia8a	262	0.945	15.913	0.252	High	alignment_9	threading_9
10	3dfaa	258	0.931	15.766	0.295	High	alignment_10	threading_10

5.Models generated by PROSPECT2
PROSPECT2 uses a score function considering sequence muations, secondary structures, solvent accessibility and pairwise residue contacts.
It uses a divide-and conquer approach to find the optimal threading.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2cl1A	250	0.902	12.141	0.992	High	alignment_1	threading_1
2	1x8bA	254	0.916	11.391	0.252	High	alignment_2	threading_2
3	2a19B	252	0.909	11.253	0.310	High	alignment_3	threading_3
4	1u5qA	261	0.942	10.826	0.284	High	alignment_4	threading_4
5	2bujA	267	0.963	10.664	0.213	High	alignment_5	threading_5
6	2c30A	262	0.945	10.561	0.286	High	alignment_6	threading_6
7	2ou7A	265	0.956	10.524	0.260	High	alignment_7	threading_7
8	1o6ya	251	0.906	10.511	0.271	High	alignment_8	threading_8
9	1f3mc	256	0.924	10.482	0.293	High	alignment_9	threading_9
10	1phk_	260	0.938	10.382	0.292	High	alignment_10	threading_10

6.Models generated by FUGUE
FUGUE uses a sequence-structure profile considering local structural environment: secondary structure, solvent accessibility, and hydrogen bonding status.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	TyrKc:1qcfa	257	0.927	37.880	0.226	High	alignment_1	threading_1
2	kinase:1hcl	217	0.783	36.180	0.295	High	alignment_2	threading_2
3	hsd1koba:hsd1koba	264	0.953	34.700	0.269	High	alignment_3	threading_3
4	hsd1tkia:hsd1tkia	263	0.949	32.490	0.221	High	alignment_4	threading_4
5	hs2acxa:hs2acxa	266	0.960	29.580	0.252	High	alignment_5	threading_5
6	hs3c4za:hs3c4za	270	0.974	27.440	0.252	High	alignment_6	threading_6
7	hs2pzia:hs2pzia	248	0.895	27.330	0.250	High	alignment_7	threading_7
8	hs2rioa:hs2rioa	254	0.916	23.130	0.220	High	alignment_8	threading_8
9	hs3cd3a:hs3cd3a	259	0.935	21.830	0.247	High	alignment_9	threading_9
10	hs3dlza:hs3dlza	266	0.960	11.190	0.154	High	alignment_10	threading_10

7.Models generated by HHSEARCH
HHsearch creates profile Hidden Markov Models (HMM) for query and template sequences. Then it uses HMM-HMM alignment to find the final alignments.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2jav_A	245	0.884	13.611	1.000	High	alignment_1	threading_1
2	2bdw_A	260	0.938	12.766	0.304	High	alignment_2	threading_2
3	3ckw_A	231	0.833	12.701	0.314	High	alignment_3	threading_3
4	3c4z_A	261	0.942	12.919	0.272	High	alignment_4	threading_4
5	1y8g_A	236	0.851	12.623	0.316	High	alignment_5	threading_5
6	1kob_A	257	0.927	12.727	0.272	High	alignment_6	threading_6
7	2vwi_A	225	0.812	12.823	0.249	High	alignment_7	threading_7
8	1omw_A	255	0.920	12.654	0.275	High	alignment_8	threading_8
9	1koa_A	255	0.920	12.540	0.239	High	alignment_9	threading_9
10	2acx_A	259	0.935	12.776	0.251	High	alignment_10	threading_10

8.Models generated by PAINT
PAINT is a PAirwise INteraciton based Threading algorithm. Like RAPTOR threading approach, it considers sequence muations,
secondary structures, solvent accessibility and pairwise residue contacts. The optimal threading is found by using linear programming.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	1x8bA	254	0.916	1.628	0.244	High	alignment_1	threading_1
2	2bfxA	262	0.945	1.272	0.271	High	alignment_2	threading_2
3	1o6ya	251	0.906	1.259	0.251	High	alignment_3	threading_3
4	1phk_	260	0.938	1.202	0.285	High	alignment_4	threading_4
5	2eueA	233	0.841	1.191	0.300	High	alignment_5	threading_5
6	1jksa	263	0.949	1.152	0.243	High	alignment_6	threading_6
7	1xqzA	248	0.895	1.093	0.270	High	alignment_7	threading_7
8	1tkia	263	0.949	1.039	0.213	High	alignment_8	threading_8
9	1u5qA	259	0.935	1.023	0.282	High	alignment_9	threading_9
10	1f3mc	254	0.916	0.799	0.287	High	alignment_10	threading_10

9.Models generated by SAM-T02
SAM-T02 is a threading algorithm that uses Hidden Markov Models (HMM). It builds multiple alignment and creates an HMM from that multiple alignment.
Then the HMM can be used for searching template library.

Rank	Template	Align_length	Coverage	Zscore	Seq_id	Confidence	Target-template alignments	3-D models from threading alignments
1	2cl1A	249	0.898	20.883	0.996	High	alignment_1	threading_1
2	3dfaA	258	0.931	18.637	0.298	High	alignment_2	threading_2
3	2j51A	257	0.927	18.416	0.272	High	alignment_3	threading_3
4	2bdwA	256	0.924	18.085	0.305	High	alignment_4	threading_4
5	2ou7A	259	0.935	18.065	0.270	High	alignment_5	threading_5
6	3c0gA	266	0.960	17.442	0.305	High	alignment_6	threading_6
7	2jamA	255	0.920	17.355	0.275	High	alignment_7	threading_7
8	2cn5A	249	0.898	17.108	0.297	High	alignment_8	threading_8
9	2qg5A	257	0.927	16.933	0.323	High	alignment_9	threading_9
10	1o6ka	255	0.920	16.629	0.275	High	alignment_10	threading_10