OPENSEQ.org - 3173 - GREMLIN Submission

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cIV_C_4_cI_J_4_Pdenitr

Genes:	A	B	A+B
Length:	273	200	432
Sequences:	2888	6534	2877
Seq/Len:	10.58	32.67	6.66
MirrorTree (Pazo et al. 2001)			0.59

>SEQ_A
AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGLADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR
>SEQ_B
MMTFAFYLFAISACVAGFMVVIGRNPVHSVLWLILAFLSAAGLFVLQGAEFVAMLLVVVYVGAVAVLFLFVVMMLDVDFAELKGELARYLPLALVIGVVLLAQLGIAFSGWTPSDQAESLRAAPVDAAVENTLGLGLVLYDRYVLMFQLAGLVLLVAMIGAIVLTMRHRKDVKRQNVLEQMWRDPAKTMELKDVKPGQGL

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	0.27
5	0.00	0.01	4.52
10	0.00	0.01	4.98
20	0.00	0.01	5.10
100	0.00	0.03	5.26
∞	0.01	0.06	6.08

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
13_P	59_V	1.20	0.95	0.30
167_D	164_L	1.14	0.93	0.25
238_Q	157_A	1.09	0.91	0.22
136_D	29_S	1.05	0.89	0.20
61_V	147_F	0.97	0.83	0.15
55_L	145_L	0.94	0.80	0.14
108_F	165_T	0.91	0.78	0.13
8_Y	55_L	0.91	0.77	0.12
205_Y	150_A	0.91	0.77	0.12
131_G	66_V	0.90	0.76	0.12
138_W	74_M	0.89	0.75	0.12
234_L	61_V	0.89	0.75	0.11
69_V	92_L	0.87	0.73	0.11
21_A	62_G	0.87	0.73	0.11
23_G	72_V	0.87	0.72	0.11
52_L	97_G	0.87	0.72	0.11
125_G	49_A	0.87	0.72	0.11
203_T	155_L	0.86	0.72	0.10
31_A	42_G	0.86	0.72	0.10
187_G	15_V	0.85	0.71	0.10
229_V	93_A	0.85	0.70	0.10
34_W	64_V	0.84	0.69	0.10
225_I	43_L	0.82	0.67	0.09
63_F	10_A	0.82	0.67	0.09
21_A	151_G	0.82	0.66	0.09
110_K	9_F	0.82	0.66	0.09
37_G	147_F	0.81	0.66	0.09
92_L	65_A	0.81	0.65	0.09
210_Y	100_L	0.81	0.64	0.08
225_I	12_S	0.81	0.64	0.08
8_Y	32_W	0.80	0.63	0.08
183_V	105_G	0.79	0.63	0.08
175_L	53_A	0.79	0.62	0.08
265_F	26_P	0.78	0.61	0.08
196_A	29_S	0.78	0.60	0.07
4_K	147_F	0.77	0.60	0.07
22_I	39_S	0.77	0.59	0.07
191_Y	150_A	0.77	0.59	0.07
21_A	16_A	0.77	0.59	0.07
169_K	8_L	0.76	0.58	0.07
201_A	122_A	0.76	0.57	0.07
138_W	72_V	0.76	0.57	0.07
201_A	76_D	0.76	0.57	0.07
187_G	19_M	0.76	0.57	0.07
203_T	153_V	0.75	0.56	0.07
86_L	160_G	0.74	0.55	0.07
187_G	47_Q	0.74	0.55	0.07
54_G	139_L	0.74	0.55	0.07
150_L	58_V	0.74	0.55	0.06
154_A	140_Y	0.74	0.54	0.06
147_I	159_I	0.74	0.54	0.06
29_T	15_V	0.73	0.54	0.06
79_T	30_V	0.73	0.54	0.06
147_I	21_V	0.73	0.53	0.06
158_A	15_V	0.73	0.53	0.06
236_K	38_L	0.73	0.53	0.06
154_A	27_V	0.72	0.52	0.06
211_M	158_M	0.71	0.50	0.06
4_K	156_V	0.71	0.50	0.06
23_G	133_L	0.71	0.50	0.06
177_V	105_G	0.71	0.49	0.06
133_V	103_Q	0.70	0.49	0.06
228_F	47_Q	0.70	0.48	0.05
228_F	139_L	0.69	0.47	0.05
182_G	56_L	0.69	0.47	0.05
229_V	87_A	0.69	0.47	0.05

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
3179	5.65	cIV_C_10_cI_J_6_Pdenitr	Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06)	0.79	Done - Shared
3178	5.68	cIV_C_6_cI_J_6_Pdenitr	Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06)	0.86	Done - Shared
3177	5.65	cIV_C_2_cI_J_6_Pdenitr	Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06)	0.85	Done - Shared
3176	5.68	cIV_C_4_cI_J_6_Pdenitr	Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06)	0.86	Done - Shared
3175	1.26	cIV_C_4_cI_J_10_Pdenitr	Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06)	0.00	Done - Shared
3174	1.24	cIV_C_4_cI_J_20_Pdenitr	Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06)	0.00	Done - Shared
3173	6.66	cIV_C_4_cI_J_4_Pdenitr	Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06)	0.30	Done - Shared
3172	6.66	cIV_C_4_cI_J_20_Pdenitr	Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06)	0.23	Done - Shared

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