OPENSEQ.org - RFAH - ECOLI GREMLIN

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RFAH - Transcription antitermination protein RfaH

UniProt:	P0AFW0	Sequence MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10839
Length:	162 (161)
Sequences:	1652
Seq/Len:	10.26

RFAH
Paralog alert: 0.29 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: NUSG RFAH

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
18_Q	22_E	4.511	1.00
90_S	94_H	4.027	1.00
27_N	58_E	3.001	1.00
117_I	160_R	2.948	1.00
139_S	159_F	2.903	1.00
34_T	45_A	2.844	1.00
132_E	140_M	2.456	1.00
34_T	47_S	2.334	1.00
114_D	161_K	2.11	1.00
33_I	48_E	1.941	1.00
138_R	155_K	1.931	1.00
17_A	75_V	1.851	1.00
37_K	48_E	1.849	1.00
120_E	158_E	1.779	1.00
59_F	65_H	1.73	1.00
115_K	127_Q	1.729	1.00
28_C	136_E	1.687	1.00
138_R	153_S	1.68	1.00
50_L	56_F	1.678	1.00
21_L	28_C	1.662	1.00
36_E	43_R	1.623	1.00
154_V	158_E	1.602	1.00
32_M	47_S	1.553	1.00
128_A	141_L	1.503	1.00
111_Y	114_D	1.46	1.00
131_T	142_L	1.432	1.00
117_I	127_Q	1.42	1.00
17_A	55_L	1.416	1.00
59_F	69_I	1.404	0.99
39_V	44_T	1.401	0.99
21_L	69_I	1.375	0.99
36_E	45_A	1.345	0.99
13_Q	74_G	1.326	0.99
26_V	58_E	1.316	0.99
10_K	13_Q	1.314	0.99
89_P	92_V	1.291	0.99
51_F	96_L	1.288	0.99
112_P	133_P	1.278	0.99
6_L	88_V	1.255	0.99
62_E	65_H	1.248	0.99
21_L	29_L	1.221	0.98
8_Y	76_S	1.218	0.98
35_L	48_E	1.206	0.98
29_L	97_S	1.206	0.98
91_A	94_H	1.204	0.98
58_E	90_S	1.199	0.98
141_L	154_V	1.198	0.98
51_F	56_F	1.184	0.98
139_S	156_N	1.18	0.98
117_I	125_G	1.172	0.98
93_I	97_S	1.171	0.98
65_H	69_I	1.17	0.97
9_C	14_L	1.162	0.97
21_L	136_E	1.161	0.97
143_L	152_H	1.152	0.97
155_K	158_E	1.147	0.97
116_V	141_L	1.143	0.97
22_E	28_C	1.138	0.97
141_L	151_K	1.119	0.96
8_Y	77_H	1.118	0.96
16_R	20_H	1.116	0.96
25_A	28_C	1.112	0.96
142_L	149_E	1.089	0.96
16_R	23_R	1.076	0.95
80_R	87_I	1.074	0.95
144_N	149_E	1.067	0.95
17_A	72_T	1.056	0.95
38_I	43_R	1.051	0.94
85_P	123_F	1.042	0.94
94_H	99_Y	1.024	0.93
66_T	70_N	1.023	0.93
19_E	23_R	1.02	0.93
88_V	93_I	1.019	0.93
154_V	159_F	1.009	0.93
40_R	44_T	1.004	0.93
115_K	129_I	1.002	0.92

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	P(%)	HHΔ		Acc
2ougA	4	0.9938	100	0.081	Contact Map	0.539
2jvvA	1	1	100	0.109	Contact Map	0.804
2lq8A	1	0.9877	100	0.144	Contact Map	0.54
1m1hA	1	1	100	0.144	Contact Map	0.629
2xhcA	1	0.9691	100	0.261	Contact Map	0.477
3p8bB	2	0.8765	100	0.304	Contact Map	0.764
1nz8A	1	0.642	99.9	0.416	Contact Map	0.457
3lpeA	4	0.5123	99.7	0.589	Contact Map	0.587
2e6zA	1	0.3642	99	0.713	Contact Map	0.665
1nz9A	1	0.3519	99	0.716	Contact Map	0.775

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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