Query psy225
Match_columns 450
No_of_seqs 435 out of 3287
Neff 10.0
Searched_HMMs 46136
Date Fri Aug 16 19:57:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy225.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/225hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03778 MATH_TRAF2 Tumor Necro 100.0 3.1E-37 6.8E-42 253.2 15.8 156 286-443 2-164 (164)
2 cd03777 MATH_TRAF3 Tumor Necro 100.0 1.2E-36 2.5E-41 258.5 19.8 177 267-444 3-185 (186)
3 cd03779 MATH_TRAF1 Tumor Necro 100.0 1E-32 2.2E-37 224.8 14.5 140 302-443 1-147 (147)
4 cd03780 MATH_TRAF5 Tumor Necro 100.0 1.6E-32 3.5E-37 225.1 14.7 141 302-443 1-148 (148)
5 cd03783 MATH_Meprin_Alpha Mepr 100.0 1.4E-30 3E-35 212.3 13.9 140 303-443 3-167 (167)
6 cd03782 MATH_Meprin_Beta Mepri 100.0 2.4E-30 5.2E-35 209.3 14.1 139 303-443 3-167 (167)
7 cd03776 MATH_TRAF6 Tumor Necro 100.0 8.9E-30 1.9E-34 212.0 14.6 142 302-443 1-147 (147)
8 cd03771 MATH_Meprin Meprin fam 100.0 1.6E-29 3.5E-34 209.7 14.2 139 303-443 3-167 (167)
9 cd03781 MATH_TRAF4 Tumor Necro 100.0 2.7E-29 5.8E-34 210.0 14.3 142 302-443 1-154 (154)
10 KOG0297|consensus 100.0 9.9E-29 2.2E-33 235.5 18.0 359 4-407 14-385 (391)
11 cd00270 MATH_TRAF_C Tumor Necr 100.0 3E-28 6.5E-33 204.1 15.5 142 302-443 1-149 (149)
12 KOG2462|consensus 99.9 6.4E-26 1.4E-30 195.6 4.2 131 103-236 129-267 (279)
13 cd03773 MATH_TRIM37 Tripartite 99.9 2.3E-22 5.1E-27 164.8 11.9 125 302-444 5-131 (132)
14 KOG2462|consensus 99.9 4.1E-23 8.9E-28 178.3 4.4 132 73-206 129-265 (279)
15 cd03775 MATH_Ubp21p Ubiquitin- 99.9 8.3E-22 1.8E-26 161.3 11.4 124 303-443 2-134 (134)
16 cd03772 MATH_HAUSP Herpesvirus 99.9 3.3E-21 7.1E-26 158.7 13.3 129 301-446 2-134 (137)
17 cd03774 MATH_SPOP Speckle-type 99.9 2.3E-21 5.1E-26 160.1 12.0 128 302-446 5-138 (139)
18 PF00917 MATH: MATH domain; I 99.8 1.5E-18 3.1E-23 139.9 10.0 119 308-444 1-119 (119)
19 KOG3608|consensus 99.8 4.2E-19 9.1E-24 157.2 6.5 185 78-268 140-345 (467)
20 cd00121 MATH MATH (meprin and 99.8 6.1E-18 1.3E-22 137.6 12.8 126 302-443 1-126 (126)
21 KOG3608|consensus 99.7 8.8E-19 1.9E-23 155.2 5.5 179 80-267 185-375 (467)
22 PLN03086 PRLI-interacting fact 99.7 1.6E-17 3.5E-22 161.6 7.4 143 74-234 407-562 (567)
23 KOG1074|consensus 99.6 2.5E-16 5.4E-21 154.5 3.9 52 212-268 880-931 (958)
24 KOG3576|consensus 99.5 2.5E-15 5.4E-20 123.3 2.2 110 128-238 114-238 (267)
25 PLN03086 PRLI-interacting fact 99.5 1.9E-14 4.2E-19 140.3 7.0 146 103-268 406-564 (567)
26 KOG1074|consensus 99.5 5.4E-15 1.2E-19 145.3 1.7 80 185-266 605-690 (958)
27 smart00061 MATH meprin and TRA 99.5 1.2E-13 2.6E-18 106.2 8.5 94 304-420 2-95 (95)
28 KOG3576|consensus 99.4 2.2E-13 4.7E-18 112.0 4.5 112 152-268 111-236 (267)
29 KOG3623|consensus 99.3 1.9E-12 4.2E-17 125.4 3.2 103 104-206 210-331 (1007)
30 KOG3623|consensus 99.2 4E-12 8.6E-17 123.3 1.8 76 129-204 892-970 (1007)
31 COG5077 Ubiquitin carboxyl-ter 99.1 3E-10 6.6E-15 111.2 7.4 134 295-446 32-172 (1089)
32 PHA00733 hypothetical protein 98.7 1E-08 2.2E-13 81.9 3.5 50 183-234 71-121 (128)
33 PHA00733 hypothetical protein 98.5 7.2E-08 1.6E-12 77.1 4.2 91 171-268 26-123 (128)
34 PF02176 zf-TRAF: TRAF-type zi 98.4 6.9E-08 1.5E-12 66.7 0.9 60 203-263 1-60 (60)
35 PF13465 zf-H2C2_2: Zinc-finge 98.4 1.8E-07 3.9E-12 52.1 1.7 26 172-197 1-26 (26)
36 PHA02768 hypothetical protein; 98.4 1.6E-07 3.6E-12 61.3 1.6 40 104-145 5-45 (55)
37 PHA02768 hypothetical protein; 98.2 5.3E-07 1.1E-11 59.0 1.9 42 212-260 6-47 (55)
38 KOG3993|consensus 98.2 5.4E-07 1.2E-11 83.1 1.9 111 158-273 356-487 (500)
39 PF13465 zf-H2C2_2: Zinc-finge 98.2 9.1E-07 2E-11 49.2 1.5 25 118-142 1-25 (26)
40 PHA00616 hypothetical protein 98.1 1E-06 2.2E-11 54.7 1.6 34 211-245 1-34 (44)
41 KOG3993|consensus 97.9 2.4E-06 5.1E-11 79.0 0.7 154 75-234 268-480 (500)
42 PHA00616 hypothetical protein 97.9 5.5E-06 1.2E-10 51.5 1.1 33 104-136 1-34 (44)
43 PF15227 zf-C3HC4_4: zinc fing 97.7 8.7E-06 1.9E-10 51.1 0.0 36 14-51 1-42 (42)
44 PF05605 zf-Di19: Drought indu 97.7 2.7E-05 5.8E-10 52.2 2.1 46 186-234 3-51 (54)
45 KOG1987|consensus 97.6 0.00057 1.2E-08 64.2 10.6 117 306-447 8-128 (297)
46 PF14835 zf-RING_6: zf-RING of 97.5 3.7E-05 8E-10 51.8 0.7 50 7-57 3-52 (65)
47 PHA00732 hypothetical protein 97.4 9.9E-05 2.1E-09 53.4 2.7 42 104-150 1-44 (79)
48 KOG3002|consensus 97.4 8.2E-05 1.8E-09 68.3 2.8 110 9-124 46-160 (299)
49 PF02176 zf-TRAF: TRAF-type zi 97.4 9E-05 2E-09 51.0 2.3 54 96-149 1-60 (60)
50 KOG0320|consensus 97.2 4.6E-05 1E-09 62.4 -1.0 47 9-57 129-179 (187)
51 PF00096 zf-C2H2: Zinc finger, 97.1 0.00022 4.8E-09 38.3 1.1 22 212-234 1-22 (23)
52 PHA00732 hypothetical protein 97.1 0.00055 1.2E-08 49.5 3.2 45 185-235 1-47 (79)
53 PLN03208 E3 ubiquitin-protein 97.1 0.00025 5.3E-09 60.0 1.5 49 7-57 14-80 (193)
54 PF05605 zf-Di19: Drought indu 97.0 0.00095 2.1E-08 44.6 3.7 19 105-123 3-21 (54)
55 smart00504 Ubox Modified RING 97.0 0.00026 5.7E-09 49.2 0.9 54 12-69 2-59 (63)
56 TIGR00599 rad18 DNA repair pro 96.8 0.00067 1.5E-08 64.7 2.1 61 5-68 20-83 (397)
57 PF00096 zf-C2H2: Zinc finger, 96.7 0.00053 1.2E-08 36.8 0.7 19 133-151 2-21 (23)
58 PF04564 U-box: U-box domain; 96.7 0.0003 6.5E-09 50.4 -0.9 60 8-70 1-64 (73)
59 PF13923 zf-C3HC4_2: Zinc fing 96.5 0.00027 5.8E-09 43.7 -1.6 36 14-51 1-39 (39)
60 PF13912 zf-C2H2_6: C2H2-type 96.5 0.0012 2.6E-08 37.0 1.1 26 211-237 1-26 (27)
61 TIGR00570 cdk7 CDK-activating 96.5 0.0018 4E-08 59.1 2.8 59 11-70 3-72 (309)
62 KOG1863|consensus 96.3 0.0035 7.5E-08 68.8 4.4 124 305-448 30-155 (1093)
63 PF13894 zf-C2H2_4: C2H2-type 96.2 0.0029 6.3E-08 34.1 1.7 23 212-235 1-23 (24)
64 KOG0317|consensus 96.2 0.0011 2.3E-08 59.1 -0.4 48 8-57 236-285 (293)
65 PF13912 zf-C2H2_6: C2H2-type 96.2 0.0025 5.4E-08 35.7 1.1 22 105-126 2-24 (27)
66 PF11789 zf-Nse: Zinc-finger o 96.1 0.0011 2.3E-08 44.7 -0.6 48 2-50 2-53 (57)
67 PF00097 zf-C3HC4: Zinc finger 96.1 0.00077 1.7E-08 42.2 -1.3 37 14-51 1-41 (41)
68 PF12756 zf-C2H2_2: C2H2 type 96.0 0.0038 8.1E-08 47.8 2.0 71 187-267 1-73 (100)
69 KOG0823|consensus 96.0 0.003 6.6E-08 54.5 1.5 48 8-57 44-96 (230)
70 PF14634 zf-RING_5: zinc-RING 95.9 0.002 4.3E-08 41.0 0.0 39 13-53 1-44 (44)
71 cd00162 RING RING-finger (Real 95.9 0.0022 4.8E-08 40.7 0.0 41 13-54 1-44 (45)
72 PF13894 zf-C2H2_4: C2H2-type 95.7 0.0058 1.3E-07 32.8 1.4 19 106-124 2-21 (24)
73 PF09237 GAGA: GAGA factor; I 95.5 0.01 2.3E-07 37.8 1.9 29 103-131 23-52 (54)
74 COG5222 Uncharacterized conser 95.5 0.0067 1.4E-07 53.9 1.4 43 11-54 274-319 (427)
75 COG5189 SFP1 Putative transcri 95.4 0.005 1.1E-07 55.3 0.5 24 183-206 347-373 (423)
76 smart00355 ZnF_C2H2 zinc finge 95.2 0.017 3.6E-07 31.5 2.2 24 212-236 1-24 (26)
77 COG5189 SFP1 Putative transcri 95.2 0.0086 1.9E-07 53.8 1.3 68 129-205 347-419 (423)
78 PF12756 zf-C2H2_2: C2H2 type 95.2 0.011 2.4E-07 45.2 1.7 20 133-152 1-21 (100)
79 PF09237 GAGA: GAGA factor; I 95.1 0.017 3.7E-07 36.9 2.2 31 208-239 21-51 (54)
80 PF13920 zf-C3HC4_3: Zinc fing 95.0 0.0019 4.1E-08 42.4 -2.7 44 11-56 2-48 (50)
81 PHA02929 N1R/p28-like protein; 94.8 0.0093 2E-07 52.9 0.6 48 9-57 172-228 (238)
82 PF03145 Sina: Seven in absent 94.6 0.02 4.3E-07 50.1 2.1 64 64-127 4-71 (198)
83 KOG0978|consensus 94.5 0.0069 1.5E-07 61.4 -1.3 47 9-57 641-690 (698)
84 COG5574 PEX10 RING-finger-cont 94.4 0.01 2.2E-07 52.2 -0.2 44 9-54 213-260 (271)
85 KOG2164|consensus 94.4 0.014 3.1E-07 56.4 0.6 45 11-57 186-237 (513)
86 KOG2879|consensus 94.3 0.025 5.3E-07 50.1 1.9 46 10-56 238-287 (298)
87 smart00355 ZnF_C2H2 zinc finge 94.3 0.035 7.5E-07 30.2 1.9 19 133-151 2-21 (26)
88 PF13913 zf-C2HC_2: zinc-finge 94.2 0.038 8.2E-07 30.2 1.8 21 133-153 4-24 (25)
89 COG5152 Uncharacterized conser 94.2 0.01 2.3E-07 49.5 -0.6 46 10-57 195-242 (259)
90 PF13913 zf-C2HC_2: zinc-finge 94.0 0.015 3.3E-07 31.7 -0.0 18 187-204 4-21 (25)
91 PF10571 UPF0547: Uncharacteri 93.6 0.045 9.8E-07 30.1 1.4 23 13-35 2-24 (26)
92 COG5432 RAD18 RING-finger-cont 93.5 0.018 3.9E-07 51.2 -0.4 47 8-57 22-71 (391)
93 PRK04860 hypothetical protein; 93.5 0.047 1E-06 45.5 2.0 37 130-169 118-154 (160)
94 KOG2231|consensus 93.4 0.17 3.8E-06 51.4 6.1 70 166-235 158-235 (669)
95 PHA02926 zinc finger-like prot 93.2 0.025 5.4E-07 48.6 -0.0 52 6-57 165-231 (242)
96 COG5236 Uncharacterized conser 93.1 0.065 1.4E-06 48.9 2.5 225 8-266 58-303 (493)
97 KOG0311|consensus 93.1 0.0036 7.7E-08 57.3 -5.5 54 8-62 40-98 (381)
98 PF05290 Baculo_IE-1: Baculovi 93.0 0.04 8.6E-07 43.2 0.8 51 3-57 74-133 (140)
99 PF13909 zf-H2C2_5: C2H2-type 92.9 0.064 1.4E-06 28.8 1.4 21 213-235 2-22 (24)
100 KOG2231|consensus 92.9 0.11 2.5E-06 52.7 4.1 78 185-267 150-235 (669)
101 KOG0287|consensus 92.3 0.011 2.5E-07 53.6 -3.3 47 8-57 20-69 (442)
102 PRK04860 hypothetical protein; 92.3 0.083 1.8E-06 44.0 1.9 26 171-196 129-154 (160)
103 PF12874 zf-met: Zinc-finger o 91.9 0.08 1.7E-06 28.7 0.9 21 213-234 2-22 (25)
104 smart00184 RING Ring finger. E 91.8 0.039 8.5E-07 33.4 -0.4 36 14-51 1-39 (39)
105 PF13639 zf-RING_2: Ring finge 91.7 0.0072 1.6E-07 38.4 -3.9 37 13-52 2-44 (44)
106 COG5048 FOG: Zn-finger [Genera 91.0 0.12 2.6E-06 51.2 1.9 58 104-161 289-354 (467)
107 PF12171 zf-C2H2_jaz: Zinc-fin 90.8 0.11 2.4E-06 28.9 0.8 17 217-233 6-22 (27)
108 PF12171 zf-C2H2_jaz: Zinc-fin 90.7 0.11 2.4E-06 28.9 0.7 20 186-205 2-22 (27)
109 PF12874 zf-met: Zinc-finger o 90.3 0.12 2.6E-06 28.0 0.7 19 133-151 2-21 (25)
110 KOG1813|consensus 90.3 0.16 3.4E-06 45.8 1.7 47 9-57 239-287 (313)
111 PF06524 NOA36: NOA36 protein; 89.6 0.14 3.1E-06 44.9 0.9 174 26-235 39-232 (314)
112 TIGR00622 ssl1 transcription f 89.4 0.34 7.4E-06 37.3 2.7 26 26-57 2-27 (112)
113 PF13445 zf-RING_UBOX: RING-ty 89.3 0.054 1.2E-06 34.0 -1.4 34 14-49 1-43 (43)
114 PRK14890 putative Zn-ribbon RN 89.2 0.68 1.5E-05 30.9 3.6 9 74-82 25-33 (59)
115 KOG1146|consensus 88.8 0.21 4.5E-06 54.1 1.6 91 180-280 460-552 (1406)
116 PRK14890 putative Zn-ribbon RN 88.8 0.31 6.7E-06 32.5 1.8 8 74-81 48-55 (59)
117 PF03604 DNA_RNApol_7kD: DNA d 88.8 0.43 9.3E-06 27.7 2.2 24 12-35 1-27 (32)
118 KOG0297|consensus 88.5 0.67 1.4E-05 45.1 4.7 84 136-222 95-178 (391)
119 COG2888 Predicted Zn-ribbon RN 88.5 0.42 9.1E-06 31.8 2.2 8 74-81 27-34 (61)
120 cd00350 rubredoxin_like Rubred 88.3 0.37 8E-06 28.3 1.8 10 44-53 16-25 (33)
121 KOG3002|consensus 88.2 0.23 5.1E-06 45.9 1.4 81 183-267 78-162 (299)
122 PF03145 Sina: Seven in absent 88.0 0.38 8.2E-06 42.0 2.5 49 217-268 23-71 (198)
123 PF09723 Zn-ribbon_8: Zinc rib 88.0 0.32 7E-06 30.4 1.5 28 26-53 6-34 (42)
124 PF12861 zf-Apc11: Anaphase-pr 87.5 0.23 4.9E-06 36.1 0.6 42 14-56 35-82 (85)
125 PF14447 Prok-RING_4: Prokaryo 87.4 0.68 1.5E-05 30.4 2.7 44 12-57 8-51 (55)
126 COG5048 FOG: Zn-finger [Genera 86.8 0.24 5.3E-06 49.0 0.7 135 130-266 288-440 (467)
127 KOG2186|consensus 86.8 0.32 6.8E-06 42.8 1.2 43 133-176 5-47 (276)
128 KOG2186|consensus 86.6 0.31 6.6E-06 42.8 1.1 47 159-206 4-50 (276)
129 cd00729 rubredoxin_SM Rubredox 86.5 0.57 1.2E-05 27.7 1.9 9 12-20 3-11 (34)
130 smart00834 CxxC_CXXC_SSSS Puta 85.7 0.54 1.2E-05 29.0 1.6 29 26-54 6-35 (41)
131 KOG2177|consensus 85.5 0.19 4E-06 47.8 -0.9 46 6-53 8-55 (386)
132 COG2888 Predicted Zn-ribbon RN 85.1 0.42 9.1E-06 31.7 0.9 8 74-81 50-57 (61)
133 PF09538 FYDLN_acid: Protein o 84.9 0.63 1.4E-05 35.9 1.9 28 8-35 6-36 (108)
134 PF13909 zf-H2C2_5: C2H2-type 84.6 0.85 1.8E-05 24.3 1.9 22 241-267 1-22 (24)
135 PF07975 C1_4: TFIIH C1-like d 84.5 0.38 8.2E-06 31.3 0.5 28 25-52 21-50 (51)
136 PRK00398 rpoP DNA-directed RNA 83.5 0.56 1.2E-05 29.9 1.0 30 25-56 3-32 (46)
137 KOG2660|consensus 82.9 0.13 2.9E-06 47.0 -2.9 51 5-56 9-61 (331)
138 KOG4739|consensus 82.5 0.94 2E-05 39.9 2.2 51 12-62 4-55 (233)
139 smart00154 ZnF_AN1 AN1-like Zi 82.1 0.97 2.1E-05 27.7 1.6 25 14-39 1-26 (39)
140 PF07754 DUF1610: Domain of un 82.0 1.7 3.6E-05 23.4 2.2 8 74-81 16-23 (24)
141 KOG4159|consensus 81.9 0.42 9.1E-06 46.0 -0.1 48 8-57 81-130 (398)
142 PHA00626 hypothetical protein 81.1 1.1 2.3E-05 29.4 1.5 12 24-35 22-33 (59)
143 TIGR02605 CxxC_CxxC_SSSS putat 80.7 1.1 2.4E-05 29.4 1.6 28 26-53 6-34 (52)
144 KOG0824|consensus 80.5 1 2.3E-05 40.8 1.9 45 11-57 7-54 (324)
145 PF09538 FYDLN_acid: Protein o 80.4 1.4 2.9E-05 34.1 2.2 29 26-57 10-38 (108)
146 COG1198 PriA Primosomal protei 79.9 1.8 3.9E-05 45.4 3.6 49 26-113 436-484 (730)
147 smart00659 RPOLCX RNA polymera 79.9 1.4 3.1E-05 27.7 1.8 11 44-54 18-28 (44)
148 KOG1146|consensus 79.7 0.58 1.3E-05 50.9 0.0 98 104-206 436-540 (1406)
149 smart00451 ZnF_U1 U1-like zinc 79.3 1.5 3.3E-05 25.8 1.8 21 212-233 4-24 (35)
150 PF12678 zf-rbx1: RING-H2 zinc 79.2 0.37 8E-06 34.4 -1.1 37 14-52 22-73 (73)
151 PF14446 Prok-RING_1: Prokaryo 78.3 0.75 1.6E-05 30.2 0.2 31 11-41 5-37 (54)
152 PRK00464 nrdR transcriptional 76.0 1.2 2.7E-05 36.8 0.9 69 186-266 1-72 (154)
153 TIGR02300 FYDLN_acid conserved 75.4 2 4.3E-05 33.7 1.9 28 8-35 6-36 (129)
154 PRK14714 DNA polymerase II lar 75.3 3.7 8E-05 45.1 4.4 37 11-56 667-703 (1337)
155 PF12773 DZR: Double zinc ribb 75.3 4.7 0.0001 26.1 3.4 38 14-54 1-38 (50)
156 PF13240 zinc_ribbon_2: zinc-r 74.1 2 4.3E-05 22.8 1.1 20 14-33 2-21 (23)
157 PRK04023 DNA polymerase II lar 74.0 3.6 7.8E-05 43.9 3.8 46 10-57 625-675 (1121)
158 PF13719 zinc_ribbon_5: zinc-r 73.3 1.5 3.2E-05 26.5 0.6 10 74-83 25-34 (37)
159 COG1592 Rubrerythrin [Energy p 72.9 2.6 5.7E-05 35.2 2.1 24 26-54 135-158 (166)
160 PF01428 zf-AN1: AN1-like Zinc 71.7 2 4.3E-05 26.9 0.9 21 17-38 6-26 (43)
161 COG1996 RPC10 DNA-directed RNA 71.6 2.4 5.2E-05 27.3 1.2 10 11-20 6-15 (49)
162 KOG4628|consensus 71.6 2.5 5.4E-05 39.8 1.9 44 12-57 230-279 (348)
163 PRK00464 nrdR transcriptional 71.5 2.9 6.3E-05 34.6 2.1 9 47-55 2-10 (154)
164 COG5151 SSL1 RNA polymerase II 70.4 3.3 7.1E-05 37.7 2.3 24 10-33 307-330 (421)
165 TIGR00622 ssl1 transcription f 69.7 5.8 0.00013 30.7 3.2 15 43-57 79-93 (112)
166 PF09986 DUF2225: Uncharacteri 69.6 2.6 5.6E-05 37.3 1.5 42 183-225 3-61 (214)
167 PF14205 Cys_rich_KTR: Cystein 69.2 2.8 6E-05 27.4 1.2 31 47-82 6-36 (55)
168 KOG2932|consensus 68.6 4.9 0.00011 36.7 2.9 42 12-54 91-132 (389)
169 PF14353 CpXC: CpXC protein 68.5 4.4 9.6E-05 32.5 2.5 9 47-55 3-11 (128)
170 TIGR02098 MJ0042_CXXC MJ0042 f 68.3 1.5 3.3E-05 26.5 -0.2 8 75-82 26-33 (38)
171 KOG1002|consensus 67.7 1.5 3.3E-05 42.8 -0.3 51 5-57 530-587 (791)
172 TIGR00595 priA primosomal prot 67.5 4.9 0.00011 40.7 3.1 34 27-82 215-248 (505)
173 PF13717 zinc_ribbon_4: zinc-r 67.0 3 6.4E-05 25.0 0.9 10 74-83 25-34 (36)
174 TIGR02300 FYDLN_acid conserved 67.0 4.6 0.0001 31.8 2.2 27 26-55 10-36 (129)
175 PF14445 Prok-RING_2: Prokaryo 66.9 0.32 7E-06 30.9 -3.3 44 10-54 6-50 (57)
176 KOG1734|consensus 66.9 1.1 2.3E-05 39.9 -1.4 47 10-57 223-282 (328)
177 COG4049 Uncharacterized protei 66.8 2.7 5.8E-05 27.5 0.7 24 208-232 14-37 (65)
178 COG3357 Predicted transcriptio 65.6 4.4 9.5E-05 29.6 1.7 31 22-54 55-85 (97)
179 COG1198 PriA Primosomal protei 64.8 6.9 0.00015 41.2 3.6 20 11-35 435-454 (730)
180 smart00734 ZnF_Rad18 Rad18-lik 64.7 5.4 0.00012 21.9 1.6 20 133-152 3-22 (26)
181 KOG3507|consensus 63.9 3.5 7.5E-05 27.3 0.8 26 10-35 19-47 (62)
182 KOG4173|consensus 63.2 2.3 5E-05 36.2 -0.1 24 239-264 143-166 (253)
183 KOG3800|consensus 62.2 3.3 7.1E-05 37.5 0.7 54 13-68 2-67 (300)
184 COG1997 RPL43A Ribosomal prote 61.3 4.8 0.00011 29.3 1.3 27 9-35 33-63 (89)
185 KOG2482|consensus 61.2 8.2 0.00018 35.8 3.0 22 185-206 195-217 (423)
186 KOG4367|consensus 61.0 2 4.4E-05 40.8 -0.8 29 9-39 2-30 (699)
187 PF13248 zf-ribbon_3: zinc-rib 60.7 5.1 0.00011 21.9 1.1 7 14-20 5-11 (26)
188 COG5243 HRD1 HRD ubiquitin lig 60.3 2.3 4.9E-05 39.7 -0.7 46 10-56 286-345 (491)
189 PF04438 zf-HIT: HIT zinc fing 60.2 5.5 0.00012 22.8 1.1 23 12-37 3-25 (30)
190 COG4049 Uncharacterized protei 60.0 7.8 0.00017 25.4 1.9 31 234-268 11-41 (65)
191 PF05191 ADK_lid: Adenylate ki 59.3 3.9 8.5E-05 24.5 0.5 29 27-55 3-31 (36)
192 PRK14714 DNA polymerase II lar 59.0 9.4 0.0002 42.1 3.5 42 12-57 680-721 (1337)
193 PF09845 DUF2072: Zn-ribbon co 58.3 5.3 0.00011 31.7 1.1 28 25-54 1-28 (131)
194 COG1773 Rubredoxin [Energy pro 58.3 14 0.00031 24.4 3.0 12 11-23 3-14 (55)
195 PRK00420 hypothetical protein; 58.3 8.4 0.00018 29.9 2.2 11 46-56 24-34 (112)
196 TIGR00373 conserved hypothetic 58.0 8.5 0.00018 32.1 2.4 32 103-143 108-140 (158)
197 smart00531 TFIIE Transcription 57.7 10 0.00023 31.2 2.9 17 181-197 95-111 (147)
198 KOG3183|consensus 56.9 6.1 0.00013 34.7 1.4 44 13-57 10-67 (250)
199 PF08209 Sgf11: Sgf11 (transcr 56.3 5.9 0.00013 23.2 0.8 23 132-154 5-27 (33)
200 smart00531 TFIIE Transcription 56.2 8.1 0.00018 31.8 2.0 37 103-143 98-135 (147)
201 COG1645 Uncharacterized Zn-fin 54.8 5.8 0.00012 31.6 0.9 24 12-35 29-54 (131)
202 PRK14873 primosome assembly pr 54.5 10 0.00022 39.8 2.8 19 27-56 385-403 (665)
203 TIGR01206 lysW lysine biosynth 54.4 7.3 0.00016 25.8 1.1 7 47-53 4-10 (54)
204 COG3364 Zn-ribbon containing p 54.2 4.1 8.8E-05 30.5 -0.1 28 25-54 2-29 (112)
205 smart00249 PHD PHD zinc finger 54.2 10 0.00022 23.5 1.9 27 14-40 2-29 (47)
206 PF15135 UPF0515: Uncharacteri 54.0 14 0.0003 32.8 3.1 73 25-114 112-184 (278)
207 PRK06266 transcription initiat 53.6 11 0.00024 32.2 2.4 32 103-143 116-148 (178)
208 PF07191 zinc-ribbons_6: zinc- 53.4 2.4 5.1E-05 29.6 -1.3 38 12-57 2-42 (70)
209 KOG2272|consensus 53.1 4.7 0.0001 35.5 0.1 62 132-197 164-233 (332)
210 COG5151 SSL1 RNA polymerase II 52.7 21 0.00044 32.8 4.0 50 185-235 362-411 (421)
211 PF14569 zf-UDP: Zinc-binding 52.7 2.5 5.4E-05 29.9 -1.3 46 12-57 10-63 (80)
212 PF01363 FYVE: FYVE zinc finge 52.6 7.5 0.00016 27.1 1.1 30 11-40 9-40 (69)
213 PF04641 Rtf2: Rtf2 RING-finge 52.3 7.7 0.00017 35.5 1.4 49 8-57 110-162 (260)
214 PRK05580 primosome assembly pr 52.1 13 0.00028 39.3 3.2 10 47-56 392-401 (679)
215 KOG2807|consensus 51.7 14 0.00031 34.1 2.9 29 22-56 273-301 (378)
216 PLN02638 cellulose synthase A 50.9 9.4 0.0002 41.5 1.9 45 13-57 19-71 (1079)
217 PRK03824 hypA hydrogenase nick 50.6 9.7 0.00021 30.8 1.6 11 44-54 106-116 (135)
218 PF09986 DUF2225: Uncharacteri 50.4 9.1 0.0002 33.8 1.5 12 46-57 49-60 (214)
219 COG5175 MOT2 Transcriptional r 50.4 4.2 9.1E-05 37.5 -0.6 50 4-56 8-64 (480)
220 PF06524 NOA36: NOA36 protein; 49.8 8.4 0.00018 34.3 1.1 17 4-20 56-72 (314)
221 TIGR00373 conserved hypothetic 49.7 14 0.00031 30.8 2.5 17 181-197 105-121 (158)
222 COG4640 Predicted membrane pro 49.4 8.7 0.00019 36.4 1.2 22 13-35 3-25 (465)
223 PF13878 zf-C2H2_3: zinc-finge 49.4 16 0.00034 22.6 2.0 22 104-125 13-37 (41)
224 COG5216 Uncharacterized conser 48.4 5.7 0.00012 26.3 -0.1 27 25-52 22-51 (67)
225 COG4647 AcxC Acetone carboxyla 47.6 4.3 9.4E-05 31.7 -0.8 20 16-37 62-81 (165)
226 PRK04023 DNA polymerase II lar 47.5 25 0.00054 38.0 4.3 12 304-315 845-856 (1121)
227 PLN02436 cellulose synthase A 46.7 14 0.00029 40.3 2.3 45 13-57 38-90 (1094)
228 KOG3039|consensus 46.4 9.2 0.0002 33.7 0.8 47 10-57 220-271 (303)
229 PF10083 DUF2321: Uncharacteri 46.2 11 0.00023 30.9 1.2 45 46-90 40-84 (158)
230 PRK06266 transcription initiat 45.9 17 0.00037 31.0 2.4 15 280-294 156-170 (178)
231 PF00628 PHD: PHD-finger; Int 45.5 6.3 0.00014 25.5 -0.2 28 13-40 1-29 (51)
232 PF05325 DUF730: Protein of un 45.4 81 0.0018 23.3 5.4 43 258-300 73-115 (122)
233 KOG2893|consensus 45.0 9.5 0.00021 33.4 0.7 20 184-203 33-53 (341)
234 PLN02400 cellulose synthase 44.5 17 0.00036 39.8 2.6 45 13-57 38-90 (1085)
235 PF01780 Ribosomal_L37ae: Ribo 44.5 9.1 0.0002 28.3 0.5 27 9-36 33-64 (90)
236 PLN02189 cellulose synthase 44.3 15 0.00033 39.9 2.2 45 13-57 36-88 (1040)
237 PF13453 zf-TFIIB: Transcripti 44.0 16 0.00035 22.5 1.5 38 47-93 1-38 (41)
238 PF00301 Rubredoxin: Rubredoxi 43.9 13 0.00027 23.9 1.0 15 6-20 29-43 (47)
239 KOG0804|consensus 43.5 9.5 0.00021 36.9 0.5 42 13-55 177-221 (493)
240 PF14570 zf-RING_4: RING/Ubox 42.6 8.2 0.00018 24.8 -0.0 40 14-55 1-47 (48)
241 KOG2807|consensus 42.6 13 0.00029 34.3 1.3 26 10-35 275-300 (378)
242 KOG1493|consensus 42.5 2.4 5.1E-05 29.8 -2.6 32 25-56 45-81 (84)
243 PLN02195 cellulose synthase A 41.9 18 0.00039 39.1 2.3 45 13-57 8-60 (977)
244 COG4530 Uncharacterized protei 41.7 20 0.00042 27.3 1.8 33 213-262 11-43 (129)
245 PF14803 Nudix_N_2: Nudix N-te 41.7 9.1 0.0002 22.6 0.1 10 48-57 3-12 (34)
246 KOG4173|consensus 41.2 13 0.00027 31.9 0.9 18 134-151 109-127 (253)
247 PF15616 TerY-C: TerY-C metal 41.2 17 0.00037 29.1 1.6 38 13-56 79-116 (131)
248 PF04216 FdhE: Protein involve 41.0 11 0.00023 35.2 0.5 10 11-20 172-181 (290)
249 PF12013 DUF3505: Protein of u 40.8 37 0.0008 26.2 3.5 21 74-94 11-31 (109)
250 COG0068 HypF Hydrogenase matur 40.2 8.1 0.00018 39.8 -0.4 70 8-85 98-184 (750)
251 COG5220 TFB3 Cdk activating ki 40.2 1.9 4.1E-05 37.6 -4.1 56 12-68 11-80 (314)
252 PF02891 zf-MIZ: MIZ/SP-RING z 39.6 5.7 0.00012 25.8 -1.1 41 12-53 3-49 (50)
253 PF04606 Ogr_Delta: Ogr/Delta- 39.6 9.1 0.0002 24.5 -0.1 30 47-79 1-30 (47)
254 PRK14873 primosome assembly pr 39.5 30 0.00064 36.4 3.5 37 10-53 382-418 (665)
255 KOG4275|consensus 39.3 6.5 0.00014 35.6 -1.1 42 10-55 299-341 (350)
256 smart00661 RPOL9 RNA polymeras 38.9 20 0.00044 23.2 1.5 8 75-82 21-28 (52)
257 PF08271 TF_Zn_Ribbon: TFIIB z 38.9 13 0.00028 23.2 0.5 10 45-54 19-28 (43)
258 PRK14559 putative protein seri 38.2 33 0.00071 35.9 3.5 23 13-35 3-25 (645)
259 TIGR00280 L37a ribosomal prote 38.0 17 0.00036 27.0 1.0 28 9-36 33-64 (91)
260 PF02892 zf-BED: BED zinc fing 37.9 16 0.00036 22.8 0.9 8 226-233 34-41 (45)
261 PF01485 IBR: IBR domain; Int 37.9 28 0.00061 23.4 2.2 36 4-40 11-55 (64)
262 PLN02915 cellulose synthase A 37.4 22 0.00047 38.8 2.1 47 11-57 15-69 (1044)
263 PRK12380 hydrogenase nickel in 36.9 22 0.00047 27.8 1.6 25 26-54 71-95 (113)
264 PF14311 DUF4379: Domain of un 36.8 22 0.00047 23.5 1.4 26 26-51 29-55 (55)
265 PRK12496 hypothetical protein; 36.5 25 0.00053 29.6 1.9 28 26-57 128-155 (164)
266 PF01096 TFIIS_C: Transcriptio 36.5 2.9 6.3E-05 25.6 -2.7 8 132-139 29-36 (39)
267 smart00440 ZnF_C2C2 C2C2 Zinc 36.5 8.6 0.00019 23.6 -0.6 10 132-141 29-38 (40)
268 smart00064 FYVE Protein presen 36.0 25 0.00053 24.4 1.6 30 11-40 10-41 (68)
269 cd00730 rubredoxin Rubredoxin; 36.0 17 0.00037 23.7 0.7 14 7-20 30-43 (50)
270 PF07649 C1_3: C1-like domain; 36.0 17 0.00037 20.5 0.6 22 13-35 2-25 (30)
271 PTZ00255 60S ribosomal protein 35.7 20 0.00043 26.5 1.1 27 9-36 34-65 (90)
272 PF07295 DUF1451: Protein of u 35.5 25 0.00054 28.9 1.7 39 178-225 101-143 (146)
273 PF05502 Dynactin_p62: Dynacti 35.4 31 0.00067 34.7 2.8 23 427-449 444-469 (483)
274 COG4306 Uncharacterized protei 35.3 23 0.0005 27.6 1.4 45 45-90 39-84 (160)
275 PRK14559 putative protein seri 35.2 39 0.00083 35.3 3.5 38 11-56 15-52 (645)
276 PF08746 zf-RING-like: RING-li 35.1 11 0.00025 23.5 -0.2 37 14-51 1-43 (43)
277 KOG4317|consensus 35.0 28 0.0006 32.1 2.1 30 9-40 5-35 (383)
278 KOG1701|consensus 34.9 19 0.00041 34.7 1.1 11 105-115 428-438 (468)
279 PHA01750 hypothetical protein 34.7 1.5E+02 0.0033 20.3 5.7 27 270-296 42-68 (75)
280 PF08946 Osmo_CC: Osmosensory 34.3 76 0.0016 20.0 3.2 29 268-296 10-38 (46)
281 COG1327 Predicted transcriptio 34.3 20 0.00044 29.2 1.0 45 210-265 27-71 (156)
282 PRK09678 DNA-binding transcrip 34.3 16 0.00036 25.8 0.5 9 106-114 3-11 (72)
283 cd00065 FYVE FYVE domain; Zinc 34.2 24 0.00052 23.3 1.3 28 13-40 4-33 (57)
284 PF11023 DUF2614: Protein of u 33.8 21 0.00047 27.4 1.0 29 25-57 69-97 (114)
285 PF06825 HSBP1: Heat shock fac 33.8 1.2E+02 0.0025 20.2 4.3 21 276-296 27-47 (54)
286 KOG1812|consensus 33.7 30 0.00064 33.7 2.3 46 11-57 146-204 (384)
287 PRK03681 hypA hydrogenase nick 33.7 26 0.00057 27.4 1.6 26 26-54 71-96 (114)
288 KOG1940|consensus 33.3 14 0.00031 33.7 0.0 10 105-114 235-244 (276)
289 PF14369 zf-RING_3: zinc-finge 33.3 27 0.00059 20.7 1.2 10 76-85 23-32 (35)
290 smart00647 IBR In Between Ring 33.2 41 0.00088 22.7 2.4 36 5-40 12-55 (64)
291 PRK03976 rpl37ae 50S ribosomal 33.2 22 0.00048 26.3 1.0 28 9-36 34-65 (90)
292 TIGR00595 priA primosomal prot 32.6 44 0.00095 34.0 3.4 37 10-53 212-248 (505)
293 PF05502 Dynactin_p62: Dynacti 32.5 35 0.00075 34.4 2.6 11 133-143 88-98 (483)
294 COG4888 Uncharacterized Zn rib 32.5 28 0.00062 26.1 1.4 12 8-19 19-30 (104)
295 KOG0802|consensus 32.1 6.9 0.00015 40.1 -2.4 42 11-54 291-339 (543)
296 PF13824 zf-Mss51: Zinc-finger 31.2 34 0.00074 22.7 1.5 12 43-54 12-23 (55)
297 KOG1785|consensus 31.0 15 0.00032 34.9 -0.3 46 10-57 367-417 (563)
298 smart00614 ZnF_BED BED zinc fi 30.8 36 0.00079 21.9 1.7 10 225-234 36-45 (50)
299 KOG0717|consensus 30.8 74 0.0016 31.2 4.3 39 241-285 293-331 (508)
300 TIGR00244 transcriptional regu 30.6 26 0.00057 28.6 1.1 45 210-265 27-71 (147)
301 COG2331 Uncharacterized protei 29.9 8.7 0.00019 27.1 -1.4 31 26-56 13-44 (82)
302 PF11793 FANCL_C: FANCL C-term 29.9 14 0.00031 26.0 -0.5 28 12-40 3-37 (70)
303 PF05443 ROS_MUCR: ROS/MUCR tr 29.8 21 0.00046 28.7 0.5 25 211-239 72-96 (132)
304 PF12760 Zn_Tnp_IS1595: Transp 29.5 33 0.00071 21.7 1.2 8 46-53 19-26 (46)
305 PF03107 C1_2: C1 domain; Int 29.4 47 0.001 18.8 1.7 21 12-32 1-22 (30)
306 COG5236 Uncharacterized conser 28.8 43 0.00093 31.3 2.3 72 184-266 190-273 (493)
307 PF13451 zf-trcl: Probable zin 27.6 25 0.00054 22.7 0.4 14 184-197 3-16 (49)
308 PF07800 DUF1644: Protein of u 27.5 39 0.00085 27.9 1.6 10 11-20 2-11 (162)
309 KOG2593|consensus 27.4 1.4E+02 0.003 29.2 5.4 33 209-245 126-158 (436)
310 PRK14892 putative transcriptio 27.2 48 0.001 25.2 1.9 10 46-55 43-52 (99)
311 PHA01750 hypothetical protein 27.1 2.1E+02 0.0046 19.6 5.3 22 273-294 52-73 (75)
312 PF09340 NuA4: Histone acetylt 27.0 1E+02 0.0022 22.3 3.5 29 271-299 3-31 (80)
313 KOG2272|consensus 26.2 53 0.0011 29.3 2.2 11 10-20 136-146 (332)
314 PF08274 PhnA_Zn_Ribbon: PhnA 26.1 35 0.00075 19.5 0.8 21 13-33 4-27 (30)
315 TIGR00100 hypA hydrogenase nic 25.7 47 0.001 26.0 1.8 25 26-54 71-95 (115)
316 PF04102 SlyX: SlyX; InterPro 25.6 2.1E+02 0.0045 20.0 4.8 28 270-297 18-45 (69)
317 PRK00564 hypA hydrogenase nick 25.6 49 0.0011 26.0 1.8 25 26-54 72-97 (117)
318 PRK05978 hypothetical protein; 25.5 38 0.00083 27.8 1.2 14 72-85 31-44 (148)
319 PF00130 C1_1: Phorbol esters/ 25.4 43 0.00093 21.7 1.3 32 8-40 8-43 (53)
320 KOG2114|consensus 25.4 30 0.00065 36.5 0.7 41 12-54 841-881 (933)
321 KOG2907|consensus 25.2 33 0.00071 26.4 0.7 39 104-142 74-113 (116)
322 PRK00295 hypothetical protein; 24.7 2.1E+02 0.0045 19.9 4.7 27 270-296 19-45 (68)
323 PRK01343 zinc-binding protein; 23.9 59 0.0013 21.8 1.7 17 10-27 8-24 (57)
324 PF07282 OrfB_Zn_ribbon: Putat 23.8 41 0.00089 23.3 1.0 13 42-54 43-55 (69)
325 COG4957 Predicted transcriptio 23.8 48 0.001 26.4 1.4 25 212-240 77-101 (148)
326 PF05495 zf-CHY: CHY zinc fing 23.8 24 0.00052 24.9 -0.2 25 173-197 29-53 (71)
327 PRK00736 hypothetical protein; 23.7 2.3E+02 0.0049 19.8 4.7 27 270-296 19-45 (68)
328 KOG4602|consensus 23.2 40 0.00088 30.0 1.0 8 26-33 269-276 (318)
329 PF07716 bZIP_2: Basic region 23.2 2.2E+02 0.0049 18.5 4.5 30 268-297 23-52 (54)
330 PF08790 zf-LYAR: LYAR-type C2 22.9 58 0.0013 18.3 1.2 19 187-205 2-20 (28)
331 KOG2923|consensus 22.8 37 0.00079 23.1 0.5 27 26-53 23-52 (67)
332 PF11672 DUF3268: Protein of u 22.8 52 0.0011 25.1 1.4 36 184-220 1-39 (102)
333 PF04959 ARS2: Arsenite-resist 22.7 1.2E+02 0.0026 26.7 3.9 32 239-274 76-107 (214)
334 PF09551 Spore_II_R: Stage II 22.7 2.9E+02 0.0062 22.2 5.6 16 258-273 19-34 (130)
335 PF05741 zf-nanos: Nanos RNA b 22.7 34 0.00073 22.8 0.3 16 10-26 32-47 (55)
336 PF04899 MbeD_MobD: MbeD/MobD 22.4 2.9E+02 0.0062 19.5 5.0 23 274-296 46-68 (70)
337 PF04508 Pox_A_type_inc: Viral 22.4 1.4E+02 0.0031 15.9 2.6 16 280-295 4-19 (23)
338 PF12013 DUF3505: Protein of u 22.1 62 0.0013 24.9 1.8 24 212-236 81-108 (109)
339 KOG2482|consensus 22.0 67 0.0014 30.1 2.2 19 186-204 145-165 (423)
340 KOG4718|consensus 22.0 21 0.00045 30.9 -0.9 43 11-55 181-226 (235)
341 PF07800 DUF1644: Protein of u 21.9 98 0.0021 25.7 2.9 56 104-159 80-138 (162)
342 PRK02793 phi X174 lysis protei 21.9 2.5E+02 0.0054 19.8 4.7 27 270-296 22-48 (72)
343 PF09963 DUF2197: Uncharacteri 21.9 42 0.00092 22.4 0.7 9 106-114 4-12 (56)
344 PRK04406 hypothetical protein; 21.7 2.5E+02 0.0055 20.0 4.7 27 270-296 25-51 (75)
345 PF10393 Matrilin_ccoil: Trime 21.5 2.3E+02 0.0051 18.1 4.7 19 279-297 25-43 (47)
346 cd00924 Cyt_c_Oxidase_Vb Cytoc 21.5 43 0.00092 25.3 0.7 14 24-37 78-91 (97)
347 PRK05580 primosome assembly pr 21.5 87 0.0019 33.2 3.3 36 11-53 381-416 (679)
348 COG3416 Uncharacterized protei 21.3 1.9E+02 0.0041 25.1 4.6 37 269-305 47-85 (233)
349 PRK04325 hypothetical protein; 21.3 2.6E+02 0.0056 19.9 4.7 27 270-296 23-49 (74)
350 PF13696 zf-CCHC_2: Zinc knuck 21.0 66 0.0014 18.7 1.2 15 6-20 3-17 (32)
351 PF02318 FYVE_2: FYVE-type zin 20.9 23 0.0005 27.9 -0.9 43 10-52 53-101 (118)
352 PRK00762 hypA hydrogenase nick 20.8 63 0.0014 25.7 1.6 28 26-54 71-101 (124)
353 PF06676 DUF1178: Protein of u 20.7 56 0.0012 26.9 1.3 28 26-54 6-41 (148)
354 PRK04351 hypothetical protein; 20.7 45 0.00099 27.5 0.8 10 26-35 113-122 (149)
355 PF10276 zf-CHCC: Zinc-finger 20.6 46 0.00099 20.5 0.6 12 184-195 28-39 (40)
356 PF01155 HypA: Hydrogenase exp 20.5 46 0.00099 26.0 0.8 9 46-54 87-95 (113)
357 PRK02119 hypothetical protein; 20.4 2.8E+02 0.0061 19.6 4.7 27 270-296 23-49 (73)
358 PF04810 zf-Sec23_Sec24: Sec23 20.3 40 0.00086 20.6 0.3 9 45-53 24-32 (40)
359 KOG2893|consensus 20.2 40 0.00087 29.6 0.4 31 188-222 13-44 (341)
No 1
>cd03778 MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF2 associates with the receptors TNFR-1, TNFR-2, RANK (which mediates differentiation and maturation of osteoclasts) and CD40 (which is important for the proliferation and activation of B cells), among others. It regulates distinct pathways that lead to the activation of nuclear factor-kappaB and Jun NH2-terminal kinases. TRAF2 also indirectly associates with death receptors through its interaction with TRADD (TNFR-associated death domain protein). It is involved in regulating oxidative stress or ROS-induced cell death and in the preconditioning of cells by sublethal stress for protection from subsequent injury. TRAF2 contains a RING finger domain, five z
Probab=100.00 E-value=3.1e-37 Score=253.19 Aligned_cols=156 Identities=39% Similarity=0.802 Sum_probs=141.5
Q ss_pred HHHHHHHHhhhh-ccCCceEEEEECCchhhhhcc-----ccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEec
Q psy225 286 ISTLKSALNKVT-LNYSGTLIWKITDYSLKCQES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLL 359 (450)
Q Consensus 286 i~~l~~~~~~l~-~~~~~~~~w~i~~~s~~~~~~-----~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~ 359 (450)
|.+|++++.+|+ ..++|.++|+|.||++++.++ ..++||+||++.+||+|+|++||||++.+.++|+||||+++
T Consensus 2 ~~~~~~~~~~l~~~~~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~~l~~ylnG~g~~~g~~LSly~~l~ 81 (164)
T cd03778 2 XADLEQKVLEXEASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVM 81 (164)
T ss_pred hhHHHHHhhhccccccCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEEEEEEEeCCCCCCCCCEEEEEEEEe
Confidence 567888888888 456999999999999988765 47999999999999999999999999999999999999999
Q ss_pred CCCCCcccCCcccceEEEEEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeecccccc-CCceeCCcEEE
Q psy225 360 PGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRK-RQFLKDDAIFI 438 (450)
Q Consensus 360 ~g~~d~~l~Wp~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~-~~fl~dd~l~i 438 (450)
+|++|..|+|||..+++|+|+||. .+.++..++.++++..+|+||.. ..+.+|||+.|+++++|.. +|||+||+|.|
T Consensus 82 ~Ge~D~~L~WPf~~~itl~llDQ~-~r~hi~~~~~pd~~~~~f~RP~~-~~n~~~G~~~Fv~l~~l~~~~~Yv~dDtlfI 159 (164)
T cd03778 82 KGPNDALLRWPFNQKVTLMLLDQN-NREHVIDAFRPDVTSSSFQRPVN-DMNIASGCPLFCPVSKXEAKNSYVRDDAIFI 159 (164)
T ss_pred cCCcCcccCCceeeEEEEEEECCC-CCCcceeEEEcCcchHhcCCCCc-ccccCcCcceEEEhhHccccCCcccCCeEEE
Confidence 999999999999999999999997 46678899999998889999974 4577899999999999975 79999999999
Q ss_pred EEEEe
Q psy225 439 RVKVD 443 (450)
Q Consensus 439 ~~~v~ 443 (450)
+|.|.
T Consensus 160 k~~Vd 164 (164)
T cd03778 160 KAIVD 164 (164)
T ss_pred EEEEC
Confidence 99884
No 2
>cd03777 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal al
Probab=100.00 E-value=1.2e-36 Score=258.49 Aligned_cols=177 Identities=36% Similarity=0.716 Sum_probs=159.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-ccCCceEEEEECCchhhhhcc---c--cccCCCcccCCCCcEEEEEEE
Q psy225 267 NVNQHMLLMCSLVSKQQQQISTLKSALNKVT-LNYSGTLIWKITDYSLKCQES---I--ELLSPSFYTSQFGYKLQVSLF 340 (450)
Q Consensus 267 ~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~-~~~~~~~~w~i~~~s~~~~~~---~--~~~S~~f~~~~~g~~w~l~~~ 340 (450)
.+..|+.++.+.+..+...|.++++++..|+ ..++|.++|+|.+|+..+..+ . .++||+||+|.+||+|+|++|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w~i~~y 82 (186)
T cd03777 3 LLESQLSRHDQMLSVHDIRLADMDLRFQVLETASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVY 82 (186)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeEEEEEE
Confidence 3557788888888999999999999999999 556999999999999887544 2 799999999999999999999
Q ss_pred ecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCcccee
Q psy225 341 LNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFV 420 (450)
Q Consensus 341 p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~ 420 (450)
|||++.+.++||||||+|++|++|+.|+|||.++++|+|+||.+.+.++..++.+++....|.||.. ..+.+||++.||
T Consensus 83 pnG~g~~~~~~iSvyl~L~~ge~D~~L~WP~~~~~tfsLlDQ~~~~~~~~~~~~p~p~~~~F~rp~~-~~n~~~G~~~Fi 161 (186)
T cd03777 83 LNGDGMGKGTHLSLFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTG-EMNIASGCPVFV 161 (186)
T ss_pred cCCCCCCCCCEEEEEEEEecCCcccccCCceeEEEEEEEEcCCCccccccceeccCCccccccCCcc-CCCCCCCchhee
Confidence 9999888899999999999999999999999999999999998777778888888877778998863 346789999999
Q ss_pred eccccccCCceeCCcEEEEEEEec
Q psy225 421 SLDTIRKRQFLKDDAIFIRVKVDP 444 (450)
Q Consensus 421 ~~~~l~~~~fl~dd~l~i~~~v~v 444 (450)
++++|+.++||+||+|+|+|.|..
T Consensus 162 ~~~~Le~~~ylkdD~l~Irv~v~~ 185 (186)
T cd03777 162 AQTVLENGTYIKDDTIFIKVIVDT 185 (186)
T ss_pred EHHHhccCCcEeCCEEEEEEEEec
Confidence 999999989999999999999975
No 3
>cd03779 MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF1 expression is the most restricted among the TRAFs. It is found exclusively in activated lymphocytes, dendritic cells and certain epithelia. TRAF1 associates, directly or indirectly through heterodimerization with TRAF2, with the TNFR family receptors TNFR-2, CD30, RANK, CD40 and LMP1, among others. It also binds the intracellular proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1 is unique among the TRAFs in that it lacks a RING domain, which is critical for the activation of nuclear factor-kappaB and Jun NH2-terminal kinase. Studies on TRAF1-deficient mice suggest that TRAF1 has a negative regulatory role in TNFR-mediat
Probab=100.00 E-value=1e-32 Score=224.80 Aligned_cols=140 Identities=47% Similarity=0.926 Sum_probs=121.2
Q ss_pred ceEEEEECCchhhhhcc-----ccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEE
Q psy225 302 GTLIWKITDYSLKCQES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVS 376 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~-----~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~ 376 (450)
|.++|.|.||+++++++ ..++||+||++++||+|+|++||||.+.+.++||||||+|++|++|..|+|||.++++
T Consensus 1 g~~~W~i~~f~~~~~~a~~~~~~~~~S~~Fyt~~~Gy~w~i~~ypnG~~~~~~~~iSv~l~l~~g~~D~~l~wpv~~~~t 80 (147)
T cd03779 1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGAGKGTHISLFFVIMKGEYDALLPWPFRHKVT 80 (147)
T ss_pred CeEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEcCCCCCCCCCEEEEEEEEecCCcccccCcceEEEEE
Confidence 57899999999888766 4799999999999999999999999988888999999999999999999999999999
Q ss_pred EEEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccccC--CceeCCcEEEEEEEe
Q psy225 377 FTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRKR--QFLKDDAIFIRVKVD 443 (450)
Q Consensus 377 ~~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~~--~fl~dd~l~i~~~v~ 443 (450)
|+|+||.+.. ....++.++.....|.||.. ..+.+||+++||++++|++. +||+||+|+|+|+|.
T Consensus 81 fsLlDq~~~~-~~~~~~~~~~~~~~F~rP~~-~~n~~~G~~~Fi~~~~Le~s~~~ylkDD~~~Irc~V~ 147 (147)
T cd03779 81 FMLLDQNNRE-HVIDAFRPDLSSASFQRPVS-DMNVASGCPLFFPLKKLQSPKHAYCKDDTIYIKCVVD 147 (147)
T ss_pred EEEECCCCCC-CCcEeecCCcccccccCccc-CCCCCcchhheeEHHHhcccCCCcEeCCEEEEEEEEC
Confidence 9999997543 33445554443467999974 34678999999999999964 999999999999984
No 4
>cd03780 MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF5 was identified as an activator of nuclear factor-kappaB and a regulator of lymphotoxin-beta receptor and CD40 signaling. Its interaction with CD40 is indirect, involving hetero-oligomerization with TRAF3. In addition, TRAF5 has been shown to associate with other TNFRs including CD27, CD30, OX40 and GITR (glucocorticoid-induced TNFR). It plays a role in modulating Th2 immune responses (driven by OX40 costimulation) and T-cell activation (triggered by GITR). It is also involved in osteoclastogenesis. TRAF5 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more dive
Probab=100.00 E-value=1.6e-32 Score=225.14 Aligned_cols=141 Identities=43% Similarity=0.894 Sum_probs=123.9
Q ss_pred ceEEEEECCchhhhhcc---c--cccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEE
Q psy225 302 GTLIWKITDYSLKCQES---I--ELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVS 376 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~---~--~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~ 376 (450)
|.++|+|.+|+.++..+ . .+.|++||++.+||+|+|++||||.+.+.++||||||.|++|++|+.|+|||.++++
T Consensus 1 g~~vwkI~~ys~~~~~~~~g~~~~i~S~~Fyt~~~Gy~w~i~~ypnG~~~~~~~~iSv~l~l~~g~~D~~l~wp~~~~~t 80 (148)
T cd03780 1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSGKGTHLSLYFVVMRGEFDSLLQWPFRQRVT 80 (148)
T ss_pred CEEEEEECCHHHHHHhhcCCCccEEECCCcccCCCCeeEEEEEEcCCCCCCCCCEEEEEEEEecCccccccCcceEEEEE
Confidence 57899999999987654 3 799999998888999999999999988889999999999999999999999999999
Q ss_pred EEEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeecccccc--CCceeCCcEEEEEEEe
Q psy225 377 FTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRK--RQFLKDDAIFIRVKVD 443 (450)
Q Consensus 377 ~~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~--~~fl~dd~l~i~~~v~ 443 (450)
|+|+||.+.+.++..++.++++...|.+|.. ..+.+||+++||++++|+. ++||+||+|+|+|.|.
T Consensus 81 fsLlDq~~~~~~~~~~~~~~~~~~~F~rp~~-~~n~~~G~~~Fi~~~~Le~s~~~ylkdD~~~Ik~~v~ 148 (148)
T cd03780 81 LMLLDQSGKKNHIMETFKADPNSSSFKRPDG-EMNIASGCPRFVAHSVLENAKNTYIKDDTLFLKVAVD 148 (148)
T ss_pred EEEECCCCCCCCcceeeecCCccccccCCCC-CCCCCcChhheeEHHHhhcccCCcCcCCEEEEEEEEC
Confidence 9999998766665666666665677999964 3467899999999999985 4999999999999884
No 5
>cd03783 MATH_Meprin_Alpha Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The alpha subunit is synthesized as a membrane spanning protein, however, it is cleaved during biosynthesis and loses its transmembrane domain. It oligomerizes into large complexes, containing 10-100 subunits (dimers that associate noncovalently), which are secreted as latent proteases and can move through extracellular spaces in a nondestructive manner. This allows delivery of the concentrated protease to sites containing activating enzymes, such as sites of inflammation, infection or cancerous growth. Meprin alpha shows preference for small or hydrophobic residues at the P1 and P1' sites of its substrate. Both
Probab=99.97 E-value=1.4e-30 Score=212.32 Aligned_cols=140 Identities=32% Similarity=0.615 Sum_probs=122.8
Q ss_pred eEEEEECCchhhhhcc---ccccCCCcccCCCCcEEEEEEEecCCCC-CCCCeEEEEEEecCCCCCcccCCc-ccceEEE
Q psy225 303 TLIWKITDYSLKCQES---IELLSPSFYTSQFGYKLQVSLFLNGNGA-GEGTHVSVYIKLLPGEYDALLKWP-FSHSVSF 377 (450)
Q Consensus 303 ~~~w~i~~~s~~~~~~---~~~~S~~f~~~~~g~~w~l~~~p~g~~~-~~~~~~s~yl~l~~g~~d~~l~Wp-~~~~~~~ 377 (450)
.++|+|.||+++++++ ..++||+||++ .||+++|++||||++. +.++|+|||+++++|++|..|+|| +..+++|
T Consensus 3 ~~iWkI~nfs~~~~~a~~~~~i~Sp~Fyt~-~GYk~~l~~~lng~~~~~~g~~lSl~~~lm~Ge~D~~L~WP~~~~~itl 81 (167)
T cd03783 3 NAVWRVRNFSQILENTTKGDVLQSPRFYSP-EGYGYGVSLYPLSNESDYSGNYTGLYFHLCSGENDAVLEWPALNRQAII 81 (167)
T ss_pred ceeEEECcHHHHHHhCcCCCeEECCCCccC-CCceEEEEEEecCCCCCCCCCEEEEEEEEecccCCCcccCCCcCCEEEE
Confidence 4699999999988765 68999999996 6999999999999864 678999999999999999999999 5789999
Q ss_pred EEEeCC---CCCcceeEeeecCC--CCCC------CCCCCC---------CCCCccCCccceeeccccccCCceeCCcEE
Q psy225 378 TLFDQS---EKPVNVVESFVPDP--TWEN------FQRPSK---------QPDSLGFGFPRFVSLDTIRKRQFLKDDAIF 437 (450)
Q Consensus 378 ~l~~~~---~~~~~~~~~~~~~~--~~~~------f~~~~~---------~~~~~~~G~~~f~~~~~l~~~~fl~dd~l~ 437 (450)
+|+||+ ..++++++++.+++ +..+ |+||.. ..++.||||+.||+++.|+.++||+||+|.
T Consensus 82 ~llDQ~~~~~~r~~~~~sf~~d~~~~~~~~~~~~~f~rP~~~~~~~~~~~~~~~~gfG~~~Fish~~L~~r~yikdDtlf 161 (167)
T cd03783 82 TVLDQDPDVRLRMSSSRSFTTDKSQTSSAINGTLRWDRPSRVGTYDTSCDCFRGIDFGWSTFISHSQLRRRSFLKNDDLI 161 (167)
T ss_pred EEEcCCcchhhccccceeeecCCCcccccccccccccCCcccccccccccccCCcccccccceeHHHHhhCCcccCCeEE
Confidence 999997 36788888898887 3233 999952 246889999999999999999999999999
Q ss_pred EEEEEe
Q psy225 438 IRVKVD 443 (450)
Q Consensus 438 i~~~v~ 443 (450)
|.++++
T Consensus 162 I~~~~~ 167 (167)
T cd03783 162 IFVDFE 167 (167)
T ss_pred EEEecC
Confidence 999874
No 6
>cd03782 MATH_Meprin_Beta Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for f
Probab=99.97 E-value=2.4e-30 Score=209.33 Aligned_cols=139 Identities=27% Similarity=0.564 Sum_probs=120.8
Q ss_pred eEEEEECCchhhhhcc---ccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCccc-ceEEEE
Q psy225 303 TLIWKITDYSLKCQES---IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFS-HSVSFT 378 (450)
Q Consensus 303 ~~~w~i~~~s~~~~~~---~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~-~~~~~~ 378 (450)
.++|+|.||++++.++ ..++||+||++ +||+++|++||||++.+ ++|+|||+++++|++|..|+|||. .+++|.
T Consensus 3 ~~iWkI~~fs~~~~~~~~~~~i~Sp~FYt~-~GYkl~l~~ylnG~g~~-~~~lsl~~~lm~Ge~D~~L~WPf~~~qit~~ 80 (167)
T cd03782 3 EHIWHIRNFTQLLATTPPNGKIYSPPFLSS-TGYSFQVGLYLNGTDDY-PGNLAIYLHLTSGPNDDQLQWPCPWQQATMM 80 (167)
T ss_pred cEEEEeCcHHHHHHhcCCCceEECCCCcCc-cCceeEEEEEecCCCCC-CCEEEEEEEEeccCCCccccCCCcCCeEEEE
Confidence 4799999999988764 78999999998 79999999999999876 789999999999999999999999 999999
Q ss_pred EEeCCC---CCcceeE--eeecCCCCC---CC--CCCCC-----CCC-------CccCCccceeeccccccCCceeCCcE
Q psy225 379 LFDQSE---KPVNVVE--SFVPDPTWE---NF--QRPSK-----QPD-------SLGFGFPRFVSLDTIRKRQFLKDDAI 436 (450)
Q Consensus 379 l~~~~~---~~~~~~~--~~~~~~~~~---~f--~~~~~-----~~~-------~~~~G~~~f~~~~~l~~~~fl~dd~l 436 (450)
|+||+. .++++.+ ++.|+.++. .| .||.. +.. +.+|||+.||+++.|..+.||+||++
T Consensus 81 LlDQ~~d~~~r~~~~~~~t~~P~~~s~~n~~f~w~rP~kvg~~~~~~~~~~~~r~~~~G~~~Fish~~L~~r~yikdD~i 160 (167)
T cd03782 81 LLDQHPDIRQRMSNQRSVTTDPNMTSTDSDEYFWDDPRKVGSEVTDTDGSTFYRGPGYGTSAFITHLRLRSRDFIKGDDV 160 (167)
T ss_pred EEcCCCchhhccceeeeEEecCCcccccCccceecCCcccCcccccccccccccccccCccceeeHHHHhhcCcccCCeE
Confidence 999973 6778888 555555544 46 99941 122 78999999999999999999999999
Q ss_pred EEEEEEe
Q psy225 437 FIRVKVD 443 (450)
Q Consensus 437 ~i~~~v~ 443 (450)
+|-++++
T Consensus 161 fi~~~~e 167 (167)
T cd03782 161 IFLLTME 167 (167)
T ss_pred EEEEecC
Confidence 9998874
No 7
>cd03776 MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kapp
Probab=99.97 E-value=8.9e-30 Score=212.02 Aligned_cols=142 Identities=35% Similarity=0.678 Sum_probs=120.1
Q ss_pred ceEEEEECCchhhhhcc---c--cccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEE
Q psy225 302 GTLIWKITDYSLKCQES---I--ELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVS 376 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~---~--~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~ 376 (450)
|.++|+|.+||.+++.. . .+.|+.|+++.+||+|+|++||||...+..++|||||.|+++++|..++||+.++++
T Consensus 1 g~h~~~I~~yS~~~~~~~~g~~~~i~S~~F~~~~gGy~W~i~~yP~G~~~~~~~~lS~~L~l~~~~~d~~l~wpv~a~~~ 80 (147)
T cd03776 1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEARCPNYISLFVHLMQGENDSHLDWPFQGTIT 80 (147)
T ss_pred CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCCCCCCEEEEEEEEeccCCCcccCCcccceeE
Confidence 57899999999765532 3 488999998666999999999999987778899999999999999999999999999
Q ss_pred EEEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccccCCceeCCcEEEEEEEe
Q psy225 377 FTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443 (450)
Q Consensus 377 ~~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~~~fl~dd~l~i~~~v~ 443 (450)
|+|+||.++..++...+.+.+....|.+|....++.+|||+.||++++|+..+||+||+|+|+|+|.
T Consensus 81 ~~lldq~~~~~~~~~~~~~~~~~~~F~~p~~~~~~~~~G~~~fi~~~~Le~~~yl~dD~l~I~c~V~ 147 (147)
T cd03776 81 LTLLDQSEPRQNIHETMMSKPELLAFQRPTTDRNPKGFGYVEFAHIEDLLQRGFVKNDTLLIKIEVN 147 (147)
T ss_pred EEEECCCcccCccEEEEEcCCChHhhcCCCcCCCCCCeeEceeeEHHHhhhCCCccCCEEEEEEEEC
Confidence 9999998766555545544444567888864445678999999999999988999999999999984
No 8
>cd03771 MATH_Meprin Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular metalloproteases, which are either anchored to the membrane or secreted into extracellular spaces. They are expressed in renal and intestinal brush border membranes, leukocytes, and cancer cells, and are capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. Meprin proteases are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. Despite their similarity, the two subunits differ in their ability to self-associate, in proteolytic processing during biosynthesis and in substrate specificity. Both subunits are synthesized as membrane spanning proteins, however, the alpha subunit is cleaved during biosynthesis and loses its transmembrane domain. Meprin beta forms homodimers or heterotetramers while meprin alpha oligomerizes into large complexes co
Probab=99.96 E-value=1.6e-29 Score=209.72 Aligned_cols=139 Identities=32% Similarity=0.687 Sum_probs=119.8
Q ss_pred eEEEEECCchhhhhcc---ccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcc-cceEEEE
Q psy225 303 TLIWKITDYSLKCQES---IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPF-SHSVSFT 378 (450)
Q Consensus 303 ~~~w~i~~~s~~~~~~---~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~-~~~~~~~ 378 (450)
.++|+|.+||.+++.. ..+.||+||+. +||+|+|++||||.+. .++||||||+|++|++|..|+||+ .++++|+
T Consensus 3 ~hvwkI~~yS~~~~~~~~g~~i~S~~Fysv-gGy~w~I~~YPnG~~~-~~~~lSlyL~L~~g~~d~~L~WP~v~a~~t~~ 80 (167)
T cd03771 3 EAVWRVRNFSQLLETTPKGTKIYSPRFYSP-EGYAFQVGLYPNGTES-YPGYTGLYFHLCSGENDDVLEWPCPNRQATMT 80 (167)
T ss_pred eEEEEEcCchhhhhcCCCCCEEECCCCCcc-CCeEEEEEEEeCCCCC-CCCcceEEEEEecCCccccccCcceeEEEEEE
Confidence 5799999999986432 57999999542 3999999999999987 788999999999999999999996 7999999
Q ss_pred EEeCC---CCCcceeEeeecCCCCCC-------CCCCCC-----CC-------CCccCCccceeeccccccCCceeCCcE
Q psy225 379 LFDQS---EKPVNVVESFVPDPTWEN-------FQRPSK-----QP-------DSLGFGFPRFVSLDTIRKRQFLKDDAI 436 (450)
Q Consensus 379 l~~~~---~~~~~~~~~~~~~~~~~~-------f~~~~~-----~~-------~~~~~G~~~f~~~~~l~~~~fl~dd~l 436 (450)
|+||. ..++++.+++.++++... |.||.. .. ++.||||+.||++++|++++||+||+|
T Consensus 81 LlDQ~~~~~~r~~~~~~~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~~~g~G~~~Fis~~~L~~r~ylk~dtl 160 (167)
T cd03771 81 LLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYRGPGYGWSTFISHSRLRRRDFLKGDDL 160 (167)
T ss_pred EECCCCcccccCcceEEEecCCcccccccccccccCCccccccccccccccccccCccccccceeHHHhccCCCCcCCEE
Confidence 99997 366788999999986544 999942 11 457999999999999999899999999
Q ss_pred EEEEEEe
Q psy225 437 FIRVKVD 443 (450)
Q Consensus 437 ~i~~~v~ 443 (450)
.|+++++
T Consensus 161 ~i~~~~~ 167 (167)
T cd03771 161 IILLDFE 167 (167)
T ss_pred EEEEEeC
Confidence 9999874
No 9
>cd03781 MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF4, including the Drosophila protein DTRAF1. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF4 is highly expressed during embryogenesis, especially in the central and peripheral nervous system. Studies using TRAF4-deficient mice show that TRAF4 is required for neurogenesis, as well as the development of the trachea and the axial skeleton. In addition, TRAF4 augments nuclear factor-kappaB activation triggered by GITR (glucocorticoid-induced TNFR), a receptor expressed in T-cells, B-cells and macrophages. It also participates in counteracting the signaling mediated by Toll-like receptors through its association with TRAF6 and TR
Probab=99.96 E-value=2.7e-29 Score=209.97 Aligned_cols=142 Identities=63% Similarity=1.247 Sum_probs=121.7
Q ss_pred ceEEEEECCchhhhhcc-----ccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEE
Q psy225 302 GTLIWKITDYSLKCQES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVS 376 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~-----~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~ 376 (450)
|+++|+|.+|+..+..+ ..+.|+.|++|.+||+|+|++||||...+.++++||||+|++|++|..|+||+.+.++
T Consensus 1 g~~~~~I~gys~~~~~~~~~~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~~~~~~vs~~l~l~~ge~d~~l~wp~~a~~~ 80 (154)
T cd03781 1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGSGEGSHLSVYIRVLPGEYDNLLEWPFSHRIT 80 (154)
T ss_pred CEEEEEECCHHHHHHHhhcCCCceEECCCeecCCCCEEEEEEEECCCCCCCCCCEEEEEEEEecCCcccccCCceeeEEE
Confidence 57899999999887531 5799999999999999999999999988888999999999999999889999999999
Q ss_pred EEEEeCCCC----CcceeEeeecCCCCCCCCCCCC---CCCCccCCccceeeccccccCCceeCCcEEEEEEEe
Q psy225 377 FTLFDQSEK----PVNVVESFVPDPTWENFQRPSK---QPDSLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443 (450)
Q Consensus 377 ~~l~~~~~~----~~~~~~~~~~~~~~~~f~~~~~---~~~~~~~G~~~f~~~~~l~~~~fl~dd~l~i~~~v~ 443 (450)
|+|+||.+. +.++...+.++++..+|.+|.. ..++.+|||..||++++|++.+||+||+|+|+|+|+
T Consensus 81 ~~llDq~~~~~~~~~~~~~~~~~~~~~~~F~rp~~~~~~~~~~~~G~~~fi~~~~Le~~~yl~dD~l~Irc~v~ 154 (154)
T cd03781 81 FTLLDQSDPSLSKPQHITETFTPDPTWKNFQKPSASRLDESTLGFGYPKFISHEDLKKRNYIKDDAIFLRASVE 154 (154)
T ss_pred EEEECCCCCccccCcceEEEEEcCCchhhhcCCcccccCCCCCccchhHeeEHHHHhhCCcccCCEEEEEEEeC
Confidence 999999754 2234455556566678998863 234678999999999999988999999999999984
No 10
>KOG0297|consensus
Probab=99.96 E-value=9.9e-29 Score=235.49 Aligned_cols=359 Identities=30% Similarity=0.540 Sum_probs=247.2
Q ss_pred cccccCceeeccCCCCcccCCCcccCCCCCcccCCCCCC--CCCCCCCCCCCCCCC--CCCCCCchhHHhhhcceeeccC
Q psy225 4 SFTSWTKTLSFPARLNTHHKQQISSKENTLSSSSSSHSS--DLPMICSQTKSRTPL--SLTPDVSDSEKDTMGSLIHCIH 79 (450)
Q Consensus 4 ~~~~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~~~~--~~~~~~~~~~~~~~~~~~~C~~ 79 (450)
+..+++.+|.|++|..+ +.+|++...|||.||..|+.. .....||.|...+.. ....+ ..+.+++.++++.|++
T Consensus 14 ~~~~~~~~l~C~~C~~v-l~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~-~~~~~~~~~l~i~c~~ 91 (391)
T KOG0297|consen 14 LGRPLDENLLCPICMSV-LRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVP-RALRRELLKLPIRCIF 91 (391)
T ss_pred cCCCCcccccCcccccc-ccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccCch-HHHHHHHHhccccccc
Confidence 44567889999999999 999999767999999988832 226799999777665 44445 7778889999999999
Q ss_pred CCCCCchHHHHhHHHHhhhcCCCCcccCCc-ccccccccHHHhHHhhhCCCCcccCcccccccChhHHHHHhhhCCCCcc
Q psy225 80 YKEGCKWYDELKSLKGHLQTCKYDAIPCNK-CLAAIPKTLMEDHSKFTCPERITTCQYCLESFSGMEMEDHTGHCSYEMV 158 (450)
Q Consensus 80 c~~~c~~~~~l~~~~~H~~~c~~~~~~C~~-C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~~~~~~~~ 158 (450)
-..||.|...|..++.|...| .+.+|+. |+..+...++..|+...+..+.-.|..|+..+....+..|... .....
T Consensus 92 ~~~GC~~~~~l~~~~~Hl~~c--~~~~C~~~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~~~~~~~~~h~~~-~~~~~ 168 (391)
T KOG0297|consen 92 ASRGCRADLELEALQGHLSTC--DPLKCPHRCGVQVPRDDLEDHLEAECPRRSLKCSLCQSDSILILLEAHEEN-PQAEV 168 (391)
T ss_pred CCCCccccccHHHHHhHhccC--CcccCccccccccchHHHHHHHhcccccccccchhhcCccchhhhhhcCCC-CCccc
Confidence 999999999999999999999 8999965 9999999999999999999999999999999988888888777 55555
Q ss_pred cccccCChhhchhHHHhhhhhcccCce-eecccccccccccchhhccccCCCCcccCCcccccCccChhHHHHHHhhhcC
Q psy225 159 YCENKCGHKIQRRLMAKHRANDCYKRL-VACRYCSKSYVADTLVTHQTKCTRAPIPCPNQCEMVALPREELDVHIKEHCN 237 (450)
Q Consensus 159 ~~c~~C~~~f~~~~l~~H~~~h~~~k~-~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~ 237 (450)
+|...|+..-....+. +.+.+.+.++ ..+..+.+. .....|.....+-+..+...|.. ...+...+.
T Consensus 169 ~c~~k~~~~~l~~~~~-~~qs~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~---- 236 (391)
T KOG0297|consen 169 SCELKCGKQKLKRRML-ANQSEEPAKRIQELIMQLKE---EFERIAALLNPRVSTSGNIQCTP----DAPLEEYIK---- 236 (391)
T ss_pred cccccchhhhhhhHHH-HHHhhhhhhhhhHHHHHHHH---hhhhhhhhcccccccccceeecC----chhHHHHHh----
Confidence 6666677654432111 1111222211 112211111 00000000000000011101110 011111110
Q ss_pred CccccccccCCCCCccccChHHHHH-hhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh-ccCCceEEEEECCchhhh
Q psy225 238 SLLVSCVFKDAGCRFKGMRGETMEK-HIEENVNQHMLLMCSLVSKQQQQISTLKSALNKVT-LNYSGTLIWKITDYSLKC 315 (450)
Q Consensus 238 ~~~~~C~~~~~gC~~~~~~~~~l~~-H~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~-~~~~~~~~w~i~~~s~~~ 315 (450)
......+|...... ..|.. |+.. ..+..+......++ ..++|.++|.|.+|+..+
T Consensus 237 -----~~l~~~~~~~~~~~-~~lE~~~~~~-----------------~~~~~~~~~~~~~~~~~~~g~~iwki~~~~~~~ 293 (391)
T KOG0297|consen 237 -----DSLKESGCTLSQRV-QLLESRHEGR-----------------QPLGDMALSVREMEVRSYDGTLIWKIPDYGRKK 293 (391)
T ss_pred -----hHHHHhhccccccH-HHhhhhhhhh-----------------hhhHHHHHHHHHhhhhccCCEEEEEecchhhhh
Confidence 01111112222221 22211 1110 11222333333333 678999999999996666
Q ss_pred hcc-----ccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEeCCCCCccee
Q psy225 316 QES-----IELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFDQSEKPVNVV 390 (450)
Q Consensus 316 ~~~-----~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~~~~~~~~~~ 390 (450)
.++ ..++|+.||+..+||+++..+|.||++.+.+.++|+|+.+++|++|..|.|||+..++|.+++| +..
T Consensus 294 ~e~~~~~~~~~~S~~f~t~~~Gyk~~~~~~lng~g~~~~~~~s~~~~~~~ge~d~~l~wpf~~~v~~~l~dq-----~~~ 368 (391)
T KOG0297|consen 294 QEAVAGATLSLFSPAFYTSKYGYKLCARIYLNGDGTGKGTHLSLYFVVMRGEYDALLPWPFRQKVTLMLLDQ-----HVI 368 (391)
T ss_pred HHHHhccCccccccccccccccHHHHhHhhhcCCCCCCcceeeeeeeecccCcccccccCCCCceEEEEecc-----ccc
Confidence 554 7889999999999999999999999999999999999999999999999999999999999999 567
Q ss_pred EeeecCCCCCCCCCCCC
Q psy225 391 ESFVPDPTWENFQRPSK 407 (450)
Q Consensus 391 ~~~~~~~~~~~f~~~~~ 407 (450)
.++.++.....|.||.+
T Consensus 369 ~~~~~~~~~~~f~r~~~ 385 (391)
T KOG0297|consen 369 DAFKPDLNSSSFQRPVG 385 (391)
T ss_pred ccccccchhhhcCCCCC
Confidence 77888888888999974
No 11
>cd00270 MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. There are at least six mammalian and three Drosophila proteins containing TRAF domains. The mammalian TRAFs display varying expression profiles, indicating independent and cell type-specific regulation. They display distinct, as well as overlapping functions and interactions with receptors. Most TRAFs, except TRAF1, share N-terminal homology and contain a RING domain, multiple zinc finger domains, and a TRAF domain. TRAFs form homo- and heterotrimers through its TRAF domain. The TRAF domain can be divided into a more divergent N-ter
Probab=99.96 E-value=3e-28 Score=204.15 Aligned_cols=142 Identities=51% Similarity=1.047 Sum_probs=118.9
Q ss_pred ceEEEEECCchhhhhc-----cccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEE
Q psy225 302 GTLIWKITDYSLKCQE-----SIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVS 376 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~-----~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~ 376 (450)
|+++|+|.+||.++.. ...+.|+.|++|.+||.|+|++||||.+.+.++++||||+|+++++|..++||+.++++
T Consensus 1 g~~~w~I~~fs~~~~~~~~~~~~~~~S~~F~vg~~G~~w~i~~yP~G~~~~~~~~lsl~L~l~~~~~d~~~~w~~~~~~~ 80 (149)
T cd00270 1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGTGKGTHLSLFVHVMKGEYDALLEWPFRGKIT 80 (149)
T ss_pred CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCCCCCCEEEEEEEEeccCCCccccCCccceEE
Confidence 5789999999998652 15789999999988999999999999877778899999999999999899999999999
Q ss_pred EEEEeCCCC--CcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccccCCceeCCcEEEEEEEe
Q psy225 377 FTLFDQSEK--PVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443 (450)
Q Consensus 377 ~~l~~~~~~--~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~~~fl~dd~l~i~~~v~ 443 (450)
|+|+||.++ +.++..++.+.+....|.+|..+..+.+|||..||++++|++.|||+||+|+|+|+|.
T Consensus 81 ~~l~d~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~fi~~~~L~~~gfl~dD~l~I~~~v~ 149 (149)
T cd00270 81 LTLLDQSDDSKRKHITETFMPDPNSSAFQRPPTGENNIGFGYPEFVPLEKLESRGYVKDDTLFIKVEVD 149 (149)
T ss_pred EEEECCCCccccCceEEEEEcCCchHhhcCCCcccCCCCcCcceEeEHHHhccCCCEeCCEEEEEEEEC
Confidence 999999864 4444455544444456765432234678999999999999987999999999999984
No 12
>KOG2462|consensus
Probab=99.92 E-value=6.4e-26 Score=195.55 Aligned_cols=131 Identities=18% Similarity=0.419 Sum_probs=118.9
Q ss_pred CcccCCcccccccc-cHHHhHHhhhCC---CCcccCcccccccChhH-HHHHhhhCCCCcccccccCChhhch-hHHHhh
Q psy225 103 DAIPCNKCLAAIPK-TLMEDHSKFTCP---ERITTCQYCLESFSGME-MEDHTGHCSYEMVYCENKCGHKIQR-RLMAKH 176 (450)
Q Consensus 103 ~~~~C~~C~~~f~~-~~l~~H~~~h~~---~~~~~C~~C~~~f~~~~-l~~H~~~~~~~~~~~c~~C~~~f~~-~~l~~H 176 (450)
..|.|++||+.+.+ ++|.+|...|+. .+.+.|++|+|.+...- |+.|+++|+ .+..|..||+.|.| -.|+-|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 56899999999999 999999999985 57789999999999997 999999998 67889999999996 788999
Q ss_pred hhhcccCceeecccccccccc-cchhhccccC-CCCcccCCcccccCccChhHHHHHHhhhc
Q psy225 177 RANDCYKRLVACRYCSKSYVA-DTLVTHQTKC-TRAPIPCPNQCEMVALPREELDVHIKEHC 236 (450)
Q Consensus 177 ~~~h~~~k~~~C~~C~~~f~~-~~l~~H~~~~-~~~~~~C~~~C~~~f~~~~~l~~H~~~h~ 236 (450)
+|+|+|||||.|++|+|.|.. ++|+.|+++| +.++|+|+ .|+|+|..++.|.+|.+.-|
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~-~C~KsFsl~SyLnKH~ES~C 267 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCP-RCGKSFALKSYLNKHSESAC 267 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCc-chhhHHHHHHHHHHhhhhcc
Confidence 999999999999999999999 9999999995 77899999 99999999999999988754
No 13
>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i
Probab=99.88 E-value=2.3e-22 Score=164.83 Aligned_cols=125 Identities=22% Similarity=0.413 Sum_probs=100.1
Q ss_pred ceEEEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEe
Q psy225 302 GTLIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFD 381 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~ 381 (450)
+++.|+|.+||.+...+..+.|+.|.+| ||.|+|.+||+|.+.+.++++||||.+.++ ..|++.++++|+|+|
T Consensus 5 ~~~~~~I~~fS~~~~~~~~~~S~~F~vg--G~~W~i~~yP~G~~~~~~~~lSl~L~l~~~-----~~~~~~~~~~l~lln 77 (132)
T cd03773 5 DSATFTLENFSTLRQSADPVYSDPLNVD--GLCWRLKVYPDGNGEVRGNFLSVFLELCSG-----LGEASKYEYRVEMVH 77 (132)
T ss_pred cccEEEECChhhhhcCCcceeCCCeEeC--CccEEEEEECCCCCCCCCCEEEEEEEeecC-----CCCceeEEEEEEEEc
Confidence 4578999999988653367999999999 999999999999877778899999998754 236788999999999
Q ss_pred CCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccccCCceeC--CcEEEEEEEec
Q psy225 382 QSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRKRQFLKD--DAIFIRVKVDP 444 (450)
Q Consensus 382 ~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~~~fl~d--d~l~i~~~v~v 444 (450)
|.++..++.... ...|. .+.+|||..||++++|++.|||+| |+|+|+|.|++
T Consensus 78 q~~~~~~~~~~~-----~~~f~------~~~~wG~~~Fi~~~~L~~~gfl~~~~D~l~i~~~v~p 131 (132)
T cd03773 78 QANPTKNIKREF-----ASDFE------VGECWGYNRFFRLDLLINEGYLLPENDTLILRFSVRP 131 (132)
T ss_pred CCCCccceEEec-----ccccc------CCCCcCHHHhccHHHHhhCCCcCCCCCEEEEEEEEeC
Confidence 964333332211 12242 145799999999999998899999 99999999975
No 14
>KOG2462|consensus
Probab=99.87 E-value=4.1e-23 Score=178.28 Aligned_cols=132 Identities=17% Similarity=0.276 Sum_probs=122.1
Q ss_pred ceeeccCCCCCCchHHHH-hHHHHhhhcCCCCcccCCcccccccc-cHHHhHHhhhCCCCcccCcccccccChhH-HHHH
Q psy225 73 SLIHCIHYKEGCKWYDEL-KSLKGHLQTCKYDAIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSGME-MEDH 149 (450)
Q Consensus 73 ~~~~C~~c~~~c~~~~~l-~~~~~H~~~c~~~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~~~-l~~H 149 (450)
-.++|+.|++.....+.| +|-+.|-..-..+.+.|+.|++.+.. ..|+.|+++|+ -+++|..|||.|.+.- |+-|
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 468999999999999999 67778874333467899999999999 99999999988 7899999999999998 9999
Q ss_pred hhhCCCCcccccccCChhhc-hhHHHhhhhhcccCceeecccccccccc-cchhhcccc
Q psy225 150 TGHCSYEMVYCENKCGHKIQ-RRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTHQTK 206 (450)
Q Consensus 150 ~~~~~~~~~~~c~~C~~~f~-~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H~~~ 206 (450)
+|+|+||+||.|..|++.|. |++|..|+++|.+.|+|+|+-|+|.|.. +-|.+|...
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999999 9999999999999999999999999999 999999977
No 15
>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.
Probab=99.87 E-value=8.3e-22 Score=161.34 Aligned_cols=124 Identities=23% Similarity=0.495 Sum_probs=97.9
Q ss_pred eEEEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCC---cccCCcccceEEEEE
Q psy225 303 TLIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYD---ALLKWPFSHSVSFTL 379 (450)
Q Consensus 303 ~~~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d---~~l~Wp~~~~~~~~l 379 (450)
++.|+|.+||.+. ..+.|+.|.+| ||.|+|.+||+|+.. .++|||||.+...+.. ...+|++.|.|+|+|
T Consensus 2 ~f~w~I~~fS~~~---~~~~S~~F~vG--G~~W~l~~yP~G~~~--~~~iSlyL~l~~~~~~~~~~~~~~~v~a~f~~~l 74 (134)
T cd03775 2 SFTWRIKNWSELE---KKVHSPKFKCG--GFEWRILLFPQGNSQ--TGGVSIYLEPHPEEEEKAPLDEDWSVCAQFALVI 74 (134)
T ss_pred cEEEEECCcccCC---cceeCCCEEEC--CeeEEEEEeCCCCCC--CCeEEEEEEecCcccccccCCCCCeEEEEEEEEE
Confidence 5899999999953 45899999999 999999999999755 6799999999764322 134799999999999
Q ss_pred EeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccc------cCCceeCCcEEEEEEEe
Q psy225 380 FDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIR------KRQFLKDDAIFIRVKVD 443 (450)
Q Consensus 380 ~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~------~~~fl~dd~l~i~~~v~ 443 (450)
+||.++..++... ....|.. .+.+|||.+||++++|+ ..|||+||+|+|++.|.
T Consensus 75 ~n~~~~~~~~~~~-----~~~~F~~-----~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~~~~~ 134 (134)
T cd03775 75 SNPGDPSIQLSNV-----AHHRFNA-----EDKDWGFTRFIELRKLAHRTPDKPSPFLENGELNITVYVR 134 (134)
T ss_pred EcCCCCccceEcc-----ceeEeCC-----CCCCCChhHcccHHHHcccccCCCCceeECCEEEEEEEEC
Confidence 9997654433221 1123542 25689999999999998 36999999999999874
No 16
>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway. It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1
Probab=99.86 E-value=3.3e-21 Score=158.66 Aligned_cols=129 Identities=14% Similarity=0.317 Sum_probs=101.3
Q ss_pred CceEEEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCC--CCCCeEEEEEEecCCCCCcccCCcccceEEEE
Q psy225 301 SGTLIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGA--GEGTHVSVYIKLLPGEYDALLKWPFSHSVSFT 378 (450)
Q Consensus 301 ~~~~~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~--~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~ 378 (450)
.+++.|.|.+||.+ . +.+.|+.|.+| ||.|+|.+||+|... +..+++||||.+.+.. . ...|++.+.|+|+
T Consensus 2 ~~~~~~~I~~~S~l-~--e~~~S~~f~vg--G~~W~i~~~P~g~~~~~~~~~~lsvyL~~~~~~-~-~~~w~i~a~~~~~ 74 (137)
T cd03772 2 EATFSFTVERFSRL-S--ESVLSPPCFVR--NLPWKIMVMPRNYPDRNPHQKSVGFFLQCNAES-D-STSWSCHAQAVLR 74 (137)
T ss_pred CcEEEEEECCcccC-C--CcEECCCEEEC--CcceEEEEEeCCCCCCCCCCCeEEEEEeeCCcC-C-CCCCeEEEEEEEE
Confidence 46889999999997 2 46899999999 999999999999654 2347999999997532 2 2379999999999
Q ss_pred EEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccc--cCCceeCCcEEEEEEEecCC
Q psy225 379 LFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIR--KRQFLKDDAIFIRVKVDPSK 446 (450)
Q Consensus 379 l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~--~~~fl~dd~l~i~~~v~v~~ 446 (450)
|+||.+...+...... ..|.+. ..+|||+.||++++|. ..|||+||+|+|+|.|+|-.
T Consensus 75 l~~~~~~~~~~~~~~~-----~~f~~~-----~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~~V~~~~ 134 (137)
T cd03772 75 IINYKDDEPSFSRRIS-----HLFFSK-----ENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQADA 134 (137)
T ss_pred EEcCCCCcccEEEeee-----eEEcCC-----CCCccchheeEHHHhcCCCCCcEECCEEEEEEEEEeeC
Confidence 9999854433322211 124222 4589999999999995 57999999999999998764
No 17
>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta
Probab=99.86 E-value=2.3e-21 Score=160.07 Aligned_cols=128 Identities=17% Similarity=0.298 Sum_probs=99.7
Q ss_pred ceEEEEECCchhhhhcc-ccccCCCcccCCCC---cEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEE
Q psy225 302 GTLIWKITDYSLKCQES-IELLSPSFYTSQFG---YKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSF 377 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~-~~~~S~~f~~~~~g---~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~ 377 (450)
-++.|.|.+||...... ..+.|+.|.+| | |+|+|.+||+|...+..+++||||.++..+ .||+.+.|+|
T Consensus 5 ~~~~w~I~~fS~~~~~~~~~i~S~~F~vg--g~~~~~W~l~~yP~G~~~~~~~~iSlyL~l~~~~-----~~~v~a~f~~ 77 (139)
T cd03774 5 FCYMWTISNFSFCREEMGEVIKSSTFSSG--ANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCP-----KSEVRAKFKF 77 (139)
T ss_pred EEEEEEECCchhhhhcCCCEEECCCeecC--CcCCceEEEEEeCCCCCCCCCCeEEEEEEEccCC-----CCcEEEEEEE
Confidence 46899999999875432 67999999999 7 599999999998666678999999997532 3689999999
Q ss_pred EEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccc--cCCceeCCcEEEEEEEecCC
Q psy225 378 TLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIR--KRQFLKDDAIFIRVKVDPSK 446 (450)
Q Consensus 378 ~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~--~~~fl~dd~l~i~~~v~v~~ 446 (450)
+|+||.+++.... .......|. ...+|||.+||++++|. ..|||+||+|+|+|+|+|++
T Consensus 78 ~l~n~~~~~~~~~----~~~~~~~f~------~~~~wG~~~fi~~~~L~~~~~g~l~dD~l~I~c~I~V~~ 138 (139)
T cd03774 78 SILNAKGEETKAM----ESQRAYRFV------QGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ 138 (139)
T ss_pred EEEecCCCeeeee----cccCcEeCC------CCCccCHHHeeeHHHhhhhhcccccCCEEEEEEEEEEEc
Confidence 9999986532211 111112242 14689999999999995 46999999999999999864
No 18
>PF00917 MATH: MATH domain; InterPro: IPR002083 Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain []. Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PDOC00604 from PROSITEDOC), a MATH domain, an EGF-like domain (see PDOC00021 from PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane []. TRAF proteins were first isolated by their ability to interact with TNF receptors []. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PDOC00449 from PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PDOC50145 from PROSITEDOC) in the middle and the MATH domain in the C-terminal part []. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD []. The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain []. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [].; GO: 0005515 protein binding; PDB: 1D00_E 1CZY_A 1D01_F 1CA9_A 1D0J_D 1F3V_B 1CA4_C 1D0A_A 1QSC_C 1CZZ_C ....
Probab=99.77 E-value=1.5e-18 Score=139.91 Aligned_cols=119 Identities=27% Similarity=0.463 Sum_probs=94.3
Q ss_pred ECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEeCCCCCc
Q psy225 308 ITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFDQSEKPV 387 (450)
Q Consensus 308 i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~~~~~~~ 387 (450)
|+|||++......+.|+.|..+ ||+|+|.++|+|. ++++++||.+..++.+..++||+.+.++|.|+++.++..
T Consensus 1 i~nfs~l~~~~~~~~s~~~~~~--g~~W~l~~~~~~~----~~~l~~~L~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~ 74 (119)
T PF00917_consen 1 IKNFSKLKEGEEYSSSFVFSHG--GYPWRLKVYPKGN----GKYLSVYLHCDKGENDSDLEWSIEAEFRFRLLNQNGKSI 74 (119)
T ss_dssp ETTGGGHHTSEEEEEEEESSTT--SEEEEEEEETTES----TTEEEEEEEEECSTTGGGSSSSEEEEEEEEEE-TTSCEE
T ss_pred CcccceEeCCCcEECCCeEEEC--CEEEEEEEEeCCC----cCcEEEEEEEeecccccccceeeeEEEEEEEecCCCCcc
Confidence 6899999843233344777777 9999999999997 569999999999988777889999999999999987653
Q ss_pred ceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccccCCceeCCcEEEEEEEec
Q psy225 388 NVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVDP 444 (450)
Q Consensus 388 ~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~~~fl~dd~l~i~~~v~v 444 (450)
..... ...|.. ..+|||.+|+++++|.+..||+||+|+|+|+|+|
T Consensus 75 ~~~~~------~~~F~~------~~~~g~~~fi~~~~l~~~~fl~dd~l~ie~~v~I 119 (119)
T PF00917_consen 75 SKRIK------SHSFNN------PSSWGWSSFISWEDLEDPYFLVDDSLTIEVEVKI 119 (119)
T ss_dssp EEEEE------CEEECT------TSEEEEEEEEEHHHHTTCTTSBTTEEEEEEEEEE
T ss_pred eeeee------eeEEee------ecccchhheeEHHHhCccCCeECCEEEEEEEEEC
Confidence 22222 122432 3589999999999999767999999999999986
No 19
>KOG3608|consensus
Probab=99.77 E-value=4.2e-19 Score=157.19 Aligned_cols=185 Identities=18% Similarity=0.383 Sum_probs=158.4
Q ss_pred cCCCCCCchHHHH-hHHHHhhhcCCC---------Cc-ccC--Ccccccccc-cHHHhHHhhhCCCCcccCcccccccCh
Q psy225 78 IHYKEGCKWYDEL-KSLKGHLQTCKY---------DA-IPC--NKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSG 143 (450)
Q Consensus 78 ~~c~~~c~~~~~l-~~~~~H~~~c~~---------~~-~~C--~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (450)
+.|+..|.....+ .|+..|.--|+| +| +.| ..|-+.|.. ..|+.|++.|++++...|+.||.-|+.
T Consensus 140 edCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~ 219 (467)
T KOG3608|consen 140 EDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRT 219 (467)
T ss_pred hhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhcc
Confidence 6789999998888 666777766665 12 457 678899999 999999999999999999999999999
Q ss_pred hH-HHHHhhhCC--CCcccccccCChhhc-hhHHHhhhhhcccCceeecccccccccc-cchhhcccc-C-CCCcccCCc
Q psy225 144 ME-MEDHTGHCS--YEMVYCENKCGHKIQ-RRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTHQTK-C-TRAPIPCPN 216 (450)
Q Consensus 144 ~~-l~~H~~~~~--~~~~~~c~~C~~~f~-~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H~~~-~-~~~~~~C~~ 216 (450)
+. |-.|.+..+ ...+|.|..|.+.|. .+.|..|+..|- .-|+|+.|+..... +.|.+|++. | ..+||+|.
T Consensus 220 ~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd- 296 (467)
T KOG3608|consen 220 KTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCD- 296 (467)
T ss_pred ccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCcccc-
Confidence 98 999988654 456889999999998 688888988774 36899999999999 999999999 6 78999999
Q ss_pred ccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhHhhH
Q psy225 217 QCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 217 ~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~ 268 (450)
.|+..+.+.++|.+|..+|. +..|.|.+.+ |.++++....|++|+.+.+
T Consensus 297 ~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~--C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 297 ECDTRCVRESDLAKHVQVHS-KTVYQCEHPD--CHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred chhhhhccHHHHHHHHHhcc-ccceecCCCC--CcHHHHHHHHHHHHHHHhc
Confidence 99999999999999999887 7789998854 9999999899999988754
No 20
>cd00121 MATH MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH doma
Probab=99.77 E-value=6.1e-18 Score=137.62 Aligned_cols=126 Identities=33% Similarity=0.658 Sum_probs=98.5
Q ss_pred ceEEEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEe
Q psy225 302 GTLIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFD 381 (450)
Q Consensus 302 ~~~~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~ 381 (450)
+++.|.|.+|+... . ..+.|+.|..+ |+.|+|.+||+|... ..+++||||.+.++... ...|++.+.++|.|+|
T Consensus 1 ~~~~~~i~~~~~~~-~-~~~~S~~f~~~--g~~W~l~~~p~~~~~-~~~~lsv~L~~~~~~~~-~~~~~~~~~~~~~l~~ 74 (126)
T cd00121 1 GKHTWKIVNFSELE-G-ESIYSPPFEVG--GYKWRIRIYPNGDGE-SGDYLSLYLELDKGESD-LEKWSVRAEFTLKLVN 74 (126)
T ss_pred CEEEEEECCCCCCC-C-cEEECCCEEEc--CEeEEEEEEcCCCCC-CCCEEEEEEEecCCCCC-CCCCcEEEEEEEEEEC
Confidence 36899999999822 2 56899999999 999999999999755 56799999999876544 5679999999999999
Q ss_pred CCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccccCCceeCCcEEEEEEEe
Q psy225 382 QSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRKRQFLKDDAIFIRVKVD 443 (450)
Q Consensus 382 ~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~~~fl~dd~l~i~~~v~ 443 (450)
+++.. +...... ..|. ...+.+|||+.||++++|...+++.||+|+|+|+|.
T Consensus 75 ~~~~~-~~~~~~~-----~~~~----~~~~~~~G~~~fi~~~~l~~~~~~~~d~l~i~~~v~ 126 (126)
T cd00121 75 QNGGK-SLSKSFT-----HVFF----SEKGSGWGFPKFISWDDLEDSYYLVDDSLTIEVEVK 126 (126)
T ss_pred CCCCc-cceEecc-----CCcC----CCCCCCCChHHeeEHHHhccCCcEECCEEEEEEEEC
Confidence 97322 2222211 1121 123679999999999999976669999999999984
No 21
>KOG3608|consensus
Probab=99.75 E-value=8.8e-19 Score=155.17 Aligned_cols=179 Identities=16% Similarity=0.306 Sum_probs=155.4
Q ss_pred CCCCCchHHHH-hHHHHhhhcCCCCcccCCcccccccc-cHHHhHHhhh--CCCCcccCcccccccChhH-HHHHhhhCC
Q psy225 80 YKEGCKWYDEL-KSLKGHLQTCKYDAIPCNKCLAAIPK-TLMEDHSKFT--CPERITTCQYCLESFSGME-MEDHTGHCS 154 (450)
Q Consensus 80 c~~~c~~~~~l-~~~~~H~~~c~~~~~~C~~C~~~f~~-~~l~~H~~~h--~~~~~~~C~~C~~~f~~~~-l~~H~~~~~ 154 (450)
|-+.+..+..| +|++.|.++ +.+.|+.||..|++ ..|-.|++.. -...+|.|..|.|.|.++. |..|+..|.
T Consensus 185 Ct~~~~~k~~LreH~r~Hs~e---KvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv 261 (467)
T KOG3608|consen 185 CTKHMGNKYRLREHIRTHSNE---KVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV 261 (467)
T ss_pred hhhhhccHHHHHHHHHhcCCC---eEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh
Confidence 44556677888 677899999 89999999999999 9999998644 3467999999999999998 999999885
Q ss_pred CCcccccccCChhhc-hhHHHhhhhh-cccCceeecccccccccc-cchhhccccCCCCcccCCc-ccccCccChhHHHH
Q psy225 155 YEMVYCENKCGHKIQ-RRLMAKHRAN-DCYKRLVACRYCSKSYVA-DTLVTHQTKCTRAPIPCPN-QCEMVALPREELDV 230 (450)
Q Consensus 155 ~~~~~~c~~C~~~f~-~~~l~~H~~~-h~~~k~~~C~~C~~~f~~-~~l~~H~~~~~~~~~~C~~-~C~~~f~~~~~l~~ 230 (450)
. -|.|+.|+.+.. ++.|..|++. |...|||+|+.|++.+.+ ++|++|..+|.+..|+|.+ .|..++.+...|.+
T Consensus 262 n--~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~r~~~q~~~ 339 (467)
T KOG3608|consen 262 N--CYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred h--cccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHHHHHHHHHH
Confidence 4 477889999887 7999999875 888999999999999999 9999999999999999982 39999999999999
Q ss_pred HHhhhc-C--CccccccccCCCCCccccChHHHHHhhHhh
Q psy225 231 HIKEHC-N--SLLVSCVFKDAGCRFKGMRGETMEKHIEEN 267 (450)
Q Consensus 231 H~~~h~-~--~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~ 267 (450)
|.+.+. + ..+|.|.. |++-|.+..+|.+|+...
T Consensus 340 H~~evhEg~np~~Y~CH~----Cdr~ft~G~~L~~HL~kk 375 (467)
T KOG3608|consen 340 HFLEVHEGNNPILYACHC----CDRFFTSGKSLSAHLMKK 375 (467)
T ss_pred HHHHhccCCCCCceeeec----chhhhccchhHHHHHHHh
Confidence 998776 3 34688888 999999999999998753
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.70 E-value=1.6e-17 Score=161.62 Aligned_cols=143 Identities=26% Similarity=0.547 Sum_probs=119.2
Q ss_pred eeeccCCCCCCchHHHHhHHHHhhhcCCCCcccCC--cccccccccHHHhHHhhhCCCCcccCcccccccChhHHHHHhh
Q psy225 74 LIHCIHYKEGCKWYDELKSLKGHLQTCKYDAIPCN--KCLAAIPKTLMEDHSKFTCPERITTCQYCLESFSGMEMEDHTG 151 (450)
Q Consensus 74 ~~~C~~c~~~c~~~~~l~~~~~H~~~c~~~~~~C~--~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~ 151 (450)
.+.|++ |.|.+.++++..|...|.+....|+ .||..|...++..|. .|+.|++.|....|..|+.
T Consensus 407 ~V~C~N----C~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~---------~C~~Cgk~f~~s~LekH~~ 473 (567)
T PLN03086 407 TVECRN----CKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHV---------HCEKCGQAFQQGEMEKHMK 473 (567)
T ss_pred eEECCC----CCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCc---------cCCCCCCccchHHHHHHHH
Confidence 578997 7889999999999999999999998 599999888888884 7999999997655999999
Q ss_pred hCCCCcccccccCChhhchhHHHhhhhhcccCceeecccccccccc-----------cchhhccccCCCCcccCCccccc
Q psy225 152 HCSYEMVYCENKCGHKIQRRLMAKHRANDCYKRLVACRYCSKSYVA-----------DTLVTHQTKCTRAPIPCPNQCEM 220 (450)
Q Consensus 152 ~~~~~~~~~c~~C~~~f~~~~l~~H~~~h~~~k~~~C~~C~~~f~~-----------~~l~~H~~~~~~~~~~C~~~C~~ 220 (450)
.|+ .++.|. ||+.+.+..|..|+.+||+++|+.|++|++.+.. +.|..|+.+|+.+++.|. .||+
T Consensus 474 ~~H--kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~-~Cgk 549 (567)
T PLN03086 474 VFH--EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCD-SCGR 549 (567)
T ss_pred hcC--CCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEcc-ccCC
Confidence 985 667777 9987778999999999999999999999998852 367777777777777777 7777
Q ss_pred CccChhHHHHHHhh
Q psy225 221 VALPREELDVHIKE 234 (450)
Q Consensus 221 ~f~~~~~l~~H~~~ 234 (450)
.+ ...+|..|+..
T Consensus 550 ~V-rlrdm~~H~~~ 562 (567)
T PLN03086 550 SV-MLKEMDIHQIA 562 (567)
T ss_pred ee-eehhHHHHHHH
Confidence 65 45567777643
No 23
>KOG1074|consensus
Probab=99.61 E-value=2.5e-16 Score=154.47 Aligned_cols=52 Identities=17% Similarity=0.375 Sum_probs=48.6
Q ss_pred ccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhHhhH
Q psy225 212 IPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~ 268 (450)
..|. .||+.|...+.|+.|+++|++++||.|.+ |++.|..+.+|++||..++
T Consensus 880 h~C~-vCgk~FsSSsALqiH~rTHtg~KPF~C~f----C~~aFttrgnLKvHMgtH~ 931 (958)
T KOG1074|consen 880 HVCN-VCGKQFSSSAALEIHMRTHTGPKPFFCHF----CEEAFTTRGNLKVHMGTHM 931 (958)
T ss_pred hhhc-cchhcccchHHHHHhhhcCCCCCCccchh----hhhhhhhhhhhhhhhcccc
Confidence 5698 99999999999999999999999999999 9999999999999998653
No 24
>KOG3576|consensus
Probab=99.53 E-value=2.5e-15 Score=123.31 Aligned_cols=110 Identities=20% Similarity=0.281 Sum_probs=82.7
Q ss_pred CCCcccCcccccccChhH-HHHHhhhCCCCcccccccCChhhc-hhHHHhhhhhcccCceeecccccccccc-cchhhcc
Q psy225 128 PERITTCQYCLESFSGME-MEDHTGHCSYEMVYCENKCGHKIQ-RRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTHQ 204 (450)
Q Consensus 128 ~~~~~~C~~C~~~f~~~~-l~~H~~~~~~~~~~~c~~C~~~f~-~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H~ 204 (450)
+...|.|..|+|.|.... |.+|++-|...+.+-|..||+.|. .-+|++|.++|+|.|||+|..|+++|++ -.|+.|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 345677888888888877 888888888888888888888887 5788888888888888888888888888 7788887
Q ss_pred cc-CC-----------CCcccCCcccccCccChhHHHHHHhhhcCC
Q psy225 205 TK-CT-----------RAPIPCPNQCEMVALPREELDVHIKEHCNS 238 (450)
Q Consensus 205 ~~-~~-----------~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~ 238 (450)
+. |+ ++.|.|. .||.+-.....+..|++.|.+.
T Consensus 194 ~kvhgv~~~yaykerr~kl~vce-dcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCE-DCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeec-ccCCCCCChhHHHHHHHhcCCC
Confidence 65 53 2346677 7776666666666666665543
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.51 E-value=1.9e-14 Score=140.33 Aligned_cols=146 Identities=24% Similarity=0.413 Sum_probs=127.1
Q ss_pred CcccCCcccccccccHHHhHHhhhCCCCcccCcc--cccccChhHHHHHhhhCCCCcccccccCChhhchhHHHhhhhhc
Q psy225 103 DAIPCNKCLAAIPKTLMEDHSKFTCPERITTCQY--CLESFSGMEMEDHTGHCSYEMVYCENKCGHKIQRRLMAKHRAND 180 (450)
Q Consensus 103 ~~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~l~~H~~~~~~~~~~~c~~C~~~f~~~~l~~H~~~h 180 (450)
....|+.|....+..+|..|.. +|......|+. |+..|....+..|. .|..|++.|....|..|++++
T Consensus 406 ~~V~C~NC~~~i~l~~l~lHe~-~C~r~~V~Cp~~~Cg~v~~r~el~~H~---------~C~~Cgk~f~~s~LekH~~~~ 475 (567)
T PLN03086 406 DTVECRNCKHYIPSRSIALHEA-YCSRHNVVCPHDGCGIVLRVEEAKNHV---------HCEKCGQAFQQGEMEKHMKVF 475 (567)
T ss_pred CeEECCCCCCccchhHHHHHHh-hCCCcceeCCcccccceeeccccccCc---------cCCCCCCccchHHHHHHHHhc
Confidence 3568999999999999999985 89888899984 99999777788884 678999999888899999987
Q ss_pred ccCceeecccccccccccchhhcccc-CCCCcccCCcccccCcc----------ChhHHHHHHhhhcCCccccccccCCC
Q psy225 181 CYKRLVACRYCSKSYVADTLVTHQTK-CTRAPIPCPNQCEMVAL----------PREELDVHIKEHCNSLLVSCVFKDAG 249 (450)
Q Consensus 181 ~~~k~~~C~~C~~~f~~~~l~~H~~~-~~~~~~~C~~~C~~~f~----------~~~~l~~H~~~h~~~~~~~C~~~~~g 249 (450)
+ +|+.|+ ||+.+....|..|+.+ |+++++.|+ .|++.+. ..+.|..|... |+.+++.|..
T Consensus 476 H--kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~-fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt~~C~~---- 546 (567)
T PLN03086 476 H--EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCR-FCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRTAPCDS---- 546 (567)
T ss_pred C--CCccCC-CCCCcchhHHHhhhhccCCCCceeCC-CCCCccccCccccchhhhhhhHHHHHHh-cCCcceEccc----
Confidence 4 899999 9987655999999988 899999999 9999884 23589999977 8999999988
Q ss_pred CCccccChHHHHHhhHhhH
Q psy225 250 CRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 250 C~~~~~~~~~l~~H~~~~~ 268 (450)
|++.+.. .+|..|+...+
T Consensus 547 Cgk~Vrl-rdm~~H~~~~h 564 (567)
T PLN03086 547 CGRSVML-KEMDIHQIAVH 564 (567)
T ss_pred cCCeeee-hhHHHHHHHhh
Confidence 9999999 99999998754
No 26
>KOG1074|consensus
Probab=99.49 E-value=5.4e-15 Score=145.28 Aligned_cols=80 Identities=21% Similarity=0.326 Sum_probs=58.7
Q ss_pred eeecccccccccc-cchhhcccc-CCCCcccCCcccccCccChhHHHHHHhhhcCCc----cccccccCCCCCccccChH
Q psy225 185 LVACRYCSKSYVA-DTLVTHQTK-CTRAPIPCPNQCEMVALPREELDVHIKEHCNSL----LVSCVFKDAGCRFKGMRGE 258 (450)
Q Consensus 185 ~~~C~~C~~~f~~-~~l~~H~~~-~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~----~~~C~~~~~gC~~~~~~~~ 258 (450)
|-+|-+|-+...- +.|+.|.++ +||+||+|. .||+.|.++.+|+.|+-.|-..- .+.||. ..-|.+.|...-
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCK-iCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~-~~ic~~kftn~V 682 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCK-ICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPS-TFICQKKFTNAV 682 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccc-cccchhccccchhhcccccccCccccccccCCc-hhhhcccccccc
Confidence 5678888888777 888888888 488888888 88888888888888887775543 356660 012888887777
Q ss_pred HHHHhhHh
Q psy225 259 TMEKHIEE 266 (450)
Q Consensus 259 ~l~~H~~~ 266 (450)
.|..|++-
T Consensus 683 ~lpQhIri 690 (958)
T KOG1074|consen 683 TLPQHIRI 690 (958)
T ss_pred cccceEEe
Confidence 77777764
No 27
>smart00061 MATH meprin and TRAF homology.
Probab=99.49 E-value=1.2e-13 Score=106.23 Aligned_cols=94 Identities=20% Similarity=0.351 Sum_probs=72.4
Q ss_pred EEEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEeCC
Q psy225 304 LIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFDQS 383 (450)
Q Consensus 304 ~~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~~~ 383 (450)
++|.|.+|+.+... ..+.|++|.++ |+.|+|.+||++ +++||||.+.+...+ ...|++.++++|+|+||+
T Consensus 2 ~~~~~~~~~~~~~~-~~~~S~~f~~~--g~~W~i~~~p~~------~~lsl~L~~~~~~~~-~~~w~v~a~~~~~l~~~~ 71 (95)
T smart00061 2 LSHTFKNVSRLEEG-ESYFSPSEEHF--NIPWRLKIYRKN------GFLSLYLHCEKEECD-SRKWSIEAEFTLKLVSQN 71 (95)
T ss_pred ceeEEEchhhcccC-ceEeCChhEEc--CceeEEEEEEcC------CEEEEEEEeCCCcCC-CCCeEEEEEEEEEEEeCC
Confidence 47999999987444 67999999998 999999999983 499999999876544 337999999999999998
Q ss_pred CCCcceeEeeecCCCCCCCCCCCCCCCCccCCcccee
Q psy225 384 EKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFV 420 (450)
Q Consensus 384 ~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~ 420 (450)
++.... .....|.+ +.+|||++||
T Consensus 72 ~~~~~~-------~~~~~F~~------~~~~G~~~fi 95 (95)
T smart00061 72 GKSLSK-------KDKHVFEK------PSGWGFSKFI 95 (95)
T ss_pred CCEEee-------eeeEEEcC------CCccceeeEC
Confidence 653311 11233542 4589999885
No 28
>KOG3576|consensus
Probab=99.40 E-value=2.2e-13 Score=112.04 Aligned_cols=112 Identities=22% Similarity=0.402 Sum_probs=99.8
Q ss_pred hCCCCcccccccCChhhc-hhHHHhhhhhcccCceeecccccccccc-cchhhcccc-CCCCcccCCcccccCccChhHH
Q psy225 152 HCSYEMVYCENKCGHKIQ-RRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTHQTK-CTRAPIPCPNQCEMVALPREEL 228 (450)
Q Consensus 152 ~~~~~~~~~c~~C~~~f~-~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H~~~-~~~~~~~C~~~C~~~f~~~~~l 228 (450)
...+...+.|..||+.|. ...|.+|++-|...|.+-|..||+.|.. -+|++|+++ +|-+||+|. .|++.|.++..|
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~-~c~kaftqrcsl 189 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCS-LCEKAFTQRCSL 189 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchh-hhhHHHHhhccH
Confidence 455667788999999999 7899999999999999999999999999 999999999 699999999 999999999999
Q ss_pred HHHHhhhcC-----------CccccccccCCCCCccccChHHHHHhhHhhH
Q psy225 229 DVHIKEHCN-----------SLLVSCVFKDAGCRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 229 ~~H~~~h~~-----------~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~ 268 (450)
..|++.-.+ ++.|.|.- |++...+...+..|++..+
T Consensus 190 eshl~kvhgv~~~yaykerr~kl~vced----cg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 190 ESHLKKVHGVQHQYAYKERRAKLYVCED----CGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred HHHHHHHcCchHHHHHHHhhhheeeecc----cCCCCCChhHHHHHHHhcC
Confidence 999986554 35678887 9999999888888988654
No 29
>KOG3623|consensus
Probab=99.27 E-value=1.9e-12 Score=125.40 Aligned_cols=103 Identities=17% Similarity=0.376 Sum_probs=89.0
Q ss_pred cccCCcccccccc-cHHHhHHhhhC--CCCcccCcccccccChhH-HHHHhhhCCC-------------CcccccccCCh
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSKFTC--PERITTCQYCLESFSGME-MEDHTGHCSY-------------EMVYCENKCGH 166 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~~h~--~~~~~~C~~C~~~f~~~~-l~~H~~~~~~-------------~~~~~c~~C~~ 166 (450)
...|+.|.+.+.+ ..|+.|++.-+ .+..|.|..|..+|.+.. |.+|+..|.. -+-|.|.+||+
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 4679999999999 99999987533 345689999999999998 9999988743 23578999999
Q ss_pred hhc-hhHHHhhhhhcccCceeecccccccccc-cchhhcccc
Q psy225 167 KIQ-RRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTHQTK 206 (450)
Q Consensus 167 ~f~-~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H~~~ 206 (450)
.|. +.+|+.|+|+|.|+|||.|+.|+|.|.. ..+..|+..
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 999 8999999999999999999999999999 788999854
No 30
>KOG3623|consensus
Probab=99.20 E-value=4e-12 Score=123.28 Aligned_cols=76 Identities=16% Similarity=0.347 Sum_probs=40.3
Q ss_pred CCcccCcccccccChhH-HHHHhhhCCCCcccccccCChhhc-hhHHHhhhhhcccCceeecccccccccc-cchhhcc
Q psy225 129 ERITTCQYCLESFSGME-MEDHTGHCSYEMVYCENKCGHKIQ-RRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTHQ 204 (450)
Q Consensus 129 ~~~~~C~~C~~~f~~~~-l~~H~~~~~~~~~~~c~~C~~~f~-~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H~ 204 (450)
+.+|.|+.|+|.|...+ |.+|.-.|+|.+||.|.+|.+.|. +.+|..|.|.|.|+|||+|+.|+|.|.. ..+..||
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHM 970 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHM 970 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhh
Confidence 34455555555555544 555555555555555555555555 4555555555555555555555555544 4444444
No 31
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=99.06 E-value=3e-10 Score=111.21 Aligned_cols=134 Identities=23% Similarity=0.439 Sum_probs=100.0
Q ss_pred hhhccCCceEEEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcc--cCCccc
Q psy225 295 KVTLNYSGTLIWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDAL--LKWPFS 372 (450)
Q Consensus 295 ~l~~~~~~~~~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~--l~Wp~~ 372 (450)
+++..-...+.|.|++|++.... ..||+|.+| |++|+|.++|.|.... .+||||.....+.+.. -.|.+-
T Consensus 32 d~Ee~~~~sftW~vk~wsel~~k---~~Sp~F~vg--~~twki~lfPqG~nq~---~~sVyLe~~pqe~e~~~gk~~~cc 103 (1089)
T COG5077 32 DVEELLEMSFTWKVKRWSELAKK---VESPPFSVG--GHTWKIILFPQGNNQC---NVSVYLEYEPQELEETGGKYYDCC 103 (1089)
T ss_pred cHHHHhhcccceecCChhhhhhh---ccCCccccc--CeeEEEEEecccCCcc---ccEEEEEeccchhhhhcCcchhhh
Confidence 44444556778999999998664 789999999 9999999999998653 3899998875442221 248899
Q ss_pred ceEEEEEEeCCCCCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeecccccc-----CCceeCCcEEEEEEEecCC
Q psy225 373 HSVSFTLFDQSEKPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIRK-----RQFLKDDAIFIRVKVDPSK 446 (450)
Q Consensus 373 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~~-----~~fl~dd~l~i~~~v~v~~ 446 (450)
++|.|.|-++..+..+...+ .-..|+. ...+|||.+|+.+..|.. ..|+.+|++.|.+.|+|++
T Consensus 104 aqFaf~Is~p~~pti~~iN~-----sHhrFs~-----~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~ItvyVRvlk 172 (1089)
T COG5077 104 AQFAFDISNPKYPTIEYINK-----SHHRFSM-----ESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVYVRVLK 172 (1089)
T ss_pred hheeeecCCCCCCchhhhhc-----ccccccc-----cccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEEEEEEe
Confidence 99999999887644333211 0122432 257999999999988762 2589999999999999865
No 32
>PHA00733 hypothetical protein
Probab=98.70 E-value=1e-08 Score=81.95 Aligned_cols=50 Identities=16% Similarity=0.261 Sum_probs=28.8
Q ss_pred Cceeecccccccccc-cchhhccccCCCCcccCCcccccCccChhHHHHHHhh
Q psy225 183 KRLVACRYCSKSYVA-DTLVTHQTKCTRAPIPCPNQCEMVALPREELDVHIKE 234 (450)
Q Consensus 183 ~k~~~C~~C~~~f~~-~~l~~H~~~~~~~~~~C~~~C~~~f~~~~~l~~H~~~ 234 (450)
.+||.|+.|++.|.. ..|..|++.+ +.++.|+ .|++.|.....|..|+..
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h-~~~~~C~-~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYT-EHSKVCP-VCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcC-CcCccCC-CCCCccCCHHHHHHHHHH
Confidence 555666666555555 5555555543 2345666 666666666666666554
No 33
>PHA00733 hypothetical protein
Probab=98.55 E-value=7.2e-08 Score=77.11 Aligned_cols=91 Identities=14% Similarity=0.138 Sum_probs=69.9
Q ss_pred hHHHhhhhhcccCceeecccccccccc-cchhh------ccccCCCCcccCCcccccCccChhHHHHHHhhhcCCccccc
Q psy225 171 RLMAKHRANDCYKRLVACRYCSKSYVA-DTLVT------HQTKCTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSC 243 (450)
Q Consensus 171 ~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~------H~~~~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C 243 (450)
..|..+...--..+++.|.+|.+.|.. ..|.. |+..++.+||.|+ .|++.|..+..|..|++.| ..++.|
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~-~Cgk~Fss~s~L~~H~r~h--~~~~~C 102 (128)
T PHA00733 26 EELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCP-LCLMPFSSSVSLKQHIRYT--EHSKVC 102 (128)
T ss_pred HHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCC-CCCCcCCCHHHHHHHHhcC--CcCccC
Confidence 444444333334577888888888776 44443 4444678999999 9999999999999999875 457899
Q ss_pred cccCCCCCccccChHHHHHhhHhhH
Q psy225 244 VFKDAGCRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 244 ~~~~~gC~~~~~~~~~l~~H~~~~~ 268 (450)
+. |++.|.+...|.+|+...+
T Consensus 103 ~~----CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 103 PV----CGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CC----CCCccCCHHHHHHHHHHhc
Confidence 88 9999999999999987643
No 34
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=98.42 E-value=6.9e-08 Score=66.74 Aligned_cols=60 Identities=38% Similarity=0.862 Sum_probs=41.8
Q ss_pred ccccCCCCcccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHh
Q psy225 203 HQTKCTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKH 263 (450)
Q Consensus 203 H~~~~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H 263 (450)
|...|+..++.|++.|+..-+.+..|..|+...|+.++++|+|..+||+..+.+ .+|.+|
T Consensus 1 H~~~C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~-~~l~~H 60 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPR-EDLEEH 60 (60)
T ss_dssp HHTTSTTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEH-HHHHHC
T ss_pred CcccCCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccch-hHHhCC
Confidence 455577788888855666656899999999989999999999999999999999 888877
No 35
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.37 E-value=1.8e-07 Score=52.08 Aligned_cols=26 Identities=23% Similarity=0.534 Sum_probs=22.5
Q ss_pred HHHhhhhhcccCceeecccccccccc
Q psy225 172 LMAKHRANDCYKRLVACRYCSKSYVA 197 (450)
Q Consensus 172 ~l~~H~~~h~~~k~~~C~~C~~~f~~ 197 (450)
+|.+|+++|++++||+|++|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47889999999999999999998863
No 36
>PHA02768 hypothetical protein; Provisional
Probab=98.36 E-value=1.6e-07 Score=61.34 Aligned_cols=40 Identities=15% Similarity=0.074 Sum_probs=27.5
Q ss_pred cccCCcccccccc-cHHHhHHhhhCCCCcccCcccccccChhH
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSGME 145 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 145 (450)
.|.|+.||+.|.+ ..|..|+++|. ++++|..|++.|...+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccc
Confidence 4577777777777 77777777766 5667777777666543
No 37
>PHA02768 hypothetical protein; Provisional
Probab=98.24 E-value=5.3e-07 Score=58.99 Aligned_cols=42 Identities=19% Similarity=0.449 Sum_probs=25.4
Q ss_pred ccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHH
Q psy225 212 IPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETM 260 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l 260 (450)
|+|+ .||+.|..+++|..|+++|. ++++|.. |++.|.+.+.|
T Consensus 6 y~C~-~CGK~Fs~~~~L~~H~r~H~--k~~kc~~----C~k~f~~~s~l 47 (55)
T PHA02768 6 YECP-ICGEIYIKRKSMITHLRKHN--TNLKLSN----CKRISLRTGEY 47 (55)
T ss_pred cCcc-hhCCeeccHHHHHHHHHhcC--CcccCCc----ccceeccccee
Confidence 5566 66666666666666666665 4555544 66666654433
No 38
>KOG3993|consensus
Probab=98.21 E-value=5.4e-07 Score=83.09 Aligned_cols=111 Identities=12% Similarity=0.114 Sum_probs=61.2
Q ss_pred ccccccCChhhch-hHHHhhhhhcccC---c--------------eeecccccccccc-cchhhccccC--CCCcccCCc
Q psy225 158 VYCENKCGHKIQR-RLMAKHRANDCYK---R--------------LVACRYCSKSYVA-DTLVTHQTKC--TRAPIPCPN 216 (450)
Q Consensus 158 ~~~c~~C~~~f~~-~~l~~H~~~h~~~---k--------------~~~C~~C~~~f~~-~~l~~H~~~~--~~~~~~C~~ 216 (450)
+|.|..|+++|.| ..|++|+.+|... + .+-|+.|+-.+.. ..-..|..-+ ......|+
T Consensus 356 i~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp- 434 (500)
T KOG3993|consen 356 IFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPP- 434 (500)
T ss_pred eeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCC-
Confidence 5667777777774 6667776555321 0 1223333333322 1111222111 11223456
Q ss_pred ccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhHhhHHHHHH
Q psy225 217 QCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIEENVNQHML 273 (450)
Q Consensus 217 ~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~~~~~~ 273 (450)
.|+..+..+..-..|.+.-..+..|.|.| |.-.|.....|.+|+...+-..+.
T Consensus 435 ~~~~ppsss~~sgg~~rlg~~~q~f~~ky----~~atfyss~~ltrhin~~Hpse~r 487 (500)
T KOG3993|consen 435 YDGSPPSSSGSSGGYGRLGIAEQGFTCKY----CPATFYSSPGLTRHINKCHPSELR 487 (500)
T ss_pred CCCCCcccCCCCCccccccchhhcccccc----chHhhhcCcchHhHhhhcChHHhh
Confidence 67766665555555555555667788888 888888878888888865444333
No 39
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.16 E-value=9.1e-07 Score=49.22 Aligned_cols=25 Identities=32% Similarity=0.578 Sum_probs=21.1
Q ss_pred HHHhHHhhhCCCCcccCcccccccC
Q psy225 118 LMEDHSKFTCPERITTCQYCLESFS 142 (450)
Q Consensus 118 ~l~~H~~~h~~~~~~~C~~C~~~f~ 142 (450)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4778888888888888888888875
No 40
>PHA00616 hypothetical protein
Probab=98.14 E-value=1e-06 Score=54.72 Aligned_cols=34 Identities=12% Similarity=0.205 Sum_probs=31.4
Q ss_pred cccCCcccccCccChhHHHHHHhhhcCCccccccc
Q psy225 211 PIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVF 245 (450)
Q Consensus 211 ~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 245 (450)
||+|+ .||+.|..+++|..|++.|+++.++.|++
T Consensus 1 pYqC~-~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCL-RCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccc-hhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 68899 99999999999999999999999999887
No 41
>KOG3993|consensus
Probab=97.94 E-value=2.4e-06 Score=78.96 Aligned_cols=154 Identities=16% Similarity=0.177 Sum_probs=100.6
Q ss_pred eeccCCCCCCchHHHHhHHHHhhhcCCC---CcccCCcccccccc-cHHHhHHhhhCCC---------------------
Q psy225 75 IHCIHYKEGCKWYDELKSLKGHLQTCKY---DAIPCNKCLAAIPK-TLMEDHSKFTCPE--------------------- 129 (450)
Q Consensus 75 ~~C~~c~~~c~~~~~l~~~~~H~~~c~~---~~~~C~~C~~~f~~-~~l~~H~~~h~~~--------------------- 129 (450)
|.|..|...+...-.|..++ |+. ..|+|++|+|.|.- .+|..|.+.|-..
T Consensus 268 yiCqLCK~kYeD~F~LAQHr-----C~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~ 342 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHR-----CPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEV 342 (500)
T ss_pred HHHHHHHHhhhhHHHHhhcc-----CCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhh
Confidence 66777766666655553332 221 46899999999999 9999998877421
Q ss_pred ------------CcccCcccccccChhH-HHHHhhhCCCCccccc--------ccCChhhchhHHHhhhhh---------
Q psy225 130 ------------RITTCQYCLESFSGME-MEDHTGHCSYEMVYCE--------NKCGHKIQRRLMAKHRAN--------- 179 (450)
Q Consensus 130 ------------~~~~C~~C~~~f~~~~-l~~H~~~~~~~~~~~c--------~~C~~~f~~~~l~~H~~~--------- 179 (450)
..|.|..|+|+|++.. |+.|+.+|.......- ..=+..+....+..|...
T Consensus 343 ~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl 422 (500)
T KOG3993|consen 343 QEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVL 422 (500)
T ss_pred hhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhccccccccccccccccccccccccee
Confidence 2378999999999998 9999888764322110 000000001222333221
Q ss_pred -ccc-Cceeecccccccccc-cchhhcccc-CCCCcccCCcccccCccChhHHHHHHhh
Q psy225 180 -DCY-KRLVACRYCSKSYVA-DTLVTHQTK-CTRAPIPCPNQCEMVALPREELDVHIKE 234 (450)
Q Consensus 180 -h~~-~k~~~C~~C~~~f~~-~~l~~H~~~-~~~~~~~C~~~C~~~f~~~~~l~~H~~~ 234 (450)
+.+ .-...|++|+..+.. ..-..|.+. +.+..|.|. +|..+|.....|..|+..
T Consensus 423 ~~a~sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~k-y~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 423 YVAGSAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCK-YCPATFYSSPGLTRHINK 480 (500)
T ss_pred eeeccccccCCCCCCCCcccCCCCCccccccchhhccccc-cchHhhhcCcchHhHhhh
Confidence 111 123458888877776 334466665 778889999 999999999999999865
No 42
>PHA00616 hypothetical protein
Probab=97.86 E-value=5.5e-06 Score=51.46 Aligned_cols=33 Identities=18% Similarity=0.252 Sum_probs=26.1
Q ss_pred cccCCcccccccc-cHHHhHHhhhCCCCcccCcc
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQY 136 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~ 136 (450)
||.|+.||+.|.. ++|..|++.|++++++.|++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 5678888888888 88888888888888877765
No 43
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.69 E-value=8.7e-06 Score=51.14 Aligned_cols=36 Identities=22% Similarity=0.206 Sum_probs=25.0
Q ss_pred ccCCCCcccCCCcccCCCCCcccCCCC------CCCCCCCCCCC
Q psy225 14 FPARLNTHHKQQISSKENTLSSSSSSH------SSDLPMICSQT 51 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~~Cg~~fc~~~~------~~~~~~~C~~C 51 (450)
|+||... +.+|+.. .|||.||..++ .....+.||+|
T Consensus 1 CpiC~~~-~~~Pv~l-~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL-FKDPVSL-PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh-hCCcccc-CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999 9999999 59999998877 12223789987
No 44
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.66 E-value=2.7e-05 Score=52.16 Aligned_cols=46 Identities=26% Similarity=0.633 Sum_probs=23.8
Q ss_pred eecccccccccccchhhcccc-CC--CCcccCCcccccCccChhHHHHHHhh
Q psy225 186 VACRYCSKSYVADTLVTHQTK-CT--RAPIPCPNQCEMVALPREELDVHIKE 234 (450)
Q Consensus 186 ~~C~~C~~~f~~~~l~~H~~~-~~--~~~~~C~~~C~~~f~~~~~l~~H~~~ 234 (450)
|.|++|++.|....|..|... |. .+.+.|| .|...+ ..+|..|+..
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CP-iC~~~~--~~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSESKNVVCP-ICSSRV--TDNLIRHLNS 51 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCCCCCccCC-Cchhhh--hhHHHHHHHH
Confidence 556666664443556666555 42 2345666 665432 2355555544
No 45
>KOG1987|consensus
Probab=97.57 E-value=0.00057 Score=64.15 Aligned_cols=117 Identities=20% Similarity=0.356 Sum_probs=86.2
Q ss_pred EEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEeCCCC
Q psy225 306 WKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFDQSEK 385 (450)
Q Consensus 306 w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~~~~~ 385 (450)
|.+.+++.... .++|..|-.+ |-.|++.+||.|+ ++++|+.+...+ +|.+.+.+.|.++|+...
T Consensus 8 ~~~~~~~~~~l---~~ys~~~~~~--~~~~~~~~~~~~~------~~~~~~~~~~~~-----~~~~~~~~~l~v~n~~~~ 71 (297)
T KOG1987|consen 8 WVISNFSSVGL---VIYSNGFVKG--GCKWRLSAYPKGN------YLSLTLSVSDSP-----GWERYAKLRLTVVNQKSE 71 (297)
T ss_pred eeeccCcchhh---hccccceeec--CceEEEEEecCCC------EEEEEEEeccCC-----CcceeEEEEEEEccCCCc
Confidence 88988877653 4789999988 8899999999996 789999887544 699999999999999765
Q ss_pred Cc-cee-EeeecCCCCCCCCCCCCCCCCccCCccceeeccccc--cCCceeCCcEEEEEEEecCCc
Q psy225 386 PV-NVV-ESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIR--KRQFLKDDAIFIRVKVDPSKI 447 (450)
Q Consensus 386 ~~-~~~-~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~--~~~fl~dd~l~i~~~v~v~~~ 447 (450)
.. ... ..+ ..|... .-...||+...++...+. ..||+.++.+.+.+.+.|.+.
T Consensus 72 ~~~~~~~~~~------~~~~~~---~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a~~~V~~~ 128 (297)
T KOG1987|consen 72 KYLSTVEEGF------SWFRFN---KVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVARSEVFEA 128 (297)
T ss_pred ceeeeeeeeE------Eecccc---ccccccCcccccChHHhhcccCcEEEcCceEEEeeecceee
Confidence 33 222 111 112111 114589999998888776 469999988888777766544
No 46
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.47 E-value=3.7e-05 Score=51.75 Aligned_cols=50 Identities=10% Similarity=0.020 Sum_probs=26.9
Q ss_pred ccCceeeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 7 SWTKTLSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 7 ~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
.+++-+.|++|... ++.|+-...|+|.||+.|+...-...||+|..+-..
T Consensus 3 ~le~lLrCs~C~~~-l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~ 52 (65)
T PF14835_consen 3 RLEELLRCSICFDI-LKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWI 52 (65)
T ss_dssp HHHHTTS-SSS-S---SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-
T ss_pred HHHHhcCCcHHHHH-hcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHH
Confidence 45667899999999 999998889999999999854444579999887543
No 47
>PHA00732 hypothetical protein
Probab=97.45 E-value=9.9e-05 Score=53.37 Aligned_cols=42 Identities=19% Similarity=0.435 Sum_probs=23.3
Q ss_pred cccCCcccccccc-cHHHhHHhh-hCCCCcccCcccccccChhHHHHHh
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSKF-TCPERITTCQYCLESFSGMEMEDHT 150 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~l~~H~ 150 (450)
||.|+.|++.|.. ..|..|++. |.+ +.|+.|++.|. .+..|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~--~l~~H~ 44 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR--RLNQHF 44 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC--Chhhhh
Confidence 3556666666666 666666653 332 35666666554 244444
No 48
>KOG3002|consensus
Probab=97.44 E-value=8.2e-05 Score=68.25 Aligned_cols=110 Identities=17% Similarity=0.230 Sum_probs=83.1
Q ss_pred CceeeccCCCCcccCCC-cccCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCCCCchH
Q psy225 9 TKTLSFPARLNTHHKQQ-ISSKENTLSSSSSSHSSDLPMICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKEGCKWY 87 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p-~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~c~~~ 87 (450)
.+-+.||+|... +..| +|| .-||..|.+|-. +....||.|+.++.. .+. +.+++.++...+.|++-..||++.
T Consensus 46 ~~lleCPvC~~~-l~~Pi~QC-~nGHlaCssC~~-~~~~~CP~Cr~~~g~--~R~-~amEkV~e~~~vpC~~~~~GC~~~ 119 (299)
T KOG3002|consen 46 LDLLDCPVCFNP-LSPPIFQC-DNGHLACSSCRT-KVSNKCPTCRLPIGN--IRC-RAMEKVAEAVLVPCKNAKLGCTKS 119 (299)
T ss_pred hhhccCchhhcc-Ccccceec-CCCcEehhhhhh-hhcccCCcccccccc--HHH-HHHHHHHHhceecccccccCCcee
Confidence 344679999998 6655 889 589999887742 567799999988773 355 778898999999999999999998
Q ss_pred HHHhHHHHhhhcCCCCcccCC----cccccccccHHHhHHh
Q psy225 88 DELKSLKGHLQTCKYDAIPCN----KCLAAIPKTLMEDHSK 124 (450)
Q Consensus 88 ~~l~~~~~H~~~c~~~~~~C~----~C~~~f~~~~l~~H~~ 124 (450)
.....-..|...|.+.++.|| .|.-.=...+|..|.+
T Consensus 120 ~~Y~~~~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~ 160 (299)
T KOG3002|consen 120 FPYGEKSKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLN 160 (299)
T ss_pred eccccccccccccccCCcCCCCCcccCCccCcHHHHHHHHH
Confidence 887555789999999888884 3333222255555554
No 49
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=97.43 E-value=9e-05 Score=51.00 Aligned_cols=54 Identities=33% Similarity=0.889 Sum_probs=39.7
Q ss_pred hhhcCCCCcccCCc--ccccccccHHHhHHhhhCCCCcccCcc----cccccChhHHHHH
Q psy225 96 HLQTCKYDAIPCNK--CLAAIPKTLMEDHSKFTCPERITTCQY----CLESFSGMEMEDH 149 (450)
Q Consensus 96 H~~~c~~~~~~C~~--C~~~f~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~~l~~H 149 (450)
|...|++.++.|+. |...+.+.+|..|+...++.++..|++ |+..+....|..|
T Consensus 1 H~~~C~~~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp HHTTSTTSEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CcccCCCCEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 56679999999977 667788899999999999999999988 7777666655554
No 50
>KOG0320|consensus
Probab=97.25 E-value=4.6e-05 Score=62.40 Aligned_cols=47 Identities=13% Similarity=0.138 Sum_probs=37.2
Q ss_pred CceeeccCCCCcccCC--CcccCCCCCcccCCCC--CCCCCCCCCCCCCCCCC
Q psy225 9 TKTLSFPARLNTHHKQ--QISSKENTLSSSSSSH--SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~--p~~c~~Cg~~fc~~~~--~~~~~~~C~~C~~~~~~ 57 (450)
+..|.|+||... ..+ |+.. .|||.||+.|+ .......||+|++.+..
T Consensus 129 ~~~~~CPiCl~~-~sek~~vsT-kCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDS-VSEKVPVST-KCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecc-hhhcccccc-ccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 456999999998 655 4445 79999999998 34567899999997665
No 51
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.10 E-value=0.00022 Score=38.33 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=15.0
Q ss_pred ccCCcccccCccChhHHHHHHhh
Q psy225 212 IPCPNQCEMVALPREELDVHIKE 234 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~~ 234 (450)
|.|+ .|++.|..+..|..|++.
T Consensus 1 y~C~-~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCP-ICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEET-TTTEEESSHHHHHHHHHH
T ss_pred CCCC-CCCCccCCHHHHHHHHhH
Confidence 4566 677777777777777765
No 52
>PHA00732 hypothetical protein
Probab=97.07 E-value=0.00055 Score=49.50 Aligned_cols=45 Identities=24% Similarity=0.472 Sum_probs=33.6
Q ss_pred eeecccccccccc-cchhhcccc-CCCCcccCCcccccCccChhHHHHHHhhh
Q psy225 185 LVACRYCSKSYVA-DTLVTHQTK-CTRAPIPCPNQCEMVALPREELDVHIKEH 235 (450)
Q Consensus 185 ~~~C~~C~~~f~~-~~l~~H~~~-~~~~~~~C~~~C~~~f~~~~~l~~H~~~h 235 (450)
||.|+.|++.|.+ ..|..|++. |. ++.|+ .|++.|. .|..|..+.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~--~~~C~-~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT--LTKCP-VCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC--CCccC-CCCCEeC---Chhhhhccc
Confidence 5778888888888 888888874 53 34788 8888885 577777653
No 53
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.06 E-value=0.00025 Score=59.95 Aligned_cols=49 Identities=10% Similarity=-0.004 Sum_probs=38.6
Q ss_pred ccCceeeccCCCCcccCCCcccCCCCCcccCCCCC------------------CCCCCCCCCCCCCCCC
Q psy225 7 SWTKTLSFPARLNTHHKQQISSKENTLSSSSSSHS------------------SDLPMICSQTKSRTPL 57 (450)
Q Consensus 7 ~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~------------------~~~~~~C~~C~~~~~~ 57 (450)
+....+.|+||... +.+|+.. .|||.||..|+. ......||+|+..+..
T Consensus 14 ~~~~~~~CpICld~-~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 14 DSGGDFDCNICLDQ-VRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred cCCCccCCccCCCc-CCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 44567999999999 9999998 599999887771 1235689999887654
No 54
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.01 E-value=0.00095 Score=44.62 Aligned_cols=19 Identities=16% Similarity=0.501 Sum_probs=7.5
Q ss_pred ccCCcccccccccHHHhHH
Q psy225 105 IPCNKCLAAIPKTLMEDHS 123 (450)
Q Consensus 105 ~~C~~C~~~f~~~~l~~H~ 123 (450)
|.||.|++.|....|..|.
T Consensus 3 f~CP~C~~~~~~~~L~~H~ 21 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHC 21 (54)
T ss_pred cCCCCCCCccCHHHHHHHH
Confidence 3444444433224444443
No 55
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=96.99 E-value=0.00026 Score=49.22 Aligned_cols=54 Identities=11% Similarity=0.021 Sum_probs=41.2
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC-CCCCCCchhHHh
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL-SLTPDVSDSEKD 69 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~-~~~~~~~~~~~~ 69 (450)
+.|+||+.. +.+|+.. .|||.|++.++ ..+ ...||.|+..+.. .+.++ ..+++.
T Consensus 2 ~~Cpi~~~~-~~~Pv~~-~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~~~l~~~-~~l~~~ 59 (63)
T smart00504 2 FLCPISLEV-MKDPVIL-PSGQTYERRAIEKWLLS-HGTDPVTGQPLTHEDLIPN-LALKSA 59 (63)
T ss_pred cCCcCCCCc-CCCCEEC-CCCCEEeHHHHHHHHHH-CCCCCCCcCCCChhhceeC-HHHHHH
Confidence 679999999 9999998 49999988777 222 5689999998865 55555 444443
No 56
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.78 E-value=0.00067 Score=64.68 Aligned_cols=61 Identities=7% Similarity=-0.023 Sum_probs=45.8
Q ss_pred ccccCceeeccCCCCcccCCCcccCCCCCcccCCCCC--CCCCCCCCCCCCCCCC-CCCCCCchhHH
Q psy225 5 FTSWTKTLSFPARLNTHHKQQISSKENTLSSSSSSHS--SDLPMICSQTKSRTPL-SLTPDVSDSEK 68 (450)
Q Consensus 5 ~~~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~--~~~~~~C~~C~~~~~~-~~~~~~~~~~~ 68 (450)
++.++..+.|+||... +.+|+.. .|||.||..|+. -.....||.|+..+.. .+..+ ..+..
T Consensus 20 l~~Le~~l~C~IC~d~-~~~Pvit-pCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N-~~L~~ 83 (397)
T TIGR00599 20 LYPLDTSLRCHICKDF-FDVPVLT-SCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSN-WLVSE 83 (397)
T ss_pred ccccccccCCCcCchh-hhCccCC-CCCCchhHHHHHHHHhCCCCCCCCCCccccccCccc-hHHHH
Confidence 4677889999999999 9999987 599999998882 1223489999988765 44444 44443
No 57
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=96.75 E-value=0.00053 Score=36.77 Aligned_cols=19 Identities=32% Similarity=0.662 Sum_probs=8.4
Q ss_pred cCcccccccChhH-HHHHhh
Q psy225 133 TCQYCLESFSGME-MEDHTG 151 (450)
Q Consensus 133 ~C~~C~~~f~~~~-l~~H~~ 151 (450)
.|+.|++.|.... |..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 3444444444444 444443
No 58
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.65 E-value=0.0003 Score=50.43 Aligned_cols=60 Identities=8% Similarity=-0.019 Sum_probs=42.2
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC-CCCCCCchhHHhh
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL-SLTPDVSDSEKDT 70 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~-~~~~~~~~~~~~~ 70 (450)
+++.|.|+|++.+ +++|+..+ +|+.|.+.++ .......||.++..+.. .+.++ ..++..+
T Consensus 1 iP~~f~CpIt~~l-M~dPVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn-~~Lk~~I 64 (73)
T PF04564_consen 1 IPDEFLCPITGEL-MRDPVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN-RALKSAI 64 (73)
T ss_dssp SSGGGB-TTTSSB--SSEEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE--HHHHHHH
T ss_pred CCcccCCcCcCcH-hhCceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC-HHHHHHH
Confidence 4678999999999 99999996 8899977666 44567899999988877 66666 5555544
No 59
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=96.53 E-value=0.00027 Score=43.72 Aligned_cols=36 Identities=11% Similarity=0.077 Sum_probs=27.0
Q ss_pred ccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCC
Q psy225 14 FPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQT 51 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C 51 (450)
|+||... +++|+....|||.||..++ ... ...||.|
T Consensus 1 C~iC~~~-~~~~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDE-LRDPVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB--SSEEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCc-ccCcCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 8999999 9999666679999998877 223 4688876
No 60
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.50 E-value=0.0012 Score=36.99 Aligned_cols=26 Identities=27% Similarity=0.653 Sum_probs=18.2
Q ss_pred cccCCcccccCccChhHHHHHHhhhcC
Q psy225 211 PIPCPNQCEMVALPREELDVHIKEHCN 237 (450)
Q Consensus 211 ~~~C~~~C~~~f~~~~~l~~H~~~h~~ 237 (450)
||.|. .|++.|.....|..|++.|++
T Consensus 1 ~~~C~-~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECD-ECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEET-TTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCC-ccCCccCChhHHHHHhHHhcC
Confidence 45666 777777777777777776653
No 61
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.49 E-value=0.0018 Score=59.07 Aligned_cols=59 Identities=14% Similarity=0.041 Sum_probs=40.1
Q ss_pred eeeccCCCCcccCCCc---ccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC-----CCCCCCchhHHhh
Q psy225 11 TLSFPARLNTHHKQQI---SSKENTLSSSSSSH---SSDLPMICSQTKSRTPL-----SLTPDVSDSEKDT 70 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~---~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~-----~~~~~~~~~~~~~ 70 (450)
.+.||+|.......|- ....|||.||.+|+ ....+..||.|+..+.. +.+.| ..+++++
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D-~~vekEV 72 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED-PTVEKEV 72 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcccccccc-HHHHHHH
Confidence 4789999983123331 22269999999998 33566799999988766 36666 5555543
No 62
>KOG1863|consensus
Probab=96.34 E-value=0.0035 Score=68.77 Aligned_cols=124 Identities=13% Similarity=0.170 Sum_probs=88.9
Q ss_pred EEEECCchhhhhccccccCCCcccCCCCcEEEEEEEecCCCCCCCCeEEEEEEecCCCCCcccCCcccceEEEEEEeCCC
Q psy225 305 IWKITDYSLKCQESIELLSPSFYTSQFGYKLQVSLFLNGNGAGEGTHVSVYIKLLPGEYDALLKWPFSHSVSFTLFDQSE 384 (450)
Q Consensus 305 ~w~i~~~s~~~~~~~~~~S~~f~~~~~g~~w~l~~~p~g~~~~~~~~~s~yl~l~~g~~d~~l~Wp~~~~~~~~l~~~~~ 384 (450)
.|...+....... ..||.|-.| +.+|++.+.|++.. ...+++|+.......+ -.|.+.+.+.+.+.|..+
T Consensus 30 ~~~~~~~~~~~~~---~~~~~~~~~--~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~--~~~s~~~~~~~~v~~~~~ 99 (1093)
T KOG1863|consen 30 TIDGIDDKSLLYR---ALSSNFGAG--ATKWKILIAPKVNS---LQSTRKKLEVMPSQSL--KSWSCGAQAVLRVKNTID 99 (1093)
T ss_pred cccCcCcchhhhH---hcCcccccc--ccceeeeeccccCc---ccceeEEeeeccCCCC--cceEecchhhhccccCCC
Confidence 3666555554432 678888888 99999999999973 3469999998755444 449999999999999333
Q ss_pred CCcceeEeeecCCCCCCCCCCCCCCCCccCCccceeeccccc--cCCceeCCcEEEEEEEecCCcc
Q psy225 385 KPVNVVESFVPDPTWENFQRPSKQPDSLGFGFPRFVSLDTIR--KRQFLKDDAIFIRVKVDPSKIV 448 (450)
Q Consensus 385 ~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~f~~~~~l~--~~~fl~dd~l~i~~~v~v~~~~ 448 (450)
....... +..+.|. .....||+..|+.++++. ..||+.+|++.+++.|.+..-+
T Consensus 100 ~~~~~~~-----~~~h~~~-----~~~~dwg~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~ 155 (1093)
T KOG1863|consen 100 NLPDPEK-----AIHHVFT-----ADERDWGFSCFSTSSDIRKPEDGYVRNGLEKLEKRVRVEQPT 155 (1093)
T ss_pred Cchhhhh-----hhhhccc-----ccccchhhccchhHhhccCcccccccccceeeeeeeeeecCC
Confidence 2221111 1112232 335789999999999997 6699999999999999886543
No 63
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.24 E-value=0.0029 Score=34.07 Aligned_cols=23 Identities=30% Similarity=0.696 Sum_probs=13.6
Q ss_pred ccCCcccccCccChhHHHHHHhhh
Q psy225 212 IPCPNQCEMVALPREELDVHIKEH 235 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~~h 235 (450)
|.|+ .|++.|..+..|..|+++|
T Consensus 1 ~~C~-~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCP-ICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-S-STS-EESSHHHHHHHHHHH
T ss_pred CCCc-CCCCcCCcHHHHHHHHHhh
Confidence 3566 6666677777777776654
No 64
>KOG0317|consensus
Probab=96.20 E-value=0.0011 Score=59.10 Aligned_cols=48 Identities=8% Similarity=-0.081 Sum_probs=37.2
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCCCC--CCCCCCCCCCCCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSHSS--DLPMICSQTKSRTPL 57 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~~~~ 57 (450)
.+..++|.+|... ..+|-..+ |||.||-+|+.+ ...-+||.|+..+..
T Consensus 236 ~~a~~kC~LCLe~-~~~pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 236 PEATRKCSLCLEN-RSNPSATP-CGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCCCceEEEecC-CCCCCcCc-CcchHHHHHHHHHHccccCCCcccccCCC
Confidence 3455899999999 88998885 999999888832 233469999987553
No 65
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=96.16 E-value=0.0025 Score=35.67 Aligned_cols=22 Identities=14% Similarity=0.548 Sum_probs=11.8
Q ss_pred ccCCcccccccc-cHHHhHHhhh
Q psy225 105 IPCNKCLAAIPK-TLMEDHSKFT 126 (450)
Q Consensus 105 ~~C~~C~~~f~~-~~l~~H~~~h 126 (450)
+.|..|++.|.. ..|..|++.|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 455555555555 5555555544
No 66
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=96.12 E-value=0.0011 Score=44.66 Aligned_cols=48 Identities=15% Similarity=0.122 Sum_probs=28.6
Q ss_pred CCcccccCceeeccCCCCcccCCCcccCCCCCcccCCCC----CCCCCCCCCC
Q psy225 2 VRSFTSWTKTLSFPARLNTHHKQQISSKENTLSSSSSSH----SSDLPMICSQ 50 (450)
Q Consensus 2 ~~~~~~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~----~~~~~~~C~~ 50 (450)
+..++...-.+.||+.... +.+|+....|||.|.+..+ ...+...||+
T Consensus 2 di~i~~~~~~~~CPiT~~~-~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 2 DIVIEGGTISLKCPITLQP-FEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -----SSB--SB-TTTSSB--SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ceEEeccEeccCCCCcCCh-hhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4445566678999999999 9999999999999966544 3566778887
No 67
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=96.10 E-value=0.00077 Score=42.20 Aligned_cols=37 Identities=11% Similarity=0.068 Sum_probs=29.9
Q ss_pred ccCCCCcccCCCcccCCCCCcccCCCC----CCCCCCCCCCC
Q psy225 14 FPARLNTHHKQQISSKENTLSSSSSSH----SSDLPMICSQT 51 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~~Cg~~fc~~~~----~~~~~~~C~~C 51 (450)
|+||... +.+|.....|||.||..++ .....+.||.|
T Consensus 1 C~iC~~~-~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEP-FEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSB-CSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcc-ccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999999 9999855579999988777 22567789887
No 68
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.04 E-value=0.0038 Score=47.84 Aligned_cols=71 Identities=17% Similarity=0.309 Sum_probs=18.8
Q ss_pred ecccccccccc-cchhhcccc-CCCCcccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhh
Q psy225 187 ACRYCSKSYVA-DTLVTHQTK-CTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHI 264 (450)
Q Consensus 187 ~C~~C~~~f~~-~~l~~H~~~-~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~ 264 (450)
+|.+|+..|.. ..|..|+.. |+...-... .+.....+..+++. .....+.|.+ |+..|.....|..|+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~-----~l~~~~~~~~~~~~-~~~~~~~C~~----C~~~f~s~~~l~~Hm 70 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQK-----YLVDPNRLLNYLRK-KVKESFRCPY----CNKTFRSREALQEHM 70 (100)
T ss_dssp ------------------------------------------------------SSEEBSS----SS-EESSHHHHHHHH
T ss_pred Ccccccccccccccccccccccccccccccc-----cccccccccccccc-ccCCCCCCCc----cCCCCcCHHHHHHHH
Confidence 47788888888 778888866 543221111 12233334344432 2223577887 888888888888888
Q ss_pred Hhh
Q psy225 265 EEN 267 (450)
Q Consensus 265 ~~~ 267 (450)
++.
T Consensus 71 ~~~ 73 (100)
T PF12756_consen 71 RSK 73 (100)
T ss_dssp HHT
T ss_pred cCc
Confidence 864
No 69
>KOG0823|consensus
Probab=96.01 E-value=0.003 Score=54.51 Aligned_cols=48 Identities=8% Similarity=-0.036 Sum_probs=39.7
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCC-----CCCCCCCCCCCCCCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSH-----SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~-----~~~~~~~C~~C~~~~~~ 57 (450)
....|.|.||... .++|+.. .|||-||-.|+ .......||+|+..+..
T Consensus 44 ~~~~FdCNICLd~-akdPVvT-lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 44 DGGFFDCNICLDL-AKDPVVT-LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCceeeeeeccc-cCCCEEe-ecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 4567999999999 9999998 69999998887 45666789999876443
No 70
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=95.94 E-value=0.002 Score=41.02 Aligned_cols=39 Identities=3% Similarity=-0.038 Sum_probs=29.3
Q ss_pred eccCCCCccc--C-CCcccCCCCCcccCCCCCC--CCCCCCCCCCC
Q psy225 13 SFPARLNTHH--K-QQISSKENTLSSSSSSHSS--DLPMICSQTKS 53 (450)
Q Consensus 13 ~C~iC~~~~~--~-~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~ 53 (450)
.|++|... + . .|+.. .|||.||..++.. .....||+|++
T Consensus 1 ~C~~C~~~-~~~~~~~~l~-~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEK-YSEERRPRLT-SCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCcc-ccCCCCeEEc-ccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 48899988 6 3 44555 6999999888743 35789999974
No 71
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=95.87 E-value=0.0022 Score=40.75 Aligned_cols=41 Identities=10% Similarity=0.068 Sum_probs=32.5
Q ss_pred eccCCCCcccCCCcccCCCCCcccCCCCC---CCCCCCCCCCCCC
Q psy225 13 SFPARLNTHHKQQISSKENTLSSSSSSHS---SDLPMICSQTKSR 54 (450)
Q Consensus 13 ~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~---~~~~~~C~~C~~~ 54 (450)
.|+||... +.+++....|||.||..++. ......||.|+..
T Consensus 1 ~C~iC~~~-~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEE-FREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCCcCchh-hhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 48999999 88888887799999887772 2346789999864
No 72
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.75 E-value=0.0058 Score=32.81 Aligned_cols=19 Identities=16% Similarity=0.464 Sum_probs=7.8
Q ss_pred cCCcccccccc-cHHHhHHh
Q psy225 106 PCNKCLAAIPK-TLMEDHSK 124 (450)
Q Consensus 106 ~C~~C~~~f~~-~~l~~H~~ 124 (450)
.|+.|++.|.. ..|..|+.
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHH
Confidence 34444444444 44444444
No 73
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.45 E-value=0.01 Score=37.82 Aligned_cols=29 Identities=17% Similarity=0.289 Sum_probs=15.6
Q ss_pred CcccCCcccccccc-cHHHhHHhhhCCCCc
Q psy225 103 DAIPCNKCLAAIPK-TLMEDHSKFTCPERI 131 (450)
Q Consensus 103 ~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~ 131 (450)
.|..|+.|+..+++ .+|+.|+.++++.+|
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 56677777777777 777777766665543
No 74
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.45 E-value=0.0067 Score=53.93 Aligned_cols=43 Identities=9% Similarity=0.082 Sum_probs=37.9
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSR 54 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~ 54 (450)
.+.|+.|+.. ++.|...++||+.||..|+ .-+..|.||.|...
T Consensus 274 ~LkCplc~~L-lrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rk 319 (427)
T COG5222 274 SLKCPLCHCL-LRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319 (427)
T ss_pred cccCcchhhh-hhCcccCccccchHHHHHHhhhhhhccccCCCcccc
Confidence 4899999999 9999999999999998888 45678999999663
No 75
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.39 E-value=0.005 Score=55.30 Aligned_cols=24 Identities=25% Similarity=0.481 Sum_probs=15.2
Q ss_pred Cceeeccc--ccccccc-cchhhcccc
Q psy225 183 KRLVACRY--CSKSYVA-DTLVTHQTK 206 (450)
Q Consensus 183 ~k~~~C~~--C~~~f~~-~~l~~H~~~ 206 (450)
+|||+|++ |.|.+.. ..|+.|+.-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lh 373 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLH 373 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhc
Confidence 36777765 6676666 556666544
No 76
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.23 E-value=0.017 Score=31.52 Aligned_cols=24 Identities=29% Similarity=0.699 Sum_probs=18.6
Q ss_pred ccCCcccccCccChhHHHHHHhhhc
Q psy225 212 IPCPNQCEMVALPREELDVHIKEHC 236 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~~h~ 236 (450)
+.|+ .|++.|.....|..|++.|.
T Consensus 1 ~~C~-~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCP-ECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCC-CCcchhCCHHHHHHHHHHhc
Confidence 4677 88888888888888887653
No 77
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=95.18 E-value=0.0086 Score=53.84 Aligned_cols=68 Identities=16% Similarity=0.273 Sum_probs=36.8
Q ss_pred CCcccCc--ccccccChhH-HHHHhhh-CCCCcccccccCChhhchhHHHhhhhhcccCceeecccccccccc-cchhhc
Q psy225 129 ERITTCQ--YCLESFSGME-MEDHTGH-CSYEMVYCENKCGHKIQRRLMAKHRANDCYKRLVACRYCSKSYVA-DTLVTH 203 (450)
Q Consensus 129 ~~~~~C~--~C~~~f~~~~-l~~H~~~-~~~~~~~~c~~C~~~f~~~~l~~H~~~h~~~k~~~C~~C~~~f~~-~~l~~H 203 (450)
++||+|+ .|+|.++... |+-|+.. |...+...-. .-..|.-.-...|||.|++|+|.+.. ..|+.|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p---------~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYH 417 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP---------SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC---------CccccccccccCCceeccccchhhccCccceec
Confidence 4777776 4777777766 7776642 2111111000 00011111234578888888888877 667776
Q ss_pred cc
Q psy225 204 QT 205 (450)
Q Consensus 204 ~~ 205 (450)
..
T Consensus 418 r~ 419 (423)
T COG5189 418 RK 419 (423)
T ss_pred cc
Confidence 53
No 78
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.15 E-value=0.011 Score=45.18 Aligned_cols=20 Identities=35% Similarity=0.800 Sum_probs=0.0
Q ss_pred cCcccccccChhH-HHHHhhh
Q psy225 133 TCQYCLESFSGME-MEDHTGH 152 (450)
Q Consensus 133 ~C~~C~~~f~~~~-l~~H~~~ 152 (450)
+|..|+..|.... |..|+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~ 21 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKK 21 (100)
T ss_dssp ---------------------
T ss_pred Ccccccccccccccccccccc
Confidence 3777777777766 7777754
No 79
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.15 E-value=0.017 Score=36.88 Aligned_cols=31 Identities=23% Similarity=0.434 Sum_probs=15.2
Q ss_pred CCCcccCCcccccCccChhHHHHHHhhhcCCc
Q psy225 208 TRAPIPCPNQCEMVALPREELDVHIKEHCNSL 239 (450)
Q Consensus 208 ~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~ 239 (450)
.+.|-.|| .|+..+.+..+|+.|++.+++.+
T Consensus 21 S~~PatCP-~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCP-ICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-T-TT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCC-cchhhccchhhHHHHHHHHhccc
Confidence 34455566 66666666666666665555444
No 80
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=94.96 E-value=0.0019 Score=42.42 Aligned_cols=44 Identities=5% Similarity=-0.022 Sum_probs=33.4
Q ss_pred eeeccCCCCcccCCCcccCCCCCc-ccCCCCC--CCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLS-SSSSSHS--SDLPMICSQTKSRTP 56 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~-fc~~~~~--~~~~~~C~~C~~~~~ 56 (450)
+..|.||... ..++...+ |||. ||..++. ......||+|+.++.
T Consensus 2 ~~~C~iC~~~-~~~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFEN-PRDVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSS-BSSEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCcc-CCceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4579999999 88888885 9999 8887762 236779999998754
No 81
>PHA02929 N1R/p28-like protein; Provisional
Probab=94.85 E-value=0.0093 Score=52.92 Aligned_cols=48 Identities=4% Similarity=-0.092 Sum_probs=34.3
Q ss_pred CceeeccCCCCcccCCCc-------ccCCCCCcccCCCCC--CCCCCCCCCCCCCCCC
Q psy225 9 TKTLSFPARLNTHHKQQI-------SSKENTLSSSSSSHS--SDLPMICSQTKSRTPL 57 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p~-------~c~~Cg~~fc~~~~~--~~~~~~C~~C~~~~~~ 57 (450)
.+...|+||... +.++. ..+.|||.||..|+. .+....||+|+..+..
T Consensus 172 ~~~~eC~ICle~-~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 172 SKDKECAICMEK-VYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCccCCcc-cccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 445789999998 65431 234699999998882 1235589999987654
No 82
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=94.63 E-value=0.02 Score=50.15 Aligned_cols=64 Identities=19% Similarity=0.211 Sum_probs=33.8
Q ss_pred chhHHhhhcceeeccCCCCCCchHHHHhHHHHhhhcCCCCcccCCc----ccccccccHHHhHHhhhC
Q psy225 64 SDSEKDTMGSLIHCIHYKEGCKWYDELKSLKGHLQTCKYDAIPCNK----CLAAIPKTLMEDHSKFTC 127 (450)
Q Consensus 64 ~~~~~~~~~~~~~C~~c~~~c~~~~~l~~~~~H~~~c~~~~~~C~~----C~~~f~~~~l~~H~~~h~ 127 (450)
..+++.+..+.+.|++...||.+...+.....|...|++.|+.||. |+-.=....|..|....+
T Consensus 4 ~alE~v~~~~~~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H 71 (198)
T PF03145_consen 4 RALEKVAESIKFPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKH 71 (198)
T ss_dssp -----------EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHT
T ss_pred HHHHHHHhhceecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHC
Confidence 3456666778899999999999998888899999999999999976 433322366666665443
No 83
>KOG0978|consensus
Probab=94.46 E-value=0.0069 Score=61.45 Aligned_cols=47 Identities=6% Similarity=-0.017 Sum_probs=38.1
Q ss_pred CceeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 9 TKTLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
..-++|++|... ..+.... .|||.||..|+ ...+.-+||.|+.+|..
T Consensus 641 K~~LkCs~Cn~R-~Kd~vI~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 641 KELLKCSVCNTR-WKDAVIT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred HhceeCCCccCc-hhhHHHH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 356789999987 6676666 69999999998 34566789999998876
No 84
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.39 E-value=0.01 Score=52.25 Aligned_cols=44 Identities=7% Similarity=-0.071 Sum_probs=35.6
Q ss_pred CceeeccCCCCcccCCCcccCCCCCcccCCCCC----CCCCCCCCCCCCC
Q psy225 9 TKTLSFPARLNTHHKQQISSKENTLSSSSSSHS----SDLPMICSQTKSR 54 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~----~~~~~~C~~C~~~ 54 (450)
...|+|.+|... ..+|.-. .|||.||..|+. .++.-.||.|+..
T Consensus 213 ~~d~kC~lC~e~-~~~ps~t-~CgHlFC~~Cl~~~~t~~k~~~CplCRak 260 (271)
T COG5574 213 LADYKCFLCLEE-PEVPSCT-PCGHLFCLSCLLISWTKKKYEFCPLCRAK 260 (271)
T ss_pred ccccceeeeecc-cCCcccc-cccchhhHHHHHHHHHhhccccCchhhhh
Confidence 468999999999 8888777 599999988873 3455559999874
No 85
>KOG2164|consensus
Probab=94.36 E-value=0.014 Score=56.38 Aligned_cols=45 Identities=13% Similarity=0.163 Sum_probs=37.3
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCC-------CCCCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSH-------SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~-------~~~~~~~C~~C~~~~~~ 57 (450)
.+.||||... ..-|.... |||.||-.|+ .-.....||+|...+..
T Consensus 186 ~~~CPICL~~-~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEP-PSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCC-CCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 7899999999 88888885 9999999888 23567899999887554
No 86
>KOG2879|consensus
Probab=94.31 E-value=0.025 Score=50.11 Aligned_cols=46 Identities=7% Similarity=-0.074 Sum_probs=38.0
Q ss_pred ceeeccCCCCcccCCCcccCCCCCcccCCCCC----CCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLSSSSSSHS----SDLPMICSQTKSRTP 56 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~----~~~~~~C~~C~~~~~ 56 (450)
..-+|++|+.. ..-|++-..|||.||.-|+. -...+.||.|+++-.
T Consensus 238 ~~~~C~~Cg~~-PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEP-PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCC-CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 44589999999 99999997899999988883 245689999998644
No 87
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.31 E-value=0.035 Score=30.19 Aligned_cols=19 Identities=21% Similarity=0.581 Sum_probs=8.7
Q ss_pred cCcccccccChhH-HHHHhh
Q psy225 133 TCQYCLESFSGME-MEDHTG 151 (450)
Q Consensus 133 ~C~~C~~~f~~~~-l~~H~~ 151 (450)
.|+.|++.|.... |..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 3444444444443 444444
No 88
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.20 E-value=0.038 Score=30.15 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=11.0
Q ss_pred cCcccccccChhHHHHHhhhC
Q psy225 133 TCQYCLESFSGMEMEDHTGHC 153 (450)
Q Consensus 133 ~C~~C~~~f~~~~l~~H~~~~ 153 (450)
.|+.||+.|....|..|+..|
T Consensus 4 ~C~~CgR~F~~~~l~~H~~~C 24 (25)
T PF13913_consen 4 PCPICGRKFNPDRLEKHEKIC 24 (25)
T ss_pred cCCCCCCEECHHHHHHHHHhc
Confidence 455555555444455555443
No 89
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=94.17 E-value=0.01 Score=49.46 Aligned_cols=46 Identities=11% Similarity=-0.111 Sum_probs=38.0
Q ss_pred ceeeccCCCCcccCCCcccCCCCCcccCCCCCC--CCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLSSSSSSHSS--DLPMICSQTKSRTPL 57 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~~~~ 57 (450)
-+|.|-||.+. ++.|+.. .|||.||..|.+. .+.-.|-+|++....
T Consensus 195 IPF~C~iCKkd-y~spvvt-~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 195 IPFLCGICKKD-YESPVVT-ECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred Cceeehhchhh-ccchhhh-hcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 47899999999 9999998 5999999988743 355689999886544
No 90
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.98 E-value=0.015 Score=31.73 Aligned_cols=18 Identities=28% Similarity=0.787 Sum_probs=7.6
Q ss_pred ecccccccccccchhhcc
Q psy225 187 ACRYCSKSYVADTLVTHQ 204 (450)
Q Consensus 187 ~C~~C~~~f~~~~l~~H~ 204 (450)
+|+.||+.|..+.|..|+
T Consensus 4 ~C~~CgR~F~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKFNPDRLEKHE 21 (25)
T ss_pred cCCCCCCEECHHHHHHHH
Confidence 344444444334444443
No 91
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=93.61 E-value=0.045 Score=30.09 Aligned_cols=23 Identities=4% Similarity=-0.154 Sum_probs=17.0
Q ss_pred eccCCCCcccCCCcccCCCCCcc
Q psy225 13 SFPARLNTHHKQQISSKENTLSS 35 (450)
Q Consensus 13 ~C~iC~~~~~~~p~~c~~Cg~~f 35 (450)
.||.|+..+....-.|+.||+.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 48888876355667788888877
No 92
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=93.51 E-value=0.018 Score=51.16 Aligned_cols=47 Identities=6% Similarity=-0.122 Sum_probs=37.0
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
++.-+.|.||... ++-|...+ |||.||.-|+ .++. .-||+|+..+..
T Consensus 22 LDs~lrC~IC~~~-i~ip~~Tt-CgHtFCslCIR~hL~~q-p~CP~Cr~~~~e 71 (391)
T COG5432 22 LDSMLRCRICDCR-ISIPCETT-CGHTFCSLCIRRHLGTQ-PFCPVCREDPCE 71 (391)
T ss_pred chhHHHhhhhhhe-eecceecc-cccchhHHHHHHHhcCC-CCCccccccHHh
Confidence 3455689999999 99999995 9999998887 4444 469999876444
No 93
>PRK04860 hypothetical protein; Provisional
Probab=93.48 E-value=0.047 Score=45.49 Aligned_cols=37 Identities=24% Similarity=0.477 Sum_probs=25.6
Q ss_pred CcccCcccccccChhHHHHHhhhCCCCcccccccCChhhc
Q psy225 130 RITTCQYCLESFSGMEMEDHTGHCSYEMVYCENKCGHKIQ 169 (450)
Q Consensus 130 ~~~~C~~C~~~f~~~~l~~H~~~~~~~~~~~c~~C~~~f~ 169 (450)
-+|.|. |+. ....+..|.++|.++++|.|..|+..|.
T Consensus 118 ~~Y~C~-C~~--~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 118 FPYRCK-CQE--HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEEcC-CCC--eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 357776 776 2223777777777777777777777765
No 94
>KOG2231|consensus
Probab=93.37 E-value=0.17 Score=51.39 Aligned_cols=70 Identities=14% Similarity=0.186 Sum_probs=31.2
Q ss_pred hhhchhHHHhhhhhccc-Cce----eecccccccccc-cchhhccccCCCCcccCC--cccccCccChhHHHHHHhhh
Q psy225 166 HKIQRRLMAKHRANDCY-KRL----VACRYCSKSYVA-DTLVTHQTKCTRAPIPCP--NQCEMVALPREELDVHIKEH 235 (450)
Q Consensus 166 ~~f~~~~l~~H~~~h~~-~k~----~~C~~C~~~f~~-~~l~~H~~~~~~~~~~C~--~~C~~~f~~~~~l~~H~~~h 235 (450)
+.+.+..|..|+..-+. ++. -.|.+|...|.. ..|.+|++..-+.-.-|+ -.++.-|..-.+|..|.+.+
T Consensus 158 k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 158 KLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred ehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhc
Confidence 33445556666554332 211 245556555555 555555554222222221 02233344445666665543
No 95
>PHA02926 zinc finger-like protein; Provisional
Probab=93.18 E-value=0.025 Score=48.64 Aligned_cols=52 Identities=6% Similarity=-0.120 Sum_probs=34.6
Q ss_pred cccCceeeccCCCCcccCCC-------cccCCCCCcccCCCCC---C-----CCCCCCCCCCCCCCC
Q psy225 6 TSWTKTLSFPARLNTHHKQQ-------ISSKENTLSSSSSSHS---S-----DLPMICSQTKSRTPL 57 (450)
Q Consensus 6 ~~~~~~~~C~iC~~~~~~~p-------~~c~~Cg~~fc~~~~~---~-----~~~~~C~~C~~~~~~ 57 (450)
....+...|.||......++ =..+.|+|.||..|+. . .....||.|+..+..
T Consensus 165 ~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 165 YRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred HhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 34556778999998623321 1244799999988871 1 124569999987664
No 96
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.14 E-value=0.065 Score=48.95 Aligned_cols=225 Identities=12% Similarity=0.158 Sum_probs=110.6
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCCC----CCCCCCCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCC-C
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSHS----SDLPMICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYK-E 82 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~----~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~-~ 82 (450)
.++.-.|.||-.. ..=.-..| |+|..|..|.. --+...|+.|+.....-++.+ .+ .-.|.+....|..-+ -
T Consensus 58 DEen~~C~ICA~~-~TYs~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V~fT~-~~-~~DI~D~~~~k~~~EK~ 133 (493)
T COG5236 58 DEENMNCQICAGS-TTYSARYP-CGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTA-SS-PADITDRRQWKGREEKV 133 (493)
T ss_pred ccccceeEEecCC-ceEEEecc-CCchHHHHHHHHHHHHHhccCCCccccccceEEEec-CC-CCcchhHhhhcccccce
Confidence 4455679999776 32222333 99998876652 235668999987533311111 00 000111111121111 1
Q ss_pred CCchHHHHhHHHHhh-hcCCCCcccCC--cccccccc-cHHHhHHhhhCCCCcccCcccccccChhHHHHHhhhCCCCcc
Q psy225 83 GCKWYDELKSLKGHL-QTCKYDAIPCN--KCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSGMEMEDHTGHCSYEMV 158 (450)
Q Consensus 83 ~c~~~~~l~~~~~H~-~~c~~~~~~C~--~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~~~~~~~~ 158 (450)
|-...+. +.+.-. .- ..|.|| .|...-.. .+|+.|.+..++ .+-|..|-+- .+.
T Consensus 134 GI~y~~E--~v~~E~~~L---L~F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~n---------------Kk~ 191 (493)
T COG5236 134 GIFYEGE--DVRDEMEDL---LSFKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGN---------------KKD 191 (493)
T ss_pred eeeecch--HHHHHHHHH---HHhcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcC---------------ccc
Confidence 1111111 111100 00 234552 34444333 667777765443 2345544210 111
Q ss_pred cccccCChh-hchhHHHhhhhhcc---cCcee-ecccccccccc-cchhhccccCCCCcccCCcccc----cCccChhHH
Q psy225 159 YCENKCGHK-IQRRLMAKHRANDC---YKRLV-ACRYCSKSYVA-DTLVTHQTKCTRAPIPCPNQCE----MVALPREEL 228 (450)
Q Consensus 159 ~~c~~C~~~-f~~~~l~~H~~~h~---~~k~~-~C~~C~~~f~~-~~l~~H~~~~~~~~~~C~~~C~----~~f~~~~~l 228 (450)
| .|.-. |.++.|..|...-- |.+-+ .|.+|...|-. ..|..|.+.-.++-+.|. .-+ .-|..-.+|
T Consensus 192 F---~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE~ChICD-~v~p~~~QYFK~Y~~L 267 (493)
T COG5236 192 F---WNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHEACHICD-MVGPIRYQYFKSYEDL 267 (493)
T ss_pred C---ccceeeeecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhhhhhhhhhh-ccCccchhhhhCHHHH
Confidence 1 12222 45677777765432 33333 59999999888 889999998444444444 222 124455678
Q ss_pred HHHHhhhcCCccccccccC--CCCCccccChHHHHHhhHh
Q psy225 229 DVHIKEHCNSLLVSCVFKD--AGCRFKGMRGETMEKHIEE 266 (450)
Q Consensus 229 ~~H~~~h~~~~~~~C~~~~--~gC~~~~~~~~~l~~H~~~ 266 (450)
..|.+. ..|-|.+.. .|=-+.|+...+|+.|+..
T Consensus 268 e~HF~~----~hy~ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 268 EAHFRN----AHYCCTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred HHHhhc----CceEEEEEEEecCcEEEeccHHHHHHHHHH
Confidence 888764 235555532 1223457776777777654
No 97
>KOG0311|consensus
Probab=93.10 E-value=0.0036 Score=57.29 Aligned_cols=54 Identities=17% Similarity=0.122 Sum_probs=44.6
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC--CCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL--SLTPD 62 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~--~~~~~ 62 (450)
+...+.|+||... +.+....+.|+|+||..|+ .......||.|++.+.. .+..|
T Consensus 40 ~~~~v~c~icl~l-lk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~D 98 (381)
T KOG0311|consen 40 FDIQVICPICLSL-LKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRID 98 (381)
T ss_pred hhhhhccHHHHHH-HHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCC
Confidence 4566789999999 9999999999999999998 45667899999998776 44444
No 98
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=92.95 E-value=0.04 Score=43.18 Aligned_cols=51 Identities=12% Similarity=0.013 Sum_probs=37.0
Q ss_pred CcccccCceeeccCCCCc----ccCCCcccCCCCCcccCCCC-----CCCCCCCCCCCCCCCCC
Q psy225 3 RSFTSWTKTLSFPARLNT----HHKQQISSKENTLSSSSSSH-----SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 3 ~~~~~~~~~~~C~iC~~~----~~~~p~~c~~Cg~~fc~~~~-----~~~~~~~C~~C~~~~~~ 57 (450)
-|.++ +-|+|.||... .+-+|-.| ||.+.|.-|. ....-..||+|+.+|.+
T Consensus 74 vF~d~--~lYeCnIC~etS~ee~FLKPneC--CgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 74 VFLDP--KLYECNICKETSAEERFLKPNEC--CGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred eecCC--CceeccCcccccchhhcCCcccc--cchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 45655 88999999986 14578888 9988765443 23345689999998876
No 99
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=92.93 E-value=0.064 Score=28.84 Aligned_cols=21 Identities=33% Similarity=0.847 Sum_probs=10.4
Q ss_pred cCCcccccCccChhHHHHHHhhh
Q psy225 213 PCPNQCEMVALPREELDVHIKEH 235 (450)
Q Consensus 213 ~C~~~C~~~f~~~~~l~~H~~~h 235 (450)
+|+ .|+.... +..|..|++.+
T Consensus 2 ~C~-~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 2 KCP-HCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp E-S-SSS-EES-HHHHHHHHHHH
T ss_pred CCC-CCCCcCC-HHHHHHHHHhh
Confidence 455 5555444 55666666554
No 100
>KOG2231|consensus
Probab=92.91 E-value=0.11 Score=52.68 Aligned_cols=78 Identities=21% Similarity=0.178 Sum_probs=59.1
Q ss_pred eeecccccccccccchhhcccc-CC-CCc----ccCCcccccCccChhHHHHHHhhhcCCcccccccc--CCCCCccccC
Q psy225 185 LVACRYCSKSYVADTLVTHQTK-CT-RAP----IPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFK--DAGCRFKGMR 256 (450)
Q Consensus 185 ~~~C~~C~~~f~~~~l~~H~~~-~~-~~~----~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~--~~gC~~~~~~ 256 (450)
.-.+..+.+.++...|..|+.. .+ ++. ..|. .|...|.....|..|++.++ +.|.++ ..|++.-|..
T Consensus 150 ~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~-~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~ 224 (669)
T KOG2231|consen 150 LKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCK-FCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYND 224 (669)
T ss_pred ceeeeeeeehehHHHHHHHHhcCCCccccccCCccch-hhhhhhccHHHHHHhhccce----eheeecCcccccchhccc
Confidence 3345556777888889999887 33 332 4688 99999999999999998654 455554 4677888888
Q ss_pred hHHHHHhhHhh
Q psy225 257 GETMEKHIEEN 267 (450)
Q Consensus 257 ~~~l~~H~~~~ 267 (450)
..+|..|.+..
T Consensus 225 ~~dLe~HfR~~ 235 (669)
T KOG2231|consen 225 YDDLEEHFRKG 235 (669)
T ss_pred chHHHHHhhhc
Confidence 89999999964
No 101
>KOG0287|consensus
Probab=92.34 E-value=0.011 Score=53.59 Aligned_cols=47 Identities=9% Similarity=-0.070 Sum_probs=38.9
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
++.-++|-||... ++-|...+ |||.||.-|+ ..+ ...||.|...+..
T Consensus 20 lD~lLRC~IC~ey-f~ip~itp-CsHtfCSlCIR~~L~~-~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 20 LDDLLRCGICFEY-FNIPMITP-CSHTFCSLCIRKFLSY-KPQCPTCCVTVTE 69 (442)
T ss_pred hHHHHHHhHHHHH-hcCceecc-ccchHHHHHHHHHhcc-CCCCCceecccch
Confidence 4566789999999 99999997 9999998887 334 4579999887766
No 102
>PRK04860 hypothetical protein; Provisional
Probab=92.26 E-value=0.083 Score=44.02 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=12.8
Q ss_pred hHHHhhhhhcccCceeeccccccccc
Q psy225 171 RLMAKHRANDCYKRLVACRYCSKSYV 196 (450)
Q Consensus 171 ~~l~~H~~~h~~~k~~~C~~C~~~f~ 196 (450)
..+.+|.++|.++++|.|..|+..|.
T Consensus 129 ~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 129 LTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred CHHHHHHHHhcCCccEECCCCCceeE
Confidence 44445555555555555555554443
No 103
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=91.88 E-value=0.08 Score=28.73 Aligned_cols=21 Identities=19% Similarity=0.433 Sum_probs=12.0
Q ss_pred cCCcccccCccChhHHHHHHhh
Q psy225 213 PCPNQCEMVALPREELDVHIKE 234 (450)
Q Consensus 213 ~C~~~C~~~f~~~~~l~~H~~~ 234 (450)
.|. .|++.|.....|..|++.
T Consensus 2 ~C~-~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 2 YCD-ICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EET-TTTEEESSHHHHHHHHTT
T ss_pred CCC-CCCCCcCCHHHHHHHHCc
Confidence 345 555566666666666543
No 104
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=91.79 E-value=0.039 Score=33.36 Aligned_cols=36 Identities=14% Similarity=0.055 Sum_probs=26.9
Q ss_pred ccCCCCcccCCCcccCCCCCcccCCCCC---CCCCCCCCCC
Q psy225 14 FPARLNTHHKQQISSKENTLSSSSSSHS---SDLPMICSQT 51 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~~Cg~~fc~~~~~---~~~~~~C~~C 51 (450)
|+||... ..++...+ |||.||..++. ......||.|
T Consensus 1 C~iC~~~-~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE-LKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC-CCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence 7889988 88888874 99999877762 2345678876
No 105
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=91.74 E-value=0.0072 Score=38.40 Aligned_cols=37 Identities=11% Similarity=0.065 Sum_probs=25.9
Q ss_pred eccCCCCccc---CCCcccCCCCCcccCCCC---CCCCCCCCCCCC
Q psy225 13 SFPARLNTHH---KQQISSKENTLSSSSSSH---SSDLPMICSQTK 52 (450)
Q Consensus 13 ~C~iC~~~~~---~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~ 52 (450)
.|+||... + ..++..+ |||.|+..++ ... ...||+|+
T Consensus 2 ~C~IC~~~-~~~~~~~~~l~-C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEE-FEDGEKVVKLP-CGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp CETTTTCB-HHTTSCEEEET-TSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCcCCChh-hcCCCeEEEcc-CCCeeCHHHHHHHHHh-CCcCCccC
Confidence 59999997 5 3566775 9999977776 222 35899884
No 106
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.97 E-value=0.12 Score=51.16 Aligned_cols=58 Identities=17% Similarity=0.262 Sum_probs=35.9
Q ss_pred cccCCcccccccc-cHHHhHHh--hhCCC--CcccCc--ccccccChhH-HHHHhhhCCCCccccc
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSK--FTCPE--RITTCQ--YCLESFSGME-MEDHTGHCSYEMVYCE 161 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~-l~~H~~~~~~~~~~~c 161 (450)
++.|..|...|.. ..|..|.+ .|.++ +++.|+ .|++.|.... +..|...|.+..+..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4556666666666 66666666 56666 666666 5666666665 6666666666554443
No 107
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=90.79 E-value=0.11 Score=28.90 Aligned_cols=17 Identities=24% Similarity=0.495 Sum_probs=7.6
Q ss_pred ccccCccChhHHHHHHh
Q psy225 217 QCEMVALPREELDVHIK 233 (450)
Q Consensus 217 ~C~~~f~~~~~l~~H~~ 233 (450)
.|++.|.....+..|++
T Consensus 6 ~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 6 ACDKYFSSENQLKQHMK 22 (27)
T ss_dssp TTTBBBSSHHHHHCCTT
T ss_pred cCCCCcCCHHHHHHHHc
Confidence 44444444444444443
No 108
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=90.69 E-value=0.11 Score=28.90 Aligned_cols=20 Identities=25% Similarity=0.584 Sum_probs=12.0
Q ss_pred eecccccccccc-cchhhccc
Q psy225 186 VACRYCSKSYVA-DTLVTHQT 205 (450)
Q Consensus 186 ~~C~~C~~~f~~-~~l~~H~~ 205 (450)
|.|..|++.|.. ..+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456666666666 55666653
No 109
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=90.30 E-value=0.12 Score=27.99 Aligned_cols=19 Identities=32% Similarity=0.667 Sum_probs=10.4
Q ss_pred cCcccccccChhH-HHHHhh
Q psy225 133 TCQYCLESFSGME-MEDHTG 151 (450)
Q Consensus 133 ~C~~C~~~f~~~~-l~~H~~ 151 (450)
.|+.|++.|.... ++.|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 4555555555554 555554
No 110
>KOG1813|consensus
Probab=90.28 E-value=0.16 Score=45.75 Aligned_cols=47 Identities=4% Similarity=-0.150 Sum_probs=37.1
Q ss_pred CceeeccCCCCcccCCCcccCCCCCcccCCCCCC--CCCCCCCCCCCCCCC
Q psy225 9 TKTLSFPARLNTHHKQQISSKENTLSSSSSSHSS--DLPMICSQTKSRTPL 57 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~~~~ 57 (450)
.-++.|.||... +.+|+.. .|||.||..|.+. .+.-.|.+|+.....
T Consensus 239 ~~Pf~c~icr~~-f~~pVvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 239 LLPFKCFICRKY-FYRPVVT-KCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cCCccccccccc-cccchhh-cCCceeehhhhccccccCCcceeccccccc
Confidence 346789999999 9999999 5999999988743 344679999875443
No 111
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=89.63 E-value=0.14 Score=44.89 Aligned_cols=174 Identities=18% Similarity=0.327 Sum_probs=93.4
Q ss_pred cccCCCCC-----cccCCCCCCCCCCCCCCCCCC---CCC----CCCCCCchhHHhhhcceeeccCCCCCCchHHHH-hH
Q psy225 26 ISSKENTL-----SSSSSSHSSDLPMICSQTKSR---TPL----SLTPDVSDSEKDTMGSLIHCIHYKEGCKWYDEL-KS 92 (450)
Q Consensus 26 ~~c~~Cg~-----~fc~~~~~~~~~~~C~~C~~~---~~~----~~~~~~~~~~~~~~~~~~~C~~c~~~c~~~~~l-~~ 92 (450)
..|..|+. .||.-|..-.+...|-.|++. +.. ..|+. ..... +...-..|..|+- |.-.- +-
T Consensus 39 MeCdkC~r~QKnRAFCYFC~s~qrlp~Ca~Cgk~KCm~k~gdCvvkH~g-~~~tG-l~mvGaiCDfCEa---wvCHgrkC 113 (314)
T PF06524_consen 39 MECDKCQRKQKNRAFCYFCQSVQRLPMCAHCGKTKCMLKTGDCVVKHPG-VFTTG-LGMVGAICDFCEA---WVCHGRKC 113 (314)
T ss_pred ccchhhhhhccccceeehhhhhhcCchhhhcCCeeeeccCCCeEEecCc-eeecc-cchhhhhhccchh---heeccccc
Confidence 34555543 366666666677788888764 222 22333 22111 1111234665542 33222 34
Q ss_pred HHHhhhcCCCCcccCCcccccccccHHHhHHhhhCCCCcccCcccccccChhHHHHHhhhCCC--CcccccccCChhhch
Q psy225 93 LKGHLQTCKYDAIPCNKCLAAIPKTLMEDHSKFTCPERITTCQYCLESFSGMEMEDHTGHCSY--EMVYCENKCGHKIQR 170 (450)
Q Consensus 93 ~~~H~~~c~~~~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~l~~H~~~~~~--~~~~~c~~C~~~f~~ 170 (450)
|..|.-.||.....|-+|.+.+. .+|.+.|.|..|..-.....--.|+..|.- ...|.|.-|.+.-+
T Consensus 114 l~~HaC~Cpl~da~C~EC~R~vw----------~hGGrif~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq- 182 (314)
T PF06524_consen 114 LSTHACTCPLQDAVCIECERGVW----------DHGGRIFKCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQ- 182 (314)
T ss_pred cccccccCcCCCcEeeeeecccc----------cCCCeEEEeecCCCeeeccchhhhhhhhhhhhcccccccccccccc-
Confidence 66888889888888988887543 567788999998766555444445554421 22233333332111
Q ss_pred hHHHhhhhhcccCceeecccccccccccchhhcccc-----CCCCcccCCcccccCccChhHHHHHHhhh
Q psy225 171 RLMAKHRANDCYKRLVACRYCSKSYVADTLVTHQTK-----CTRAPIPCPNQCEMVALPREELDVHIKEH 235 (450)
Q Consensus 171 ~~l~~H~~~h~~~k~~~C~~C~~~f~~~~l~~H~~~-----~~~~~~~C~~~C~~~f~~~~~l~~H~~~h 235 (450)
|.|--|.--|- ..|.+. -..+++.|| .||.......+|..-.++|
T Consensus 183 ---------------~sCLRCK~cfC----ddHvrrKg~ky~k~k~~PCP-KCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 183 ---------------YSCLRCKICFC----DDHVRRKGFKYEKGKPIPCP-KCGYETQETKDLSMSTRSH 232 (314)
T ss_pred ---------------hhhhheeeeeh----hhhhhhcccccccCCCCCCC-CCCCcccccccceeeeecc
Confidence 11111111111 234332 245788999 9998777777776655554
No 112
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.39 E-value=0.34 Score=37.28 Aligned_cols=26 Identities=15% Similarity=0.170 Sum_probs=17.2
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
|.|++|+...| +-|-.||+|+-.|..
T Consensus 2 Y~CPrC~skvC------~LP~~CpiCgLtLVs 27 (112)
T TIGR00622 2 YFCPQCRAKVC------ELPVECPICGLTLIL 27 (112)
T ss_pred ccCCCCCCCcc------CCCCcCCcCCCEEec
Confidence 66777777665 245678888776544
No 113
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=89.32 E-value=0.054 Score=34.02 Aligned_cols=34 Identities=9% Similarity=-0.005 Sum_probs=16.0
Q ss_pred ccCCCCccc---CCCcccCCCCCcccCCCC-----CC-CCCCCCC
Q psy225 14 FPARLNTHH---KQQISSKENTLSSSSSSH-----SS-DLPMICS 49 (450)
Q Consensus 14 C~iC~~~~~---~~p~~c~~Cg~~fc~~~~-----~~-~~~~~C~ 49 (450)
|+||... . ..|+..+ |||.||..++ .+ ...++||
T Consensus 1 CpIc~e~-~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKEF-STEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCccccc-cCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 7888773 3 2488886 9999988777 11 3567776
No 114
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=89.17 E-value=0.68 Score=30.89 Aligned_cols=9 Identities=22% Similarity=0.338 Sum_probs=4.1
Q ss_pred eeeccCCCC
Q psy225 74 LIHCIHYKE 82 (450)
Q Consensus 74 ~~~C~~c~~ 82 (450)
.|.||+||.
T Consensus 25 ~F~CPnCG~ 33 (59)
T PRK14890 25 KFLCPNCGE 33 (59)
T ss_pred EeeCCCCCC
Confidence 344554443
No 115
>KOG1146|consensus
Probab=88.82 E-value=0.21 Score=54.13 Aligned_cols=91 Identities=14% Similarity=0.271 Sum_probs=55.6
Q ss_pred cccCceeecccccccccc-cchhhcccc-CCCCcccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccCh
Q psy225 180 DCYKRLVACRYCSKSYVA-DTLVTHQTK-CTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRG 257 (450)
Q Consensus 180 h~~~k~~~C~~C~~~f~~-~~l~~H~~~-~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~ 257 (450)
|...+.+.|+.|+..|+. ..|..|++. |.+-.- . .|.. +..-..+.+-.-..++-+++.|.. |...+..+
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~-~c~~-gq~~~~~arg~~~~~~~~p~~C~~----C~~stttn 531 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--A-YCKA-GQNHPRLARGEVYRCPGKPYPCRA----CNYSTTTN 531 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccch--h-HhHh-ccccccccccccccCCCCccccee----eeeeeecc
Confidence 556678888888888888 788888888 643221 1 2221 111111111111225566777777 99999999
Q ss_pred HHHHHhhHhhHHHHHHHHHHHHH
Q psy225 258 ETMEKHIEENVNQHMLLMCSLVS 280 (450)
Q Consensus 258 ~~l~~H~~~~~~~~~~~~~~~~~ 280 (450)
.+|..|+++. .|...|.....
T Consensus 532 g~LsihlqS~--~h~~~lee~~~ 552 (1406)
T KOG1146|consen 532 GNLSIHLQSD--LHRNELEEAEE 552 (1406)
T ss_pred hHHHHHHHHH--hhHHHHHHHHh
Confidence 9999999986 44444433333
No 116
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.82 E-value=0.31 Score=32.48 Aligned_cols=8 Identities=13% Similarity=0.193 Sum_probs=4.9
Q ss_pred eeeccCCC
Q psy225 74 LIHCIHYK 81 (450)
Q Consensus 74 ~~~C~~c~ 81 (450)
+|.||.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 56666664
No 117
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=88.78 E-value=0.43 Score=27.73 Aligned_cols=24 Identities=8% Similarity=-0.199 Sum_probs=14.6
Q ss_pred eeccCCCCcc---cCCCcccCCCCCcc
Q psy225 12 LSFPARLNTH---HKQQISSKENTLSS 35 (450)
Q Consensus 12 ~~C~iC~~~~---~~~p~~c~~Cg~~f 35 (450)
|.|..|+..+ ..+|.+|+.||++.
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeE
Confidence 5677777641 24667777777763
No 118
>KOG0297|consensus
Probab=88.52 E-value=0.67 Score=45.09 Aligned_cols=84 Identities=20% Similarity=0.542 Sum_probs=64.7
Q ss_pred ccccccChhHHHHHhhhCCCCcccccccCChhhchhHHHhhhhhcccCceeecccccccccccchhhccccCCCCcccCC
Q psy225 136 YCLESFSGMEMEDHTGHCSYEMVYCENKCGHKIQRRLMAKHRANDCYKRLVACRYCSKSYVADTLVTHQTKCTRAPIPCP 215 (450)
Q Consensus 136 ~C~~~f~~~~l~~H~~~~~~~~~~~c~~C~~~f~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~ 215 (450)
.|........++.|...| ....|.+.|+..+.+..+..|+...|..+.-.|.+|+..+....+..|... +..++.|+
T Consensus 95 GC~~~~~l~~~~~Hl~~c--~~~~C~~~C~~~~~~~d~~~hl~~~C~~~~~~c~~~~~~~~~~~~~~h~~~-~~~~~~c~ 171 (391)
T KOG0297|consen 95 GCRADLELEALQGHLSTC--DPLKCPHRCGVQVPRDDLEDHLEAECPRRSLKCSLCQSDSILILLEAHEEN-PQAEVSCE 171 (391)
T ss_pred CccccccHHHHHhHhccC--CcccCccccccccchHHHHHHHhcccccccccchhhcCccchhhhhhcCCC-CCcccccc
Confidence 565555555688888877 334444559988889999999988899999999999988888888888877 77778887
Q ss_pred cccccCc
Q psy225 216 NQCEMVA 222 (450)
Q Consensus 216 ~~C~~~f 222 (450)
+.|+..-
T Consensus 172 ~k~~~~~ 178 (391)
T KOG0297|consen 172 LKCGKQK 178 (391)
T ss_pred ccchhhh
Confidence 5577544
No 119
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=88.49 E-value=0.42 Score=31.75 Aligned_cols=8 Identities=13% Similarity=0.264 Sum_probs=3.8
Q ss_pred eeeccCCC
Q psy225 74 LIHCIHYK 81 (450)
Q Consensus 74 ~~~C~~c~ 81 (450)
.|.||+||
T Consensus 27 ~F~CPnCG 34 (61)
T COG2888 27 KFPCPNCG 34 (61)
T ss_pred EeeCCCCC
Confidence 34455554
No 120
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=88.33 E-value=0.37 Score=28.28 Aligned_cols=10 Identities=20% Similarity=0.614 Sum_probs=5.3
Q ss_pred CCCCCCCCCC
Q psy225 44 LPMICSQTKS 53 (450)
Q Consensus 44 ~~~~C~~C~~ 53 (450)
.+..||+|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 3455666644
No 121
>KOG3002|consensus
Probab=88.25 E-value=0.23 Score=45.89 Aligned_cols=81 Identities=22% Similarity=0.388 Sum_probs=58.6
Q ss_pred Cceeecccccccccccchhhcccc-CCCCcccCCc---ccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChH
Q psy225 183 KRLVACRYCSKSYVADTLVTHQTK-CTRAPIPCPN---QCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGE 258 (450)
Q Consensus 183 ~k~~~C~~C~~~f~~~~l~~H~~~-~~~~~~~C~~---~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~ 258 (450)
+.+..|+.|...+.. ....++.. .+...+.|++ .|.+.|..... ..|.+. |.-.++.||+....|++...- .
T Consensus 78 ~~~~~CP~Cr~~~g~-~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~-C~f~~~~CP~p~~~C~~~G~~-~ 153 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGN-IRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKV-CEFRPCSCPVPGAECKYTGSY-K 153 (299)
T ss_pred hhcccCCcccccccc-HHHHHHHHHHHhceecccccccCCceeeccccc-cccccc-cccCCcCCCCCcccCCccCcH-H
Confidence 556678888777763 23344433 5556667764 58888876666 778765 777999999987789999998 8
Q ss_pred HHHHhhHhh
Q psy225 259 TMEKHIEEN 267 (450)
Q Consensus 259 ~l~~H~~~~ 267 (450)
+|..|....
T Consensus 154 ~l~~H~~~~ 162 (299)
T KOG3002|consen 154 DLYAHLNDT 162 (299)
T ss_pred HHHHHHHhh
Confidence 898998764
No 122
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=88.01 E-value=0.38 Score=42.05 Aligned_cols=49 Identities=27% Similarity=0.580 Sum_probs=32.9
Q ss_pred ccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhHhhH
Q psy225 217 QCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 217 ~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~ 268 (450)
.|... ..-..+..|.+. |+-+|+.||....+|++.... ..|..|+...|
T Consensus 23 GC~~~-~~~~~~~~HE~~-C~~~p~~CP~~~~~C~~~G~~-~~l~~Hl~~~H 71 (198)
T PF03145_consen 23 GCTET-FPYSEKREHEEE-CPFRPCSCPFPGSGCDWQGSY-KELLDHLRDKH 71 (198)
T ss_dssp T---E-E-GGGHHHHHHT--TTSEEE-SSSSTT---EEEC-CCHHHHHHHHT
T ss_pred CCccc-ccccChhhHhcc-CCCcCCcCCCCCCCccccCCH-HHHHHHHHHHC
Confidence 46655 477788999965 999999999977899999988 88999998743
No 123
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=87.97 E-value=0.32 Score=30.36 Aligned_cols=28 Identities=25% Similarity=0.211 Sum_probs=18.5
Q ss_pred cccCCCCCcccCC-CCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSS-SHSSDLPMICSQTKS 53 (450)
Q Consensus 26 ~~c~~Cg~~fc~~-~~~~~~~~~C~~C~~ 53 (450)
|.|+.||+.|-.. .+.....-.||.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 6777888888322 223356778888887
No 124
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=87.49 E-value=0.23 Score=36.15 Aligned_cols=42 Identities=5% Similarity=-0.061 Sum_probs=25.9
Q ss_pred ccCCCCcccCC-CcccCCCCCcccCCCC-----CCCCCCCCCCCCCCCC
Q psy225 14 FPARLNTHHKQ-QISSKENTLSSSSSSH-----SSDLPMICSQTKSRTP 56 (450)
Q Consensus 14 C~iC~~~~~~~-p~~c~~Cg~~fc~~~~-----~~~~~~~C~~C~~~~~ 56 (450)
|+.|..+ ..+ |.....|+|.|...|+ +......||.|+..+.
T Consensus 35 Cp~Ck~P-gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 35 CPDCKFP-GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCccCC-CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 4444444 333 4444579999966555 2234579999998654
No 125
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=87.36 E-value=0.68 Score=30.44 Aligned_cols=44 Identities=2% Similarity=-0.216 Sum_probs=35.7
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
..|-.|+.. ..+....+ |||..|..++.+++--.||.|++++..
T Consensus 8 ~~~~~~~~~-~~~~~~~p-CgH~I~~~~f~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 8 QPCVFCGFV-GTKGTVLP-CGHLICDNCFPGERYNGCPFCGTPFEF 51 (55)
T ss_pred eeEEEcccc-cccccccc-ccceeeccccChhhccCCCCCCCcccC
Confidence 356677777 66666664 999999999999999999999998764
No 126
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=86.85 E-value=0.24 Score=49.00 Aligned_cols=135 Identities=17% Similarity=0.117 Sum_probs=93.1
Q ss_pred CcccCcccccccChhH-HHHHhh--hCCCC--cccccc--cCChhhch-hHHHhhhhhcccCceeeccc--ccccccc-c
Q psy225 130 RITTCQYCLESFSGME-MEDHTG--HCSYE--MVYCEN--KCGHKIQR-RLMAKHRANDCYKRLVACRY--CSKSYVA-D 198 (450)
Q Consensus 130 ~~~~C~~C~~~f~~~~-l~~H~~--~~~~~--~~~~c~--~C~~~f~~-~~l~~H~~~h~~~k~~~C~~--C~~~f~~-~ 198 (450)
.++.|..|...|.... +..|.+ .|.++ +++.|. .|++.|.+ ..+..|...|.+.+++.+.. +...+.. .
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 3688999999999988 999999 79999 899887 79999984 78889999998888887765 3333333 2
Q ss_pred chhhcc------ccCCCCcccCC-cccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhHh
Q psy225 199 TLVTHQ------TKCTRAPIPCP-NQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIEE 266 (450)
Q Consensus 199 ~l~~H~------~~~~~~~~~C~-~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~~ 266 (450)
.-..+. .........+. +.|-..+..+..+..|...|....+..|.. .+|...+.+...+..|++.
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 440 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKN--PPCSKSFNRHYNLIPHKKI 440 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCC--CcchhhccCcccccccccc
Confidence 211111 11344444444 246667777777888887777766555543 4588888886666666553
No 127
>KOG2186|consensus
Probab=86.77 E-value=0.32 Score=42.77 Aligned_cols=43 Identities=28% Similarity=0.569 Sum_probs=18.8
Q ss_pred cCcccccccChhHHHHHhhhCCCCcccccccCChhhchhHHHhh
Q psy225 133 TCQYCLESFSGMEMEDHTGHCSYEMVYCENKCGHKIQRRLMAKH 176 (450)
Q Consensus 133 ~C~~C~~~f~~~~l~~H~~~~~~~~~~~c~~C~~~f~~~~l~~H 176 (450)
.|..||.......+.+|+..|++ .-|.|-.|++.|.+.....|
T Consensus 5 tCnvCgEsvKKp~vekH~srCrn-~~fSCIDC~k~F~~~sYknH 47 (276)
T KOG2186|consen 5 TCNVCGESVKKPQVEKHMSRCRN-AYFSCIDCGKTFERVSYKNH 47 (276)
T ss_pred ehhhhhhhccccchHHHHHhccC-CeeEEeecccccccchhhhh
Confidence 34444444444444444444444 22333344444444444444
No 128
>KOG2186|consensus
Probab=86.64 E-value=0.31 Score=42.85 Aligned_cols=47 Identities=21% Similarity=0.528 Sum_probs=27.1
Q ss_pred cccccCChhhchhHHHhhhhhcccCceeecccccccccccchhhcccc
Q psy225 159 YCENKCGHKIQRRLMAKHRANDCYKRLVACRYCSKSYVADTLVTHQTK 206 (450)
Q Consensus 159 ~~c~~C~~~f~~~~l~~H~~~h~~~k~~~C~~C~~~f~~~~l~~H~~~ 206 (450)
|.|+.||....+-.+.+|+. .|...-|.|-.|++.|...+...|..-
T Consensus 4 FtCnvCgEsvKKp~vekH~s-rCrn~~fSCIDC~k~F~~~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKKPQVEKHMS-RCRNAYFSCIDCGKTFERVSYKNHTKC 50 (276)
T ss_pred EehhhhhhhccccchHHHHH-hccCCeeEEeecccccccchhhhhhhh
Confidence 45666666666656666653 333355666666666666555566543
No 129
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=86.54 E-value=0.57 Score=27.71 Aligned_cols=9 Identities=11% Similarity=-0.123 Sum_probs=5.1
Q ss_pred eeccCCCCc
Q psy225 12 LSFPARLNT 20 (450)
Q Consensus 12 ~~C~iC~~~ 20 (450)
|.|.+||.+
T Consensus 3 ~~C~~CG~i 11 (34)
T cd00729 3 WVCPVCGYI 11 (34)
T ss_pred EECCCCCCE
Confidence 556666554
No 130
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=85.67 E-value=0.54 Score=29.03 Aligned_cols=29 Identities=10% Similarity=0.068 Sum_probs=16.3
Q ss_pred cccCCCCCcccCCC-CCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSS-HSSDLPMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~-~~~~~~~~C~~C~~~ 54 (450)
|+|+.||+.|-... ........||.|+..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 56667777663211 122455678888764
No 131
>KOG2177|consensus
Probab=85.47 E-value=0.19 Score=47.77 Aligned_cols=46 Identities=11% Similarity=0.203 Sum_probs=36.3
Q ss_pred cccCceeeccCCCCcccCCCcccCCCCCcccCCCCCC--CCCCCCCCCCC
Q psy225 6 TSWTKTLSFPARLNTHHKQQISSKENTLSSSSSSHSS--DLPMICSQTKS 53 (450)
Q Consensus 6 ~~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~ 53 (450)
....+.+.|+||... +.+|... .|||.||..|+.. .....||.|+.
T Consensus 8 ~~~~~~~~C~iC~~~-~~~p~~l-~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 8 EVLQEELTCPICLEY-FREPVLL-PCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred hhccccccChhhHHH-hhcCccc-cccchHhHHHHHHhcCCCcCCcccCC
Confidence 455678899999999 9999444 5999999888732 15589999983
No 132
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.14 E-value=0.42 Score=31.74 Aligned_cols=8 Identities=13% Similarity=0.231 Sum_probs=5.4
Q ss_pred eeeccCCC
Q psy225 74 LIHCIHYK 81 (450)
Q Consensus 74 ~~~C~~c~ 81 (450)
+|.||+||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 67777764
No 133
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=84.85 E-value=0.63 Score=35.91 Aligned_cols=28 Identities=11% Similarity=0.011 Sum_probs=13.7
Q ss_pred cCceeeccCCCCcc---cCCCcccCCCCCcc
Q psy225 8 WTKTLSFPARLNTH---HKQQISSKENTLSS 35 (450)
Q Consensus 8 ~~~~~~C~iC~~~~---~~~p~~c~~Cg~~f 35 (450)
+..+..|+.||..| -++|..||.||..|
T Consensus 6 lGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred cCCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 34445555555541 13455555555555
No 134
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=84.62 E-value=0.85 Score=24.32 Aligned_cols=22 Identities=14% Similarity=0.614 Sum_probs=16.7
Q ss_pred ccccccCCCCCccccChHHHHHhhHhh
Q psy225 241 VSCVFKDAGCRFKGMRGETMEKHIEEN 267 (450)
Q Consensus 241 ~~C~~~~~gC~~~~~~~~~l~~H~~~~ 267 (450)
|.|+. |++... +..|.+|++..
T Consensus 1 y~C~~----C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPH----CSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SS----SS-EES-HHHHHHHHHHH
T ss_pred CCCCC----CCCcCC-HHHHHHHHHhh
Confidence 46888 999998 79999999864
No 135
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=84.46 E-value=0.38 Score=31.31 Aligned_cols=28 Identities=4% Similarity=-0.027 Sum_probs=15.9
Q ss_pred CcccCCCCCcccCCCC--CCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSSSSH--SSDLPMICSQTK 52 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~--~~~~~~~C~~C~ 52 (450)
.|+|+.|++.||..|- ..+..+.||-|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred eEECCCCCCccccCcChhhhccccCCcCCC
Confidence 3899999999987653 567778888774
No 136
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.45 E-value=0.56 Score=29.94 Aligned_cols=30 Identities=7% Similarity=-0.030 Sum_probs=16.3
Q ss_pred CcccCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSSSSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~ 56 (450)
.|.|+.||..|-..... ....||.|+..+.
T Consensus 3 ~y~C~~CG~~~~~~~~~--~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYG--TGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCC--CceECCCCCCeEE
Confidence 45666666666332211 1567777776544
No 137
>KOG2660|consensus
Probab=82.86 E-value=0.13 Score=47.02 Aligned_cols=51 Identities=8% Similarity=-0.036 Sum_probs=41.2
Q ss_pred ccccCceeeccCCCCcccCCCcccCCCCCcccCCCCCC--CCCCCCCCCCCCCC
Q psy225 5 FTSWTKTLSFPARLNTHHKQQISSKENTLSSSSSSHSS--DLPMICSQTKSRTP 56 (450)
Q Consensus 5 ~~~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~~~ 56 (450)
+.++.....|.+|+.. +.|+-...+|-|.||++|+.. +..-.||.|+..+.
T Consensus 9 ~~~~n~~itC~LC~GY-liDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 9 LTELNPHITCRLCGGY-LIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred hhhcccceehhhccce-eecchhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 4566777899999999 999999999999999999921 23668999976543
No 138
>KOG4739|consensus
Probab=82.53 E-value=0.94 Score=39.90 Aligned_cols=51 Identities=8% Similarity=0.077 Sum_probs=36.8
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCCC-CCCCC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTPL-SLTPD 62 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~-~~~~~ 62 (450)
..|..|+..-..+|+-.+.|+|.||..|.....+-.|++|++++.. ++..+
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~i~l~~s 55 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRIIQLNRS 55 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCccccccccceeeeeecccc
Confidence 4688887641456777778999999999865555599999998665 44433
No 139
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=82.11 E-value=0.97 Score=27.68 Aligned_cols=25 Identities=0% Similarity=-0.255 Sum_probs=19.2
Q ss_pred ccCCCCcccCC-CcccCCCCCcccCCC
Q psy225 14 FPARLNTHHKQ-QISSKENTLSSSSSS 39 (450)
Q Consensus 14 C~iC~~~~~~~-p~~c~~Cg~~fc~~~ 39 (450)
|.+|+.. ..- |+.|..|+..||..-
T Consensus 1 C~~C~~~-~~l~~f~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRKK-VGLTGFKCRHCGNLFCGEH 26 (39)
T ss_pred CcccCCc-ccccCeECCccCCcccccc
Confidence 6678776 444 999988999998643
No 140
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=81.98 E-value=1.7 Score=23.37 Aligned_cols=8 Identities=13% Similarity=0.256 Sum_probs=5.3
Q ss_pred eeeccCCC
Q psy225 74 LIHCIHYK 81 (450)
Q Consensus 74 ~~~C~~c~ 81 (450)
.|.||+||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 56677665
No 141
>KOG4159|consensus
Probab=81.92 E-value=0.42 Score=46.03 Aligned_cols=48 Identities=8% Similarity=-0.069 Sum_probs=39.1
Q ss_pred cCceeeccCCCCcccCCCcccCCCCCcccCCCC--CCCCCCCCCCCCCCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQISSKENTLSSSSSSH--SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~--~~~~~~~C~~C~~~~~~ 57 (450)
+...|.|.+|... +.+|... .|||.||..|+ .....-.||.|+..+..
T Consensus 81 ~~sef~c~vc~~~-l~~pv~t-pcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 81 IRSEFECCVCSRA-LYPPVVT-PCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred ccchhhhhhhHhh-cCCCccc-cccccccHHHHHHHhccCCCCccccccccc
Confidence 4678999999999 9999999 49999998876 22355689999887764
No 142
>PHA00626 hypothetical protein
Probab=81.11 E-value=1.1 Score=29.42 Aligned_cols=12 Identities=0% Similarity=-0.036 Sum_probs=5.6
Q ss_pred CCcccCCCCCcc
Q psy225 24 QQISSKENTLSS 35 (450)
Q Consensus 24 ~p~~c~~Cg~~f 35 (450)
..|.|+.||..|
T Consensus 22 nrYkCkdCGY~f 33 (59)
T PHA00626 22 DDYVCCDCGYND 33 (59)
T ss_pred cceEcCCCCCee
Confidence 344444444444
No 143
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.73 E-value=1.1 Score=29.40 Aligned_cols=28 Identities=11% Similarity=0.018 Sum_probs=17.1
Q ss_pred cccCCCCCcccCC-CCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSS-SHSSDLPMICSQTKS 53 (450)
Q Consensus 26 ~~c~~Cg~~fc~~-~~~~~~~~~C~~C~~ 53 (450)
|.|+.||+.|-.. ....+..-.||.|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 5677777777322 112235567999987
No 144
>KOG0824|consensus
Probab=80.52 E-value=1 Score=40.77 Aligned_cols=45 Identities=7% Similarity=-0.127 Sum_probs=37.2
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCCCC---CCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSHSS---DLPMICSQTKSRTPL 57 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~---~~~~~C~~C~~~~~~ 57 (450)
.-.|+||... ..-|... .|+|.||..|+.+ .+...|++|+.++..
T Consensus 7 ~~eC~IC~nt-~n~Pv~l-~C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 7 KKECLICYNT-GNCPVNL-YCFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred CCcceeeecc-CCcCccc-cccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 3469999999 9999887 5999999988854 355679999998776
No 145
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=80.44 E-value=1.4 Score=34.08 Aligned_cols=29 Identities=10% Similarity=0.185 Sum_probs=16.9
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
..|+.||.+|.- .+..|..||.|+..+..
T Consensus 10 R~Cp~CG~kFYD---Lnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 10 RTCPSCGAKFYD---LNKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCCCcchhcc---CCCCCccCCCCCCccCc
Confidence 567777777731 23356667777665543
No 146
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=79.92 E-value=1.8 Score=45.37 Aligned_cols=49 Identities=12% Similarity=0.205 Sum_probs=28.8
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCCCCchHHHHhHHHHhhhcCCCCcc
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKEGCKWYDELKSLKGHLQTCKYDAI 105 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~c~~~~~l~~~~~H~~~c~~~~~ 105 (450)
..|..||+.+ +||.|...+.. |.. .+ ...|.+|+..- . .|.
T Consensus 436 l~C~~Cg~v~-----------~Cp~Cd~~lt~--H~~----~~-----~L~CH~Cg~~~--------------~---~p~ 476 (730)
T COG1198 436 LLCRDCGYIA-----------ECPNCDSPLTL--HKA----TG-----QLRCHYCGYQE--------------P---IPQ 476 (730)
T ss_pred eecccCCCcc-----------cCCCCCcceEE--ecC----CC-----eeEeCCCCCCC--------------C---CCC
Confidence 4577777776 57777776553 332 12 55677765421 1 466
Q ss_pred cCCccccc
Q psy225 106 PCNKCLAA 113 (450)
Q Consensus 106 ~C~~C~~~ 113 (450)
.|+.||..
T Consensus 477 ~Cp~Cgs~ 484 (730)
T COG1198 477 SCPECGSE 484 (730)
T ss_pred CCCCCCCC
Confidence 77777764
No 147
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.89 E-value=1.4 Score=27.75 Aligned_cols=11 Identities=18% Similarity=0.232 Sum_probs=5.2
Q ss_pred CCCCCCCCCCC
Q psy225 44 LPMICSQTKSR 54 (450)
Q Consensus 44 ~~~~C~~C~~~ 54 (450)
.+..||.|+..
T Consensus 18 ~~irC~~CG~r 28 (44)
T smart00659 18 DVVRCRECGYR 28 (44)
T ss_pred CceECCCCCce
Confidence 34455555443
No 148
>KOG1146|consensus
Probab=79.72 E-value=0.58 Score=50.90 Aligned_cols=98 Identities=16% Similarity=0.262 Sum_probs=65.3
Q ss_pred cccCCcccccccc-cHHHhHHh-hhCCCCcccCcccccccChhH-HHHHhhh-CCC-CcccccccCChhhc-hhHHHhhh
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSK-FTCPERITTCQYCLESFSGME-MEDHTGH-CSY-EMVYCENKCGHKIQ-RRLMAKHR 177 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~-l~~H~~~-~~~-~~~~~c~~C~~~f~-~~~l~~H~ 177 (450)
...|..|+..+.+ +.+..|+. .+.-.+.++|+.|+..++... |..|+|. |+. ...+| . .+. .-.+.+-.
T Consensus 436 l~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c----~-~gq~~~~~arg~ 510 (1406)
T KOG1146|consen 436 LVELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYC----K-AGQNHPRLARGE 510 (1406)
T ss_pred cccccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHh----H-hccccccccccc
Confidence 4456666666666 66666653 466678999999999999998 9999996 322 22111 0 011 11112212
Q ss_pred hhcccCceeecccccccccc-cchhhcccc
Q psy225 178 ANDCYKRLVACRYCSKSYVA-DTLVTHQTK 206 (450)
Q Consensus 178 ~~h~~~k~~~C~~C~~~f~~-~~l~~H~~~ 206 (450)
...++.++|.|..|...++. .+|..|+..
T Consensus 511 ~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 511 VYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 23567889999999999998 888888755
No 149
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=79.26 E-value=1.5 Score=25.77 Aligned_cols=21 Identities=19% Similarity=0.499 Sum_probs=11.8
Q ss_pred ccCCcccccCccChhHHHHHHh
Q psy225 212 IPCPNQCEMVALPREELDVHIK 233 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~ 233 (450)
+.|. .|++.|.....+..|+.
T Consensus 4 ~~C~-~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCK-LCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEcc-ccCCccCCHHHHHHHHC
Confidence 4455 56655655555555554
No 150
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=79.17 E-value=0.37 Score=34.39 Aligned_cols=37 Identities=5% Similarity=-0.138 Sum_probs=23.8
Q ss_pred ccCCCCcccCCC------------cccCCCCCcccCCCC---CCCCCCCCCCCC
Q psy225 14 FPARLNTHHKQQ------------ISSKENTLSSSSSSH---SSDLPMICSQTK 52 (450)
Q Consensus 14 C~iC~~~~~~~p------------~~c~~Cg~~fc~~~~---~~~~~~~C~~C~ 52 (450)
|.||... +.++ ..-..|||.|...|+ .... ..||.|+
T Consensus 22 C~IC~~~-l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-~~CP~CR 73 (73)
T PF12678_consen 22 CAICREP-LEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-NTCPLCR 73 (73)
T ss_dssp ETTTTSB-TTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-SB-TTSS
T ss_pred ccccChh-hhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-CcCCCCC
Confidence 9999998 6432 233459999965555 3222 2899985
No 151
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=78.32 E-value=0.75 Score=30.22 Aligned_cols=31 Identities=6% Similarity=-0.041 Sum_probs=23.4
Q ss_pred eeeccCCCCcc--cCCCcccCCCCCcccCCCCC
Q psy225 11 TLSFPARLNTH--HKQQISSKENTLSSSSSSHS 41 (450)
Q Consensus 11 ~~~C~iC~~~~--~~~p~~c~~Cg~~fc~~~~~ 41 (450)
...|++|++.| ..+.++|+.||..+.+.|+.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 44799999983 24678899999888776663
No 152
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=75.96 E-value=1.2 Score=36.77 Aligned_cols=69 Identities=17% Similarity=0.276 Sum_probs=36.8
Q ss_pred eecccccccccc---cchhhccccCCCCcccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHH
Q psy225 186 VACRYCSKSYVA---DTLVTHQTKCTRAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEK 262 (450)
Q Consensus 186 ~~C~~C~~~f~~---~~l~~H~~~~~~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~ 262 (450)
++||+||-..+. +.+..- ...-.+.++|+ .||++|..-..+..=+ .=..+-.|-...|.. ..+..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~-~~~~~~~~~c~-~c~~~f~~~e~~~~~~---------i~VIKRDG~~v~Fd~-~KI~~ 68 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED-GNAIRRRRECL-ACGKRFTTFERVELVP---------LLVIKKDGRREPFDR-EKLRR 68 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC-CCceeeeeecc-ccCCcceEeEeccCcc---------cEEEecCCcCCCcCH-HHHHH
Confidence 368888866543 111111 11222338899 9999996543332211 113344567777777 66655
Q ss_pred hhHh
Q psy225 263 HIEE 266 (450)
Q Consensus 263 H~~~ 266 (450)
=+..
T Consensus 69 AI~k 72 (154)
T PRK00464 69 GLRR 72 (154)
T ss_pred HHHH
Confidence 5543
No 153
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=75.41 E-value=2 Score=33.74 Aligned_cols=28 Identities=7% Similarity=-0.075 Sum_probs=14.2
Q ss_pred cCceeeccCCCCcc---cCCCcccCCCCCcc
Q psy225 8 WTKTLSFPARLNTH---HKQQISSKENTLSS 35 (450)
Q Consensus 8 ~~~~~~C~iC~~~~---~~~p~~c~~Cg~~f 35 (450)
+..+..|+.|+..| .+.|..|+.||..|
T Consensus 6 lGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred hCccccCCCcCccccccCCCCccCCCcCCcc
Confidence 34455566555541 13455555555555
No 154
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.34 E-value=3.7 Score=45.07 Aligned_cols=37 Identities=8% Similarity=0.151 Sum_probs=25.3
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~ 56 (450)
.++||.|+.. ... ..|+.||... +..+.||.|+..+.
T Consensus 667 ~rkCPkCG~~-t~~-~fCP~CGs~t-------e~vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTE-TYE-NRCPDCGTHT-------EPVYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCc-ccc-ccCcccCCcC-------CCceeCccCCCccC
Confidence 4689999987 443 3788888775 23567888877543
No 155
>PF12773 DZR: Double zinc ribbon
Probab=75.26 E-value=4.7 Score=26.08 Aligned_cols=38 Identities=8% Similarity=0.037 Sum_probs=19.0
Q ss_pred ccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 14 FPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
|+.|+..+..+..-|+.||...- ........||.|+..
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~---~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP---PPDQSKKICPNCGAE 38 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh---hccCCCCCCcCCcCC
Confidence 55566652233444555555543 112334567777664
No 156
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=74.05 E-value=2 Score=22.83 Aligned_cols=20 Identities=5% Similarity=-0.160 Sum_probs=8.6
Q ss_pred ccCCCCcccCCCcccCCCCC
Q psy225 14 FPARLNTHHKQQISSKENTL 33 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~~Cg~ 33 (450)
|+.|+..+..+.-.|+.||.
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCCcCcchhhhCC
Confidence 55555541222333444443
No 157
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.99 E-value=3.6 Score=43.95 Aligned_cols=46 Identities=4% Similarity=-0.159 Sum_probs=34.4
Q ss_pred ceeeccCCCCcccCCCcccCCCCCc-----ccCCCCCCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLS-----SSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~-----fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
....|+.|+.. . -...|+.||.. ||..|-....++.||.|+..+..
T Consensus 625 g~RfCpsCG~~-t-~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 625 GRRKCPSCGKE-T-FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred cCccCCCCCCc-C-CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 45579999998 5 44789999964 68777666667889999876544
No 158
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.31 E-value=1.5 Score=26.50 Aligned_cols=10 Identities=10% Similarity=0.222 Sum_probs=4.8
Q ss_pred eeeccCCCCC
Q psy225 74 LIHCIHYKEG 83 (450)
Q Consensus 74 ~~~C~~c~~~ 83 (450)
.+.|+.|+..
T Consensus 25 ~vrC~~C~~~ 34 (37)
T PF13719_consen 25 KVRCPKCGHV 34 (37)
T ss_pred EEECCCCCcE
Confidence 4555555443
No 159
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=72.93 E-value=2.6 Score=35.20 Aligned_cols=24 Identities=8% Similarity=0.177 Sum_probs=17.4
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
|.|+.||+.+ .++.|-.||+|+.+
T Consensus 135 ~vC~vCGy~~-----~ge~P~~CPiCga~ 158 (166)
T COG1592 135 WVCPVCGYTH-----EGEAPEVCPICGAP 158 (166)
T ss_pred EEcCCCCCcc-----cCCCCCcCCCCCCh
Confidence 7788888776 24677888888753
No 160
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=71.71 E-value=2 Score=26.92 Aligned_cols=21 Identities=10% Similarity=-0.168 Sum_probs=13.4
Q ss_pred CCCcccCCCcccCCCCCcccCC
Q psy225 17 RLNTHHKQQISSKENTLSSSSS 38 (450)
Q Consensus 17 C~~~~~~~p~~c~~Cg~~fc~~ 38 (450)
|+.. ..-|+.|+.|+..||..
T Consensus 6 C~~~-~~~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 6 CKKK-DFLPFKCKHCGKSFCLK 26 (43)
T ss_dssp T--B-CTSHEE-TTTS-EE-TT
T ss_pred CcCc-cCCCeECCCCCcccCcc
Confidence 8887 66899999999999854
No 161
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=71.64 E-value=2.4 Score=27.29 Aligned_cols=10 Identities=0% Similarity=-0.247 Sum_probs=5.5
Q ss_pred eeeccCCCCc
Q psy225 11 TLSFPARLNT 20 (450)
Q Consensus 11 ~~~C~iC~~~ 20 (450)
.|.|..|+..
T Consensus 6 ~Y~C~~Cg~~ 15 (49)
T COG1996 6 EYKCARCGRE 15 (49)
T ss_pred EEEhhhcCCe
Confidence 4555555554
No 162
>KOG4628|consensus
Probab=71.62 E-value=2.5 Score=39.81 Aligned_cols=44 Identities=7% Similarity=-0.048 Sum_probs=31.7
Q ss_pred eeccCCCCcccC---CCcccCCCCCcccCCC---CCCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHK---QQISSKENTLSSSSSS---HSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 12 ~~C~iC~~~~~~---~p~~c~~Cg~~fc~~~---~~~~~~~~C~~C~~~~~~ 57 (450)
..|.||... +. +-...| |+|.|...| |..+....||+|+.....
T Consensus 230 ~~CaIClEd-Y~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 589999986 54 344565 999995444 466777889999885443
No 163
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=71.55 E-value=2.9 Score=34.62 Aligned_cols=9 Identities=11% Similarity=0.158 Sum_probs=5.9
Q ss_pred CCCCCCCCC
Q psy225 47 ICSQTKSRT 55 (450)
Q Consensus 47 ~C~~C~~~~ 55 (450)
+||.|+.+.
T Consensus 2 ~cp~c~~~~ 10 (154)
T PRK00464 2 RCPFCGHPD 10 (154)
T ss_pred cCCCCCCCC
Confidence 577777654
No 164
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=70.41 E-value=3.3 Score=37.67 Aligned_cols=24 Identities=17% Similarity=0.043 Sum_probs=12.8
Q ss_pred ceeeccCCCCcccCCCcccCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTL 33 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~ 33 (450)
.-|.||.|....-.-|..||.|+-
T Consensus 307 gGy~CP~CktkVCsLPi~CP~Csl 330 (421)
T COG5151 307 GGYECPVCKTKVCSLPISCPICSL 330 (421)
T ss_pred CceeCCcccceeecCCccCcchhH
Confidence 345666665431344666666653
No 165
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.68 E-value=5.8 Score=30.67 Aligned_cols=15 Identities=13% Similarity=0.219 Sum_probs=10.6
Q ss_pred CCCCCCCCCCCCCCC
Q psy225 43 DLPMICSQTKSRTPL 57 (450)
Q Consensus 43 ~~~~~C~~C~~~~~~ 57 (450)
...|+|+.|+..|-.
T Consensus 79 ~~~y~C~~C~~~FC~ 93 (112)
T TIGR00622 79 SHRYVCAVCKNVFCV 93 (112)
T ss_pred ccceeCCCCCCcccc
Confidence 456788888877654
No 166
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=69.64 E-value=2.6 Score=37.28 Aligned_cols=42 Identities=21% Similarity=0.587 Sum_probs=26.4
Q ss_pred Cceeecccccccccc-cchhhcccc-------C----CCCc-----ccCCcccccCccCh
Q psy225 183 KRLVACRYCSKSYVA-DTLVTHQTK-------C----TRAP-----IPCPNQCEMVALPR 225 (450)
Q Consensus 183 ~k~~~C~~C~~~f~~-~~l~~H~~~-------~----~~~~-----~~C~~~C~~~f~~~ 225 (450)
++.+.||+|++.|.. .-.....+. + +..| ..|| .||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP-~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCP-HCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECC-CCCCccccc
Confidence 356789999999887 333344432 1 1222 4799 999887543
No 167
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=69.21 E-value=2.8 Score=27.43 Aligned_cols=31 Identities=19% Similarity=0.341 Sum_probs=15.2
Q ss_pred CCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCC
Q psy225 47 ICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKE 82 (450)
Q Consensus 47 ~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 82 (450)
.||.|+.....++..| ..+.+.++.||.|..
T Consensus 6 ~CP~CgnKTR~kir~D-----T~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIRED-----TVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecC-----ceeccccccCCCCCc
Confidence 4677765433333343 223344666766643
No 168
>KOG2932|consensus
Probab=68.56 E-value=4.9 Score=36.66 Aligned_cols=42 Identities=12% Similarity=-0.138 Sum_probs=28.1
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
.-|..|++.+..--... -|.|.||..|...+....||.|...
T Consensus 91 HfCd~Cd~PI~IYGRmI-PCkHvFCl~CAr~~~dK~Cp~C~d~ 132 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMI-PCKHVFCLECARSDSDKICPLCDDR 132 (389)
T ss_pred EeecccCCcceeeeccc-ccchhhhhhhhhcCccccCcCcccH
Confidence 45888887622112223 3889999988866667789988664
No 169
>PF14353 CpXC: CpXC protein
Probab=68.49 E-value=4.4 Score=32.45 Aligned_cols=9 Identities=11% Similarity=0.331 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q psy225 47 ICSQTKSRT 55 (450)
Q Consensus 47 ~C~~C~~~~ 55 (450)
+||.|+..+
T Consensus 3 tCP~C~~~~ 11 (128)
T PF14353_consen 3 TCPHCGHEF 11 (128)
T ss_pred CCCCCCCee
Confidence 455555443
No 170
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=68.27 E-value=1.5 Score=26.54 Aligned_cols=8 Identities=13% Similarity=0.422 Sum_probs=3.9
Q ss_pred eeccCCCC
Q psy225 75 IHCIHYKE 82 (450)
Q Consensus 75 ~~C~~c~~ 82 (450)
+.|++|+.
T Consensus 26 v~C~~C~~ 33 (38)
T TIGR02098 26 VRCGKCGH 33 (38)
T ss_pred EECCCCCC
Confidence 44555544
No 171
>KOG1002|consensus
Probab=67.73 E-value=1.5 Score=42.78 Aligned_cols=51 Identities=6% Similarity=-0.055 Sum_probs=39.5
Q ss_pred ccccCceeeccCCCCcccCCCcccCCCCCcccCCCC-------CCCCCCCCCCCCCCCCC
Q psy225 5 FTSWTKTLSFPARLNTHHKQQISSKENTLSSSSSSH-------SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 5 ~~~~~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~-------~~~~~~~C~~C~~~~~~ 57 (450)
+.+......|.+|..+ ..+++.. .|.|.||+-|+ .......||.|-..|..
T Consensus 530 ~~enk~~~~C~lc~d~-aed~i~s-~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi 587 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDP-AEDYIES-SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI 587 (791)
T ss_pred CccccCceeecccCCh-hhhhHhh-hhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence 3444556789999999 9999888 59999998887 22344899999877654
No 172
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.51 E-value=4.9 Score=40.74 Aligned_cols=34 Identities=9% Similarity=0.094 Sum_probs=19.3
Q ss_pred ccCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCC
Q psy225 27 SSKENTLSSSSSSHSSDLPMICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKE 82 (450)
Q Consensus 27 ~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~ 82 (450)
.|..||+.. .||.|.-++.. |.. .+ ...|..|+.
T Consensus 215 ~C~~Cg~~~-----------~C~~C~~~l~~--h~~----~~-----~l~Ch~Cg~ 248 (505)
T TIGR00595 215 LCRSCGYIL-----------CCPNCDVSLTY--HKK----EG-----KLRCHYCGY 248 (505)
T ss_pred EhhhCcCcc-----------CCCCCCCceEE--ecC----CC-----eEEcCCCcC
Confidence 466666555 67777766553 222 11 456777754
No 173
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=67.01 E-value=3 Score=25.00 Aligned_cols=10 Identities=10% Similarity=0.248 Sum_probs=5.1
Q ss_pred eeeccCCCCC
Q psy225 74 LIHCIHYKEG 83 (450)
Q Consensus 74 ~~~C~~c~~~ 83 (450)
.++|+.|+..
T Consensus 25 ~v~C~~C~~~ 34 (36)
T PF13717_consen 25 KVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCE
Confidence 4555555443
No 174
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=66.96 E-value=4.6 Score=31.78 Aligned_cols=27 Identities=7% Similarity=-0.054 Sum_probs=14.5
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSRT 55 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~ 55 (450)
..|+.||.+|.- .+..|..||.|+..+
T Consensus 10 r~Cp~cg~kFYD---Lnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYD---LNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccc---cCCCCccCCCcCCcc
Confidence 456666666621 233556666666543
No 175
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=66.90 E-value=0.32 Score=30.88 Aligned_cols=44 Identities=9% Similarity=-0.007 Sum_probs=33.4
Q ss_pred ceeeccCCCCcc-cCCCcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTH-HKQQISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 10 ~~~~C~iC~~~~-~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
..|.|+.|+..+ ..+..||-.||..-|.+|+..+ -|.|..|+--
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~de-YY~CksC~Gi 50 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDE-YYTCKSCNGI 50 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhh-HhHHHhhhch
Confidence 468899999861 3456889999999999998653 6778777653
No 176
>KOG1734|consensus
Probab=66.86 E-value=1.1 Score=39.92 Aligned_cols=47 Identities=6% Similarity=-0.097 Sum_probs=32.3
Q ss_pred ceeeccCCCCcc---------cCCCcccCCCCCcccCCCC----CCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTH---------HKQQISSKENTLSSSSSSH----SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 10 ~~~~C~iC~~~~---------~~~p~~c~~Cg~~fc~~~~----~~~~~~~C~~C~~~~~~ 57 (450)
++-.|.+|+..+ ..+.|+. .|+|.|...|+ .-.+...||.|++....
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence 344799999862 2267888 49999844444 33456689999886554
No 177
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=66.85 E-value=2.7 Score=27.48 Aligned_cols=24 Identities=29% Similarity=0.596 Sum_probs=11.2
Q ss_pred CCCcccCCcccccCccChhHHHHHH
Q psy225 208 TRAPIPCPNQCEMVALPREELDVHI 232 (450)
Q Consensus 208 ~~~~~~C~~~C~~~f~~~~~l~~H~ 232 (450)
||.-+.|| .||+.|..+.+...|+
T Consensus 14 GE~~lrCP-RC~~~FR~~K~Y~RHV 37 (65)
T COG4049 14 GEEFLRCP-RCGMVFRRRKDYIRHV 37 (65)
T ss_pred CceeeeCC-chhHHHHHhHHHHHHh
Confidence 33444444 4554444444444444
No 178
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=65.59 E-value=4.4 Score=29.62 Aligned_cols=31 Identities=16% Similarity=0.192 Sum_probs=22.1
Q ss_pred cCCCcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 22 HKQQISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 22 ~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
+-.|-+|..||..|-.. .-..|..||.|.+.
T Consensus 55 lv~Pa~CkkCGfef~~~--~ik~pSRCP~CKSE 85 (97)
T COG3357 55 LVRPARCKKCGFEFRDD--KIKKPSRCPKCKSE 85 (97)
T ss_pred EecChhhcccCcccccc--ccCCcccCCcchhh
Confidence 44688898999988542 23457889999763
No 179
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.84 E-value=6.9 Score=41.18 Aligned_cols=20 Identities=5% Similarity=-0.260 Sum_probs=16.6
Q ss_pred eeeccCCCCcccCCCcccCCCCCcc
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSS 35 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~f 35 (450)
...|..|+.+ .+|+.|+..+
T Consensus 435 ~l~C~~Cg~v-----~~Cp~Cd~~l 454 (730)
T COG1198 435 LLLCRDCGYI-----AECPNCDSPL 454 (730)
T ss_pred eeecccCCCc-----ccCCCCCcce
Confidence 4579999999 7899998776
No 180
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=64.69 E-value=5.4 Score=21.88 Aligned_cols=20 Identities=15% Similarity=0.459 Sum_probs=10.0
Q ss_pred cCcccccccChhHHHHHhhh
Q psy225 133 TCQYCLESFSGMEMEDHTGH 152 (450)
Q Consensus 133 ~C~~C~~~f~~~~l~~H~~~ 152 (450)
.|+.|++.+....+..|+..
T Consensus 3 ~CPiC~~~v~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREVPENLINSHLDS 22 (26)
T ss_pred cCCCCcCcccHHHHHHHHHH
Confidence 45555555533335555543
No 181
>KOG3507|consensus
Probab=63.88 E-value=3.5 Score=27.33 Aligned_cols=26 Identities=8% Similarity=-0.096 Sum_probs=18.4
Q ss_pred ceeeccCCCCc---ccCCCcccCCCCCcc
Q psy225 10 KTLSFPARLNT---HHKQQISSKENTLSS 35 (450)
Q Consensus 10 ~~~~C~iC~~~---~~~~p~~c~~Cg~~f 35 (450)
-.|.|-.|+.- ...++++|.+||++.
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~RI 47 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGYRI 47 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcchHH
Confidence 35788888763 135788888888875
No 182
>KOG4173|consensus
Probab=63.20 E-value=2.3 Score=36.23 Aligned_cols=24 Identities=21% Similarity=0.432 Sum_probs=12.0
Q ss_pred ccccccccCCCCCccccChHHHHHhh
Q psy225 239 LLVSCVFKDAGCRFKGMRGETMEKHI 264 (450)
Q Consensus 239 ~~~~C~~~~~gC~~~~~~~~~l~~H~ 264 (450)
-.|+|-+ .||+.+|....+-.+|+
T Consensus 143 dMy~Clv--EgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 143 DMYQCLV--EGCTEKFKTSRDRKDHM 166 (253)
T ss_pred cHHHHHH--HhhhhhhhhhhhhhhHH
Confidence 3455544 24665555544444444
No 183
>KOG3800|consensus
Probab=62.20 E-value=3.3 Score=37.51 Aligned_cols=54 Identities=17% Similarity=0.041 Sum_probs=35.5
Q ss_pred eccCCCCcccCCC----cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC-----CCCCCCchhHH
Q psy225 13 SFPARLNTHHKQQ----ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL-----SLTPDVSDSEK 68 (450)
Q Consensus 13 ~C~iC~~~~~~~p----~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~-----~~~~~~~~~~~ 68 (450)
.||+|....+..| +.- .|||..|.+|. ..-+++.||.|+..|.. +++.+ ..+++
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in-~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~fED-~~vek 67 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMIN-ECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQTFED-PTVEK 67 (300)
T ss_pred CCcccccceecCccceeeec-cccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhhcch-hHHHH
Confidence 4788865313333 222 69999998887 45678999999887654 45555 44444
No 184
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.27 E-value=4.8 Score=29.26 Aligned_cols=27 Identities=7% Similarity=-0.134 Sum_probs=13.2
Q ss_pred CceeeccCCCCcc----cCCCcccCCCCCcc
Q psy225 9 TKTLSFPARLNTH----HKQQISSKENTLSS 35 (450)
Q Consensus 9 ~~~~~C~iC~~~~----~~~p~~c~~Cg~~f 35 (450)
..+|.||.|+... ..--.+|..||..|
T Consensus 33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred hcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3455666665530 11235555555555
No 185
>KOG2482|consensus
Probab=61.21 E-value=8.2 Score=35.79 Aligned_cols=22 Identities=36% Similarity=0.711 Sum_probs=17.8
Q ss_pred eeecccccccccc-cchhhcccc
Q psy225 185 LVACRYCSKSYVA-DTLVTHQTK 206 (450)
Q Consensus 185 ~~~C~~C~~~f~~-~~l~~H~~~ 206 (450)
.++|-+|.+.|.. ..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 3678888888888 778888876
No 186
>KOG4367|consensus
Probab=60.98 E-value=2 Score=40.80 Aligned_cols=29 Identities=10% Similarity=0.045 Sum_probs=25.1
Q ss_pred CceeeccCCCCcccCCCcccCCCCCcccCCC
Q psy225 9 TKTLSFPARLNTHHKQQISSKENTLSSSSSS 39 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~ 39 (450)
++.++|++|+.. +++|...+ |+|..|..|
T Consensus 2 eeelkc~vc~~f-~~epiil~-c~h~lc~~c 30 (699)
T KOG4367|consen 2 EEELKCPVCGSF-YREPIILP-CSHNLCQAC 30 (699)
T ss_pred cccccCceehhh-ccCceEee-cccHHHHHH
Confidence 567899999999 99999996 999986544
No 187
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=60.67 E-value=5.1 Score=21.91 Aligned_cols=7 Identities=14% Similarity=-0.021 Sum_probs=3.3
Q ss_pred ccCCCCc
Q psy225 14 FPARLNT 20 (450)
Q Consensus 14 C~iC~~~ 20 (450)
|+.|+..
T Consensus 5 Cp~Cg~~ 11 (26)
T PF13248_consen 5 CPNCGAE 11 (26)
T ss_pred CcccCCc
Confidence 4444443
No 188
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=60.32 E-value=2.3 Score=39.75 Aligned_cols=46 Identities=2% Similarity=-0.082 Sum_probs=32.6
Q ss_pred ceeeccCCCCcc------------cCCCcccCCCCCcccCCCCCC--CCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTH------------HKQQISSKENTLSSSSSSHSS--DLPMICSQTKSRTP 56 (450)
Q Consensus 10 ~~~~C~iC~~~~------------~~~p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~~~ 56 (450)
.+-.|.||.... -.+|-..+ |||.+...|+.. |+...||+|+.++.
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i 345 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI 345 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence 445799998741 12467775 999997666632 66789999998743
No 189
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=60.18 E-value=5.5 Score=22.76 Aligned_cols=23 Identities=9% Similarity=-0.154 Sum_probs=14.3
Q ss_pred eeccCCCCcccCCCcccCCCCCcccC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSS 37 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~ 37 (450)
-.|.+|+.. ..|.|+.|+..+|+
T Consensus 3 ~~C~vC~~~---~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGNP---AKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSSE---ESEE-TTT--EESS
T ss_pred CCCccCcCC---CEEECCCcCCceeC
Confidence 357888775 46888888888764
No 190
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=59.95 E-value=7.8 Score=25.41 Aligned_cols=31 Identities=13% Similarity=0.271 Sum_probs=26.3
Q ss_pred hhcCCccccccccCCCCCccccChHHHHHhhHhhH
Q psy225 234 EHCNSLLVSCVFKDAGCRFKGMRGETMEKHIEENV 268 (450)
Q Consensus 234 ~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~ 268 (450)
+--++.-+.||- |+..|.+..+..+|+..++
T Consensus 11 ~RDGE~~lrCPR----C~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 11 DRDGEEFLRCPR----CGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred ccCCceeeeCCc----hhHHHHHhHHHHHHhhHHh
Confidence 345777889998 9999999999999998753
No 191
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=59.33 E-value=3.9 Score=24.49 Aligned_cols=29 Identities=3% Similarity=-0.003 Sum_probs=13.7
Q ss_pred ccCCCCCcccCCCCCCCCCCCCCCCCCCC
Q psy225 27 SSKENTLSSSSSSHSSDLPMICSQTKSRT 55 (450)
Q Consensus 27 ~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~ 55 (450)
.|+.||..|-.........-.|+.|+..|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 34555555533332233445666666543
No 192
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=59.01 E-value=9.4 Score=42.11 Aligned_cols=42 Identities=5% Similarity=0.008 Sum_probs=31.5
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
..|+.|+.. ...++.|+.||...-..... ...||.|+..+..
T Consensus 680 ~fCP~CGs~-te~vy~CPsCGaev~~des~---a~~CP~CGtplv~ 721 (1337)
T PRK14714 680 NRCPDCGTH-TEPVYVCPDCGAEVPPDESG---RVECPRCDVELTP 721 (1337)
T ss_pred ccCcccCCc-CCCceeCccCCCccCCCccc---cccCCCCCCcccc
Confidence 489999999 88889999999976322211 4579999987655
No 193
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=58.31 E-value=5.3 Score=31.71 Aligned_cols=28 Identities=7% Similarity=0.052 Sum_probs=18.5
Q ss_pred CcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
|++|..||+.|-.... +-..-||.|+..
T Consensus 1 PH~Ct~Cg~~f~dgs~--eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSK--EILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcH--HHHccCcccCCc
Confidence 7889999999954331 122359999754
No 194
>COG1773 Rubredoxin [Energy production and conversion]
Probab=58.29 E-value=14 Score=24.42 Aligned_cols=12 Identities=0% Similarity=-0.305 Sum_probs=8.4
Q ss_pred eeeccCCCCcccC
Q psy225 11 TLSFPARLNTHHK 23 (450)
Q Consensus 11 ~~~C~iC~~~~~~ 23 (450)
+|+|.+|+.+ +.
T Consensus 3 ~~~C~~CG~v-Yd 14 (55)
T COG1773 3 RWRCSVCGYV-YD 14 (55)
T ss_pred ceEecCCceE-ec
Confidence 5777777776 54
No 195
>PRK00420 hypothetical protein; Validated
Probab=58.27 E-value=8.4 Score=29.89 Aligned_cols=11 Identities=9% Similarity=-0.085 Sum_probs=6.2
Q ss_pred CCCCCCCCCCC
Q psy225 46 MICSQTKSRTP 56 (450)
Q Consensus 46 ~~C~~C~~~~~ 56 (450)
..||.|+.+|.
T Consensus 24 ~~CP~Cg~pLf 34 (112)
T PRK00420 24 KHCPVCGLPLF 34 (112)
T ss_pred CCCCCCCCcce
Confidence 35666665543
No 196
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=58.02 E-value=8.5 Score=32.15 Aligned_cols=32 Identities=19% Similarity=0.158 Sum_probs=22.3
Q ss_pred CcccCCcccccccc-cHHHhHHhhhCCCCcccCcccccccCh
Q psy225 103 DAIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSG 143 (450)
Q Consensus 103 ~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (450)
.-|.|+.|+..|.. ..+. ..|.|+.||.....
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLDY 140 (158)
T ss_pred CeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEeee
Confidence 56788888887777 4443 25888888877544
No 197
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.68 E-value=10 Score=31.19 Aligned_cols=17 Identities=18% Similarity=0.460 Sum_probs=10.2
Q ss_pred ccCceeecccccccccc
Q psy225 181 CYKRLVACRYCSKSYVA 197 (450)
Q Consensus 181 ~~~k~~~C~~C~~~f~~ 197 (450)
....-|.|+.|+..|..
T Consensus 95 ~~~~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 95 TNNAYYKCPNCQSKYTF 111 (147)
T ss_pred cCCcEEECcCCCCEeeH
Confidence 34445667766666665
No 198
>KOG3183|consensus
Probab=56.90 E-value=6.1 Score=34.71 Aligned_cols=44 Identities=7% Similarity=-0.094 Sum_probs=31.6
Q ss_pred ecc--CCCCcccCCCcccCCCCCcccCCCC------------CCCCCCCCCCCCCCCCC
Q psy225 13 SFP--ARLNTHHKQQISSKENTLSSSSSSH------------SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 13 ~C~--iC~~~~~~~p~~c~~Cg~~fc~~~~------------~~~~~~~C~~C~~~~~~ 57 (450)
.|. .|... ..-|+.|..|+..||..-. ..+....||.|.++...
T Consensus 10 HCs~~~Ckql-DFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~ 67 (250)
T KOG3183|consen 10 HCSVPYCKQL-DFLPFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPT 67 (250)
T ss_pred ccCcchhhhc-cccceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCC
Confidence 355 78888 8889999999999986432 23455678888766543
No 199
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=56.34 E-value=5.9 Score=23.19 Aligned_cols=23 Identities=17% Similarity=0.492 Sum_probs=11.5
Q ss_pred ccCcccccccChhHHHHHhhhCC
Q psy225 132 TTCQYCLESFSGMEMEDHTGHCS 154 (450)
Q Consensus 132 ~~C~~C~~~f~~~~l~~H~~~~~ 154 (450)
+.|+.|++.+....+..|+..|.
T Consensus 5 ~~C~nC~R~v~a~RfA~HLekCm 27 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPHLEKCM 27 (33)
T ss_dssp EE-TTTSSEEEGGGHHHHHHHHT
T ss_pred EECCCCcCCcchhhhHHHHHHHH
Confidence 44555555555444555555544
No 200
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=56.19 E-value=8.1 Score=31.84 Aligned_cols=37 Identities=16% Similarity=0.251 Sum_probs=22.9
Q ss_pred CcccCCcccccccc-cHHHhHHhhhCCCCcccCcccccccCh
Q psy225 103 DAIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSG 143 (450)
Q Consensus 103 ~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (450)
..|.|+.|+..|.. ..+.. .. ....|.|+.||.....
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~-~d---~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL-LD---MDGTFTCPRCGEELEE 135 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh-cC---CCCcEECCCCCCEEEE
Confidence 46888888887776 22211 11 2344888888877643
No 201
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=54.85 E-value=5.8 Score=31.57 Aligned_cols=24 Identities=4% Similarity=-0.039 Sum_probs=14.4
Q ss_pred eeccCCCCcccCC--CcccCCCCCcc
Q psy225 12 LSFPARLNTHHKQ--QISSKENTLSS 35 (450)
Q Consensus 12 ~~C~iC~~~~~~~--p~~c~~Cg~~f 35 (450)
+.||.|+.++|++ -+-||.||+++
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~~ 54 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYRE 54 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCceE
Confidence 5799999983332 24455555544
No 202
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.45 E-value=10 Score=39.81 Aligned_cols=19 Identities=5% Similarity=0.102 Sum_probs=12.1
Q ss_pred ccCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q psy225 27 SSKENTLSSSSSSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 27 ~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~ 56 (450)
.|..||+.+ .||.|.-+|.
T Consensus 385 ~C~~Cg~~~-----------~C~~C~~~L~ 403 (665)
T PRK14873 385 ACARCRTPA-----------RCRHCTGPLG 403 (665)
T ss_pred EhhhCcCee-----------ECCCCCCcee
Confidence 566666655 5777766655
No 203
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=54.37 E-value=7.3 Score=25.79 Aligned_cols=7 Identities=14% Similarity=0.458 Sum_probs=3.0
Q ss_pred CCCCCCC
Q psy225 47 ICSQTKS 53 (450)
Q Consensus 47 ~C~~C~~ 53 (450)
+||.|+.
T Consensus 4 ~CP~CG~ 10 (54)
T TIGR01206 4 ECPDCGA 10 (54)
T ss_pred CCCCCCC
Confidence 3444444
No 204
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=54.25 E-value=4.1 Score=30.46 Aligned_cols=28 Identities=7% Similarity=0.029 Sum_probs=19.0
Q ss_pred CcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
|++|..||+.|.... .+-..-||.|+..
T Consensus 2 pH~CtrCG~vf~~g~--~~il~GCp~CG~n 29 (112)
T COG3364 2 PHQCTRCGEVFDDGS--EEILSGCPKCGCN 29 (112)
T ss_pred Cceeccccccccccc--HHHHccCccccch
Confidence 789999999995431 1223459999764
No 205
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=54.01 E-value=14 Score=32.76 Aligned_cols=73 Identities=14% Similarity=0.193 Sum_probs=41.8
Q ss_pred CcccCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCCCCchHHHHhHHHHhhhcCCCCc
Q psy225 25 QISSKENTLSSSSSSHSSDLPMICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKEGCKWYDELKSLKGHLQTCKYDA 104 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~c~~~~~l~~~~~H~~~c~~~~ 104 (450)
-|.|..|++...+..-..+....|.-|++.+.. + +. .++..--.|.|++|+..|.-.+.+. .+
T Consensus 112 qFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDP-V-P~----dkmwG~aef~C~~C~h~F~G~~qm~-----------v~ 174 (278)
T PF15135_consen 112 QFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDP-V-PC----DKMWGIAEFHCPKCRHNFRGFAQMG-----------VP 174 (278)
T ss_pred eeeccccchHHHhccCcccccccccccccccCC-C-cc----ccccceeeeecccccccchhhhhcC-----------CC
Confidence 355666666654444445556778888776543 1 11 1222223688888888776554432 35
Q ss_pred ccCCcccccc
Q psy225 105 IPCNKCLAAI 114 (450)
Q Consensus 105 ~~C~~C~~~f 114 (450)
-.|-.|+...
T Consensus 175 sPCy~C~~~v 184 (278)
T PF15135_consen 175 SPCYGCGNPV 184 (278)
T ss_pred CCccCCCCcc
Confidence 5676676543
No 207
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.57 E-value=11 Score=32.19 Aligned_cols=32 Identities=22% Similarity=0.288 Sum_probs=21.7
Q ss_pred CcccCCcccccccc-cHHHhHHhhhCCCCcccCcccccccCh
Q psy225 103 DAIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFSG 143 (450)
Q Consensus 103 ~~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~~ 143 (450)
..|.|+.|+..|.. ..+. ..|.|+.||.....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 46788888877777 4332 35788888877654
No 208
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=53.36 E-value=2.4 Score=29.60 Aligned_cols=38 Identities=5% Similarity=0.062 Sum_probs=19.8
Q ss_pred eeccCCCCcccC---CCcccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHK---QQISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 12 ~~C~iC~~~~~~---~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
..||.|... +. ..|.|+.|+..|-. ...||.|+.+|..
T Consensus 2 ~~CP~C~~~-L~~~~~~~~C~~C~~~~~~-------~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 2 NTCPKCQQE-LEWQGGHYHCEACQKDYKK-------EAFCPDCGQPLEV 42 (70)
T ss_dssp -B-SSS-SB-EEEETTEEEETTT--EEEE-------EEE-TTT-SB-EE
T ss_pred CcCCCCCCc-cEEeCCEEECcccccccee-------cccCCCcccHHHH
Confidence 468888887 53 35778888877732 3368888876654
No 209
>KOG2272|consensus
Probab=53.05 E-value=4.7 Score=35.55 Aligned_cols=62 Identities=18% Similarity=0.328 Sum_probs=34.0
Q ss_pred ccCcccccccChhH--HHHHh---hhCCCCcccccccCChhhc-h--hHHHhhhhhcccCceeecccccccccc
Q psy225 132 TTCQYCLESFSGME--MEDHT---GHCSYEMVYCENKCGHKIQ-R--RLMAKHRANDCYKRLVACRYCSKSYVA 197 (450)
Q Consensus 132 ~~C~~C~~~f~~~~--l~~H~---~~~~~~~~~~c~~C~~~f~-~--~~l~~H~~~h~~~k~~~C~~C~~~f~~ 197 (450)
|+|..|++...+.. ++.-+ +-|.......|..|.+.+. + ..|-+|.. ..-|.|..|.+.|.-
T Consensus 164 FkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWH----veHFvCa~CekPFlG 233 (332)
T KOG2272|consen 164 FKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWH----VEHFVCAKCEKPFLG 233 (332)
T ss_pred eecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccc----hhheeehhcCCcccc
Confidence 57888888876653 33321 1222233334444555554 3 34455532 334788889888865
No 210
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=52.72 E-value=21 Score=32.76 Aligned_cols=50 Identities=12% Similarity=0.285 Sum_probs=32.7
Q ss_pred eeecccccccccccchhhccccCCCCcccCCcccccCccChhHHHHHHhhh
Q psy225 185 LVACRYCSKSYVADTLVTHQTKCTRAPIPCPNQCEMVALPREELDVHIKEH 235 (450)
Q Consensus 185 ~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~~C~~~f~~~~~l~~H~~~h 235 (450)
.--|-.|.-.|+......--.....-.|+|+ .|...|-.--+.-.|...|
T Consensus 362 s~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce-~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 362 STHCFVCQGPFPKPPVSPFDESTSSGRYQCE-LCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred CccceeccCCCCCCCCCcccccccccceech-hhhhhhhhhhHHHHHHHHh
Confidence 3458888888876222222222445678999 9998887777777777554
No 211
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=52.69 E-value=2.5 Score=29.92 Aligned_cols=46 Identities=11% Similarity=0.083 Sum_probs=18.3
Q ss_pred eeccCCCCccc----CCC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHH----KQQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 12 ~~C~iC~~~~~----~~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
-.|+||+..+. -++ +.|..|+.-.|+.|. ..+....||.|++.+..
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr 63 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKR 63 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B---
T ss_pred cccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCccc
Confidence 46999987412 133 457777777777776 45677889999976654
No 212
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=52.59 E-value=7.5 Score=27.12 Aligned_cols=30 Identities=7% Similarity=-0.066 Sum_probs=16.5
Q ss_pred eeeccCCCCcc--cCCCcccCCCCCcccCCCC
Q psy225 11 TLSFPARLNTH--HKQQISSKENTLSSSSSSH 40 (450)
Q Consensus 11 ~~~C~iC~~~~--~~~p~~c~~Cg~~fc~~~~ 40 (450)
.-.|.+|+..| ++..+.|..||..||..+.
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs 40 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCS 40 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchh
Confidence 34699998862 4677889999999987775
No 213
>PF04641 Rtf2: Rtf2 RING-finger
Probab=52.31 E-value=7.7 Score=35.49 Aligned_cols=49 Identities=6% Similarity=-0.074 Sum_probs=34.7
Q ss_pred cCceeeccCCCCcccCCC---cccCCCCCcccCCCCCCCC-CCCCCCCCCCCCC
Q psy225 8 WTKTLSFPARLNTHHKQQ---ISSKENTLSSSSSSHSSDL-PMICSQTKSRTPL 57 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p---~~c~~Cg~~fc~~~~~~~~-~~~C~~C~~~~~~ 57 (450)
....|.|||.+.. +..- +-...||+.|+...+..-+ ...||+|+.+|..
T Consensus 110 ~~~~~~CPvt~~~-~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 110 SEGRFICPVTGKE-FNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTE 162 (260)
T ss_pred CCceeECCCCCcc-cCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcccc
Confidence 5788999999998 6432 1223599999776663222 4579999998875
No 214
>PRK05580 primosome assembly protein PriA; Validated
Probab=52.06 E-value=13 Score=39.31 Aligned_cols=10 Identities=10% Similarity=0.338 Sum_probs=6.5
Q ss_pred CCCCCCCCCC
Q psy225 47 ICSQTKSRTP 56 (450)
Q Consensus 47 ~C~~C~~~~~ 56 (450)
.||.|..++.
T Consensus 392 ~C~~C~~~l~ 401 (679)
T PRK05580 392 ECPHCDASLT 401 (679)
T ss_pred CCCCCCCcee
Confidence 5777766654
No 215
>KOG2807|consensus
Probab=51.74 E-value=14 Score=34.05 Aligned_cols=29 Identities=14% Similarity=0.100 Sum_probs=15.8
Q ss_pred cCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q psy225 22 HKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 22 ~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~ 56 (450)
...-|.||.|+.+.|. -|-.||.|+..|.
T Consensus 273 ~~~Gy~CP~CkakvCs------LP~eCpiC~ltLV 301 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCS------LPIECPICSLTLV 301 (378)
T ss_pred ccCceeCCcccCeeec------CCccCCccceeEe
Confidence 3345666666666552 3455666665544
No 216
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=50.88 E-value=9.4 Score=41.53 Aligned_cols=45 Identities=9% Similarity=0.039 Sum_probs=35.0
Q ss_pred eccCCCCccc----CCC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHH----KQQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 13 ~C~iC~~~~~----~~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
.|+|||.-+. -+| +.|.+||.-.|+.|. ..+....||+|+..+..
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr 71 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKR 71 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhh
Confidence 7999998412 133 568899999999998 56778899999987764
No 217
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.65 E-value=9.7 Score=30.85 Aligned_cols=11 Identities=27% Similarity=0.437 Sum_probs=8.1
Q ss_pred CCCCCCCCCCC
Q psy225 44 LPMICSQTKSR 54 (450)
Q Consensus 44 ~~~~C~~C~~~ 54 (450)
..+.||.|+..
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 44679999864
No 218
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=50.42 E-value=9.1 Score=33.82 Aligned_cols=12 Identities=8% Similarity=0.144 Sum_probs=9.1
Q ss_pred CCCCCCCCCCCC
Q psy225 46 MICSQTKSRTPL 57 (450)
Q Consensus 46 ~~C~~C~~~~~~ 57 (450)
..||.|+-+...
T Consensus 49 ~vCP~CgyA~~~ 60 (214)
T PF09986_consen 49 WVCPHCGYAAFE 60 (214)
T ss_pred EECCCCCCcccc
Confidence 479999987554
No 219
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=50.42 E-value=4.2 Score=37.47 Aligned_cols=50 Identities=6% Similarity=0.028 Sum_probs=34.3
Q ss_pred cccccCceeeccCCCCcccC----CCcccCCCCCcccCCCC---CCCCCCCCCCCCCCCC
Q psy225 4 SFTSWTKTLSFPARLNTHHK----QQISSKENTLSSSSSSH---SSDLPMICSQTKSRTP 56 (450)
Q Consensus 4 ~~~~~~~~~~C~iC~~~~~~----~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~ 56 (450)
+-.+.+++| ||.|... +. .=+-| .||...|.-|+ ...-...||-|+..+.
T Consensus 8 ~~sedeed~-cplcie~-mditdknf~pc-~cgy~ic~fc~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 8 HNSEDEEDY-CPLCIEP-MDITDKNFFPC-PCGYQICQFCYNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred ccccccccc-Ccccccc-cccccCCcccC-CcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence 345667777 9999886 43 23557 49998776665 3455678999976543
No 220
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=49.81 E-value=8.4 Score=34.27 Aligned_cols=17 Identities=12% Similarity=-0.210 Sum_probs=10.8
Q ss_pred cccccCceeeccCCCCc
Q psy225 4 SFTSWTKTLSFPARLNT 20 (450)
Q Consensus 4 ~~~~~~~~~~C~iC~~~ 20 (450)
|-..+.+--.|..|++.
T Consensus 56 FC~s~qrlp~Ca~Cgk~ 72 (314)
T PF06524_consen 56 FCQSVQRLPMCAHCGKT 72 (314)
T ss_pred hhhhhhcCchhhhcCCe
Confidence 44455555578888873
No 221
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=49.68 E-value=14 Score=30.81 Aligned_cols=17 Identities=6% Similarity=0.155 Sum_probs=8.9
Q ss_pred ccCceeecccccccccc
Q psy225 181 CYKRLVACRYCSKSYVA 197 (450)
Q Consensus 181 ~~~k~~~C~~C~~~f~~ 197 (450)
....-|.|+.|+..|+.
T Consensus 105 ~~~~~Y~Cp~c~~r~tf 121 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTF 121 (158)
T ss_pred cCCCeEECCCCCcEeeH
Confidence 34444556555555554
No 222
>COG4640 Predicted membrane protein [Function unknown]
Probab=49.44 E-value=8.7 Score=36.44 Aligned_cols=22 Identities=5% Similarity=-0.032 Sum_probs=16.1
Q ss_pred eccCCC-CcccCCCcccCCCCCcc
Q psy225 13 SFPARL-NTHHKQQISSKENTLSS 35 (450)
Q Consensus 13 ~C~iC~-~~~~~~p~~c~~Cg~~f 35 (450)
.|+-|| .- ..+.++|++||+.|
T Consensus 3 fC~kcG~qk-~Ed~~qC~qCG~~~ 25 (465)
T COG4640 3 FCPKCGSQK-AEDDVQCTQCGHKF 25 (465)
T ss_pred ccccccccc-ccccccccccCCcC
Confidence 477888 44 67777788888877
No 223
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=49.35 E-value=16 Score=22.64 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=12.0
Q ss_pred cccCCcccccccc---cHHHhHHhh
Q psy225 104 AIPCNKCLAAIPK---TLMEDHSKF 125 (450)
Q Consensus 104 ~~~C~~C~~~f~~---~~l~~H~~~ 125 (450)
...|+.||..+.. .+-..|.+-
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~y 37 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKY 37 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHH
Confidence 4566666666555 444445443
No 224
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=48.35 E-value=5.7 Score=26.29 Aligned_cols=27 Identities=4% Similarity=-0.009 Sum_probs=18.2
Q ss_pred CcccCCCCCcccC--CCC-CCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSS--SSH-SSDLPMICSQTK 52 (450)
Q Consensus 25 p~~c~~Cg~~fc~--~~~-~~~~~~~C~~C~ 52 (450)
.|-|| ||-+|-. ..+ .++..-.||.|.
T Consensus 22 tyPCP-CGDRFeIsLeDl~~GE~VArCPSCS 51 (67)
T COG5216 22 TYPCP-CGDRFEISLEDLRNGEVVARCPSCS 51 (67)
T ss_pred EecCC-CCCEeEEEHHHhhCCceEEEcCCce
Confidence 36686 9999832 222 567778888884
No 225
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=47.57 E-value=4.3 Score=31.67 Aligned_cols=20 Identities=20% Similarity=0.074 Sum_probs=13.5
Q ss_pred CCCCcccCCCcccCCCCCcccC
Q psy225 16 ARLNTHHKQQISSKENTLSSSS 37 (450)
Q Consensus 16 iC~~~~~~~p~~c~~Cg~~fc~ 37 (450)
||... -.+-..| .|||.|+.
T Consensus 62 i~qs~-~~rv~rc-ecghsf~d 81 (165)
T COG4647 62 ICQSA-QKRVIRC-ECGHSFGD 81 (165)
T ss_pred EEecc-cccEEEE-eccccccC
Confidence 34455 4556778 59999963
No 226
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.51 E-value=25 Score=38.00 Aligned_cols=12 Identities=8% Similarity=0.263 Sum_probs=6.2
Q ss_pred EEEEECCchhhh
Q psy225 304 LIWKITDYSLKC 315 (450)
Q Consensus 304 ~~w~i~~~s~~~ 315 (450)
.+-+|-+|+...
T Consensus 845 vvgRIIGft~a~ 856 (1121)
T PRK04023 845 VVGRIIGFTKAN 856 (1121)
T ss_pred eeeeeeeeeccc
Confidence 344555665543
No 227
>PLN02436 cellulose synthase A
Probab=46.72 E-value=14 Score=40.33 Aligned_cols=45 Identities=11% Similarity=0.113 Sum_probs=34.6
Q ss_pred eccCCCCccc----CCC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHH----KQQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 13 ~C~iC~~~~~----~~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
.|+||+.-+. -+| +.|..|+.-.|..|. ..+....||.|++.+..
T Consensus 38 iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 38 TCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKR 90 (1094)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhh
Confidence 7999998411 234 568889999999988 45677899999987764
No 228
>KOG3039|consensus
Probab=46.37 E-value=9.2 Score=33.75 Aligned_cols=47 Identities=11% Similarity=-0.000 Sum_probs=32.6
Q ss_pred ceeeccCCCCcccCCCccc---CCCCCcccCCCC--CCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISS---KENTLSSSSSSH--SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c---~~Cg~~fc~~~~--~~~~~~~C~~C~~~~~~ 57 (450)
++|.|++|... +.+...| ..||+.++..|. .-.+...||+|++++..
T Consensus 220 ~ryiCpvtrd~-LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 220 KRYICPVTRDT-LTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred cceecccchhh-hcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence 67888888887 7665554 248888877665 23445678888887654
No 229
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=46.17 E-value=11 Score=30.91 Aligned_cols=45 Identities=7% Similarity=0.069 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCCCCchHHHH
Q psy225 46 MICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKEGCKWYDEL 90 (450)
Q Consensus 46 ~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~c~~~~~l 90 (450)
-.||.|+.++....+.+-...-..-...|..|.+||+.+.|....
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHHH
Confidence 468999888766332210110011122477788888888887543
No 230
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=45.93 E-value=17 Score=31.03 Aligned_cols=15 Identities=27% Similarity=0.441 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHHh
Q psy225 280 SKQQQQISTLKSALN 294 (450)
Q Consensus 280 ~~~~~~i~~l~~~~~ 294 (450)
..++++|++|++.+.
T Consensus 156 ~~l~~~I~~l~~~~~ 170 (178)
T PRK06266 156 KELKEQIKELEEELK 170 (178)
T ss_pred HHHHHHHHHHHHHhc
Confidence 334444555554443
No 231
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=45.45 E-value=6.3 Score=25.52 Aligned_cols=28 Identities=7% Similarity=-0.059 Sum_probs=19.5
Q ss_pred eccCCCCcc-cCCCcccCCCCCcccCCCC
Q psy225 13 SFPARLNTH-HKQQISSKENTLSSSSSSH 40 (450)
Q Consensus 13 ~C~iC~~~~-~~~p~~c~~Cg~~fc~~~~ 40 (450)
.|.+|+... ..+-.+|..|+..|...++
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 478888740 2356889899988866665
No 232
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=45.39 E-value=81 Score=23.30 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=28.7
Q ss_pred HHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC
Q psy225 258 ETMEKHIEENVNQHMLLMCSLVSKQQQQISTLKSALNKVTLNY 300 (450)
Q Consensus 258 ~~l~~H~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~~~ 300 (450)
.++.+-....+...+......+..|.++|=-++++++.|+..|
T Consensus 73 fdmikee~~emkkdleaankrve~q~ekiflmekkfe~lekky 115 (122)
T PF05325_consen 73 FDMIKEETIEMKKDLEAANKRVESQAEKIFLMEKKFETLEKKY 115 (122)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHH
Confidence 4555555555666666666777777777777777777776544
No 233
>KOG2893|consensus
Probab=45.04 E-value=9.5 Score=33.37 Aligned_cols=20 Identities=25% Similarity=0.572 Sum_probs=10.8
Q ss_pred ceeecccccccccc-cchhhc
Q psy225 184 RLVACRYCSKSYVA-DTLVTH 203 (450)
Q Consensus 184 k~~~C~~C~~~f~~-~~l~~H 203 (450)
|-|+|.+|.|..-+ -.|..|
T Consensus 33 khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 33 KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ccceeeeehhhhccCCCceee
Confidence 44666666665444 444444
No 234
>PLN02400 cellulose synthase
Probab=44.55 E-value=17 Score=39.77 Aligned_cols=45 Identities=13% Similarity=0.077 Sum_probs=34.6
Q ss_pred eccCCCCcccC----CC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHHK----QQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 13 ~C~iC~~~~~~----~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
.|+||+.-+.. +| +.|..|+.-.|+.|. ..+....||+|+..+..
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR 90 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRR 90 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCcccc
Confidence 79999984121 34 568889988899988 45778899999987664
No 235
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=44.45 E-value=9.1 Score=28.28 Aligned_cols=27 Identities=11% Similarity=-0.077 Sum_probs=18.3
Q ss_pred CceeeccCCCCcccC-----CCcccCCCCCccc
Q psy225 9 TKTLSFPARLNTHHK-----QQISSKENTLSSS 36 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~-----~p~~c~~Cg~~fc 36 (450)
..+|.||.|+.. .. --.+|..||+.|.
T Consensus 33 ~~ky~Cp~Cgk~-~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 33 HAKYTCPFCGKT-SVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp HS-BEESSSSSS-EEEEEETTEEEETTTTEEEE
T ss_pred hCCCcCCCCCCc-eeEEeeeEEeecCCCCCEEe
Confidence 467889999885 32 2367888888773
No 236
>PLN02189 cellulose synthase
Probab=44.27 E-value=15 Score=39.85 Aligned_cols=45 Identities=11% Similarity=0.042 Sum_probs=34.5
Q ss_pred eccCCCCccc----CCC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHH----KQQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 13 ~C~iC~~~~~----~~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
.|+||+..+. .+| +.|..|+.-.|+.|. ..+....||+|++.+..
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKR 88 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhh
Confidence 7999998512 123 568889998899988 45678899999987764
No 237
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=43.99 E-value=16 Score=22.47 Aligned_cols=38 Identities=16% Similarity=0.042 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCCCCCCchhHHhhhcceeeccCCCCCCchHHHHhHH
Q psy225 47 ICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIHYKEGCKWYDELKSL 93 (450)
Q Consensus 47 ~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~c~~~c~~~~~l~~~ 93 (450)
.||.|+..+......+ . ....|+.|+--+-..+.+..+
T Consensus 1 ~CP~C~~~l~~~~~~~----~-----~id~C~~C~G~W~d~~el~~~ 38 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGD----V-----EIDVCPSCGGIWFDAGELEKL 38 (41)
T ss_pred CcCCCCcccceEEECC----E-----EEEECCCCCeEEccHHHHHHH
Confidence 4888887655411111 0 145688887666666665443
No 238
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=43.92 E-value=13 Score=23.88 Aligned_cols=15 Identities=7% Similarity=-0.026 Sum_probs=7.0
Q ss_pred cccCceeeccCCCCc
Q psy225 6 TSWTKTLSFPARLNT 20 (450)
Q Consensus 6 ~~~~~~~~C~iC~~~ 20 (450)
+++++.|.||+|+..
T Consensus 29 ~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 29 EDLPDDWVCPVCGAP 43 (47)
T ss_dssp GGS-TT-B-TTTSSB
T ss_pred HHCCCCCcCcCCCCc
Confidence 355666666666654
No 239
>KOG0804|consensus
Probab=43.45 E-value=9.5 Score=36.86 Aligned_cols=42 Identities=12% Similarity=-0.011 Sum_probs=31.1
Q ss_pred eccCCCCcccCCCc---ccCCCCCcccCCCCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHHKQQI---SSKENTLSSSSSSHSSDLPMICSQTKSRT 55 (450)
Q Consensus 13 ~C~iC~~~~~~~p~---~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~ 55 (450)
+||+|... +.... ....|.|.|.-.|+..-.--.||+|+...
T Consensus 177 TCpVCLER-MD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q 221 (493)
T KOG0804|consen 177 TCPVCLER-MDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQ 221 (493)
T ss_pred CcchhHhh-cCccccceeeeecccccchHHHhhcccCcChhhhhhc
Confidence 69999987 66543 55579999966676655667899997643
No 240
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=42.63 E-value=8.2 Score=24.81 Aligned_cols=40 Identities=10% Similarity=-0.029 Sum_probs=17.3
Q ss_pred ccCCCCccc----CCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCC
Q psy225 14 FPARLNTHH----KQQISSKENTLSSSSSSH---SSDLPMICSQTKSRT 55 (450)
Q Consensus 14 C~iC~~~~~----~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~ 55 (450)
|++|... + .+-+-| .||...|..++ .......||-|++++
T Consensus 1 cp~C~e~-~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEE-LDETDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B---CCCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccc-cccCCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 5677665 4 233557 59998877765 334577899998754
No 241
>KOG2807|consensus
Probab=42.56 E-value=13 Score=34.29 Aligned_cols=26 Identities=12% Similarity=-0.046 Sum_probs=19.7
Q ss_pred ceeeccCCCCcccCCCcccCCCCCcc
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLSS 35 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~f 35 (450)
.-|.||.|....-.-|..|+.|+-..
T Consensus 275 ~Gy~CP~CkakvCsLP~eCpiC~ltL 300 (378)
T KOG2807|consen 275 GGYFCPQCKAKVCSLPIECPICSLTL 300 (378)
T ss_pred CceeCCcccCeeecCCccCCccceeE
Confidence 46889999875245688999888765
No 242
>KOG1493|consensus
Probab=42.54 E-value=2.4 Score=29.84 Aligned_cols=32 Identities=3% Similarity=-0.101 Sum_probs=19.1
Q ss_pred CcccCCCCCcccCCCC-----CCCCCCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSSSSH-----SSDLPMICSQTKSRTP 56 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~-----~~~~~~~C~~C~~~~~ 56 (450)
|..-..|.|.|...|+ +......||.|+..+.
T Consensus 45 PLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 45 PLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred ccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 4444456777744443 3345578999987543
No 243
>PLN02195 cellulose synthase A
Probab=41.87 E-value=18 Score=39.07 Aligned_cols=45 Identities=4% Similarity=-0.013 Sum_probs=34.9
Q ss_pred eccCCCCccc----CCC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHH----KQQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 13 ~C~iC~~~~~----~~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
.|.|||..+. -+| +.|..|+.-.|+.|. ..++...||+|+..+..
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk~ 60 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYDA 60 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCcccc
Confidence 6999998412 234 568899999999998 46778899999988773
No 244
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.74 E-value=20 Score=27.32 Aligned_cols=33 Identities=12% Similarity=-0.030 Sum_probs=23.3
Q ss_pred cCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHH
Q psy225 213 PCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEK 262 (450)
Q Consensus 213 ~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~ 262 (450)
.|| .||+.|. .-...|+.||| |+++|++ +.+..
T Consensus 11 idP-etg~KFY-----------DLNrdPiVsPy----tG~s~P~-s~fe~ 43 (129)
T COG4530 11 IDP-ETGKKFY-----------DLNRDPIVSPY----TGKSYPR-SYFEE 43 (129)
T ss_pred cCc-cccchhh-----------ccCCCccccCc----ccccchH-HHHHh
Confidence 467 8888772 23446888998 9999988 65543
No 245
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=41.71 E-value=9.1 Score=22.60 Aligned_cols=10 Identities=20% Similarity=0.285 Sum_probs=4.3
Q ss_pred CCCCCCCCCC
Q psy225 48 CSQTKSRTPL 57 (450)
Q Consensus 48 C~~C~~~~~~ 57 (450)
||.|+.++..
T Consensus 3 C~~CG~~l~~ 12 (34)
T PF14803_consen 3 CPQCGGPLER 12 (34)
T ss_dssp -TTT--B-EE
T ss_pred cccccChhhh
Confidence 7888877655
No 246
>KOG4173|consensus
Probab=41.23 E-value=13 Score=31.93 Aligned_cols=18 Identities=22% Similarity=0.687 Sum_probs=9.1
Q ss_pred CcccccccChhH-HHHHhh
Q psy225 134 CQYCLESFSGME-MEDHTG 151 (450)
Q Consensus 134 C~~C~~~f~~~~-l~~H~~ 151 (450)
|..|.+.|.+.. |..|+.
T Consensus 109 Cs~C~r~~Pt~hLLd~HI~ 127 (253)
T KOG4173|consen 109 CSFCKRAFPTGHLLDAHIL 127 (253)
T ss_pred hHHHHHhCCchhhhhHHHH
Confidence 555555555544 444443
No 247
>PF15616 TerY-C: TerY-C metal binding domain
Probab=41.21 E-value=17 Score=29.12 Aligned_cols=38 Identities=8% Similarity=-0.064 Sum_probs=24.9
Q ss_pred eccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q psy225 13 SFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 13 ~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~ 56 (450)
-||.|+.. . --..| .||+.+|. .++....||-|+....
T Consensus 79 gCP~CGn~-~-~fa~C-~CGkl~Ci---~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 79 GCPHCGNQ-Y-AFAVC-GCGKLFCI---DGEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCcCh-h-cEEEe-cCCCEEEe---CCCCCEECCCCCCeee
Confidence 48888775 2 11234 68888864 4466789999987543
No 248
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=41.03 E-value=11 Score=35.19 Aligned_cols=10 Identities=10% Similarity=-0.170 Sum_probs=4.0
Q ss_pred eeeccCCCCc
Q psy225 11 TLSFPARLNT 20 (450)
Q Consensus 11 ~~~C~iC~~~ 20 (450)
.=.||+||..
T Consensus 172 ~g~CPvCGs~ 181 (290)
T PF04216_consen 172 RGYCPVCGSP 181 (290)
T ss_dssp -SS-TTT---
T ss_pred CCcCCCCCCc
Confidence 3479999884
No 249
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=40.83 E-value=37 Score=26.19 Aligned_cols=21 Identities=10% Similarity=0.172 Sum_probs=11.0
Q ss_pred eeeccCCCCCCchHHHHhHHH
Q psy225 74 LIHCIHYKEGCKWYDELKSLK 94 (450)
Q Consensus 74 ~~~C~~c~~~c~~~~~l~~~~ 94 (450)
...|..|+.+..-..-..|++
T Consensus 11 vlIC~~C~~av~~~~v~~HL~ 31 (109)
T PF12013_consen 11 VLICRQCQYAVQPSEVESHLR 31 (109)
T ss_pred EEEeCCCCcccCchHHHHHHH
Confidence 456777766654422224554
No 250
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=40.21 E-value=8.1 Score=39.81 Aligned_cols=70 Identities=7% Similarity=-0.065 Sum_probs=41.5
Q ss_pred cCceeeccCCCCcccCCC--------c-ccCCCCCcccCC-CC------CCCC-CCCCCCCCCCCCCCCCCCCchhHHhh
Q psy225 8 WTKTLSFPARLNTHHKQQ--------I-SSKENTLSSSSS-SH------SSDL-PMICSQTKSRTPLSLTPDVSDSEKDT 70 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~~~p--------~-~c~~Cg~~fc~~-~~------~~~~-~~~C~~C~~~~~~~~~~~~~~~~~~~ 70 (450)
+++--.|+.|..- +.+| + .|+.||-+|... .+ +.-. =.-||.|.+.+.. ..+ +..
T Consensus 98 ~pD~a~C~~Cl~E-i~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~d--P~n-----RRf 169 (750)
T COG0068 98 PPDAATCEDCLEE-IFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKD--PLN-----RRF 169 (750)
T ss_pred CCchhhhHHHHHH-hcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcC--ccc-----ccc
Confidence 3445579999886 5554 2 499999999432 22 2222 2469999775443 111 112
Q ss_pred hcceeeccCCCCCCc
Q psy225 71 MGSLIHCIHYKEGCK 85 (450)
Q Consensus 71 ~~~~~~C~~c~~~c~ 85 (450)
...++.||.||-.-.
T Consensus 170 HAQp~aCp~CGP~~~ 184 (750)
T COG0068 170 HAQPIACPKCGPHLF 184 (750)
T ss_pred ccccccCcccCCCeE
Confidence 223889999986443
No 251
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=40.19 E-value=1.9 Score=37.61 Aligned_cols=56 Identities=16% Similarity=0.013 Sum_probs=36.7
Q ss_pred eeccCCCCcccCC----CcccCCCCCcccCCCC---CCCCCCCCC--CCCCCCCC-----CCCCCCchhHH
Q psy225 12 LSFPARLNTHHKQ----QISSKENTLSSSSSSH---SSDLPMICS--QTKSRTPL-----SLTPDVSDSEK 68 (450)
Q Consensus 12 ~~C~iC~~~~~~~----p~~c~~Cg~~fc~~~~---~~~~~~~C~--~C~~~~~~-----~~~~~~~~~~~ 68 (450)
-.||+|..--+.. -+.-|.|-|+.|.+|. ...+|-+|| .|++-|.. +.+.| ..+++
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD-~~vEk 80 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFED-ITVEK 80 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccch-hhhhh
Confidence 3799998631222 3555679999988887 456788999 68765433 55566 44444
No 252
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=39.60 E-value=5.7 Score=25.83 Aligned_cols=41 Identities=10% Similarity=0.100 Sum_probs=20.3
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCC--C----CCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSS--H----SSDLPMICSQTKS 53 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~--~----~~~~~~~C~~C~~ 53 (450)
+.|++-... ++-|.+-..|.|.-|-+- + .......||+|++
T Consensus 3 L~CPls~~~-i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQR-IRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB--SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCE-EEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcC
Confidence 578998888 888888888888754221 1 2234488999875
No 253
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=39.59 E-value=9.1 Score=24.47 Aligned_cols=30 Identities=13% Similarity=0.237 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCCCCCCCchhHHhhhcceeeccC
Q psy225 47 ICSQTKSRTPLSLTPDVSDSEKDTMGSLIHCIH 79 (450)
Q Consensus 47 ~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~C~~ 79 (450)
.||.|+..... ... ..+...+.++-+.|.|
T Consensus 1 ~CP~Cg~~a~i--r~S-~~~s~~~~~~Y~qC~N 30 (47)
T PF04606_consen 1 RCPHCGSKARI--RTS-RQLSPLTRELYCQCTN 30 (47)
T ss_pred CcCCCCCeeEE--EEc-hhhCcceEEEEEEECC
Confidence 47888775432 111 1112233445667766
No 254
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.47 E-value=30 Score=36.40 Aligned_cols=37 Identities=11% Similarity=-0.018 Sum_probs=23.5
Q ss_pred ceeeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKS 53 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~ 53 (450)
.-+.|..|+.. ..|+.|+-..... ...+...|..|+.
T Consensus 382 p~l~C~~Cg~~-----~~C~~C~~~L~~h--~~~~~l~Ch~CG~ 418 (665)
T PRK14873 382 PSLACARCRTP-----ARCRHCTGPLGLP--SAGGTPRCRWCGR 418 (665)
T ss_pred CeeEhhhCcCe-----eECCCCCCceeEe--cCCCeeECCCCcC
Confidence 34579999988 6788887655221 1234556777765
No 255
>KOG4275|consensus
Probab=39.31 E-value=6.5 Score=35.61 Aligned_cols=42 Identities=5% Similarity=-0.032 Sum_probs=31.3
Q ss_pred ceeeccCCCCcccCCCcccCCCCCcc-cCCCCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLSS-SSSSHSSDLPMICSQTKSRT 55 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~f-c~~~~~~~~~~~C~~C~~~~ 55 (450)
.++.|.||... .++=+-. .|||.. |..| +...-.||+|+..+
T Consensus 299 ~~~LC~ICmDa-P~DCvfL-eCGHmVtCt~C--Gkrm~eCPICRqyi 341 (350)
T KOG4275|consen 299 TRRLCAICMDA-PRDCVFL-ECGHMVTCTKC--GKRMNECPICRQYI 341 (350)
T ss_pred HHHHHHHHhcC-CcceEEe-ecCcEEeehhh--ccccccCchHHHHH
Confidence 37889999999 7777777 499986 6666 33444899997644
No 256
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=38.89 E-value=20 Score=23.16 Aligned_cols=8 Identities=13% Similarity=0.185 Sum_probs=3.6
Q ss_pred eeccCCCC
Q psy225 75 IHCIHYKE 82 (450)
Q Consensus 75 ~~C~~c~~ 82 (450)
+.|+.|+.
T Consensus 21 ~vC~~Cg~ 28 (52)
T smart00661 21 FVCRKCGY 28 (52)
T ss_pred EECCcCCC
Confidence 44554443
No 257
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=38.86 E-value=13 Score=23.19 Aligned_cols=10 Identities=10% Similarity=0.411 Sum_probs=4.3
Q ss_pred CCCCCCCCCC
Q psy225 45 PMICSQTKSR 54 (450)
Q Consensus 45 ~~~C~~C~~~ 54 (450)
.+.|+.|+..
T Consensus 19 ~~vC~~CG~V 28 (43)
T PF08271_consen 19 ELVCPNCGLV 28 (43)
T ss_dssp EEEETTT-BB
T ss_pred eEECCCCCCE
Confidence 3455555443
No 258
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.16 E-value=33 Score=35.86 Aligned_cols=23 Identities=9% Similarity=-0.090 Sum_probs=12.8
Q ss_pred eccCCCCcccCCCcccCCCCCcc
Q psy225 13 SFPARLNTHHKQQISSKENTLSS 35 (450)
Q Consensus 13 ~C~iC~~~~~~~p~~c~~Cg~~f 35 (450)
.|+.|+........-|+.||..+
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l 25 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSL 25 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCC
Confidence 57777765123344466666654
No 259
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=38.01 E-value=17 Score=26.99 Aligned_cols=28 Identities=4% Similarity=-0.048 Sum_probs=17.6
Q ss_pred CceeeccCCCCcc-cC---CCcccCCCCCccc
Q psy225 9 TKTLSFPARLNTH-HK---QQISSKENTLSSS 36 (450)
Q Consensus 9 ~~~~~C~iC~~~~-~~---~p~~c~~Cg~~fc 36 (450)
..+|.|+.|+..- -+ -...|..|+..|.
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 4577888886640 11 2467777777774
No 260
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=37.95 E-value=16 Score=22.78 Aligned_cols=8 Identities=38% Similarity=0.650 Sum_probs=4.4
Q ss_pred hHHHHHHh
Q psy225 226 EELDVHIK 233 (450)
Q Consensus 226 ~~l~~H~~ 233 (450)
+.|..|++
T Consensus 34 s~l~~HL~ 41 (45)
T PF02892_consen 34 SNLKRHLK 41 (45)
T ss_dssp HHHHHHHH
T ss_pred HHHHHhhh
Confidence 45555653
No 261
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=37.94 E-value=28 Score=23.43 Aligned_cols=36 Identities=6% Similarity=-0.138 Sum_probs=16.9
Q ss_pred cccccCceeeccC--CCCcccC-----CC--cccCCCCCcccCCCC
Q psy225 4 SFTSWTKTLSFPA--RLNTHHK-----QQ--ISSKENTLSSSSSSH 40 (450)
Q Consensus 4 ~~~~~~~~~~C~i--C~~~~~~-----~p--~~c~~Cg~~fc~~~~ 40 (450)
|++..+..-.|+- |... +. .. .+|+.|+..||..|.
T Consensus 11 ~~~~~~~~~~Cp~~~C~~~-~~~~~~~~~~~~~C~~C~~~fC~~C~ 55 (64)
T PF01485_consen 11 YLESDPNIRWCPNPDCEYI-IEKDDGCNSPIVTCPSCGTEFCFKCG 55 (64)
T ss_dssp ---S---CC--TTSST----ECS-SSTTS--CCTTSCCSEECSSST
T ss_pred HHHCCCCccCCCCCCCccc-EEecCCCCCCeeECCCCCCcCccccC
Confidence 3433333346876 8876 32 22 789889999987664
No 262
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=37.35 E-value=22 Score=38.78 Aligned_cols=47 Identities=11% Similarity=0.038 Sum_probs=35.5
Q ss_pred eeeccCCCCcccC----CC-cccCCCCCcccCCCC---CCCCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHK----QQ-ISSKENTLSSSSSSH---SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 11 ~~~C~iC~~~~~~----~p-~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~~~ 57 (450)
...|+|||.-+.. +| +.|..|+.-.|+.|. ..+....||.|+..+..
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhh
Confidence 3479999984122 34 568899999999988 45778899999987664
No 263
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.90 E-value=22 Score=27.78 Aligned_cols=25 Identities=4% Similarity=-0.008 Sum_probs=13.4
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
..|..||+.|-. .+..+.||.|+..
T Consensus 71 ~~C~~Cg~~~~~----~~~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVEI----HQHDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEec----CCcCccCcCCCCC
Confidence 446666655532 1233458888753
No 264
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.82 E-value=22 Score=23.53 Aligned_cols=26 Identities=8% Similarity=-0.065 Sum_probs=13.6
Q ss_pred cccCCCCCcccCCCCCC-CCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSS-DLPMICSQT 51 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~-~~~~~C~~C 51 (450)
..|+.|||.|...-..+ .....||.|
T Consensus 29 W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 29 WKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred EECCCCCCeeEccHhhhccCCCCCCCC
Confidence 45777777773221111 345567765
No 265
>PRK12496 hypothetical protein; Provisional
Probab=36.53 E-value=25 Score=29.62 Aligned_cols=28 Identities=11% Similarity=-0.046 Sum_probs=18.8
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
++|+-||..|-.. ...-.||.||.++..
T Consensus 128 ~~C~gC~~~~~~~----~~~~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPED----YPDDVCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccCC----CCCCcCCCCCChhhh
Confidence 6788888888321 122469999987654
No 266
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=36.49 E-value=2.9 Score=25.58 Aligned_cols=8 Identities=25% Similarity=0.555 Sum_probs=3.5
Q ss_pred ccCccccc
Q psy225 132 TTCQYCLE 139 (450)
Q Consensus 132 ~~C~~C~~ 139 (450)
|.|..|+.
T Consensus 29 y~C~~C~~ 36 (39)
T PF01096_consen 29 YVCCNCGH 36 (39)
T ss_dssp EEESSSTE
T ss_pred EEeCCCCC
Confidence 34444443
No 267
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=36.48 E-value=8.6 Score=23.63 Aligned_cols=10 Identities=20% Similarity=0.614 Sum_probs=4.7
Q ss_pred ccCccccccc
Q psy225 132 TTCQYCLESF 141 (450)
Q Consensus 132 ~~C~~C~~~f 141 (450)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 4455554443
No 268
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=35.97 E-value=17 Score=23.66 Aligned_cols=14 Identities=7% Similarity=-0.054 Sum_probs=9.7
Q ss_pred ccCceeeccCCCCc
Q psy225 7 SWTKTLSFPARLNT 20 (450)
Q Consensus 7 ~~~~~~~C~iC~~~ 20 (450)
++++.+.||+|+..
T Consensus 30 ~Lp~~w~CP~C~a~ 43 (50)
T cd00730 30 DLPDDWVCPVCGAG 43 (50)
T ss_pred HCCCCCCCCCCCCc
Confidence 46777777777754
No 270
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=35.96 E-value=17 Score=20.54 Aligned_cols=22 Identities=9% Similarity=-0.156 Sum_probs=7.5
Q ss_pred eccCCCCcccC--CCcccCCCCCcc
Q psy225 13 SFPARLNTHHK--QQISSKENTLSS 35 (450)
Q Consensus 13 ~C~iC~~~~~~--~p~~c~~Cg~~f 35 (450)
.|.+|+.. .. -.|.|+.|+..+
T Consensus 2 ~C~~C~~~-~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKP-IDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS-----S--EEE-TTT----
T ss_pred cCCcCCCc-CCCCceEECccCCCcc
Confidence 57778777 54 467777776544
No 271
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=35.71 E-value=20 Score=26.53 Aligned_cols=27 Identities=7% Similarity=-0.146 Sum_probs=16.9
Q ss_pred CceeeccCCCCcccC-----CCcccCCCCCccc
Q psy225 9 TKTLSFPARLNTHHK-----QQISSKENTLSSS 36 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~-----~p~~c~~Cg~~fc 36 (450)
..+|.||.|+.. .. -...|..|+..|.
T Consensus 34 ~a~y~CpfCgk~-~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 34 HAKYFCPFCGKH-AVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred hCCccCCCCCCC-ceeeeeeEEEEcCCCCCEEe
Confidence 456778888654 22 2366777777773
No 272
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=35.52 E-value=25 Score=28.89 Aligned_cols=39 Identities=18% Similarity=0.447 Sum_probs=21.1
Q ss_pred hhcccCc----eeecccccccccccchhhccccCCCCcccCCcccccCccCh
Q psy225 178 ANDCYKR----LVACRYCSKSYVADTLVTHQTKCTRAPIPCPNQCEMVALPR 225 (450)
Q Consensus 178 ~~h~~~k----~~~C~~C~~~f~~~~l~~H~~~~~~~~~~C~~~C~~~f~~~ 225 (450)
..++|+. .+.|..||..... .++...-.|| .||.....|
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~~~~--------~~~~~l~~Cp-~C~~~~F~R 143 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHEVEL--------THPERLPPCP-KCGHTEFTR 143 (146)
T ss_pred CeecCcEecCceEecccCCCEEEe--------cCCCcCCCCC-CCCCCeeee
Confidence 3455655 3778888753211 1344555677 777654333
No 273
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=35.45 E-value=31 Score=34.69 Aligned_cols=23 Identities=13% Similarity=0.079 Sum_probs=17.2
Q ss_pred cCCcee---CCcEEEEEEEecCCccC
Q psy225 427 KRQFLK---DDAIFIRVKVDPSKIVA 449 (450)
Q Consensus 427 ~~~fl~---dd~l~i~~~v~v~~~~~ 449 (450)
+.|.|. .+.+.|.++|.+....|
T Consensus 444 e~~~i~~R~~N~~~i~leVvP~~~~~ 469 (483)
T PF05502_consen 444 EPGKIWERGRNWTSIVLEVVPGSLPG 469 (483)
T ss_pred cCCceEEeCCCeEEEEEEEECCccCC
Confidence 446665 68899999998876653
No 274
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.26 E-value=23 Score=27.63 Aligned_cols=45 Identities=9% Similarity=0.097 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCCCCCC-CchhHHhhhcceeeccCCCCCCchHHHH
Q psy225 45 PMICSQTKSRTPLSLTPD-VSDSEKDTMGSLIHCIHYKEGCKWYDEL 90 (450)
Q Consensus 45 ~~~C~~C~~~~~~~~~~~-~~~~~~~~~~~~~~C~~c~~~c~~~~~l 90 (450)
.-.||.|..++....+.. +..+. .--+.|-.|.+|++.|.|...-
T Consensus 39 i~qcp~csasirgd~~vegvlglg-~dye~psfchncgs~fpwterk 84 (160)
T COG4306 39 ITQCPICSASIRGDYYVEGVLGLG-GDYEPPSFCHNCGSRFPWTERK 84 (160)
T ss_pred HhcCCccCCcccccceeeeeeccC-CCCCCcchhhcCCCCCCcHHHH
Confidence 357999988766521111 00000 1112256788888888886543
No 275
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=35.22 E-value=39 Score=35.34 Aligned_cols=38 Identities=5% Similarity=-0.112 Sum_probs=24.5
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~ 56 (450)
.-.|+.||.. +.. -.|+.||... .....-||.||..+.
T Consensus 15 akFC~~CG~~-l~~-~~Cp~CG~~~------~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 15 NRFCQKCGTS-LTH-KPCPQCGTEV------PVDEAHCPNCGAETG 52 (645)
T ss_pred CccccccCCC-CCC-CcCCCCCCCC------CcccccccccCCccc
Confidence 3458888888 642 3688888774 233446888876543
No 276
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=35.14 E-value=11 Score=23.52 Aligned_cols=37 Identities=8% Similarity=0.008 Sum_probs=16.1
Q ss_pred ccCCCCcccCCCcccC--CCCCcccCCCC----CCCCCCCCCCC
Q psy225 14 FPARLNTHHKQQISSK--ENTLSSSSSSH----SSDLPMICSQT 51 (450)
Q Consensus 14 C~iC~~~~~~~p~~c~--~Cg~~fc~~~~----~~~~~~~C~~C 51 (450)
|.+|..+ ......|+ .|+-++...++ .......||.|
T Consensus 1 C~~C~~i-v~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEI-VTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB--SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccchh-HeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 6788888 77788887 58777633332 22222268876
No 277
>KOG4317|consensus
Probab=35.03 E-value=28 Score=32.06 Aligned_cols=30 Identities=10% Similarity=-0.029 Sum_probs=23.6
Q ss_pred CceeeccCCCCcccCCCcccCCCCCcccC-CCC
Q psy225 9 TKTLSFPARLNTHHKQQISSKENTLSSSS-SSH 40 (450)
Q Consensus 9 ~~~~~C~iC~~~~~~~p~~c~~Cg~~fc~-~~~ 40 (450)
....-|+||+.- .+. |.||.|+..||. .|.
T Consensus 5 s~~~~C~ic~vq-~~~-YtCPRCn~~YCsl~CY 35 (383)
T KOG4317|consen 5 SSFLACGICGVQ-KRE-YTCPRCNLLYCSLKCY 35 (383)
T ss_pred Cceeeccccccc-ccc-ccCCCCCccceeeeee
Confidence 345679999998 777 999999999975 344
No 278
>KOG1701|consensus
Probab=34.85 E-value=19 Score=34.69 Aligned_cols=11 Identities=18% Similarity=0.591 Sum_probs=7.2
Q ss_pred ccCCccccccc
Q psy225 105 IPCNKCLAAIP 115 (450)
Q Consensus 105 ~~C~~C~~~f~ 115 (450)
|+|+.||....
T Consensus 428 Y~CEDCg~~LS 438 (468)
T KOG1701|consen 428 YKCEDCGLLLS 438 (468)
T ss_pred eehhhcCcccc
Confidence 66777776554
No 279
>PHA01750 hypothetical protein
Probab=34.74 E-value=1.5e+02 Score=20.29 Aligned_cols=27 Identities=4% Similarity=0.105 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..+...+.....+++++++++.++
T Consensus 42 ~ELdNL~~ei~~~kikqDnl~~qv~ei 68 (75)
T PHA01750 42 SELDNLKTEIEELKIKQDELSRQVEEI 68 (75)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 333333333333333333344444333
No 280
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=34.32 E-value=76 Score=20.00 Aligned_cols=29 Identities=14% Similarity=0.251 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 268 VNQHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 268 ~~~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
+.+|-..+.+.+..++++|.+|+.+-+.|
T Consensus 10 Lqe~~d~IEqkiedid~qIaeLe~KR~~L 38 (46)
T PF08946_consen 10 LQEHYDNIEQKIEDIDEQIAELEAKRQRL 38 (46)
T ss_dssp -----THHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhHHHhHHHHHHHHHHHHHHHHHH
Confidence 34445555666777777888887766555
No 281
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=34.27 E-value=20 Score=29.21 Aligned_cols=45 Identities=22% Similarity=0.188 Sum_probs=22.1
Q ss_pred CcccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhH
Q psy225 210 APIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIE 265 (450)
Q Consensus 210 ~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~ 265 (450)
+.-.|+ .|+..|.+-.... ....-.++..|=...|.+ ..|.+-+.
T Consensus 27 RRReC~-~C~~RFTTfE~~E---------l~~~~VvKkdg~Re~F~r-~Kl~~gl~ 71 (156)
T COG1327 27 RRRECL-ECGERFTTFERAE---------LRPLIVVKKDGRREPFDR-EKLRRGLI 71 (156)
T ss_pred hhhccc-ccccccchhheee---------eccceEECcCCCcCCCCH-HHHHHHHH
Confidence 445677 7777775432111 111112233455556666 66655554
No 282
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=34.25 E-value=16 Score=25.79 Aligned_cols=9 Identities=33% Similarity=0.671 Sum_probs=4.4
Q ss_pred cCCcccccc
Q psy225 106 PCNKCLAAI 114 (450)
Q Consensus 106 ~C~~C~~~f 114 (450)
.|+.||..-
T Consensus 3 ~CP~Cg~~a 11 (72)
T PRK09678 3 HCPLCQHAA 11 (72)
T ss_pred cCCCCCCcc
Confidence 455555443
No 283
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=34.19 E-value=24 Score=23.30 Aligned_cols=28 Identities=7% Similarity=-0.081 Sum_probs=20.2
Q ss_pred eccCCCCcc--cCCCcccCCCCCcccCCCC
Q psy225 13 SFPARLNTH--HKQQISSKENTLSSSSSSH 40 (450)
Q Consensus 13 ~C~iC~~~~--~~~p~~c~~Cg~~fc~~~~ 40 (450)
.|..|+..| +...+.|..||+.||..+.
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~ 33 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCS 33 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHc
Confidence 477887751 3466888889999877665
No 284
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=33.83 E-value=21 Score=27.42 Aligned_cols=29 Identities=14% Similarity=0.095 Sum_probs=18.8
Q ss_pred CcccCCCCCcccCCCCCCCCCCCCCCCCCCCCC
Q psy225 25 QISSKENTLSSSSSSHSSDLPMICSQTKSRTPL 57 (450)
Q Consensus 25 p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~~~~ 57 (450)
.++||.|++...- ..+...|+.|++++..
T Consensus 69 ~V~CP~C~K~TKm----LGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 69 QVECPNCGKQTKM----LGRVDACMHCKEPLTL 97 (114)
T ss_pred eeECCCCCChHhh----hchhhccCcCCCcCcc
Confidence 4668877776521 1233589999888764
No 285
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=33.79 E-value=1.2e+02 Score=20.20 Aligned_cols=21 Identities=10% Similarity=0.289 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q psy225 276 CSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 276 ~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+++.+...|.+|++.+..|
T Consensus 27 ~~riDeM~~RIDdLE~si~dl 47 (54)
T PF06825_consen 27 LGRIDEMSSRIDDLEKSIADL 47 (54)
T ss_dssp HHHHHHHHHHHHCCHHHH---
T ss_pred HHHHHHHHhhHHHHHHHHHHH
Confidence 333444444444444444443
No 286
>KOG1812|consensus
Probab=33.71 E-value=30 Score=33.68 Aligned_cols=46 Identities=13% Similarity=0.035 Sum_probs=28.5
Q ss_pred eeeccCCCCcccC---CCcccCCCCCcccCCCC--------CCCCCCCCCC--CCCCCCC
Q psy225 11 TLSFPARLNTHHK---QQISSKENTLSSSSSSH--------SSDLPMICSQ--TKSRTPL 57 (450)
Q Consensus 11 ~~~C~iC~~~~~~---~p~~c~~Cg~~fc~~~~--------~~~~~~~C~~--C~~~~~~ 57 (450)
...|.||..- .. +.+....|+|.||..|+ .......||. |...+..
T Consensus 146 ~~~C~iC~~e-~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~ 204 (384)
T KOG1812|consen 146 KEECGICFVE-DPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTL 204 (384)
T ss_pred cccCccCccc-cccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCH
Confidence 5679999843 21 22334579999998877 2245677877 4444443
No 287
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=33.71 E-value=26 Score=27.40 Aligned_cols=26 Identities=8% Similarity=-0.037 Sum_probs=12.6
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
..|..||..|-... ...+.||.|+..
T Consensus 71 ~~C~~Cg~~~~~~~---~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYVTLLT---QRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCeeecCC---ccCCcCcCcCCC
Confidence 34555665552211 112457777753
No 288
>KOG1940|consensus
Probab=33.30 E-value=14 Score=33.68 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=5.8
Q ss_pred ccCCcccccc
Q psy225 105 IPCNKCLAAI 114 (450)
Q Consensus 105 ~~C~~C~~~f 114 (450)
..|+.|+..-
T Consensus 235 i~cndC~~~~ 244 (276)
T KOG1940|consen 235 ILCNDCGSGT 244 (276)
T ss_pred eeccCCCCCC
Confidence 4566666543
No 289
>PF14369 zf-RING_3: zinc-finger
Probab=33.26 E-value=27 Score=20.71 Aligned_cols=10 Identities=20% Similarity=0.405 Sum_probs=6.0
Q ss_pred eccCCCCCCc
Q psy225 76 HCIHYKEGCK 85 (450)
Q Consensus 76 ~C~~c~~~c~ 85 (450)
.||.|+.||-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4666666653
No 290
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=33.21 E-value=41 Score=22.65 Aligned_cols=36 Identities=8% Similarity=-0.065 Sum_probs=21.9
Q ss_pred ccccCceeecc--CCCCcccC------CCcccCCCCCcccCCCC
Q psy225 5 FTSWTKTLSFP--ARLNTHHK------QQISSKENTLSSSSSSH 40 (450)
Q Consensus 5 ~~~~~~~~~C~--iC~~~~~~------~p~~c~~Cg~~fc~~~~ 40 (450)
++..++.-.|| -|...+.. ....|+.||+.||..|.
T Consensus 12 i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~ 55 (64)
T smart00647 12 VESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCK 55 (64)
T ss_pred HhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCC
Confidence 33333333488 88765111 24678789999987664
No 291
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=33.19 E-value=22 Score=26.32 Aligned_cols=28 Identities=4% Similarity=-0.057 Sum_probs=18.1
Q ss_pred CceeeccCCCCcc-cC---CCcccCCCCCccc
Q psy225 9 TKTLSFPARLNTH-HK---QQISSKENTLSSS 36 (450)
Q Consensus 9 ~~~~~C~iC~~~~-~~---~p~~c~~Cg~~fc 36 (450)
..+|.|+.|+..- -+ -...|..|+..|.
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 34 RAKHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred hcCccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 4678888886541 12 2477888888774
No 292
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.59 E-value=44 Score=33.95 Aligned_cols=37 Identities=14% Similarity=0.090 Sum_probs=22.5
Q ss_pred ceeeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKS 53 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~ 53 (450)
.-+.|..|+.+ .+|+.|+-.... +...+...|..|+.
T Consensus 212 ~~~~C~~Cg~~-----~~C~~C~~~l~~--h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 212 KNLLCRSCGYI-----LCCPNCDVSLTY--HKKEGKLRCHYCGY 248 (505)
T ss_pred CeeEhhhCcCc-----cCCCCCCCceEE--ecCCCeEEcCCCcC
Confidence 34579999998 678888755421 11233455666655
No 293
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=32.50 E-value=35 Score=34.35 Aligned_cols=11 Identities=36% Similarity=0.767 Sum_probs=7.6
Q ss_pred cCcccccccCh
Q psy225 133 TCQYCLESFSG 143 (450)
Q Consensus 133 ~C~~C~~~f~~ 143 (450)
.|.+|.+....
T Consensus 88 ~C~~C~Wss~~ 98 (483)
T PF05502_consen 88 SCSYCRWSSRD 98 (483)
T ss_pred ECCCceeeccc
Confidence 78888776543
No 294
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=32.46 E-value=28 Score=26.13 Aligned_cols=12 Identities=25% Similarity=0.263 Sum_probs=6.5
Q ss_pred cCceeeccCCCC
Q psy225 8 WTKTLSFPARLN 19 (450)
Q Consensus 8 ~~~~~~C~iC~~ 19 (450)
+++.|.|+.|+.
T Consensus 19 L~k~FtCp~Cgh 30 (104)
T COG4888 19 LPKTFTCPRCGH 30 (104)
T ss_pred CCceEecCccCC
Confidence 455555555554
No 295
>KOG0802|consensus
Probab=32.10 E-value=6.9 Score=40.07 Aligned_cols=42 Identities=10% Similarity=-0.054 Sum_probs=32.0
Q ss_pred eeeccCCCCcccCC-----CcccCCCCCcccCCCCCC--CCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQ-----QISSKENTLSSSSSSHSS--DLPMICSQTKSR 54 (450)
Q Consensus 11 ~~~C~iC~~~~~~~-----p~~c~~Cg~~fc~~~~~~--~~~~~C~~C~~~ 54 (450)
.-.|.||... +.. |-..+ |||.|+..|+.. +....||.|+..
T Consensus 291 ~~~C~IC~e~-l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~ 339 (543)
T KOG0802|consen 291 DELCIICLEE-LHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTV 339 (543)
T ss_pred CCeeeeechh-hccccccccceee-cccchHHHHHHHHHHHhCcCCcchhh
Confidence 4579999998 776 66774 999997776622 347799999884
No 296
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=31.20 E-value=34 Score=22.72 Aligned_cols=12 Identities=8% Similarity=0.243 Sum_probs=7.4
Q ss_pred CCCCCCCCCCCC
Q psy225 43 DLPMICSQTKSR 54 (450)
Q Consensus 43 ~~~~~C~~C~~~ 54 (450)
.-.|.||.||-+
T Consensus 12 ~v~~~Cp~cGip 23 (55)
T PF13824_consen 12 HVNFECPDCGIP 23 (55)
T ss_pred ccCCcCCCCCCc
Confidence 345677777664
No 297
>KOG1785|consensus
Probab=30.97 E-value=15 Score=34.94 Aligned_cols=46 Identities=13% Similarity=0.044 Sum_probs=32.1
Q ss_pred cee-eccCCCCcccCCCcccCCCCCcccCCCC----CCCCCCCCCCCCCCCCC
Q psy225 10 KTL-SFPARLNTHHKQQISSKENTLSSSSSSH----SSDLPMICSQTKSRTPL 57 (450)
Q Consensus 10 ~~~-~C~iC~~~~~~~p~~c~~Cg~~fc~~~~----~~~~~~~C~~C~~~~~~ 57 (450)
..| .|.||... -.+ +.-+-|||..|..|+ .......||.|+..+..
T Consensus 367 sTFeLCKICaen-dKd-vkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 367 STFELCKICAEN-DKD-VKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred chHHHHHHhhcc-CCC-cccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 344 39999887 444 444569999988887 23447789999876544
No 298
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=30.85 E-value=36 Score=21.91 Aligned_cols=10 Identities=20% Similarity=0.484 Sum_probs=5.9
Q ss_pred hhHHHHHHhh
Q psy225 225 REELDVHIKE 234 (450)
Q Consensus 225 ~~~l~~H~~~ 234 (450)
.+.|..|++.
T Consensus 36 Ts~L~rHl~~ 45 (50)
T smart00614 36 TSNLRRHLRR 45 (50)
T ss_pred cHHHHHHHHh
Confidence 3566666663
No 299
>KOG0717|consensus
Probab=30.83 E-value=74 Score=31.25 Aligned_cols=39 Identities=15% Similarity=0.319 Sum_probs=26.9
Q ss_pred ccccccCCCCCccccChHHHHHhhHhhHHHHHHHHHHHHHHHHHH
Q psy225 241 VSCVFKDAGCRFKGMRGETMEKHIEENVNQHMLLMCSLVSKQQQQ 285 (450)
Q Consensus 241 ~~C~~~~~gC~~~~~~~~~l~~H~~~~~~~~~~~~~~~~~~~~~~ 285 (450)
+-|+. |++.|.....|..|..+- .|...|..+...++++
T Consensus 293 lyC~v----CnKsFKseKq~kNHEnSK--KHkenv~eLrqemEEE 331 (508)
T KOG0717|consen 293 LYCVV----CNKSFKSEKQLKNHENSK--KHKENVAELRQEMEEE 331 (508)
T ss_pred eEEee----ccccccchHHHHhhHHHH--HHHHHHHHHHHHHHHh
Confidence 66877 999999999999999864 5555554444444333
No 300
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=30.56 E-value=26 Score=28.55 Aligned_cols=45 Identities=22% Similarity=0.257 Sum_probs=21.9
Q ss_pred CcccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCccccChHHHHHhhH
Q psy225 210 APIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFKGMRGETMEKHIE 265 (450)
Q Consensus 210 ~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~~~~~~~l~~H~~ 265 (450)
+.-.|. .|++.|++-..... .+ .=..+-.|=...|.+ ..|..-+.
T Consensus 27 RRReC~-~C~~RFTTyErve~--------~~-l~ViKkdG~re~Fdr-~Kl~~gl~ 71 (147)
T TIGR00244 27 RRRECL-ECHERFTTFERAEL--------LP-PTVIKQDGVREPFNR-EKLLRGMV 71 (147)
T ss_pred ecccCC-ccCCccceeeeccc--------cc-cEEEcCCCCCCCCCH-HHHHHHHH
Confidence 345677 77777754322211 11 112233455566666 55555544
No 301
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.94 E-value=8.7 Score=27.05 Aligned_cols=31 Identities=13% Similarity=0.115 Sum_probs=16.9
Q ss_pred cccCCCCCcccC-CCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSS-SSHSSDLPMICSQTKSRTP 56 (450)
Q Consensus 26 ~~c~~Cg~~fc~-~~~~~~~~~~C~~C~~~~~ 56 (450)
|.|..||++|-. ..+.....-.||.|+..+.
T Consensus 13 Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~~k 44 (82)
T COG2331 13 YECTECGNRFDVVQAMTDDPLTTCEECGARLK 44 (82)
T ss_pred EeecccchHHHHHHhcccCccccChhhChHHH
Confidence 667777777722 1222233346777766543
No 302
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=29.91 E-value=14 Score=25.97 Aligned_cols=28 Identities=4% Similarity=-0.177 Sum_probs=9.8
Q ss_pred eeccCCCCcccC-C---C-cccC--CCCCcccCCCC
Q psy225 12 LSFPARLNTHHK-Q---Q-ISSK--ENTLSSSSSSH 40 (450)
Q Consensus 12 ~~C~iC~~~~~~-~---p-~~c~--~Cg~~fc~~~~ 40 (450)
..|.||... .. . | ..|+ .|+..|...|+
T Consensus 3 ~~C~IC~~~-~~~~~~~p~~~C~n~~C~~~fH~~CL 37 (70)
T PF11793_consen 3 LECGICYSY-RLDDGEIPDVVCPNPSCGKKFHLLCL 37 (70)
T ss_dssp -S-SSS--S-S-TT-----B--S-TT----B-SGGG
T ss_pred CCCCcCCcE-ecCCCCcCceEcCCcccCCHHHHHHH
Confidence 469999876 33 2 2 4565 78888866666
No 303
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=29.82 E-value=21 Score=28.69 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=13.2
Q ss_pred cccCCcccccCccChhHHHHHHhhhcCCc
Q psy225 211 PIPCPNQCEMVALPREELDVHIKEHCNSL 239 (450)
Q Consensus 211 ~~~C~~~C~~~f~~~~~l~~H~~~h~~~~ 239 (450)
-+.|- +||+.|. .|+.|+++|.+..
T Consensus 72 ~i~cl-ecGk~~k---~LkrHL~~~~glt 96 (132)
T PF05443_consen 72 YIICL-ECGKKFK---TLKRHLRTHHGLT 96 (132)
T ss_dssp -EE-T-BT--EES---BHHHHHHHTT-S-
T ss_pred eeEEc-cCCcccc---hHHHHHHHccCCC
Confidence 35676 7888773 5578888775543
No 304
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=29.51 E-value=33 Score=21.71 Aligned_cols=8 Identities=25% Similarity=0.767 Sum_probs=4.3
Q ss_pred CCCCCCCC
Q psy225 46 MICSQTKS 53 (450)
Q Consensus 46 ~~C~~C~~ 53 (450)
+.||.|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44555554
No 305
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.43 E-value=47 Score=18.76 Aligned_cols=21 Identities=5% Similarity=-0.222 Sum_probs=12.5
Q ss_pred eeccCCCCcccCC-CcccCCCC
Q psy225 12 LSFPARLNTHHKQ-QISSKENT 32 (450)
Q Consensus 12 ~~C~iC~~~~~~~-p~~c~~Cg 32 (450)
+.|.+|+...... -|.|..|+
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCC
Confidence 4577777751223 56777666
No 306
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.82 E-value=43 Score=31.29 Aligned_cols=72 Identities=18% Similarity=0.274 Sum_probs=46.3
Q ss_pred ceeecccccccccccchhhcccc-CCC---Cc-ccCCcccccCccChhHHHHHHhhhcCCccccccccCCCCCcc-----
Q psy225 184 RLVACRYCSKSYVADTLVTHQTK-CTR---AP-IPCPNQCEMVALPREELDVHIKEHCNSLLVSCVFKDAGCRFK----- 253 (450)
Q Consensus 184 k~~~C~~C~~~f~~~~l~~H~~~-~~~---~~-~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~~~~gC~~~----- 253 (450)
+.|.|.+ ..|+++.|+.|... -.+ +- =.|. .|...|-.-..|..|.+..+ -.|-+ |++.
T Consensus 190 k~F~~E~--~lF~~~~Lr~H~~~G~~e~GFKGHP~C~-FC~~~FYdDDEL~~HcR~~H----E~ChI----CD~v~p~~~ 258 (493)
T COG5236 190 KDFWNEI--RLFRSSTLRDHKNGGLEEEGFKGHPLCI-FCKIYFYDDDELRRHCRLRH----EACHI----CDMVGPIRY 258 (493)
T ss_pred ccCccce--eeeecccccccccCCccccCcCCCchhh-hccceecChHHHHHHHHhhh----hhhhh----hhccCccch
Confidence 4455554 34666888888877 222 22 2577 88888888888888877532 23444 4433
Q ss_pred --ccChHHHHHhhHh
Q psy225 254 --GMRGETMEKHIEE 266 (450)
Q Consensus 254 --~~~~~~l~~H~~~ 266 (450)
|+...+|.+|.+.
T Consensus 259 QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 259 QYFKSYEDLEAHFRN 273 (493)
T ss_pred hhhhCHHHHHHHhhc
Confidence 6677788888874
No 307
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=27.59 E-value=25 Score=22.72 Aligned_cols=14 Identities=21% Similarity=0.788 Sum_probs=7.9
Q ss_pred ceeecccccccccc
Q psy225 184 RLVACRYCSKSYVA 197 (450)
Q Consensus 184 k~~~C~~C~~~f~~ 197 (450)
+++.|..||..|..
T Consensus 3 k~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCKDCGAEFVF 16 (49)
T ss_pred eeEEcccCCCeEEE
Confidence 44556666665554
No 308
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=27.50 E-value=39 Score=27.90 Aligned_cols=10 Identities=10% Similarity=0.351 Sum_probs=7.4
Q ss_pred eeeccCCCCc
Q psy225 11 TLSFPARLNT 20 (450)
Q Consensus 11 ~~~C~iC~~~ 20 (450)
...|+||...
T Consensus 2 d~~CpICme~ 11 (162)
T PF07800_consen 2 DVTCPICMEH 11 (162)
T ss_pred CccCceeccC
Confidence 3579999874
No 309
>KOG2593|consensus
Probab=27.44 E-value=1.4e+02 Score=29.16 Aligned_cols=33 Identities=21% Similarity=0.251 Sum_probs=15.8
Q ss_pred CCcccCCcccccCccChhHHHHHHhhhcCCccccccc
Q psy225 209 RAPIPCPNQCEMVALPREELDVHIKEHCNSLLVSCVF 245 (450)
Q Consensus 209 ~~~~~C~~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 245 (450)
..-|.|| .|.+.|..-..++ ...-..-.|.|.+
T Consensus 126 ~~~Y~Cp-~C~kkyt~Lea~~---L~~~~~~~F~C~~ 158 (436)
T KOG2593|consen 126 VAGYVCP-NCQKKYTSLEALQ---LLDNETGEFHCEN 158 (436)
T ss_pred cccccCC-ccccchhhhHHHH---hhcccCceEEEec
Confidence 3446666 6666664332222 2222234566766
No 310
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.16 E-value=48 Score=25.18 Aligned_cols=10 Identities=20% Similarity=0.385 Sum_probs=5.9
Q ss_pred CCCCCCCCCC
Q psy225 46 MICSQTKSRT 55 (450)
Q Consensus 46 ~~C~~C~~~~ 55 (450)
..|+.|+...
T Consensus 43 ~~C~~CG~y~ 52 (99)
T PRK14892 43 ITCGNCGLYT 52 (99)
T ss_pred EECCCCCCcc
Confidence 4577776543
No 311
>PHA01750 hypothetical protein
Probab=27.09 E-value=2.1e+02 Score=19.60 Aligned_cols=22 Identities=14% Similarity=0.128 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q psy225 273 LLMCSLVSKQQQQISTLKSALN 294 (450)
Q Consensus 273 ~~~~~~~~~~~~~i~~l~~~~~ 294 (450)
..+....+.+++++.+++++++
T Consensus 52 ~~~kikqDnl~~qv~eik~k~d 73 (75)
T PHA01750 52 EELKIKQDELSRQVEEIKRKLD 73 (75)
T ss_pred HHHHHhHHHHHHHHHHHHHhhc
Confidence 3333344445555555555544
No 312
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=26.97 E-value=1e+02 Score=22.35 Aligned_cols=29 Identities=7% Similarity=0.130 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q psy225 271 HMLLMCSLVSKQQQQISTLKSALNKVTLN 299 (450)
Q Consensus 271 ~~~~~~~~~~~~~~~i~~l~~~~~~l~~~ 299 (450)
.|..+...-.+++.++..|+.+|-++|..
T Consensus 3 ~L~~l~~~k~~Le~~L~~lE~qIy~~Et~ 31 (80)
T PF09340_consen 3 ELKELLQKKKKLEKDLAALEKQIYDKETS 31 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666677888888999988888743
No 313
>KOG2272|consensus
Probab=26.17 E-value=53 Score=29.25 Aligned_cols=11 Identities=0% Similarity=-0.251 Sum_probs=8.2
Q ss_pred ceeeccCCCCc
Q psy225 10 KTLSFPARLNT 20 (450)
Q Consensus 10 ~~~~C~iC~~~ 20 (450)
..|.|..|...
T Consensus 136 g~YvC~KCh~~ 146 (332)
T KOG2272|consen 136 GRYVCQKCHAH 146 (332)
T ss_pred ceeehhhhhhh
Confidence 47888888775
No 314
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=26.08 E-value=35 Score=19.52 Aligned_cols=21 Identities=10% Similarity=-0.001 Sum_probs=7.2
Q ss_pred eccCCCCc---ccCCCcccCCCCC
Q psy225 13 SFPARLNT---HHKQQISSKENTL 33 (450)
Q Consensus 13 ~C~iC~~~---~~~~p~~c~~Cg~ 33 (450)
.|+.|+.. ....-+.|+.|++
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCcceeccCCEEeCCcccc
Confidence 35666553 0123455555554
No 315
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=25.72 E-value=47 Score=26.01 Aligned_cols=25 Identities=8% Similarity=0.013 Sum_probs=14.6
Q ss_pred cccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
..|..||+.|-.. +..+.||.|+..
T Consensus 71 ~~C~~Cg~~~~~~----~~~~~CP~Cgs~ 95 (115)
T TIGR00100 71 CECEDCSEEVSPE----IDLYRCPKCHGI 95 (115)
T ss_pred EEcccCCCEEecC----CcCccCcCCcCC
Confidence 4466666666322 124668888764
No 316
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=25.63 E-value=2.1e+02 Score=19.99 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKVT 297 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l~ 297 (450)
..+..+...+..+..+|..|++++..|.
T Consensus 18 ~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~ 45 (69)
T PF04102_consen 18 DTIEELNDVVTEQQRQIDRLQRQLRLLR 45 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555666666666666666654
No 317
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.56 E-value=49 Score=26.03 Aligned_cols=25 Identities=16% Similarity=0.381 Sum_probs=12.5
Q ss_pred cccCCCCCcccCCCCCCCCCC-CCCCCCCC
Q psy225 26 ISSKENTLSSSSSSHSSDLPM-ICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~~~~~~~~-~C~~C~~~ 54 (450)
..|..||..|-.. +..+ .||.|+..
T Consensus 72 ~~C~~Cg~~~~~~----~~~~~~CP~Cgs~ 97 (117)
T PRK00564 72 LECKDCSHVFKPN----ALDYGVCEKCHSK 97 (117)
T ss_pred EEhhhCCCccccC----CccCCcCcCCCCC
Confidence 3455566555221 1122 48888764
No 318
>PRK05978 hypothetical protein; Provisional
Probab=25.52 E-value=38 Score=27.82 Aligned_cols=14 Identities=29% Similarity=0.228 Sum_probs=8.3
Q ss_pred cceeeccCCCCCCc
Q psy225 72 GSLIHCIHYKEGCK 85 (450)
Q Consensus 72 ~~~~~C~~c~~~c~ 85 (450)
.+.-+||+|++|=-
T Consensus 31 Gl~grCP~CG~G~L 44 (148)
T PRK05978 31 GFRGRCPACGEGKL 44 (148)
T ss_pred HHcCcCCCCCCCcc
Confidence 34556777776633
No 319
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=25.44 E-value=43 Score=21.70 Aligned_cols=32 Identities=13% Similarity=-0.081 Sum_probs=22.4
Q ss_pred cCceeeccCCCCccc----CCCcccCCCCCcccCCCC
Q psy225 8 WTKTLSFPARLNTHH----KQQISSKENTLSSSSSSH 40 (450)
Q Consensus 8 ~~~~~~C~iC~~~~~----~~p~~c~~Cg~~fc~~~~ 40 (450)
+..+-.|.+|+.. + ...|.|..|+...-..|.
T Consensus 8 ~~~~~~C~~C~~~-i~g~~~~g~~C~~C~~~~H~~C~ 43 (53)
T PF00130_consen 8 FSKPTYCDVCGKF-IWGLGKQGYRCSWCGLVCHKKCL 43 (53)
T ss_dssp SSSTEB-TTSSSB-ECSSSSCEEEETTTT-EEETTGG
T ss_pred CCCCCCCcccCcc-cCCCCCCeEEECCCCChHhhhhh
Confidence 3566689999998 5 667889989888755554
No 320
>KOG2114|consensus
Probab=25.38 E-value=30 Score=36.52 Aligned_cols=41 Identities=12% Similarity=-0.073 Sum_probs=33.5
Q ss_pred eeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCCC
Q psy225 12 LSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKSR 54 (450)
Q Consensus 12 ~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~~ 54 (450)
-+|..|+.. +.-|..==.|||.|...|+. ++...||.|...
T Consensus 841 skCs~C~~~-LdlP~VhF~CgHsyHqhC~e-~~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGT-LDLPFVHFLCGHSYHQHCLE-DKEDKCPKCLPE 881 (933)
T ss_pred eeecccCCc-cccceeeeecccHHHHHhhc-cCcccCCccchh
Confidence 479999999 88887655799999877765 667899999774
No 321
>KOG2907|consensus
Probab=25.19 E-value=33 Score=26.40 Aligned_cols=39 Identities=21% Similarity=0.261 Sum_probs=18.0
Q ss_pred cccCCcccccccc-cHHHhHHhhhCCCCcccCcccccccC
Q psy225 104 AIPCNKCLAAIPK-TLMEDHSKFTCPERITTCQYCLESFS 142 (450)
Q Consensus 104 ~~~C~~C~~~f~~-~~l~~H~~~h~~~~~~~C~~C~~~f~ 142 (450)
..+|+.||..=.. ..|+......-+.--|.|+.|+.+|.
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 3566666653222 33322222222233466666666654
No 322
>PRK00295 hypothetical protein; Provisional
Probab=24.73 E-value=2.1e+02 Score=19.95 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..+...+.++..+|..|++++..|
T Consensus 19 ~tie~Ln~~v~~Qq~~I~~L~~ql~~L 45 (68)
T PRK00295 19 DTIQALNDVLVEQQRVIERLQLQMAAL 45 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555566666666666666655
No 323
>PRK01343 zinc-binding protein; Provisional
Probab=23.90 E-value=59 Score=21.78 Aligned_cols=17 Identities=12% Similarity=0.034 Sum_probs=10.5
Q ss_pred ceeeccCCCCcccCCCcc
Q psy225 10 KTLSFPARLNTHHKQQIS 27 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~~ 27 (450)
....|++|++. ...++.
T Consensus 8 p~~~CP~C~k~-~~~~~r 24 (57)
T PRK01343 8 PTRPCPECGKP-STREAY 24 (57)
T ss_pred CCCcCCCCCCc-CcCCCC
Confidence 34568888887 554443
No 324
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.78 E-value=41 Score=23.31 Aligned_cols=13 Identities=15% Similarity=0.204 Sum_probs=8.2
Q ss_pred CCCCCCCCCCCCC
Q psy225 42 SDLPMICSQTKSR 54 (450)
Q Consensus 42 ~~~~~~C~~C~~~ 54 (450)
....+.||.|+..
T Consensus 43 ~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 43 SGRVFTCPNCGFE 55 (69)
T ss_pred ccceEEcCCCCCE
Confidence 3455677777664
No 325
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=23.76 E-value=48 Score=26.45 Aligned_cols=25 Identities=20% Similarity=0.212 Sum_probs=19.6
Q ss_pred ccCCcccccCccChhHHHHHHhhhcCCcc
Q psy225 212 IPCPNQCEMVALPREELDVHIKEHCNSLL 240 (450)
Q Consensus 212 ~~C~~~C~~~f~~~~~l~~H~~~h~~~~~ 240 (450)
+.|- ++|+.| ..|++|+.+|.+..|
T Consensus 77 IicL-EDGkkf---KSLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICL-EDGKKF---KSLKRHLTTHYGLTP 101 (148)
T ss_pred EEEe-ccCcch---HHHHHHHhcccCCCH
Confidence 5677 889888 589999999877554
No 326
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=23.76 E-value=24 Score=24.89 Aligned_cols=25 Identities=16% Similarity=0.281 Sum_probs=9.0
Q ss_pred HHhhhhhcccCceeecccccccccc
Q psy225 173 MAKHRANDCYKRLVACRYCSKSYVA 197 (450)
Q Consensus 173 l~~H~~~h~~~k~~~C~~C~~~f~~ 197 (450)
+..|.......+...|..|+..++.
T Consensus 29 ~~~H~~~~~~~~~v~Cg~C~~~~~~ 53 (71)
T PF05495_consen 29 LEDHPFDRWPVKRVICGKCRTEQPI 53 (71)
T ss_dssp CSSS---TTT--EEEETTT--EEES
T ss_pred hccCccccccccCeECCCCCCccCh
Confidence 3344333334445666666655444
No 327
>PRK00736 hypothetical protein; Provisional
Probab=23.69 E-value=2.3e+02 Score=19.79 Aligned_cols=27 Identities=7% Similarity=0.268 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..+...+.++..+|..|.+++..|
T Consensus 19 ~tie~Ln~~v~~Qq~~i~~L~~ql~~L 45 (68)
T PRK00736 19 KTIEELSDQLAEQWKTVEQMRKKLDAL 45 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555666666666666666665
No 328
>KOG4602|consensus
Probab=23.22 E-value=40 Score=30.00 Aligned_cols=8 Identities=0% Similarity=-0.371 Sum_probs=3.5
Q ss_pred cccCCCCC
Q psy225 26 ISSKENTL 33 (450)
Q Consensus 26 ~~c~~Cg~ 33 (450)
|.|+.||.
T Consensus 269 YVCPiCGA 276 (318)
T KOG4602|consen 269 YVCPICGA 276 (318)
T ss_pred hcCccccc
Confidence 44444443
No 329
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=23.17 E-value=2.2e+02 Score=18.53 Aligned_cols=30 Identities=10% Similarity=0.117 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy225 268 VNQHMLLMCSLVSKQQQQISTLKSALNKVT 297 (450)
Q Consensus 268 ~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~ 297 (450)
...++..+...+..+..++..|..++..|+
T Consensus 23 kk~~~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 23 KKQREEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345556666667777777777777777664
No 330
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=22.92 E-value=58 Score=18.28 Aligned_cols=19 Identities=32% Similarity=0.719 Sum_probs=9.0
Q ss_pred ecccccccccccchhhccc
Q psy225 187 ACRYCSKSYVADTLVTHQT 205 (450)
Q Consensus 187 ~C~~C~~~f~~~~l~~H~~ 205 (450)
.|-.|++.|.....+.|..
T Consensus 2 sCiDC~~~F~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEEEGGGTTT---
T ss_pred eeecCCCCcCcCCcCCCCc
Confidence 4555666664455555543
No 331
>KOG2923|consensus
Probab=22.80 E-value=37 Score=23.12 Aligned_cols=27 Identities=4% Similarity=-0.090 Sum_probs=17.2
Q ss_pred cccCCCCCcccCC--CC-CCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSSSS--SH-SSDLPMICSQTKS 53 (450)
Q Consensus 26 ~~c~~Cg~~fc~~--~~-~~~~~~~C~~C~~ 53 (450)
|-|| ||-+|-.. .+ .++..-.||.|.-
T Consensus 23 yPCp-CGDrf~It~edL~~ge~Va~CpsCSL 52 (67)
T KOG2923|consen 23 YPCP-CGDRFQITLEDLENGEDVARCPSCSL 52 (67)
T ss_pred cCCC-CCCeeeecHHHHhCCCeeecCCCceE
Confidence 4565 88888332 22 5677788888843
No 332
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.80 E-value=52 Score=25.12 Aligned_cols=36 Identities=17% Similarity=0.434 Sum_probs=18.4
Q ss_pred ceeecccccccccc---cchhhccccCCCCcccCCccccc
Q psy225 184 RLVACRYCSKSYVA---DTLVTHQTKCTRAPIPCPNQCEM 220 (450)
Q Consensus 184 k~~~C~~C~~~f~~---~~l~~H~~~~~~~~~~C~~~C~~ 220 (450)
||..|++||..... +.+--|....+...|.|+ .|+.
T Consensus 1 ~p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~-~C~A 39 (102)
T PF11672_consen 1 KPIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCT-PCDA 39 (102)
T ss_pred CCcccCCCCCeeEEcccchhcCccCCCCceeEECC-CCCc
Confidence 46778888865433 112111111222337888 7774
No 333
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=22.69 E-value=1.2e+02 Score=26.72 Aligned_cols=32 Identities=19% Similarity=0.091 Sum_probs=17.7
Q ss_pred ccccccccCCCCCccccChHHHHHhhHhhHHHHHHH
Q psy225 239 LLVSCVFKDAGCRFKGMRGETMEKHIEENVNQHMLL 274 (450)
Q Consensus 239 ~~~~C~~~~~gC~~~~~~~~~l~~H~~~~~~~~~~~ 274 (450)
..+.|+. |++.|.-..-..+|+...|.+.+..
T Consensus 76 ~K~~C~l----c~KlFkg~eFV~KHI~nKH~e~ve~ 107 (214)
T PF04959_consen 76 DKWRCPL----CGKLFKGPEFVRKHIFNKHPEKVEE 107 (214)
T ss_dssp EEEEE-S----SS-EESSHHHHHHHHHHH-HHHHHH
T ss_pred CEECCCC----CCcccCChHHHHHHHhhcCHHHHHH
Confidence 3466666 7777777566667777655444443
No 334
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=22.68 E-value=2.9e+02 Score=22.24 Aligned_cols=16 Identities=6% Similarity=0.237 Sum_probs=8.4
Q ss_pred HHHHHhhHhhHHHHHH
Q psy225 258 ETMEKHIEENVNQHML 273 (450)
Q Consensus 258 ~~l~~H~~~~~~~~~~ 273 (450)
..|+..++....+.+.
T Consensus 19 Q~lKl~VRD~Vl~~l~ 34 (130)
T PF09551_consen 19 QALKLKVRDAVLEYLS 34 (130)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4566666654444444
No 335
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=22.68 E-value=34 Score=22.77 Aligned_cols=16 Identities=13% Similarity=0.019 Sum_probs=3.8
Q ss_pred ceeeccCCCCcccCCCc
Q psy225 10 KTLSFPARLNTHHKQQI 26 (450)
Q Consensus 10 ~~~~C~iC~~~~~~~p~ 26 (450)
..|.|++|+.. ..+.+
T Consensus 32 r~y~Cp~CgAt-Gd~AH 47 (55)
T PF05741_consen 32 RKYVCPICGAT-GDNAH 47 (55)
T ss_dssp GG---TTT----GGG--
T ss_pred hcCcCCCCcCc-Ccccc
Confidence 34555555555 44443
No 336
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=22.38 E-value=2.9e+02 Score=19.48 Aligned_cols=23 Identities=22% Similarity=0.378 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q psy225 274 LMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 274 ~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
.+...++.+..++..|..+++.|
T Consensus 46 ~L~~qv~~Ls~qv~~Ls~ql~rL 68 (70)
T PF04899_consen 46 ALSEQVNNLSQQVQRLSEQLERL 68 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Confidence 34444444444444454444443
No 337
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=22.38 E-value=1.4e+02 Score=15.90 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHhh
Q psy225 280 SKQQQQISTLKSALNK 295 (450)
Q Consensus 280 ~~~~~~i~~l~~~~~~ 295 (450)
+.+...|.+|++++..
T Consensus 4 ~rlr~rI~dLer~L~~ 19 (23)
T PF04508_consen 4 NRLRNRISDLERQLSE 19 (23)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4455566666666543
No 338
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=22.11 E-value=62 Score=24.91 Aligned_cols=24 Identities=17% Similarity=0.596 Sum_probs=16.4
Q ss_pred ccC----CcccccCccChhHHHHHHhhhc
Q psy225 212 IPC----PNQCEMVALPREELDVHIKEHC 236 (450)
Q Consensus 212 ~~C----~~~C~~~f~~~~~l~~H~~~h~ 236 (450)
|.| + .|+..+.+...|..|.+.+.
T Consensus 81 ~~C~~~~~-~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPP-HCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCC-CCCcEeccHHHHHHHHHHhc
Confidence 556 5 77777777777777776543
No 339
>KOG2482|consensus
Probab=22.00 E-value=67 Score=30.10 Aligned_cols=19 Identities=16% Similarity=0.649 Sum_probs=10.5
Q ss_pred eecccccccccc--cchhhcc
Q psy225 186 VACRYCSKSYVA--DTLVTHQ 204 (450)
Q Consensus 186 ~~C~~C~~~f~~--~~l~~H~ 204 (450)
.+|-+|...+.- +..-.|+
T Consensus 145 lqClFCn~e~lgnRs~~l~Hl 165 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHL 165 (423)
T ss_pred eEEEEecchhcccHHHHHHHH
Confidence 467777665554 4444454
No 340
>KOG4718|consensus
Probab=21.97 E-value=21 Score=30.87 Aligned_cols=43 Identities=9% Similarity=-0.075 Sum_probs=32.7
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCC---CCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSH---SSDLPMICSQTKSRT 55 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~~~~ 55 (450)
-+.|.+|... ...-..|..||-.+...|+ .++ ...||.|+--+
T Consensus 181 lk~Cn~Ch~L-vIqg~rCg~c~i~~h~~c~qty~q~-~~~cphc~d~w 226 (235)
T KOG4718|consen 181 LKNCNLCHCL-VIQGIRCGSCNIQYHRGCIQTYLQR-RDICPHCGDLW 226 (235)
T ss_pred HHHHhHhHHH-hheeeccCcccchhhhHHHHHHhcc-cCcCCchhccc
Confidence 3469999998 8888899999988866655 333 67899997643
No 341
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=21.88 E-value=98 Score=25.66 Aligned_cols=56 Identities=13% Similarity=0.194 Sum_probs=26.0
Q ss_pred cccCCcccccccccHHHhHHhhhCCCCcccC--cccccccChhHHHHHhh-hCCCCccc
Q psy225 104 AIPCNKCLAAIPKTLMEDHSKFTCPERITTC--QYCLESFSGMEMEDHTG-HCSYEMVY 159 (450)
Q Consensus 104 ~~~C~~C~~~f~~~~l~~H~~~h~~~~~~~C--~~C~~~f~~~~l~~H~~-~~~~~~~~ 159 (450)
...||.|.-...-..+..-.+.+-..++=.| +.|...-.+.+|+.|.+ .|+..+|.
T Consensus 80 ~L~CPLCRG~V~GWtvve~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP~ 138 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTVVEPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARPS 138 (162)
T ss_pred cccCccccCceeceEEchHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCCc
Confidence 3566666433332111111222333333334 35655555556777765 46655553
No 342
>PRK02793 phi X174 lysis protein; Provisional
Probab=21.86 E-value=2.5e+02 Score=19.82 Aligned_cols=27 Identities=11% Similarity=0.194 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..+...+.++..+|..|++++..|
T Consensus 22 ~tIe~Ln~~v~~Qq~~I~~L~~~l~~L 48 (72)
T PRK02793 22 ITIEELNVTVTAHEMEMAKLRDHLRLL 48 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555556666666666666555
No 343
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=21.85 E-value=42 Score=22.36 Aligned_cols=9 Identities=22% Similarity=0.372 Sum_probs=4.0
Q ss_pred cCCcccccc
Q psy225 106 PCNKCLAAI 114 (450)
Q Consensus 106 ~C~~C~~~f 114 (450)
+|-.|++.+
T Consensus 4 kC~lCdk~~ 12 (56)
T PF09963_consen 4 KCILCDKKE 12 (56)
T ss_pred EEEecCCEE
Confidence 344444443
No 344
>PRK04406 hypothetical protein; Provisional
Probab=21.74 E-value=2.5e+02 Score=20.03 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..+...+.++..+|..|++++..|
T Consensus 25 ~tIe~LN~~v~~Qq~~I~~L~~ql~~L 51 (75)
T PRK04406 25 QTIEELNDALSQQQLLITKMQDQMKYV 51 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555556666666666666655
No 345
>PF10393 Matrilin_ccoil: Trimeric coiled-coil oligomerisation domain of matrilin; InterPro: IPR019466 This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain (IPR006209 from INTERPRO), thereby spanning the VWA domain of the protein (IPR002035 from INTERPRO).This domain is likely to be responsible for protein trimerisation []. ; PDB: 1AQ5_C.
Probab=21.53 E-value=2.3e+02 Score=18.15 Aligned_cols=19 Identities=11% Similarity=0.286 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q psy225 279 VSKQQQQISTLKSALNKVT 297 (450)
Q Consensus 279 ~~~~~~~i~~l~~~~~~l~ 297 (450)
+..+..+++++.++++.|+
T Consensus 25 lq~Lt~kL~~vs~RLe~LE 43 (47)
T PF10393_consen 25 LQSLTQKLDAVSKRLEALE 43 (47)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555554
No 346
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=21.48 E-value=43 Score=25.34 Aligned_cols=14 Identities=7% Similarity=-0.199 Sum_probs=11.9
Q ss_pred CCcccCCCCCcccC
Q psy225 24 QQISSKENTLSSSS 37 (450)
Q Consensus 24 ~p~~c~~Cg~~fc~ 37 (450)
+|++|+.||+.|..
T Consensus 78 ~~~rC~eCG~~fkL 91 (97)
T cd00924 78 KPKRCPECGHVFKL 91 (97)
T ss_pred CceeCCCCCcEEEE
Confidence 68999999999943
No 347
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.46 E-value=87 Score=33.23 Aligned_cols=36 Identities=11% Similarity=-0.057 Sum_probs=18.0
Q ss_pred eeeccCCCCcccCCCcccCCCCCcccCCCCCCCCCCCCCCCCC
Q psy225 11 TLSFPARLNTHHKQQISSKENTLSSSSSSHSSDLPMICSQTKS 53 (450)
Q Consensus 11 ~~~C~iC~~~~~~~p~~c~~Cg~~fc~~~~~~~~~~~C~~C~~ 53 (450)
.+.|..|+.. ..|+.|+-.... +...+...|..|+.
T Consensus 381 ~~~C~~Cg~~-----~~C~~C~~~l~~--h~~~~~l~Ch~Cg~ 416 (679)
T PRK05580 381 FLLCRDCGWV-----AECPHCDASLTL--HRFQRRLRCHHCGY 416 (679)
T ss_pred ceEhhhCcCc-----cCCCCCCCceeE--ECCCCeEECCCCcC
Confidence 3456666666 456666544311 01233445666655
No 348
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.30 E-value=1.9e+02 Score=25.14 Aligned_cols=37 Identities=22% Similarity=0.314 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhc--cCCceEE
Q psy225 269 NQHMLLMCSLVSKQQQQISTLKSALNKVTL--NYSGTLI 305 (450)
Q Consensus 269 ~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~--~~~~~~~ 305 (450)
...+.++.+.++++..+|++|++++..|+. .-.+.|+
T Consensus 47 aQ~vliqE~ALk~a~~~i~eLe~ri~~lq~~~~~sgsFL 85 (233)
T COG3416 47 AQRVLIQEQALKKASTQIKELEKRIAILQAGEAGSGSFL 85 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcchh
Confidence 344445556678889999999999999875 3444443
No 349
>PRK04325 hypothetical protein; Provisional
Probab=21.28 E-value=2.6e+02 Score=19.87 Aligned_cols=27 Identities=22% Similarity=0.268 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..|...+.++..+|..|++++..|
T Consensus 23 ~tIe~LN~vv~~Qq~~I~~L~~ql~~L 49 (74)
T PRK04325 23 DLIDGLNATVARQQQTLDLLQAQLRLL 49 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555666666666666666655
No 350
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.97 E-value=66 Score=18.72 Aligned_cols=15 Identities=0% Similarity=-0.345 Sum_probs=12.1
Q ss_pred cccCceeeccCCCCc
Q psy225 6 TSWTKTLSFPARLNT 20 (450)
Q Consensus 6 ~~~~~~~~C~iC~~~ 20 (450)
..++..|.|.+|+..
T Consensus 3 k~pP~~Y~C~~C~~~ 17 (32)
T PF13696_consen 3 KKPPPGYVCHRCGQK 17 (32)
T ss_pred CCCCCCCEeecCCCC
Confidence 357788999999887
No 351
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=20.86 E-value=23 Score=27.88 Aligned_cols=43 Identities=2% Similarity=-0.048 Sum_probs=27.5
Q ss_pred ceeeccCCCCcc---cCCCcccCCCCCcccCCCC---CCCCCCCCCCCC
Q psy225 10 KTLSFPARLNTH---HKQQISSKENTLSSSSSSH---SSDLPMICSQTK 52 (450)
Q Consensus 10 ~~~~C~iC~~~~---~~~p~~c~~Cg~~fc~~~~---~~~~~~~C~~C~ 52 (450)
....|.+|+.+| ......|..|.+.+|..|- .++....|.+|.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~ 101 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQ 101 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhH
Confidence 345799998751 2457889999999988775 234445566663
No 352
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.84 E-value=63 Score=25.70 Aligned_cols=28 Identities=11% Similarity=0.107 Sum_probs=14.2
Q ss_pred cccCCCCCcccCCC--CCCCC-CCCCCCCCCC
Q psy225 26 ISSKENTLSSSSSS--HSSDL-PMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc~~~--~~~~~-~~~C~~C~~~ 54 (450)
..| .||+.|-... +.... .+.||.|+..
T Consensus 71 ~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 71 IEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred EEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 456 6776663321 11111 2568888753
No 353
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=20.72 E-value=56 Score=26.86 Aligned_cols=28 Identities=14% Similarity=0.076 Sum_probs=18.2
Q ss_pred cccCCCCCccc--CCCC------CCCCCCCCCCCCCC
Q psy225 26 ISSKENTLSSS--SSSH------SSDLPMICSQTKSR 54 (450)
Q Consensus 26 ~~c~~Cg~~fc--~~~~------~~~~~~~C~~C~~~ 54 (450)
.+|. +||.|- ..+. ...+...||+|+..
T Consensus 6 L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~ 41 (148)
T PF06676_consen 6 LRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGST 41 (148)
T ss_pred EecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCC
Confidence 4674 899981 1111 34567899999875
No 354
>PRK04351 hypothetical protein; Provisional
Probab=20.66 E-value=45 Score=27.50 Aligned_cols=10 Identities=0% Similarity=-0.160 Sum_probs=4.4
Q ss_pred cccCCCCCcc
Q psy225 26 ISSKENTLSS 35 (450)
Q Consensus 26 ~~c~~Cg~~f 35 (450)
|+|..||..+
T Consensus 113 Y~C~~Cg~~~ 122 (149)
T PRK04351 113 YECQSCGQQY 122 (149)
T ss_pred EECCCCCCEe
Confidence 4444444443
No 355
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=20.60 E-value=46 Score=20.50 Aligned_cols=12 Identities=42% Similarity=1.060 Sum_probs=9.5
Q ss_pred ceeecccccccc
Q psy225 184 RLVACRYCSKSY 195 (450)
Q Consensus 184 k~~~C~~C~~~f 195 (450)
.+..|++|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 468899998876
No 356
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=20.49 E-value=46 Score=25.97 Aligned_cols=9 Identities=22% Similarity=0.479 Sum_probs=4.3
Q ss_pred CCCCCCCCC
Q psy225 46 MICSQTKSR 54 (450)
Q Consensus 46 ~~C~~C~~~ 54 (450)
+.||.|+..
T Consensus 87 ~~CP~Cgs~ 95 (113)
T PF01155_consen 87 FSCPRCGSP 95 (113)
T ss_dssp HH-SSSSSS
T ss_pred CCCcCCcCC
Confidence 346666553
No 357
>PRK02119 hypothetical protein; Provisional
Probab=20.36 E-value=2.8e+02 Score=19.64 Aligned_cols=27 Identities=15% Similarity=0.126 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy225 270 QHMLLMCSLVSKQQQQISTLKSALNKV 296 (450)
Q Consensus 270 ~~~~~~~~~~~~~~~~i~~l~~~~~~l 296 (450)
..+..+...+.++..+|..|++++..|
T Consensus 23 ~tie~LN~~v~~Qq~~id~L~~ql~~L 49 (73)
T PRK02119 23 NLLEELNQALIEQQFVIDKMQVQLRYM 49 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555566666666666666655
No 358
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=20.35 E-value=40 Score=20.64 Aligned_cols=9 Identities=22% Similarity=0.475 Sum_probs=3.6
Q ss_pred CCCCCCCCC
Q psy225 45 PMICSQTKS 53 (450)
Q Consensus 45 ~~~C~~C~~ 53 (450)
...|+.|+.
T Consensus 24 ~w~C~~C~~ 32 (40)
T PF04810_consen 24 TWICNFCGT 32 (40)
T ss_dssp EEEETTT--
T ss_pred EEECcCCCC
Confidence 445555543
No 359
>KOG2893|consensus
Probab=20.16 E-value=40 Score=29.64 Aligned_cols=31 Identities=26% Similarity=0.702 Sum_probs=16.9
Q ss_pred cccccccccc-cchhhccccCCCCcccCCcccccCc
Q psy225 188 CRYCSKSYVA-DTLVTHQTKCTRAPIPCPNQCEMVA 222 (450)
Q Consensus 188 C~~C~~~f~~-~~l~~H~~~~~~~~~~C~~~C~~~f 222 (450)
|=+|++.|-. ..|.+|++. +-|+|. .|.+..
T Consensus 13 cwycnrefddekiliqhqka---khfkch-ichkkl 44 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA---KHFKCH-ICHKKL 44 (341)
T ss_pred eeecccccchhhhhhhhhhh---ccceee-eehhhh
Confidence 5566666665 555555544 225555 555543
Done!