OPENSEQ.org - 12352 - GREMLIN Submission

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2KC8

Genes:	A	B	A+B
Length:	415	112	509
Sequences:	4078	2544	1445
Seq/Len:	9.83	22.71	2.84
MirrorTree (Pazo et al. 2001)			0.26

>SEQ_A
APAVAHHHHHHAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAYNA
>SEQ_B
MKLVTVIIKPFKLEDVREALSSIGIQGLTVTEVKGFGRQKGHAELYRGAEYSVNFLPKVKIDVAIADDQLDEVIDIVSKAAYTGKIGDGKIFVAELQRVIRIRTGEADEAAL

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.

Δgene	Ratio of paralogs		Joined
Δgene	A	B	Seq/Len
1	0.02	0.04	2.66
2	0.04	0.06	2.72
5	0.04	0.06	2.72
10	0.05	0.06	2.73
20	0.05	0.06	2.74
100	0.06	0.07	2.84
∞	0.13	0.19	3.24

Paired alignment generation


0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20

Sequence A	E-value:
	Iterations:
Sequence B	E-value:
	Iterations:
Δgene MSA

Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment.

Figure 2: Distribution of Δgene across all genomes.

Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!

GREMLIN results (Scaled_score > 1):

Figure 4: The darker and larger the blue dots, the higher strength in coevolution.

Text file of predictions (includes both intra[A,B] and inter[AB] preds)
Generate restraints for ROSETTA Structure Modeling

Inter Residue pairs sorted by strength in coevolution signal:

i	j	Scaled Score	Prob	I_Prob
397_E	85_K	1.39	0.92	0.47
251_I	8_I	0.91	0.53	0.12
314_L	79_K	0.77	0.36	0.07
369_A	75_D	0.70	0.28	0.05
292_G	96_L	0.70	0.28	0.05
307_G	99_V	0.70	0.28	0.05
258_E	44_E	0.69	0.27	0.05
259_W	40_K	0.67	0.25	0.04
252_L	93_V	0.67	0.25	0.04
126_G	108_D	0.67	0.25	0.04
124_I	94_A	0.67	0.25	0.04
47_G	48_G	0.66	0.24	0.04
58_T	71_D	0.64	0.23	0.04
381_I	107_A	0.64	0.23	0.04
133_R	18_E	0.63	0.22	0.04
360_Q	16_V	0.63	0.22	0.04
44_L	45_L	0.63	0.21	0.04
369_A	79_K	0.62	0.21	0.03
76_A	110_A	0.62	0.21	0.03
78_G	96_L	0.61	0.20	0.03
126_G	90_K	0.61	0.20	0.03
398_Q	96_L	0.61	0.20	0.03
336_I	109_E	0.60	0.20	0.03
384_K	59_V	0.60	0.19	0.03
193_K	76_I	0.60	0.19	0.03
395_P	61_I	0.60	0.19	0.03

Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)

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