OPENSEQ.org - 10526 - GREMLIN Submission

May 4, 2021 - We are working on upgrading the webserver, some pages may not work.

ExbD-TonB

Genes:	A	B	A+B
Length:	141	239	369
Sequences:	4093	127	80
Seq/Len:	29.03	0.53	0.22
MirrorTree (Pazo et al. 2001)			0.28

>SEQ_A
MAMHLNENLDDNGEMHDINVTPFIDVMLVLLIIFMVAAPLATVDVKVNLPASTSTPQPRPEKPVYLSVKADNSMFIGNDPVTDETMITALNALTEGKKDTTIFFRADKTVDYETLMKVMDTLHQAGYLKIGLVGEETAKAK
>SEQ_B
MTLDLPRRFPWPTLLSVCIHGAVVAGLLYTSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEIQ

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	0.10	0.00	0.02
2	0.10	0.00	0.02
5	0.10	0.00	0.02
10	0.10	0.00	0.02
20	0.10	0.00	0.02
100	0.14	0.00	0.02
∞	0.24	0.00	0.21

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
83_D	33_H	1.28	0.23	0.00
88_T	216_E	1.27	0.23	0.00
31_L	212_R	1.15	0.18	0.00
88_T	211_R	1.12	0.17	0.00
91_N	236_T	1.11	0.17	0.00
87_I	233_N	1.01	0.14	0.00
81_V	237_E	1.01	0.13	0.00
83_D	146_V	0.99	0.13	0.00
125_A	158_R	0.98	0.12	0.00
31_L	77_P	0.96	0.12	0.00
42_T	39_P	0.95	0.12	0.00
112_Y	153_P	0.95	0.12	0.00
79_D	68_V	0.93	0.11	0.00
53_T	63_P	0.93	0.11	0.00
31_L	73_P	0.93	0.11	0.00
88_T	140_A	0.93	0.11	0.00
83_D	226_V	0.93	0.11	0.00
88_T	7_R	0.92	0.11	0.00
53_T	193_I	0.92	0.11	0.00
29_V	204_R	0.92	0.11	0.00
49_L	204_R	0.92	0.11	0.00
54_S	212_R	0.91	0.11	0.00
91_N	60_A	0.90	0.10	0.00
76_I	225_V	0.89	0.10	0.00
76_I	232_I	0.89	0.10	0.00
54_S	47_V	0.89	0.10	0.00
31_L	100_P	0.88	0.10	0.00
104_F	188_V	0.88	0.10	0.00
81_V	51_T	0.88	0.10	0.00
122_L	166_R	0.86	0.10	0.00
79_D	236_T	0.86	0.10	0.00
91_N	235_T	0.86	0.10	0.00
56_P	57_P	0.85	0.10	0.00
80_P	169_A	0.85	0.09	0.00
67_S	180_F	0.85	0.09	0.00
76_I	42_A	0.85	0.09	0.00
30_L	163_Y	0.85	0.09	0.00
30_L	164_P	0.85	0.09	0.00
30_L	174_G	0.85	0.09	0.00
30_L	186_G	0.85	0.09	0.00
34_F	163_Y	0.85	0.09	0.00
34_F	164_P	0.85	0.09	0.00
34_F	174_G	0.85	0.09	0.00
34_F	186_G	0.85	0.09	0.00
50_P	163_Y	0.85	0.09	0.00
50_P	164_P	0.85	0.09	0.00
50_P	174_G	0.85	0.09	0.00
50_P	186_G	0.85	0.09	0.00
84_E	203_E	0.85	0.09	0.00
126_G	163_Y	0.85	0.09	0.00
126_G	164_P	0.85	0.09	0.00
126_G	174_G	0.85	0.09	0.00
126_G	186_G	0.85	0.09	0.00
33_I	204_R	0.85	0.09	0.00
93_L	143_S	0.85	0.09	0.00
109_T	36_I	0.85	0.09	0.00
79_D	162_Q	0.84	0.09	0.00
42_T	28_L	0.84	0.09	0.00
109_T	90_E	0.83	0.09	0.00
94_T	225_V	0.83	0.09	0.00
66_L	235_T	0.83	0.09	0.00

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
10530	18.75	ExbD-TonB	Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132)	0.10	Done
10528	11.86	ExbD-TonB	Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132)	0.00	Done
10526	0.22	ExbD-TonB	Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)	0.00	Done
8585	21.61	Dale 6-20	Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132)	0.60	Done - Shared
8568	19.56	DT gene 8, -6 jack	Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (r132)	0.40	Done - Shared
8566	0.22	DT gene 8 -6	Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06)	0.00	Done - Shared
8565	0.02	DT -6	Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06)		Killed - Shared
8564	0.02	DT gene 100	Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)		Killed - Shared
8563	16.31	DT -10 Jack	Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132)	0.45	Done - Shared
8562	0.02	DT -10	Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2015_06)		Killed - Shared
8561	17.39	Dale	Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (r132)	0.61	Done - Shared
7825	9.5	DT	Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132)	0.18	Done - Shared
7822	0.02	DT	Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)		Killed - Shared

Page generated in 0.549 seconds.