OPENSEQ.org - 5586 - GREMLIN Submission

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cI_A_4_cytb_4_human

Genes:	A	B	A+B
Length:	115	378	490
Sequences:	6650	4516	3845
Seq/Len:	57.83	11.95	7.85
MirrorTree (Pazo et al. 2001)			0.76

>SEQ_A
MNFALILMINTLLALLLMIITFWLPQLNGYMEKSTPYECGFDPMSPARVPFSMKFFLVAITFLLFDLEIALLLPLPWAXQTTNLPLMVMSSLLLIIILALSLAYEWLQKGLDWAE
>SEQ_B
MTPMRKINPLMKLINHSLIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDASTAFSSIAHITRDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYSETWNIGIILLLATMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFFTFHFILPFIIAALATLHLLFLHETGSNNPLGITSHSDKITFHPYYTIKDALGLLLFILSLMTLTLFSPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTILRSVPNKLGGVLALLLSILILAMIPILHMSKQQSMMFRPLSQSLYWLLAADLLILTWIGGQPVSYPFTIIGQVASVLYFTTILILMPTISLIENKMLK

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

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

Δgene	Ratio of paralogs		Joined
Δgene	A	B	Seq/Len
1	0.00	0.00	0.13
2	0.00	0.00	0.39
5	0.00	0.00	5.56
10	0.00	0.00	6.48
20	0.00	0.00	6.55
100	0.00	0.00	6.69
∞	0.01	0.00	7.80

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
71_L	301_L	1.00	0.89	0.03
64_L	361_T	0.97	0.87	0.03
94_L	123_T	0.88	0.78	0.02
27_L	27_I	0.87	0.77	0.02
21_T	129_M	0.84	0.74	0.02
37_Y	269_K	0.84	0.74	0.02
12_L	46_T	0.81	0.69	0.02
28_N	330_A	0.80	0.68	0.02
31_M	169_S	0.79	0.67	0.02
94_L	257_T	0.79	0.67	0.02
70_A	129_M	0.79	0.67	0.02
84_L	353_V	0.78	0.66	0.02
4_A	46_T	0.78	0.66	0.02
67_L	318_R	0.77	0.64	0.02
18_M	350_I	0.76	0.62	0.01
54_K	105_G	0.76	0.62	0.01
7_L	241_T	0.75	0.61	0.01
108_Q	29_A	0.75	0.61	0.01
29_G	356_V	0.75	0.61	0.01
77_W	164_I	0.74	0.60	0.01
65_F	137_Q	0.73	0.58	0.01
56_F	25_S	0.73	0.58	0.01
59_A	62_A	0.72	0.57	0.01
100_L	46_T	0.71	0.55	0.01
75_L	371_L	0.70	0.53	0.01
77_W	318_R	0.70	0.53	0.01
101_S	107_F	0.69	0.52	0.01
95_I	112_T	0.69	0.52	0.01
29_G	243_T	0.69	0.51	0.01
60_I	58_D	0.68	0.51	0.01
5_L	364_I	0.68	0.50	0.01
72_L	162_Q	0.68	0.50	0.01
52_S	252_D	0.68	0.50	0.01
100_L	377_L	0.67	0.48	0.01
73_L	222_P	0.67	0.48	0.01
47_A	181_F	0.67	0.48	0.01
60_I	206_N	0.67	0.48	0.01
104_Y	64_S	0.66	0.47	0.01
53_M	189_I	0.66	0.47	0.01
95_I	364_I	0.66	0.47	0.01
88_V	235_F	0.66	0.47	0.01
90_S	192_L	0.66	0.46	0.01
19_I	357_L	0.65	0.46	0.01
37_Y	344_S	0.65	0.46	0.01
94_L	261_P	0.65	0.44	0.01
45_S	160_L	0.64	0.44	0.01
83_N	184_I	0.64	0.43	0.01
19_I	296_L	0.64	0.43	0.01
54_K	108_L	0.64	0.43	0.01
60_I	96_L	0.63	0.42	0.01
16_L	47_T	0.63	0.42	0.01
39_C	53_M	0.63	0.42	0.01
63_L	11_M	0.63	0.42	0.01
73_L	179_F	0.62	0.40	0.01
30_Y	317_F	0.62	0.40	0.01
44_M	47_T	0.61	0.39	0.01
71_L	239_L	0.61	0.39	0.01
37_Y	355_S	0.61	0.39	0.01
112_D	122_A	0.61	0.38	0.01

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)

ID	Seq/Len	Name	Options	I_Prob	Status
5614	1.96	cI_A_40_cytb_6_human	Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2016_06b)	0.88	Done - Shared
5613	1.95	cI_A_40_cytb_10_human	Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b)	0.92	Done - Shared
5612	7.03	cI_A_20_cytb_20_human	Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b)	0.21	Done - Shared
5611	1.93	cI_A_40_cytb_20_human	Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b)	0.89	Done - Shared
5610	1.94	cI_A_40_cytb_60_human	Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b)	0.85	Done - Shared
5596	0	cI_A_60_cytb_60_human	Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b)		Killed - Shared
5593	0	cI_A_80_cytb_80_human	Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2016_06b)		Killed - Shared
5591	1.95	cI_A_40_cytb_40_human	Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b)	0.85	Done - Shared
5586	7.85	cI_A_4_cytb_4_human	Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b)	0.03	Done - Shared

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