Query 040047
Match_columns 240
No_of_seqs 148 out of 848
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 04:34:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040047.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040047hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02340 ZZ_NBR1_like Zinc fing 98.7 1.4E-08 3.1E-13 65.5 3.3 40 23-68 1-41 (43)
2 PF07649 C1_3: C1-like domain; 98.6 2.1E-08 4.6E-13 59.6 1.2 29 23-51 1-30 (30)
3 PF07649 C1_3: C1-like domain; 98.4 8E-08 1.7E-12 57.1 0.9 29 80-108 1-30 (30)
4 cd02339 ZZ_Mind_bomb Zinc fing 98.3 5.7E-07 1.2E-11 58.5 3.6 41 23-68 1-43 (45)
5 cd02249 ZZ Zinc finger, ZZ typ 98.3 5.8E-07 1.3E-11 58.7 3.6 43 23-68 1-44 (46)
6 PF03107 C1_2: C1 domain; Int 98.3 3.4E-07 7.3E-12 54.4 2.2 29 80-108 1-30 (30)
7 cd02344 ZZ_HERC2 Zinc finger, 98.3 8.4E-07 1.8E-11 57.6 3.4 31 23-53 1-33 (45)
8 PF03107 C1_2: C1 domain; Int 98.2 1.2E-06 2.6E-11 52.1 2.1 29 23-51 1-30 (30)
9 cd02338 ZZ_PCMF_like Zinc fing 98.1 2.6E-06 5.6E-11 56.4 3.2 45 23-69 1-48 (49)
10 cd02342 ZZ_UBA_plant Zinc fing 98.1 2.3E-06 5.1E-11 54.6 2.0 33 23-55 1-35 (43)
11 cd02334 ZZ_dystrophin Zinc fin 98.0 6.2E-06 1.3E-10 54.6 3.0 44 23-68 1-47 (49)
12 KOG0696 Serine/threonine prote 98.0 1.6E-06 3.4E-11 80.7 0.0 86 21-111 55-156 (683)
13 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.9 8E-06 1.7E-10 53.8 3.0 42 23-68 1-46 (48)
14 cd02343 ZZ_EF Zinc finger, ZZ 97.9 7.8E-06 1.7E-10 53.7 2.9 35 23-57 1-36 (48)
15 cd02340 ZZ_NBR1_like Zinc fing 97.9 9.3E-06 2E-10 52.3 2.4 31 81-111 2-33 (43)
16 cd02345 ZZ_dah Zinc finger, ZZ 97.8 1.3E-05 2.7E-10 53.1 2.6 32 24-55 2-35 (49)
17 cd02335 ZZ_ADA2 Zinc finger, Z 97.8 3.2E-05 6.9E-10 51.1 3.8 45 23-69 1-48 (49)
18 cd02249 ZZ Zinc finger, ZZ typ 97.7 2.6E-05 5.5E-10 50.8 2.9 33 80-112 1-34 (46)
19 KOG4236 Serine/threonine prote 97.7 2.6E-06 5.7E-11 81.3 -2.6 45 7-53 143-190 (888)
20 PF00569 ZZ: Zinc finger, ZZ t 97.7 1.5E-05 3.2E-10 52.0 1.0 34 21-54 3-38 (46)
21 smart00291 ZnF_ZZ Zinc-binding 97.6 4.1E-05 8.9E-10 49.4 2.5 33 22-54 4-37 (44)
22 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.6 4.5E-05 9.6E-10 50.3 2.5 33 80-112 1-37 (48)
23 cd02337 ZZ_CBP Zinc finger, ZZ 97.6 4.3E-05 9.3E-10 48.7 2.3 30 23-53 1-31 (41)
24 cd02339 ZZ_Mind_bomb Zinc fing 97.5 6.9E-05 1.5E-09 48.7 2.5 30 81-110 2-33 (45)
25 KOG4582 Uncharacterized conser 97.5 6.4E-05 1.4E-09 67.1 2.9 42 23-69 153-196 (278)
26 KOG1280 Uncharacterized conser 97.5 0.00011 2.5E-09 66.3 4.0 67 21-89 7-89 (381)
27 cd02337 ZZ_CBP Zinc finger, ZZ 97.4 8.3E-05 1.8E-09 47.4 1.7 38 80-124 1-39 (41)
28 cd02338 ZZ_PCMF_like Zinc fing 97.4 0.00012 2.6E-09 48.4 2.5 43 81-125 2-48 (49)
29 cd02344 ZZ_HERC2 Zinc finger, 97.4 0.00015 3.2E-09 47.1 2.7 30 81-110 2-33 (45)
30 PF00130 C1_1: Phorbol esters/ 97.3 0.00016 3.6E-09 48.0 2.6 43 10-54 1-46 (53)
31 cd02343 ZZ_EF Zinc finger, ZZ 97.2 0.00017 3.7E-09 47.4 1.7 32 81-112 2-34 (48)
32 cd02342 ZZ_UBA_plant Zinc fing 97.2 0.00016 3.5E-09 46.2 1.4 31 81-111 2-34 (43)
33 cd02335 ZZ_ADA2 Zinc finger, Z 97.2 0.00036 7.7E-09 46.1 2.7 33 80-112 1-35 (49)
34 PF00569 ZZ: Zinc finger, ZZ t 97.1 0.00018 4E-09 46.8 0.9 32 79-110 4-37 (46)
35 cd02345 ZZ_dah Zinc finger, ZZ 97.1 0.00027 5.9E-09 46.7 1.8 31 81-111 2-34 (49)
36 cd02334 ZZ_dystrophin Zinc fin 97.1 0.00038 8.2E-09 46.0 2.3 31 81-111 2-34 (49)
37 smart00291 ZnF_ZZ Zinc-binding 97.1 0.00032 6.9E-09 45.2 1.9 33 79-111 4-37 (44)
38 KOG1280 Uncharacterized conser 97.1 0.00041 9E-09 62.8 3.2 72 78-149 7-89 (381)
39 PF00130 C1_1: Phorbol esters/ 97.0 0.0019 4.1E-08 42.8 5.1 39 138-176 10-48 (53)
40 cd00029 C1 Protein kinase C co 96.8 0.0012 2.7E-08 42.8 2.7 34 21-54 10-46 (50)
41 smart00109 C1 Protein kinase C 96.4 0.0019 4.1E-08 41.6 1.7 33 21-53 10-44 (49)
42 KOG4582 Uncharacterized conser 96.0 0.0038 8.3E-08 55.8 2.3 32 80-111 153-186 (278)
43 KOG0956 PHD finger protein AF1 95.9 0.01 2.2E-07 58.3 4.5 128 23-175 6-158 (900)
44 KOG0957 PHD finger protein [Ge 95.9 0.0032 6.9E-08 59.7 1.0 142 21-176 118-277 (707)
45 cd00029 C1 Protein kinase C co 95.7 0.0087 1.9E-07 38.7 2.4 33 78-110 10-45 (50)
46 smart00109 C1 Protein kinase C 95.3 0.0093 2E-07 38.2 1.3 33 78-110 10-44 (49)
47 KOG0696 Serine/threonine prote 95.2 0.0034 7.5E-08 58.9 -1.1 100 64-175 45-157 (683)
48 KOG4286 Dystrophin-like protei 93.3 0.047 1E-06 54.3 2.1 47 22-70 603-652 (966)
49 KOG0457 Histone acetyltransfer 92.8 0.088 1.9E-06 49.3 3.0 52 20-72 12-65 (438)
50 cd02336 ZZ_RSC8 Zinc finger, Z 92.7 0.081 1.7E-06 34.3 1.9 30 80-109 1-31 (45)
51 KOG0694 Serine/threonine prote 92.2 0.04 8.7E-07 54.3 -0.1 86 21-110 168-275 (694)
52 KOG0954 PHD finger protein [Ge 91.3 0.19 4E-06 50.1 3.4 140 19-176 268-415 (893)
53 PF13832 zf-HC5HC2H_2: PHD-zin 89.2 0.34 7.3E-06 36.8 2.7 85 81-176 2-90 (110)
54 KOG4286 Dystrophin-like protei 89.1 0.16 3.5E-06 50.7 0.9 45 78-124 602-650 (966)
55 cd02336 ZZ_RSC8 Zinc finger, Z 88.8 0.3 6.6E-06 31.6 1.8 31 23-53 1-32 (45)
56 PF00628 PHD: PHD-finger; Int 88.3 0.64 1.4E-05 30.1 3.2 34 141-176 1-34 (51)
57 PF13832 zf-HC5HC2H_2: PHD-zin 88.0 0.51 1.1E-05 35.8 2.9 84 24-111 2-88 (110)
58 KOG4236 Serine/threonine prote 85.4 0.15 3.2E-06 49.7 -1.6 43 9-53 267-312 (888)
59 PF00628 PHD: PHD-finger; Int 82.5 1.6 3.4E-05 28.2 2.9 33 81-113 1-34 (51)
60 KOG1244 Predicted transcriptio 82.3 0.87 1.9E-05 40.5 2.0 85 79-176 224-316 (336)
61 KOG1169 Diacylglycerol kinase 81.6 2.1 4.6E-05 42.3 4.6 141 24-172 46-210 (634)
62 KOG2807 RNA polymerase II tran 81.0 0.64 1.4E-05 42.3 0.7 43 138-182 329-371 (378)
63 COG5114 Histone acetyltransfer 81.0 0.89 1.9E-05 41.3 1.6 49 21-72 4-56 (432)
64 KOG0193 Serine/threonine prote 80.2 0.95 2.1E-05 44.6 1.6 33 21-53 188-220 (678)
65 PF13842 Tnp_zf-ribbon_2: DDE_ 79.8 1.6 3.5E-05 26.1 2.0 28 141-169 2-29 (32)
66 KOG1169 Diacylglycerol kinase 78.3 0.98 2.1E-05 44.6 1.1 94 79-176 44-149 (634)
67 PF14446 Prok-RING_1: Prokaryo 77.9 1.7 3.8E-05 29.2 1.9 33 78-110 4-38 (54)
68 KOG0695 Serine/threonine prote 77.5 0.81 1.8E-05 42.4 0.3 34 21-54 140-176 (593)
69 TIGR00622 ssl1 transcription f 77.4 2.8 6.1E-05 32.5 3.2 32 79-110 55-98 (112)
70 KOG0956 PHD finger protein AF1 77.2 1.5 3.3E-05 43.7 2.0 90 20-110 46-156 (900)
71 KOG2807 RNA polymerase II tran 77.1 1.4 3E-05 40.2 1.6 89 20-110 261-362 (378)
72 PF14446 Prok-RING_1: Prokaryo 76.5 2.3 4.9E-05 28.7 2.1 36 21-56 4-41 (54)
73 PF07975 C1_4: TFIIH C1-like d 75.4 1.5 3.3E-05 29.1 1.1 30 24-53 1-38 (51)
74 smart00249 PHD PHD zinc finger 73.7 2.6 5.6E-05 25.9 1.8 34 141-176 1-34 (47)
75 KOG1701 Focal adhesion adaptor 73.5 0.24 5.1E-06 46.5 -4.3 32 21-52 273-304 (468)
76 KOG0457 Histone acetyltransfer 73.4 2 4.4E-05 40.5 1.8 33 78-110 13-47 (438)
77 KOG4301 Beta-dystrobrevin [Cyt 71.9 1.3 2.8E-05 40.7 0.1 33 21-53 239-273 (434)
78 KOG0955 PHD finger protein BR1 71.9 3.7 8.1E-05 43.1 3.4 133 20-176 217-365 (1051)
79 smart00249 PHD PHD zinc finger 71.8 3.8 8.2E-05 25.1 2.3 33 81-113 1-34 (47)
80 PF07754 DUF1610: Domain of un 69.4 4.2 9E-05 22.8 1.8 20 82-101 1-24 (24)
81 TIGR00622 ssl1 transcription f 68.5 2.8 6.1E-05 32.4 1.3 32 22-53 55-98 (112)
82 COG5114 Histone acetyltransfer 68.0 4 8.6E-05 37.3 2.3 46 138-185 4-50 (432)
83 PF08746 zf-RING-like: RING-li 65.6 2.3 5.1E-05 27.0 0.3 31 142-176 1-33 (43)
84 PF10367 Vps39_2: Vacuolar sor 65.4 4.6 0.0001 29.9 1.9 33 20-52 76-108 (109)
85 PF02318 FYVE_2: FYVE-type zin 63.7 1.9 4E-05 33.5 -0.5 57 78-158 53-116 (118)
86 PF00643 zf-B_box: B-box zinc 63.6 5.3 0.00011 24.6 1.7 31 139-174 3-33 (42)
87 PHA00369 H minor spike protein 62.7 8.3 0.00018 33.7 3.2 20 207-226 140-159 (325)
88 PF10367 Vps39_2: Vacuolar sor 62.1 7.6 0.00016 28.7 2.6 31 139-172 78-108 (109)
89 PF13831 PHD_2: PHD-finger; PD 59.1 5.4 0.00012 24.4 1.1 20 92-111 3-22 (36)
90 KOG1512 PHD Zn-finger protein 58.7 2.7 5.8E-05 37.8 -0.5 71 93-176 279-349 (381)
91 PF12773 DZR: Double zinc ribb 58.0 9.2 0.0002 24.5 2.1 21 79-99 29-49 (50)
92 COG2888 Predicted Zn-ribbon RN 57.8 4.4 9.5E-05 27.8 0.5 22 139-165 38-59 (61)
93 PRK14890 putative Zn-ribbon RN 56.4 5.3 0.00011 27.4 0.8 21 140-165 37-57 (59)
94 PF01363 FYVE: FYVE zinc finge 55.5 13 0.00027 25.5 2.6 38 138-176 8-45 (69)
95 PF14569 zf-UDP: Zinc-binding 55.4 5.5 0.00012 28.8 0.8 33 78-110 8-45 (80)
96 PF10571 UPF0547: Uncharacteri 54.1 7.1 0.00015 22.2 1.0 23 81-103 2-24 (26)
97 KOG0694 Serine/threonine prote 54.1 4.2 9.1E-05 40.6 -0.0 97 79-175 169-277 (694)
98 PF11781 RRN7: RNA polymerase 54.0 7.6 0.00016 23.8 1.1 27 139-165 8-34 (36)
99 PF04687 Microvir_H: Microviru 53.6 15 0.00032 32.1 3.2 19 208-226 125-143 (310)
100 KOG0957 PHD finger protein [Ge 53.4 6.1 0.00013 38.2 0.9 55 78-148 543-598 (707)
101 PF04438 zf-HIT: HIT zinc fing 53.2 9 0.0002 22.4 1.3 23 80-105 3-25 (30)
102 PF08271 TF_Zn_Ribbon: TFIIB z 52.7 21 0.00046 22.3 3.1 36 141-177 2-40 (43)
103 KOG0193 Serine/threonine prote 52.2 7.3 0.00016 38.6 1.3 32 79-110 189-220 (678)
104 KOG2996 Rho guanine nucleotide 48.4 7.2 0.00016 38.5 0.6 42 10-53 524-568 (865)
105 KOG1829 Uncharacterized conser 47.8 24 0.00051 34.9 4.0 92 137-229 338-440 (580)
106 PF01363 FYVE: FYVE zinc finge 47.4 14 0.0003 25.3 1.8 33 78-110 8-42 (69)
107 PF09943 DUF2175: Uncharacteri 47.2 18 0.00038 27.5 2.4 35 139-176 2-36 (101)
108 PF14569 zf-UDP: Zinc-binding 46.8 7 0.00015 28.3 0.2 39 21-59 8-51 (80)
109 PF02148 zf-UBP: Zn-finger in 46.5 3.7 8E-05 28.0 -1.3 58 25-88 1-58 (63)
110 smart00064 FYVE Protein presen 44.8 16 0.00035 24.9 1.8 34 21-54 9-44 (68)
111 KOG1512 PHD Zn-finger protein 44.1 8.6 0.00019 34.6 0.4 82 21-110 257-346 (381)
112 KOG1244 Predicted transcriptio 43.9 12 0.00026 33.5 1.2 68 36-111 246-314 (336)
113 KOG3507 DNA-directed RNA polym 43.5 12 0.00025 25.6 0.9 25 79-103 20-47 (62)
114 KOG0695 Serine/threonine prote 43.4 15 0.00033 34.3 1.8 38 139-176 141-178 (593)
115 PF07282 OrfB_Zn_ribbon: Putat 43.0 19 0.0004 24.7 1.9 30 138-168 27-58 (69)
116 KOG1170 Diacylglycerol kinase 42.5 18 0.00039 37.1 2.3 97 137-233 116-227 (1099)
117 PF09297 zf-NADH-PPase: NADH p 42.3 23 0.0005 20.7 2.0 26 139-165 3-30 (32)
118 cd00065 FYVE FYVE domain; Zinc 42.0 12 0.00026 24.5 0.7 37 140-177 3-39 (57)
119 smart00547 ZnF_RBZ Zinc finger 41.5 14 0.0003 20.3 0.8 23 79-101 2-24 (26)
120 KOG4301 Beta-dystrobrevin [Cyt 41.4 8.4 0.00018 35.6 -0.1 32 78-109 239-272 (434)
121 PRK12380 hydrogenase nickel in 40.5 20 0.00044 27.5 1.9 25 138-163 69-93 (113)
122 smart00659 RPOLCX RNA polymera 40.4 24 0.00052 22.5 1.9 26 140-165 3-28 (44)
123 PLN02436 cellulose synthase A 39.6 28 0.00061 36.8 3.3 80 138-218 35-134 (1094)
124 PF13909 zf-H2C2_5: C2H2-type 38.9 16 0.00035 19.5 0.9 10 37-46 1-10 (24)
125 smart00396 ZnF_UBR1 Putative z 38.9 25 0.00054 24.7 2.0 29 143-172 1-33 (71)
126 PF09862 DUF2089: Protein of u 38.8 22 0.00048 27.6 1.9 63 142-231 1-63 (113)
127 PHA00626 hypothetical protein 38.0 23 0.0005 24.0 1.6 25 139-168 11-35 (59)
128 PF07191 zinc-ribbons_6: zinc- 37.3 16 0.00036 25.8 0.9 10 139-148 17-26 (70)
129 COG5151 SSL1 RNA polymerase II 36.6 7.5 0.00016 35.4 -1.2 37 138-175 361-407 (421)
130 smart00039 CRF corticotropin-r 36.5 99 0.0021 19.5 4.2 29 212-240 12-40 (40)
131 PF09487 HrpB2: Bacterial type 36.4 47 0.001 25.9 3.3 31 206-236 75-105 (117)
132 TIGR00270 conserved hypothetic 36.3 91 0.002 25.4 5.2 34 141-175 2-35 (154)
133 cd00729 rubredoxin_SM Rubredox 35.8 17 0.00037 21.8 0.7 23 140-163 3-25 (34)
134 cd00350 rubredoxin_like Rubred 35.6 19 0.00041 21.3 0.8 23 140-163 2-24 (33)
135 PF13240 zinc_ribbon_2: zinc-r 35.3 19 0.00042 19.7 0.8 21 82-102 2-22 (23)
136 KOG2996 Rho guanine nucleotide 34.9 13 0.00028 36.7 0.1 35 138-172 533-567 (865)
137 smart00661 RPOL9 RNA polymeras 34.5 32 0.0007 22.0 1.9 27 141-167 2-31 (52)
138 TIGR00100 hypA hydrogenase nic 34.0 30 0.00065 26.6 1.9 25 138-163 69-93 (115)
139 KOG0825 PHD Zn-finger protein 33.7 22 0.00048 36.4 1.4 33 79-111 215-249 (1134)
140 KOG4443 Putative transcription 33.3 17 0.00037 36.2 0.6 83 79-176 18-103 (694)
141 COG0675 Transposase and inacti 32.5 50 0.0011 29.0 3.4 29 77-106 307-335 (364)
142 KOG2186 Cell growth-regulating 32.4 19 0.00042 31.8 0.7 38 139-176 3-56 (276)
143 PF03604 DNA_RNApol_7kD: DNA d 31.9 16 0.00035 21.8 0.1 22 81-102 2-26 (32)
144 PRK00564 hypA hydrogenase nick 31.5 36 0.00078 26.3 2.0 25 138-163 70-95 (117)
145 KOG1011 Neurotransmitter relea 31.2 15 0.00032 36.9 -0.3 43 9-53 172-217 (1283)
146 PLN03044 GTP cyclohydrolase I; 31.0 28 0.00062 29.4 1.5 19 220-238 112-130 (188)
147 cd00642 GTP_cyclohydro1 GTP cy 31.0 28 0.0006 29.3 1.4 18 221-238 112-129 (185)
148 PF13248 zf-ribbon_3: zinc-rib 30.3 27 0.00058 19.5 0.8 22 80-101 3-24 (26)
149 PRK03681 hypA hydrogenase nick 29.9 40 0.00086 25.9 2.0 25 138-163 69-94 (114)
150 TIGR00063 folE GTP cyclohydrol 29.8 30 0.00065 29.0 1.4 18 221-238 107-124 (180)
151 PF14803 Nudix_N_2: Nudix N-te 29.7 50 0.0011 19.9 2.0 11 154-164 20-30 (34)
152 KOG1705 Uncharacterized conser 29.4 30 0.00066 25.8 1.2 24 76-99 52-75 (110)
153 PF14379 Myb_CC_LHEQLE: MYB-CC 28.6 1.4E+02 0.0031 19.8 4.1 10 212-221 6-15 (51)
154 smart00154 ZnF_AN1 AN1-like Zi 28.6 43 0.00094 20.7 1.6 23 25-47 1-23 (39)
155 COG1996 RPC10 DNA-directed RNA 28.3 41 0.0009 22.1 1.6 29 138-166 5-34 (49)
156 PF08792 A2L_zn_ribbon: A2L zi 28.0 51 0.0011 19.7 1.8 27 139-165 3-30 (33)
157 PF00301 Rubredoxin: Rubredoxi 27.9 47 0.001 21.6 1.8 43 36-88 1-43 (47)
158 PF00641 zf-RanBP: Zn-finger i 27.9 14 0.00031 21.2 -0.6 23 78-100 3-25 (30)
159 PF00473 CRF: Corticotropin-re 27.7 1.5E+02 0.0033 18.5 3.9 27 212-238 11-37 (39)
160 PRK04023 DNA polymerase II lar 26.6 46 0.00099 35.1 2.3 21 140-165 652-672 (1121)
161 PF09392 MxiH: Type III secret 26.2 1.4E+02 0.0031 21.5 4.4 28 211-238 54-81 (90)
162 PF09332 Mcm10: Mcm10 replicat 25.7 37 0.00079 31.5 1.3 62 36-110 252-320 (344)
163 PRK09347 folE GTP cyclohydrola 25.6 37 0.00081 28.6 1.2 19 220-238 114-132 (188)
164 PF13901 DUF4206: Domain of un 25.6 46 0.001 28.2 1.8 37 137-173 150-189 (202)
165 PF15446 zf-PHD-like: PHD/FYVE 25.5 35 0.00076 28.4 1.0 35 141-176 1-37 (175)
166 PRK12606 GTP cyclohydrolase I; 25.4 40 0.00088 28.8 1.4 19 220-238 126-144 (201)
167 PF13639 zf-RING_2: Ring finge 25.3 39 0.00085 20.8 1.1 31 141-173 2-32 (44)
168 PF03660 PHF5: PHF5-like prote 25.1 33 0.00071 26.2 0.7 23 77-99 53-76 (106)
169 PF12647 RNHCP: RNHCP domain; 25.0 80 0.0017 23.6 2.7 29 78-106 3-37 (92)
170 PF04687 Microvir_H: Microviru 24.9 85 0.0018 27.5 3.3 25 206-230 134-158 (310)
171 PF13771 zf-HC5HC2H: PHD-like 24.8 55 0.0012 23.4 1.9 34 20-54 34-69 (90)
172 KOG4443 Putative transcription 24.3 31 0.00066 34.5 0.5 77 23-111 19-101 (694)
173 PF09862 DUF2089: Protein of u 24.0 53 0.0011 25.5 1.7 22 82-103 1-22 (113)
174 PLN02638 cellulose synthase A 23.6 70 0.0015 34.0 3.0 43 21-63 16-63 (1079)
175 PF01155 HypA: Hydrogenase exp 23.6 25 0.00053 27.0 -0.2 25 138-163 69-93 (113)
176 cd00021 BBOX B-Box-type zinc f 23.3 51 0.0011 19.4 1.3 20 155-174 11-30 (39)
177 KOG1356 Putative transcription 23.3 45 0.00097 34.3 1.5 33 78-110 228-260 (889)
178 KOG1356 Putative transcription 23.0 47 0.001 34.2 1.6 36 137-175 227-262 (889)
179 KOG4317 Predicted Zn-finger pr 22.9 47 0.001 30.4 1.4 34 138-176 6-40 (383)
180 PRK00398 rpoP DNA-directed RNA 22.6 60 0.0013 20.5 1.5 26 139-164 3-29 (46)
181 PTZ00303 phosphatidylinositol 22.2 61 0.0013 33.5 2.1 31 23-53 461-498 (1374)
182 COG0675 Transposase and inacti 21.8 56 0.0012 28.7 1.7 30 20-50 307-336 (364)
183 COG0375 HybF Zn finger protein 21.7 83 0.0018 24.5 2.4 25 138-163 69-93 (115)
184 PF10166 DUF2368: Uncharacteri 21.6 90 0.002 24.8 2.7 9 227-235 37-45 (131)
185 PF02207 zf-UBR: Putative zinc 21.4 65 0.0014 22.4 1.7 31 144-175 2-37 (71)
186 KOG0955 PHD finger protein BR1 21.1 67 0.0015 34.1 2.3 40 137-176 217-256 (1051)
187 PHA00369 H minor spike protein 20.9 85 0.0018 27.6 2.5 25 206-230 150-174 (325)
188 TIGR03021 pilP_fam type IV pil 20.8 1.1E+02 0.0024 23.8 3.0 25 207-231 10-34 (119)
189 KOG2698 GTP cyclohydrolase I [ 20.8 93 0.002 26.9 2.7 18 221-238 173-190 (247)
190 PF08394 Arc_trans_TRASH: Arch 20.6 68 0.0015 19.8 1.4 11 142-152 1-11 (37)
191 PF12874 zf-met: Zinc-finger o 20.6 48 0.001 17.6 0.7 11 140-150 1-11 (25)
192 PTZ00484 GTP cyclohydrolase I; 20.5 61 0.0013 28.8 1.6 18 221-238 186-203 (259)
193 TIGR02558 HrpB2 type III secre 20.2 1.3E+02 0.0029 23.6 3.3 30 206-235 82-111 (124)
No 1
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=98.70 E-value=1.4e-08 Score=65.46 Aligned_cols=40 Identities=33% Similarity=0.714 Sum_probs=34.1
Q ss_pred ccccccccCCCCceEeeCCC-CCcchhhhccccccccCCCCCCcceE
Q 040047 23 YSCSACELIISGSAYGCWEC-KFFLHEQCGNASRAMQHTSHPMHHLT 68 (240)
Q Consensus 23 ~~C~~C~~~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i~h~~Hp~H~L~ 68 (240)
..||+|+++|.|.+|+|..| ||+|+..|.... . |+.|+|.
T Consensus 1 v~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~---~---H~~H~f~ 41 (43)
T cd02340 1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG---V---HPEHAML 41 (43)
T ss_pred CCCCCCCCcCcCCeEECCCCCCccchHHhhCcC---C---CCCCCEE
Confidence 47999999999999999999 899999999865 3 4556765
No 2
>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=98.57 E-value=2.1e-08 Score=59.64 Aligned_cols=29 Identities=48% Similarity=1.047 Sum_probs=14.2
Q ss_pred ccccccccCCCC-ceEeeCCCCCcchhhhc
Q 040047 23 YSCSACELIISG-SAYGCWECKFFLHEQCG 51 (240)
Q Consensus 23 ~~C~~C~~~~~g-~~Y~C~~C~f~lH~~Ca 51 (240)
+.|++|++++.+ ..|.|.+|||+||..||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp ---TTTS----S--EEE-TTT-----HHHH
T ss_pred CcCCcCCCcCCCCceEECccCCCccChhcC
Confidence 479999999988 78999999999999996
No 3
>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=98.41 E-value=8e-08 Score=57.11 Aligned_cols=29 Identities=52% Similarity=1.248 Sum_probs=14.1
Q ss_pred ccccccCCCCCc-eeEEcCCCCcccccccc
Q 040047 80 FLCNACGEPGSA-FSFCCPLCDFDLHVQCA 108 (240)
Q Consensus 80 ~~Cd~C~~~~~g-~~Y~C~~C~f~lH~~Ca 108 (240)
+.|++|++.+.+ +.|+|.+|+|++|..||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp ---TTTS----S--EEE-TTT-----HHHH
T ss_pred CcCCcCCCcCCCCceEECccCCCccChhcC
Confidence 479999999987 99999999999999996
No 4
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=98.33 E-value=5.7e-07 Score=58.51 Aligned_cols=41 Identities=27% Similarity=0.588 Sum_probs=32.7
Q ss_pred ccccccc-cCCCCceEeeCCC-CCcchhhhccccccccCCCCCCcceE
Q 040047 23 YSCSACE-LIISGSAYGCWEC-KFFLHEQCGNASRAMQHTSHPMHHLT 68 (240)
Q Consensus 23 ~~C~~C~-~~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i~h~~Hp~H~L~ 68 (240)
..||+|+ .+|.|.+|+|..| ||||+..|.... .| ++.|+|.
T Consensus 1 i~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~---~H--~~~H~f~ 43 (45)
T cd02339 1 IICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGD---KH--DLEHRFY 43 (45)
T ss_pred CCCCCCCCCCcccCeEECCCCCCccchHHHhCCC---CC--CCCCCEE
Confidence 3799998 6888999999999 899999999841 22 2456764
No 5
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=98.33 E-value=5.8e-07 Score=58.69 Aligned_cols=43 Identities=37% Similarity=0.743 Sum_probs=34.6
Q ss_pred ccccccccCCCCceEeeCCC-CCcchhhhccccccccCCCCCCcceE
Q 040047 23 YSCSACELIISGSAYGCWEC-KFFLHEQCGNASRAMQHTSHPMHHLT 68 (240)
Q Consensus 23 ~~C~~C~~~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i~h~~Hp~H~L~ 68 (240)
+.||+|+.+|.|.+|+|.+| ||+|+..|..... -.|+ +.|++.
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~-~~H~--~~H~~~ 44 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK-KGHP--PDHSFT 44 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc-CCCC--CCCCEe
Confidence 47999999999999999999 7999999999765 2332 146665
No 6
>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=98.32 E-value=3.4e-07 Score=54.45 Aligned_cols=29 Identities=41% Similarity=1.012 Sum_probs=27.2
Q ss_pred ccccccCCCCCce-eEEcCCCCcccccccc
Q 040047 80 FLCNACGEPGSAF-SFCCPLCDFDLHVQCA 108 (240)
Q Consensus 80 ~~Cd~C~~~~~g~-~Y~C~~C~f~lH~~Ca 108 (240)
+.|++|++.+.++ +|+|..|+|++|+.||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 4799999999999 9999999999999997
No 7
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.27 E-value=8.4e-07 Score=57.63 Aligned_cols=31 Identities=29% Similarity=0.855 Sum_probs=28.3
Q ss_pred cccccccc-CCCCceEeeCCC-CCcchhhhccc
Q 040047 23 YSCSACEL-IISGSAYGCWEC-KFFLHEQCGNA 53 (240)
Q Consensus 23 ~~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~ 53 (240)
..||+|+. +|.|.+|+|.+| ||||++.|...
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 47999974 899999999999 89999999986
No 8
>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=98.16 E-value=1.2e-06 Score=52.08 Aligned_cols=29 Identities=41% Similarity=0.928 Sum_probs=27.2
Q ss_pred ccccccccCCCCc-eEeeCCCCCcchhhhc
Q 040047 23 YSCSACELIISGS-AYGCWECKFFLHEQCG 51 (240)
Q Consensus 23 ~~C~~C~~~~~g~-~Y~C~~C~f~lH~~Ca 51 (240)
+.|++|++.+.|. +|+|..|+|+||..||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 5799999999999 9999999999999996
No 9
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=98.11 E-value=2.6e-06 Score=56.41 Aligned_cols=45 Identities=24% Similarity=0.541 Sum_probs=35.2
Q ss_pred ccccccc-cCCCCceEeeCCC-CCcchhhhccccccccCCCC-CCcceEE
Q 040047 23 YSCSACE-LIISGSAYGCWEC-KFFLHEQCGNASRAMQHTSH-PMHHLTL 69 (240)
Q Consensus 23 ~~C~~C~-~~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i~h~~H-p~H~L~l 69 (240)
..|++|+ .+|.|.+|+|..| ||+|+..|.....+. ..| +.|++.+
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~--~~H~~~H~~~~ 48 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTT--ERHLFDHPMQC 48 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcC--CCCCCCCCEEE
Confidence 3799998 7899999999999 999999999966432 233 2567654
No 10
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.06 E-value=2.3e-06 Score=54.58 Aligned_cols=33 Identities=21% Similarity=0.389 Sum_probs=29.0
Q ss_pred cccccccc-CCCCceEeeCCC-CCcchhhhccccc
Q 040047 23 YSCSACEL-IISGSAYGCWEC-KFFLHEQCGNASR 55 (240)
Q Consensus 23 ~~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~p~ 55 (240)
..||+|+. +|.|.+|+|..| ||||++.|.....
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 47999975 899999999999 9999999987543
No 11
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=97.98 E-value=6.2e-06 Score=54.60 Aligned_cols=44 Identities=27% Similarity=0.637 Sum_probs=33.7
Q ss_pred cccccccc-CCCCceEeeCCC-CCcchhhhccccccc-cCCCCCCcceE
Q 040047 23 YSCSACEL-IISGSAYGCWEC-KFFLHEQCGNASRAM-QHTSHPMHHLT 68 (240)
Q Consensus 23 ~~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i-~h~~Hp~H~L~ 68 (240)
..||+|+. +|.|.+|+|..| ||||+..|...-... .|.. .||+.
T Consensus 1 ~~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~--~Hp~~ 47 (49)
T cd02334 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKN--SHPMK 47 (49)
T ss_pred CCCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCC--CCCee
Confidence 36999985 799999999999 999999999865433 3432 45654
No 12
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=97.97 E-value=1.6e-06 Score=80.70 Aligned_cols=86 Identities=23% Similarity=0.543 Sum_probs=68.7
Q ss_pred CcccccccccCCCCc---eEeeCCCCCcchhhhccc-----cccc-----cCCCCCCcceEEeeccCCCCCCccccccCC
Q 040047 21 NEYSCSACELIISGS---AYGCWECKFFLHEQCGNA-----SRAM-----QHTSHPMHHLTLVPTTTYSAGNFLCNACGE 87 (240)
Q Consensus 21 ~~~~C~~C~~~~~g~---~Y~C~~C~f~lH~~Ca~~-----p~~i-----~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~ 87 (240)
.+..|+.|...|||+ +|.|.+|-|.+|+.|.+. |.+- ..|.- +|.++..++. ++..||-||.
T Consensus 55 qPTfCsHCkDFiwGfgKQGfQCqvC~fvvHkrChefVtF~CPGadkg~dtDdpr~-kHkf~~~tYs----sPTFCDhCGs 129 (683)
T KOG0696|consen 55 QPTFCSHCKDFIWGFGKQGFQCQVCCFVVHKRCHEFVTFSCPGADKGPDTDDPRS-KHKFKIHTYS----SPTFCDHCGS 129 (683)
T ss_pred CCchhhhhhhheeccccCceeeeEEeehhhhhhcceEEEECCCCCCCCCCCCccc-ccceeeeecC----CCchhhhHHH
Confidence 689999999999986 699999999999999875 3221 22333 6888887654 4789999998
Q ss_pred CCCce---eEEcCCCCcccccccccCC
Q 040047 88 PGSAF---SFCCPLCDFDLHVQCAFLP 111 (240)
Q Consensus 88 ~~~g~---~Y~C~~C~f~lH~~Ca~lP 111 (240)
...|. ..+|+.|+..+|..|...-
T Consensus 130 LLyGl~HQGmKC~~C~mNVH~rCv~nV 156 (683)
T KOG0696|consen 130 LLYGLIHQGMKCDTCDMNVHHRCVENV 156 (683)
T ss_pred HHHHHHhcccccccccchHHHHHhhcC
Confidence 76543 4789999999999999653
No 13
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.94 E-value=8e-06 Score=53.82 Aligned_cols=42 Identities=33% Similarity=0.773 Sum_probs=34.0
Q ss_pred cccccccc-CCCCceEeeCCCC---CcchhhhccccccccCCCCCCcceE
Q 040047 23 YSCSACEL-IISGSAYGCWECK---FFLHEQCGNASRAMQHTSHPMHHLT 68 (240)
Q Consensus 23 ~~C~~C~~-~~~g~~Y~C~~C~---f~lH~~Ca~~p~~i~h~~Hp~H~L~ 68 (240)
+.||+|+. +|.|.+|+|..|. |||+..|..... .|. +.|+|.
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~--~H~--~~H~~~ 46 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE--SHQ--EDHWLV 46 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC--CCC--CCCcee
Confidence 47999987 9999999999996 999999999765 332 346664
No 14
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.94 E-value=7.8e-06 Score=53.72 Aligned_cols=35 Identities=26% Similarity=0.533 Sum_probs=30.2
Q ss_pred ccccccccCCCCceEeeCCC-CCcchhhhccccccc
Q 040047 23 YSCSACELIISGSAYGCWEC-KFFLHEQCGNASRAM 57 (240)
Q Consensus 23 ~~C~~C~~~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i 57 (240)
+.||+|...+.|.+|+|..| ||||+.+|.....+.
T Consensus 1 i~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~ 36 (48)
T cd02343 1 ISCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKP 36 (48)
T ss_pred CCCCCCCCcCCCceEECCCCCCchhHHHHHhCCccC
Confidence 36999998888889999999 999999999875544
No 15
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=97.87 E-value=9.3e-06 Score=52.28 Aligned_cols=31 Identities=29% Similarity=0.806 Sum_probs=29.0
Q ss_pred cccccCCCCCceeEEcCCC-CcccccccccCC
Q 040047 81 LCNACGEPGSAFSFCCPLC-DFDLHVQCAFLP 111 (240)
Q Consensus 81 ~Cd~C~~~~~g~~Y~C~~C-~f~lH~~Ca~lP 111 (240)
.||.|++.+.|.+|+|..| +|||+..|....
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~ 33 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG 33 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC
Confidence 6999999889999999999 899999999865
No 16
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=97.84 E-value=1.3e-05 Score=53.13 Aligned_cols=32 Identities=41% Similarity=0.740 Sum_probs=29.3
Q ss_pred ccccccc-CCCCceEeeCCC-CCcchhhhccccc
Q 040047 24 SCSACEL-IISGSAYGCWEC-KFFLHEQCGNASR 55 (240)
Q Consensus 24 ~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~p~ 55 (240)
.|++|.. +|.|.+|+|..| ||+|+..|.....
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~ 35 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGR 35 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCC
Confidence 6999988 999999999999 9999999998654
No 17
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.78 E-value=3.2e-05 Score=51.13 Aligned_cols=45 Identities=31% Similarity=0.614 Sum_probs=34.1
Q ss_pred ccccccccCCCC-ceEeeCCC-CCcchhhhccccccc-cCCCCCCcceEE
Q 040047 23 YSCSACELIISG-SAYGCWEC-KFFLHEQCGNASRAM-QHTSHPMHHLTL 69 (240)
Q Consensus 23 ~~C~~C~~~~~g-~~Y~C~~C-~f~lH~~Ca~~p~~i-~h~~Hp~H~L~l 69 (240)
+.||+|.+.+.+ .+|+|.+| ||+|+..|.....+. .|. +.|++.+
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~--~~H~~~~ 48 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHR--NDHNYRV 48 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCC--CCCCeEe
Confidence 469999987765 79999999 999999999976543 332 2466543
No 18
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=97.74 E-value=2.6e-05 Score=50.84 Aligned_cols=33 Identities=30% Similarity=0.779 Sum_probs=29.9
Q ss_pred ccccccCCCCCceeEEcCCC-CcccccccccCCc
Q 040047 80 FLCNACGEPGSAFSFCCPLC-DFDLHVQCAFLPE 112 (240)
Q Consensus 80 ~~Cd~C~~~~~g~~Y~C~~C-~f~lH~~Ca~lP~ 112 (240)
+.|+.|+..+.|.+|+|..| +|+|+..|.....
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 47999999888999999999 7999999998765
No 19
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=97.74 E-value=2.6e-06 Score=81.26 Aligned_cols=45 Identities=22% Similarity=0.494 Sum_probs=39.2
Q ss_pred CCCCCCeeeeecCCCcccccccccCCCCc---eEeeCCCCCcchhhhccc
Q 040047 7 SHPHNLRIYQVQHGNEYSCSACELIISGS---AYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 7 ~H~H~L~l~~~~~~~~~~C~~C~~~~~g~---~Y~C~~C~f~lH~~Ca~~ 53 (240)
.|||.|....+. .+.+||-|++-++|. +.+|..|+..+|+.||..
T Consensus 143 i~PH~l~vhSY~--~PtFCD~CGEmL~GLvrQGlKC~gCglNyHKRCa~k 190 (888)
T KOG4236|consen 143 IRPHTLFVHSYK--APTFCDFCGEMLFGLVRQGLKCEGCGLNYHKRCAFK 190 (888)
T ss_pred eecceeeeeccc--CchHHHHHHHHHHHHHHccccccCCCCcHhhhhhhc
Confidence 477888887766 899999999998885 699999999999999964
No 20
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=97.67 E-value=1.5e-05 Score=52.02 Aligned_cols=34 Identities=32% Similarity=0.769 Sum_probs=27.1
Q ss_pred Cccccccccc-CCCCceEeeCCC-CCcchhhhcccc
Q 040047 21 NEYSCSACEL-IISGSAYGCWEC-KFFLHEQCGNAS 54 (240)
Q Consensus 21 ~~~~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~p 54 (240)
..+.|++|+. +|.|.+|+|..| ||+|+..|....
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g 38 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKG 38 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH-
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCc
Confidence 3689999988 888999999999 899999999853
No 21
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=97.63 E-value=4.1e-05 Score=49.43 Aligned_cols=33 Identities=33% Similarity=0.760 Sum_probs=30.2
Q ss_pred cccccccccCCCCceEeeCCC-CCcchhhhcccc
Q 040047 22 EYSCSACELIISGSAYGCWEC-KFFLHEQCGNAS 54 (240)
Q Consensus 22 ~~~C~~C~~~~~g~~Y~C~~C-~f~lH~~Ca~~p 54 (240)
.+.|++|+.+|.|.+|+|..| ||+|+..|....
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~ 37 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKG 37 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCc
Confidence 578999999999999999999 999999999854
No 22
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.60 E-value=4.5e-05 Score=50.28 Aligned_cols=33 Identities=39% Similarity=0.921 Sum_probs=29.4
Q ss_pred ccccccCC-CCCceeEEcCCCC---cccccccccCCc
Q 040047 80 FLCNACGE-PGSAFSFCCPLCD---FDLHVQCAFLPE 112 (240)
Q Consensus 80 ~~Cd~C~~-~~~g~~Y~C~~C~---f~lH~~Ca~lP~ 112 (240)
+.||+|+. .+.|.+|+|.+|. |||+..|.....
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~ 37 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE 37 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC
Confidence 47999998 7889999999997 999999998764
No 23
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=97.60 E-value=4.3e-05 Score=48.68 Aligned_cols=30 Identities=27% Similarity=0.697 Sum_probs=26.3
Q ss_pred ccccccccCCCCceEeeCCC-CCcchhhhccc
Q 040047 23 YSCSACELIISGSAYGCWEC-KFFLHEQCGNA 53 (240)
Q Consensus 23 ~~C~~C~~~~~g~~Y~C~~C-~f~lH~~Ca~~ 53 (240)
+.|++|.. +.|.+|+|..| ||||+..|...
T Consensus 1 y~C~~C~~-~~~~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 1 YTCNECKH-HVETRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred CcCCCCCC-cCCCceECCCCcchhhHHHHhCC
Confidence 46999987 45789999999 89999999986
No 24
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=97.52 E-value=6.9e-05 Score=48.71 Aligned_cols=30 Identities=23% Similarity=0.700 Sum_probs=26.9
Q ss_pred cccccCC-CCCceeEEcCCC-CcccccccccC
Q 040047 81 LCNACGE-PGSAFSFCCPLC-DFDLHVQCAFL 110 (240)
Q Consensus 81 ~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~l 110 (240)
.||.|++ .+.|.+|+|..| ||||+..|...
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC
Confidence 6999995 567999999999 99999999884
No 25
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=97.50 E-value=6.4e-05 Score=67.14 Aligned_cols=42 Identities=29% Similarity=0.635 Sum_probs=35.8
Q ss_pred cccccccc-CCCCceEeeCCC-CCcchhhhccccccccCCCCCCcceEE
Q 040047 23 YSCSACEL-IISGSAYGCWEC-KFFLHEQCGNASRAMQHTSHPMHHLTL 69 (240)
Q Consensus 23 ~~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i~h~~Hp~H~L~l 69 (240)
..||+|+. +|.|.+|+|.+| ||||++.|.... +.|.+|.|..
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~-----~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN-----EHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC-----CCCcccceee
Confidence 79999999 899999999999 999999998754 4566677655
No 26
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.46 E-value=0.00011 Score=66.34 Aligned_cols=67 Identities=24% Similarity=0.528 Sum_probs=46.4
Q ss_pred CcccccccccC-CCCceEeeCCC-CCcchhhhccccccccCCCCC-CcceEEeecc-------------CCCCCCccccc
Q 040047 21 NEYSCSACELI-ISGSAYGCWEC-KFFLHEQCGNASRAMQHTSHP-MHHLTLVPTT-------------TYSAGNFLCNA 84 (240)
Q Consensus 21 ~~~~C~~C~~~-~~g~~Y~C~~C-~f~lH~~Ca~~p~~i~h~~Hp-~H~L~l~~~~-------------~~~~~~~~Cd~ 84 (240)
+.+.||||++. +.+.+|+|..| ||||+.+|.+.-. .-+.|+ .||+..+-.+ -|....|.|-.
T Consensus 7 e~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~--tt~~H~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPy 84 (381)
T KOG1280|consen 7 EGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGA--TTPIHDEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPY 84 (381)
T ss_pred CCceeccccccceeeeeeEeeeecchhHHHHHhhcCC--CCcccCCCCceeEEeeccceeeEecCccccccccccccCCc
Confidence 67899999775 45678999999 9999999999653 333333 5676654221 12234677888
Q ss_pred cCCCC
Q 040047 85 CGEPG 89 (240)
Q Consensus 85 C~~~~ 89 (240)
|++.+
T Consensus 85 C~~~G 89 (381)
T KOG1280|consen 85 CGIMG 89 (381)
T ss_pred ccccc
Confidence 87765
No 27
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=97.41 E-value=8.3e-05 Score=47.36 Aligned_cols=38 Identities=29% Similarity=0.797 Sum_probs=30.9
Q ss_pred ccccccCCCCCceeEEcCCC-CcccccccccCCceeeeCCCceeeE
Q 040047 80 FLCNACGEPGSAFSFCCPLC-DFDLHVQCAFLPEILIHDSHFHSLN 124 (240)
Q Consensus 80 ~~Cd~C~~~~~g~~Y~C~~C-~f~lH~~Ca~lP~~i~~~~H~H~L~ 124 (240)
+.|+.|.. +.+.+|+|..| ||||+..|... ..|+|.|.
T Consensus 1 y~C~~C~~-~~~~r~~C~~C~dfDLC~~C~~~------~~H~H~~~ 39 (41)
T cd02337 1 YTCNECKH-HVETRWHCTVCEDYDLCITCYNT------KNHPHKME 39 (41)
T ss_pred CcCCCCCC-cCCCceECCCCcchhhHHHHhCC------CCCCcccc
Confidence 46999987 45799999999 99999999875 45677663
No 28
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=97.40 E-value=0.00012 Score=48.44 Aligned_cols=43 Identities=26% Similarity=0.652 Sum_probs=33.3
Q ss_pred cccccC-CCCCceeEEcCCC-CcccccccccCCceeeeCCCc--eeeEE
Q 040047 81 LCNACG-EPGSAFSFCCPLC-DFDLHVQCAFLPEILIHDSHF--HSLNL 125 (240)
Q Consensus 81 ~Cd~C~-~~~~g~~Y~C~~C-~f~lH~~Ca~lP~~i~~~~H~--H~L~l 125 (240)
.|+.|+ ..+.|.+|+|..| ||||+..|...... ...|. |++.+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~--~~~H~~~H~~~~ 48 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVT--TERHLFDHPMQC 48 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCc--CCCCCCCCCEEE
Confidence 699999 5678999999999 99999999986543 23343 66543
No 29
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.38 E-value=0.00015 Score=47.11 Aligned_cols=30 Identities=33% Similarity=0.730 Sum_probs=27.4
Q ss_pred cccccCC-CCCceeEEcCCC-CcccccccccC
Q 040047 81 LCNACGE-PGSAFSFCCPLC-DFDLHVQCAFL 110 (240)
Q Consensus 81 ~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~l 110 (240)
.||.|+. .+.|.+|+|..| ||||+..|...
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 6999996 578999999999 89999999886
No 30
>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=97.33 E-value=0.00016 Score=48.02 Aligned_cols=43 Identities=23% Similarity=0.515 Sum_probs=31.4
Q ss_pred CCCeeeeecCCCcccccccccCCCC---ceEeeCCCCCcchhhhcccc
Q 040047 10 HNLRIYQVQHGNEYSCSACELIISG---SAYGCWECKFFLHEQCGNAS 54 (240)
Q Consensus 10 H~L~l~~~~~~~~~~C~~C~~~~~g---~~Y~C~~C~f~lH~~Ca~~p 54 (240)
|.++..+. ..+..|+.|++.|+| .+|+|..|++.+|++|.+..
T Consensus 1 H~f~~~~~--~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 1 HHFVPTTF--SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp -EEEEEES--SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CeEEEccC--CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 33344443 378999999999954 47999999999999999853
No 31
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.23 E-value=0.00017 Score=47.40 Aligned_cols=32 Identities=28% Similarity=0.615 Sum_probs=28.5
Q ss_pred cccccCCCCCceeEEcCCC-CcccccccccCCc
Q 040047 81 LCNACGEPGSAFSFCCPLC-DFDLHVQCAFLPE 112 (240)
Q Consensus 81 ~Cd~C~~~~~g~~Y~C~~C-~f~lH~~Ca~lP~ 112 (240)
.||.|.+.+.+++|+|..| ||||+..|...-.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~ 34 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGV 34 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCc
Confidence 5999999878999999999 9999999987543
No 32
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=97.21 E-value=0.00016 Score=46.20 Aligned_cols=31 Identities=26% Similarity=0.515 Sum_probs=27.3
Q ss_pred cccccCC-CCCceeEEcCCC-CcccccccccCC
Q 040047 81 LCNACGE-PGSAFSFCCPLC-DFDLHVQCAFLP 111 (240)
Q Consensus 81 ~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~lP 111 (240)
.||+||. ++.|.+|+|..| ||||+..|....
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 6999997 568999999999 999999998643
No 33
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.16 E-value=0.00036 Score=46.09 Aligned_cols=33 Identities=27% Similarity=0.711 Sum_probs=28.9
Q ss_pred ccccccCCCCC-ceeEEcCCC-CcccccccccCCc
Q 040047 80 FLCNACGEPGS-AFSFCCPLC-DFDLHVQCAFLPE 112 (240)
Q Consensus 80 ~~Cd~C~~~~~-g~~Y~C~~C-~f~lH~~Ca~lP~ 112 (240)
+.||+|++.+. |.+|+|..| +|||+..|.....
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~ 35 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSAGA 35 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcC
Confidence 36999999875 699999999 9999999998653
No 34
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=97.11 E-value=0.00018 Score=46.82 Aligned_cols=32 Identities=31% Similarity=0.884 Sum_probs=25.9
Q ss_pred CccccccCC-CCCceeEEcCCC-CcccccccccC
Q 040047 79 NFLCNACGE-PGSAFSFCCPLC-DFDLHVQCAFL 110 (240)
Q Consensus 79 ~~~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~l 110 (240)
.+.|++|+. .+.|.+|+|..| ||||+..|...
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 679999998 667999999999 89999999864
No 35
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=97.10 E-value=0.00027 Score=46.70 Aligned_cols=31 Identities=32% Similarity=0.735 Sum_probs=28.4
Q ss_pred cccccCC-CCCceeEEcCCC-CcccccccccCC
Q 040047 81 LCNACGE-PGSAFSFCCPLC-DFDLHVQCAFLP 111 (240)
Q Consensus 81 ~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~lP 111 (240)
.|++|++ .+.|.+|+|..| ||||+..|....
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~ 34 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKG 34 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCC
Confidence 5999998 788999999999 999999999865
No 36
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=97.09 E-value=0.00038 Score=46.05 Aligned_cols=31 Identities=39% Similarity=0.921 Sum_probs=27.7
Q ss_pred cccccCC-CCCceeEEcCCC-CcccccccccCC
Q 040047 81 LCNACGE-PGSAFSFCCPLC-DFDLHVQCAFLP 111 (240)
Q Consensus 81 ~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~lP 111 (240)
.||.|+. .+.|.+|+|..| ||||+..|...-
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g 34 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSG 34 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCC
Confidence 6999997 578999999999 999999999754
No 37
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=97.08 E-value=0.00032 Score=45.22 Aligned_cols=33 Identities=30% Similarity=0.862 Sum_probs=29.8
Q ss_pred CccccccCCCCCceeEEcCCC-CcccccccccCC
Q 040047 79 NFLCNACGEPGSAFSFCCPLC-DFDLHVQCAFLP 111 (240)
Q Consensus 79 ~~~Cd~C~~~~~g~~Y~C~~C-~f~lH~~Ca~lP 111 (240)
...|+.|+..+.|.+|+|..| +|||+..|....
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~ 37 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKG 37 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCc
Confidence 578999999888999999999 999999998754
No 38
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.08 E-value=0.00041 Score=62.80 Aligned_cols=72 Identities=21% Similarity=0.455 Sum_probs=48.8
Q ss_pred CCccccccCCCC-CceeEEcCCC-CcccccccccCCceeeeCCCceeeEEeecC---------CccCCCCccceeccccc
Q 040047 78 GNFLCNACGEPG-SAFSFCCPLC-DFDLHVQCAFLPEILIHDSHFHSLNLSYAL---------PAAHHYESSSYVCDICH 146 (240)
Q Consensus 78 ~~~~Cd~C~~~~-~g~~Y~C~~C-~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~---------~~~~~~~~~~~~C~vC~ 146 (240)
....||+|++.. .+.+|+|..| |||||..|...-.+.....+.||+..+... .++.-|....|.|-+|+
T Consensus 7 e~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPyC~ 86 (381)
T KOG1280|consen 7 EGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPYCG 86 (381)
T ss_pred CCceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccceeeEecCccccccccccccCCccc
Confidence 468899999975 5888999999 999999999765443333345776643221 11112224578899998
Q ss_pred ccc
Q 040047 147 KQL 149 (240)
Q Consensus 147 ~~~ 149 (240)
+.+
T Consensus 87 ~~G 89 (381)
T KOG1280|consen 87 IMG 89 (381)
T ss_pred ccc
Confidence 853
No 39
>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=97.00 E-value=0.0019 Score=42.84 Aligned_cols=39 Identities=23% Similarity=0.440 Sum_probs=29.6
Q ss_pred cceecccccccccCCcceeEEeCCCCeeeecccccCccc
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
...+|++|++.+.+....+|+|.+|++.+|.+|+.....
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~ 48 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPP 48 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSS
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCC
Confidence 457999999998422157999999999999999876543
No 40
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=96.77 E-value=0.0012 Score=42.81 Aligned_cols=34 Identities=26% Similarity=0.570 Sum_probs=30.2
Q ss_pred CcccccccccCCCC---ceEeeCCCCCcchhhhcccc
Q 040047 21 NEYSCSACELIISG---SAYGCWECKFFLHEQCGNAS 54 (240)
Q Consensus 21 ~~~~C~~C~~~~~g---~~Y~C~~C~f~lH~~Ca~~p 54 (240)
.+..|+.|.+.++| .+|+|..|++.+|+.|+...
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchhhhhhccC
Confidence 57789999999987 58999999999999999853
No 41
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=96.39 E-value=0.0019 Score=41.56 Aligned_cols=33 Identities=30% Similarity=0.630 Sum_probs=29.6
Q ss_pred CcccccccccCCCCc--eEeeCCCCCcchhhhccc
Q 040047 21 NEYSCSACELIISGS--AYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 21 ~~~~C~~C~~~~~g~--~Y~C~~C~f~lH~~Ca~~ 53 (240)
.+..|+.|.+.|++. +|+|..|++..|+.|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 578899999999873 899999999999999985
No 42
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=96.04 E-value=0.0038 Score=55.82 Aligned_cols=32 Identities=28% Similarity=0.722 Sum_probs=29.4
Q ss_pred ccccccCC-CCCceeEEcCCC-CcccccccccCC
Q 040047 80 FLCNACGE-PGSAFSFCCPLC-DFDLHVQCAFLP 111 (240)
Q Consensus 80 ~~Cd~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~lP 111 (240)
..||.|+. .+.|.+|+|.+| |||||..|-...
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 68999999 788999999999 999999998754
No 43
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=95.87 E-value=0.01 Score=58.33 Aligned_cols=128 Identities=23% Similarity=0.470 Sum_probs=85.4
Q ss_pred cccccc-ccCCCCc--eEeeC--CCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCCCceeEEcC
Q 040047 23 YSCSAC-ELIISGS--AYGCW--ECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPGSAFSFCCP 97 (240)
Q Consensus 23 ~~C~~C-~~~~~g~--~Y~C~--~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~g~~Y~C~ 97 (240)
.-|-+| .|.+|-. --.|. .|...+|..|.... ..| -|.|+|.-|...-...+++|.
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIv----------------qVP---tGpWfCrKCesqeraarvrCe 66 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIV----------------QVP---TGPWFCRKCESQERAARVRCE 66 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeE----------------ecC---CCchhhhhhhhhhhhccceee
Confidence 347777 6677743 47788 69999999998742 122 267889888887667778888
Q ss_pred CCCcc------------cccccccC-Cceeee-CCCc-eeeEEeecCCccCCCCccceecccccccccCCc---ceeEEe
Q 040047 98 LCDFD------------LHVQCAFL-PEILIH-DSHF-HSLNLSYALPAAHHYESSSYVCDICHKQLDQKC---FWSYNC 159 (240)
Q Consensus 98 ~C~f~------------lH~~Ca~l-P~~i~~-~~H~-H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~~~~---~~~Y~C 159 (240)
.|-++ .|.-||.+ |++ +. .-|. -|+.|-+.+. + .-+..|-+|++.+..+. +....|
T Consensus 67 LCP~kdGALKkTDn~GWAHVVCALYIPEV-rFgNV~TMEPIiLq~VP~--d---RfnKtCYIC~E~GrpnkA~~GACMtC 140 (900)
T KOG0956|consen 67 LCPHKDGALKKTDNGGWAHVVCALYIPEV-RFGNVHTMEPIILQDVPH--D---RFNKTCYICNEEGRPNKAAKGACMTC 140 (900)
T ss_pred cccCcccceecccCCCceEEEEEeeccce-eecccccccceeeccCch--h---hhcceeeeecccCCccccccccceec
Confidence 88544 79999964 543 33 2222 3455544331 1 24678999998754221 456777
Q ss_pred C--CCCeeeecccccCcc
Q 040047 160 F--ACNFHAHVSCTRNRN 175 (240)
Q Consensus 160 ~--~C~~~lH~~C~~~~~ 175 (240)
+ .|.-.+|+.|+....
T Consensus 141 NKs~CkqaFHVTCAQ~~G 158 (900)
T KOG0956|consen 141 NKSGCKQAFHVTCAQRAG 158 (900)
T ss_pred ccccchhhhhhhHhhhhc
Confidence 7 578899999986443
No 44
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.86 E-value=0.0032 Score=59.74 Aligned_cols=142 Identities=21% Similarity=0.352 Sum_probs=86.5
Q ss_pred Cccccccccc-CC--CCceEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCCCceeEEcC
Q 040047 21 NEYSCSACEL-II--SGSAYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPGSAFSFCCP 97 (240)
Q Consensus 21 ~~~~C~~C~~-~~--~g~~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~g~~Y~C~ 97 (240)
...+|-+|.. .+ .|....|..|+..+|+.|..-...+.-++-. ....-.+|+|++|.-.+.- =+|.
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~---------s~~stepWfCeaC~~Gvs~--P~CE 186 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGS---------SDCSTEPWFCEACLYGVSL--PHCE 186 (707)
T ss_pred cceEEEEeecCccccccceeeccccCceecccccccccccccCCCC---------ccCCCCchhhhhHhcCCCC--Cccc
Confidence 3458999933 33 3557999999999999999854433322210 1111247999999765431 2344
Q ss_pred CC------------CcccccccccCCceeeeCCCceeeEEeecCCccCCCC-ccceecccccccccCCcceeEEeC--CC
Q 040047 98 LC------------DFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYE-SSSYVCDICHKQLDQKCFWSYNCF--AC 162 (240)
Q Consensus 98 ~C------------~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~-~~~~~C~vC~~~~~~~~~~~Y~C~--~C 162 (240)
-| +-.+|.-||....-|... ..|.|.-+..... .|. -+...|.+|...+-.+.|..-+|. .|
T Consensus 187 lCPn~~GifKetDigrWvH~iCALYvpGVafg-~~~~l~~Vtl~em--~ysk~Gak~Cs~Ced~~fARtGvci~CdaGMC 263 (707)
T KOG0957|consen 187 LCPNRFGIFKETDIGRWVHAICALYVPGVAFG-QTHTLCGVTLEEM--DYSKFGAKTCSACEDKIFARTGVCIRCDAGMC 263 (707)
T ss_pred cCCCcCCcccccchhhHHHHHHHhhcCccccc-cccccccccHHHh--hhhhhccchhccccchhhhhcceeeeccchhh
Confidence 44 345899999765444321 1233322111100 121 256789999998764435667777 68
Q ss_pred CeeeecccccCccc
Q 040047 163 NFHAHVSCTRNRNN 176 (240)
Q Consensus 163 ~~~lH~~C~~~~~~ 176 (240)
.-++|+.|+....-
T Consensus 264 k~YfHVTCAQk~Gl 277 (707)
T KOG0957|consen 264 KEYFHVTCAQKLGL 277 (707)
T ss_pred hhhhhhhHHhhhcc
Confidence 89999999865553
No 45
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=95.69 E-value=0.0087 Score=38.71 Aligned_cols=33 Identities=21% Similarity=0.500 Sum_probs=28.6
Q ss_pred CCccccccCCCCCc---eeEEcCCCCcccccccccC
Q 040047 78 GNFLCNACGEPGSA---FSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~~g---~~Y~C~~C~f~lH~~Ca~l 110 (240)
....|+.|++.+.+ ..|+|+.|++.+|.+|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 35689999998864 7899999999999999864
No 46
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=95.26 E-value=0.0093 Score=38.24 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=28.3
Q ss_pred CCccccccCCCCCc--eeEEcCCCCcccccccccC
Q 040047 78 GNFLCNACGEPGSA--FSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~~g--~~Y~C~~C~f~lH~~Ca~l 110 (240)
....|+.|++.+.+ ..|+|..|++.+|.+|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 36789999998865 3799999999999999864
No 47
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=95.21 E-value=0.0034 Score=58.95 Aligned_cols=100 Identities=22% Similarity=0.388 Sum_probs=66.2
Q ss_pred CcceEEeeccCCCCCCccccccCCCCCce---eEEcCCCCcccccccccCC-----ceeee-----CCCceeeEEeecCC
Q 040047 64 MHHLTLVPTTTYSAGNFLCNACGEPGSAF---SFCCPLCDFDLHVQCAFLP-----EILIH-----DSHFHSLNLSYALP 130 (240)
Q Consensus 64 ~H~L~l~~~~~~~~~~~~Cd~C~~~~~g~---~Y~C~~C~f~lH~~Ca~lP-----~~i~~-----~~H~H~L~l~~~~~ 130 (240)
.|.+...-. ..+..|.-|..-+.|+ .+.|..|.|.+|.+|-..- ..-+. +...|.+.+..-
T Consensus 45 ~HkF~aRFF----KqPTfCsHCkDFiwGfgKQGfQCqvC~fvvHkrChefVtF~CPGadkg~dtDdpr~kHkf~~~tY-- 118 (683)
T KOG0696|consen 45 SHKFIARFF----KQPTFCSHCKDFIWGFGKQGFQCQVCCFVVHKRCHEFVTFSCPGADKGPDTDDPRSKHKFKIHTY-- 118 (683)
T ss_pred cceeeehhc----cCCchhhhhhhheeccccCceeeeEEeehhhhhhcceEEEECCCCCCCCCCCCcccccceeeeec--
Confidence 456654322 2467999999877554 5999999999999998542 11111 222354443221
Q ss_pred ccCCCCccceecccccccccCCcceeEEeCCCCeeeecccccCcc
Q 040047 131 AAHHYESSSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRN 175 (240)
Q Consensus 131 ~~~~~~~~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~ 175 (240)
+....||-|+..+.+-..-..+|..|++.+|.+|+....
T Consensus 119 ------ssPTFCDhCGsLLyGl~HQGmKC~~C~mNVH~rCv~nVP 157 (683)
T KOG0696|consen 119 ------SSPTFCDHCGSLLYGLIHQGMKCDTCDMNVHHRCVENVP 157 (683)
T ss_pred ------CCCchhhhHHHHHHHHHhcccccccccchHHHHHhhcCC
Confidence 245799999998652102478999999999999986543
No 48
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=93.33 E-value=0.047 Score=54.32 Aligned_cols=47 Identities=21% Similarity=0.364 Sum_probs=36.8
Q ss_pred ccccccccc-CCCCceEeeCCC-CCcchhhhccccccc-cCCCCCCcceEEe
Q 040047 22 EYSCSACEL-IISGSAYGCWEC-KFFLHEQCGNASRAM-QHTSHPMHHLTLV 70 (240)
Q Consensus 22 ~~~C~~C~~-~~~g~~Y~C~~C-~f~lH~~Ca~~p~~i-~h~~Hp~H~L~l~ 70 (240)
.-+|++|++ +|.|++|+|..| |++||..|+..-+.- .|..| ||+.-.
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~--~pM~Ey 652 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMH--YPMVEY 652 (966)
T ss_pred hhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCC--CCceee
Confidence 468999955 899999999999 999999999875543 45444 676644
No 49
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=92.82 E-value=0.088 Score=49.34 Aligned_cols=52 Identities=31% Similarity=0.567 Sum_probs=39.7
Q ss_pred CCcccccccccCCCCc-eEeeCCC-CCcchhhhccccccccCCCCCCcceEEeec
Q 040047 20 GNEYSCSACELIISGS-AYGCWEC-KFFLHEQCGNASRAMQHTSHPMHHLTLVPT 72 (240)
Q Consensus 20 ~~~~~C~~C~~~~~g~-~Y~C~~C-~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~ 72 (240)
++.+.|++|...+.|. +.+|-+| |||||..|+..-.++. +-++.|+.+++..
T Consensus 12 g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~-~H~~~H~Yrim~~ 65 (438)
T KOG0457|consen 12 GGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETG-KHQNDHPYRIMDT 65 (438)
T ss_pred CCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccC-CCCCCCCceeecC
Confidence 4689999999999887 4999999 7999999998644332 1134577777654
No 50
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=92.73 E-value=0.081 Score=34.30 Aligned_cols=30 Identities=20% Similarity=0.506 Sum_probs=27.1
Q ss_pred ccccccCCCCCceeEEcCCC-Cccccccccc
Q 040047 80 FLCNACGEPGSAFSFCCPLC-DFDLHVQCAF 109 (240)
Q Consensus 80 ~~Cd~C~~~~~g~~Y~C~~C-~f~lH~~Ca~ 109 (240)
+.|+.||......+|+|... +++|++.|..
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~ 31 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQ 31 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHh
Confidence 36999999998999999998 7999999985
No 51
>KOG0694 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=92.20 E-value=0.04 Score=54.34 Aligned_cols=86 Identities=21% Similarity=0.459 Sum_probs=60.4
Q ss_pred CcccccccccCCCC--c-eEeeCCCCCcchhhhcccccc----ccC-----------CCCCC-cceEEeeccCCCCCCcc
Q 040047 21 NEYSCSACELIISG--S-AYGCWECKFFLHEQCGNASRA----MQH-----------TSHPM-HHLTLVPTTTYSAGNFL 81 (240)
Q Consensus 21 ~~~~C~~C~~~~~g--~-~Y~C~~C~f~lH~~Ca~~p~~----i~h-----------~~Hp~-H~L~l~~~~~~~~~~~~ 81 (240)
....|+.|.+.++| . +|.|..|.++.|+.|..+.-. ... +.++. |.+.... ..+...
T Consensus 168 Qpt~Cs~C~kFi~gL~kqGyQCqvC~~vvHKkCh~kvv~~C~~~~~~n~e~q~~~~~~~~~~Phrf~~~~----~q~ptF 243 (694)
T KOG0694|consen 168 QPTFCSWCQKFIWGLRKQGYQCQVCWRVVHKKCHVKVVTLCDFLDNLNSEPQGFLFEFTFRNPHRFVKLN----RQRPTF 243 (694)
T ss_pred CcchhhhhhhheeccCCCceEEeeeeehHhhhhHHHHHHhccCcCccCcCCccccccccccCCCcchhhh----ccCccH
Confidence 68999999999988 3 699999999999999864211 011 11110 2221111 135789
Q ss_pred ccccCCCCCc---eeEEcCCCCcccccccccC
Q 040047 82 CNACGEPGSA---FSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 82 Cd~C~~~~~g---~~Y~C~~C~f~lH~~Ca~l 110 (240)
|+-||....+ -...|..|+..+|..|...
T Consensus 244 c~hCGs~L~r~~qqGlkCs~Cg~n~H~~c~~~ 275 (694)
T KOG0694|consen 244 CDHCGSVLYRLRQQGLKCSTCGRNVHNRCVEN 275 (694)
T ss_pred HHhcchhhhhhcccCeeehhhhccccHHHHHh
Confidence 9999997643 4588999999999999954
No 52
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=91.35 E-value=0.19 Score=50.11 Aligned_cols=140 Identities=19% Similarity=0.295 Sum_probs=76.6
Q ss_pred CCCcccccccccCCCC---ceEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCCCceeEE
Q 040047 19 HGNEYSCSACELIISG---SAYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPGSAFSFC 95 (240)
Q Consensus 19 ~~~~~~C~~C~~~~~g---~~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~g~~Y~ 95 (240)
+++...||.|..+-.. .---|..||.-+|..|+..... |.- ++.-..=. -.....|..|-+.+...-|.
T Consensus 268 ~dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~---p~g---pWlCr~Ca--lg~~ppCvLCPkkGGamK~~ 339 (893)
T KOG0954|consen 268 YDEDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEV---PEG---PWLCRTCA--LGIEPPCVLCPKKGGAMKPT 339 (893)
T ss_pred ccccceeceecCCCccccceeEEeccchhHHHHhhhceeec---CCC---Ceeehhcc--ccCCCCeeeccccCCccccc
Confidence 4578999999887432 2477999999999999984311 111 00000000 00122344444433222222
Q ss_pred cCCCCcccccccccC-CceeeeCCCc--eeeEEeecCCccCCCCccceecccccccccCCcceeEEeC--CCCeeeeccc
Q 040047 96 CPLCDFDLHVQCAFL-PEILIHDSHF--HSLNLSYALPAAHHYESSSYVCDICHKQLDQKCFWSYNCF--ACNFHAHVSC 170 (240)
Q Consensus 96 C~~C~f~lH~~Ca~l-P~~i~~~~H~--H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~~~~~~~Y~C~--~C~~~lH~~C 170 (240)
=+.- -..|..||.. |++. ...-. -|++-...-+ .......|.+|.... |..-+|. .|--.+|+.|
T Consensus 340 ~sgT-~wAHvsCALwIPEVs-ie~~ekmePItkfs~Ip----esRwslvC~LCk~k~----GACIqCs~k~C~t~fHv~C 409 (893)
T KOG0954|consen 340 KSGT-KWAHVSCALWIPEVS-IECPEKMEPITKFSHIP----ESRWSLVCNLCKVKS----GACIQCSNKTCRTAFHVTC 409 (893)
T ss_pred CCCC-eeeEeeeeeccceee-ccCHhhcCcccccCCCc----HHHHHHHHHHhcccC----cceEEecccchhhhccchh
Confidence 1111 3478899965 5443 32211 2333222110 113457899999985 4566776 6888999999
Q ss_pred ccCccc
Q 040047 171 TRNRNN 176 (240)
Q Consensus 171 ~~~~~~ 176 (240)
+.....
T Consensus 410 A~~aG~ 415 (893)
T KOG0954|consen 410 AFEAGL 415 (893)
T ss_pred hhhcCC
Confidence 975553
No 53
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=89.22 E-value=0.34 Score=36.79 Aligned_cols=85 Identities=20% Similarity=0.290 Sum_probs=54.3
Q ss_pred cccccCCCCCceeEEcCCCCcccccccccCCceee-eCCCc-eeeEEeecCCccCCCCccceecccccccccCCcceeEE
Q 040047 81 LCNACGEPGSAFSFCCPLCDFDLHVQCAFLPEILI-HDSHF-HSLNLSYALPAAHHYESSSYVCDICHKQLDQKCFWSYN 158 (240)
Q Consensus 81 ~Cd~C~~~~~g~~Y~C~~C~f~lH~~Ca~lP~~i~-~~~H~-H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~~~~~~~Y~ 158 (240)
.|..|... +-.++-..-+-.+|..|+..-..+. ..... =+..+... ........|.+|++.. |..-+
T Consensus 2 ~C~lC~~~--~Galk~t~~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i-----~~~~~~~~C~iC~~~~----G~~i~ 70 (110)
T PF13832_consen 2 SCVLCPKR--GGALKRTSDGQWVHVLCALWIPEVIFNNGESMEPVDISNI-----PPSRFKLKCSICGKSG----GACIK 70 (110)
T ss_pred ccEeCCCC--CCcccCccCCcEEEeEccceeCccEEeechhcCcccceee-----cchhcCCcCcCCCCCC----ceeEE
Confidence 57888875 3345666667889999997633322 21111 11111111 1113578999999983 66889
Q ss_pred eCC--CCeeeecccccCccc
Q 040047 159 CFA--CNFHAHVSCTRNRNN 176 (240)
Q Consensus 159 C~~--C~~~lH~~C~~~~~~ 176 (240)
|.. |...+|+.|+.....
T Consensus 71 C~~~~C~~~fH~~CA~~~g~ 90 (110)
T PF13832_consen 71 CSHPGCSTAFHPTCARKAGL 90 (110)
T ss_pred cCCCCCCcCCCHHHHHHCCC
Confidence 997 999999999976554
No 54
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=89.08 E-value=0.16 Score=50.68 Aligned_cols=45 Identities=20% Similarity=0.331 Sum_probs=35.3
Q ss_pred CCccccccCCC-CCceeEEcCCC-CcccccccccCCceeeeCCCc--eeeE
Q 040047 78 GNFLCNACGEP-GSAFSFCCPLC-DFDLHVQCAFLPEILIHDSHF--HSLN 124 (240)
Q Consensus 78 ~~~~Cd~C~~~-~~g~~Y~C~~C-~f~lH~~Ca~lP~~i~~~~H~--H~L~ 124 (240)
...+|++|++. |.|++|+|..| |+|+|..|.+.-.. ..+|. ||+.
T Consensus 602 H~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgra--ak~hk~~~pM~ 650 (966)
T KOG4286|consen 602 HQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRA--AKGHKMHYPMV 650 (966)
T ss_pred hhhhcchhhhCccceeeeeehhhcChhHHhhHhhhccc--ccCCCCCCCce
Confidence 46799999984 68999999999 99999999976543 34453 5654
No 55
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=88.77 E-value=0.3 Score=31.60 Aligned_cols=31 Identities=23% Similarity=0.416 Sum_probs=27.6
Q ss_pred ccccccccCCCCceEeeCCC-CCcchhhhccc
Q 040047 23 YSCSACELIISGSAYGCWEC-KFFLHEQCGNA 53 (240)
Q Consensus 23 ~~C~~C~~~~~g~~Y~C~~C-~f~lH~~Ca~~ 53 (240)
+.|+.|+..+...+|+|..+ +++|+..|...
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhC
Confidence 36999999998889999998 69999999874
No 56
>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=88.34 E-value=0.64 Score=30.13 Aligned_cols=34 Identities=21% Similarity=0.418 Sum_probs=28.1
Q ss_pred ecccccccccCCcceeEEeCCCCeeeecccccCccc
Q 040047 141 VCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 141 ~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
+|.+|++.. .. ...-.|..|+..+|..|+..+..
T Consensus 1 ~C~vC~~~~-~~-~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSD-DD-GDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSC-TT-SSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcC-CC-CCeEEcCCCChhhCcccCCCChh
Confidence 588999943 33 67899999999999999988775
No 57
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=87.99 E-value=0.51 Score=35.78 Aligned_cols=84 Identities=20% Similarity=0.352 Sum_probs=53.2
Q ss_pred cccccccCCCCceEeeCCCCCcchhhhccccccccCC-CCCCcceEEeeccCCCCCCccccccCCCCCceeEEcCC--CC
Q 040047 24 SCSACELIISGSAYGCWECKFFLHEQCGNASRAMQHT-SHPMHHLTLVPTTTYSAGNFLCNACGEPGSAFSFCCPL--CD 100 (240)
Q Consensus 24 ~C~~C~~~~~g~~Y~C~~C~f~lH~~Ca~~p~~i~h~-~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~g~~Y~C~~--C~ 100 (240)
.|-.|... |..++-..-+-.+|..|+..-..+... ....=+..+...+ .......|..|++. .|..-+|.. |.
T Consensus 2 ~C~lC~~~--~Galk~t~~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~-~~~~~~~C~iC~~~-~G~~i~C~~~~C~ 77 (110)
T PF13832_consen 2 SCVLCPKR--GGALKRTSDGQWVHVLCALWIPEVIFNNGESMEPVDISNIP-PSRFKLKCSICGKS-GGACIKCSHPGCS 77 (110)
T ss_pred ccEeCCCC--CCcccCccCCcEEEeEccceeCccEEeechhcCcccceeec-chhcCCcCcCCCCC-CceeEEcCCCCCC
Confidence 46677664 334665666789999999864333211 1100011111111 12347899999987 678889998 99
Q ss_pred cccccccccCC
Q 040047 101 FDLHVQCAFLP 111 (240)
Q Consensus 101 f~lH~~Ca~lP 111 (240)
..+|+.||...
T Consensus 78 ~~fH~~CA~~~ 88 (110)
T PF13832_consen 78 TAFHPTCARKA 88 (110)
T ss_pred cCCCHHHHHHC
Confidence 99999999753
No 58
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=85.42 E-value=0.15 Score=49.68 Aligned_cols=43 Identities=26% Similarity=0.669 Sum_probs=35.7
Q ss_pred CCCCeeeeecCCCcccccccccCCCCc---eEeeCCCCCcchhhhccc
Q 040047 9 PHNLRIYQVQHGNEYSCSACELIISGS---AYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 9 ~H~L~l~~~~~~~~~~C~~C~~~~~g~---~Y~C~~C~f~lH~~Ca~~ 53 (240)
||.+....++ .+..|..|++-+.|. +.+|+.|.|..|++||..
T Consensus 267 PHTf~vHSY~--rpTVCq~CkkLLkGL~rQGlqCkDCk~NcHkrCa~~ 312 (888)
T KOG4236|consen 267 PHTFIVHSYT--RPTVCQYCKKLLKGLFRQGLQCKDCKFNCHKRCAMK 312 (888)
T ss_pred CeeEEEeecc--CchHHHHHHHHHHHHHhcCcccccCCcchhhhhhhh
Confidence 5777766665 889999998877663 699999999999999964
No 59
>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=82.50 E-value=1.6 Score=28.21 Aligned_cols=33 Identities=27% Similarity=0.587 Sum_probs=27.2
Q ss_pred cccccCCCC-CceeEEcCCCCcccccccccCCce
Q 040047 81 LCNACGEPG-SAFSFCCPLCDFDLHVQCAFLPEI 113 (240)
Q Consensus 81 ~Cd~C~~~~-~g~~Y~C~~C~f~lH~~Ca~lP~~ 113 (240)
.|.+|++.. .+....|..|+-.+|..|..++..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 478898854 478899999999999999987643
No 60
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=82.25 E-value=0.87 Score=40.50 Aligned_cols=85 Identities=18% Similarity=0.305 Sum_probs=57.2
Q ss_pred CccccccCCCC-----Cc---eeEEcCCCCcccccccccCCceeeeCCCceeeEEeecCCccCCCCccceeccccccccc
Q 040047 79 NFLCNACGEPG-----SA---FSFCCPLCDFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQLD 150 (240)
Q Consensus 79 ~~~Cd~C~~~~-----~g---~~Y~C~~C~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~ 150 (240)
...||.|-... .| ....|++|+-.=|+.|..+...+...- -++.|. . ..-..|++|++.-+
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~av----k~yrwq--c-----ieck~csicgtsen 292 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAV----KTYRWQ--C-----IECKYCSICGTSEN 292 (336)
T ss_pred CcccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHH----Hhheee--e-----eecceeccccCcCC
Confidence 45788884332 12 346799999999999987654432210 011111 1 13468999999754
Q ss_pred CCcceeEEeCCCCeeeecccccCccc
Q 040047 151 QKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 151 ~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
+ .-...|.+||-.+|.-|...+.+
T Consensus 293 d--dqllfcddcdrgyhmyclsppm~ 316 (336)
T KOG1244|consen 293 D--DQLLFCDDCDRGYHMYCLSPPMV 316 (336)
T ss_pred C--ceeEeecccCCceeeEecCCCcC
Confidence 2 46889999999999999998886
No 61
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=81.62 E-value=2.1 Score=42.34 Aligned_cols=141 Identities=18% Similarity=0.348 Sum_probs=82.5
Q ss_pred cccccccCCCCceEeeCCCCCcchhhhcccccc---------ccCCCCC---CcceEEeeccCCCCCCccccccCCCC--
Q 040047 24 SCSACELIISGSAYGCWECKFFLHEQCGNASRA---------MQHTSHP---MHHLTLVPTTTYSAGNFLCNACGEPG-- 89 (240)
Q Consensus 24 ~C~~C~~~~~g~~Y~C~~C~f~lH~~Ca~~p~~---------i~h~~Hp---~H~L~l~~~~~~~~~~~~Cd~C~~~~-- 89 (240)
.|..|.....-..-.|..|+..+|..|.....+ ..+-.|. .|..+.... ..+..|..|.+..
T Consensus 46 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~s~~~~~~~~~~~~~~~k~~~~~~~~~~~~----~~~~~c~~c~~~c~~ 121 (634)
T KOG1169|consen 46 VCCVCLWSEMAPSVDCDVDGGVSHEECVSGAASDCPLLVLLGFENQRHKTDGDHVWRPKHL----WKPAYCFVCPKSCGS 121 (634)
T ss_pred hhhhhhhcccccccceeccccchhhhhhcccccchHHHHHHHhhhhhhhccCceeccCCCC----CCCceEEeccccccc
Confidence 788887743334688999999999999875321 1122221 233333222 2356777776653
Q ss_pred C----ceeEEcCCCCcccccccccCCce--eee--CCCceeeEEeecCCccCCCCccceeccccccccc--CCcceeEEe
Q 040047 90 S----AFSFCCPLCDFDLHVQCAFLPEI--LIH--DSHFHSLNLSYALPAAHHYESSSYVCDICHKQLD--QKCFWSYNC 159 (240)
Q Consensus 90 ~----g~~Y~C~~C~f~lH~~Ca~lP~~--i~~--~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~--~~~~~~Y~C 159 (240)
. +..+.|.-|.+.+|..|...+.+ ... ..+--.+.+ ......+ ......|+.|.+.+. .+ ...++|
T Consensus 122 ~~~~~~~g~~C~~C~~~vh~~C~~~~~~~~~~~~~~~~~r~~v~--~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~c 197 (634)
T KOG1169|consen 122 CGVGIKQGLCCDWCGRTVHERCVRRADPECQCKCDLGRLRKIVL--DHPWVKG-NAGEAKCDQCLKSVKADQG-LTGPRC 197 (634)
T ss_pred hhhcccCceeeccccchHHHHHHhhcCcccccccccccccceee--cCccccc-ccCCccchhhhcccccccc-cccccc
Confidence 1 23489999999999999965322 111 000001111 1000000 124677888888643 23 458899
Q ss_pred CCCCeeeeccccc
Q 040047 160 FACNFHAHVSCTR 172 (240)
Q Consensus 160 ~~C~~~lH~~C~~ 172 (240)
.+|...+|..|..
T Consensus 198 ~~~~~~~h~~~~~ 210 (634)
T KOG1169|consen 198 GWCQIRVHDKCKS 210 (634)
T ss_pred ceeeeeeecchHH
Confidence 9999999999954
No 62
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=81.01 E-value=0.64 Score=42.32 Aligned_cols=43 Identities=23% Similarity=0.349 Sum_probs=29.6
Q ss_pred cceecccccccccCCcceeEEeCCCCeeeecccccCccccCCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNNSDSAKP 182 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~~~~~~p 182 (240)
+...|-+|+.... + ..+|+|..|.-.+++.|-.....+-+..|
T Consensus 329 ~~~~Cf~C~~~~~-~-~~~y~C~~Ck~~FCldCDv~iHesLh~Cp 371 (378)
T KOG2807|consen 329 GSRFCFACQGELL-S-SGRYRCESCKNVFCLDCDVFIHESLHNCP 371 (378)
T ss_pred CCcceeeeccccC-C-CCcEEchhccceeeccchHHHHhhhhcCC
Confidence 4456999954432 2 56999999998899888766555444444
No 63
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=80.96 E-value=0.89 Score=41.33 Aligned_cols=49 Identities=20% Similarity=0.375 Sum_probs=36.5
Q ss_pred CcccccccccCCCC-ceEeeCCC-CCcchhhhcccc--ccccCCCCCCcceEEeec
Q 040047 21 NEYSCSACELIISG-SAYGCWEC-KFFLHEQCGNAS--RAMQHTSHPMHHLTLVPT 72 (240)
Q Consensus 21 ~~~~C~~C~~~~~g-~~Y~C~~C-~f~lH~~Ca~~p--~~i~h~~Hp~H~L~l~~~ 72 (240)
.++-||.|...+.. .+-+|.+| +|||+..|+... ..+.||+| +.+....
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH---~YRiiet 56 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYH---GYRIIET 56 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCC---CeeEeec
Confidence 57899999888754 47999999 999999999753 33455565 5555443
No 64
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=80.22 E-value=0.95 Score=44.60 Aligned_cols=33 Identities=18% Similarity=0.494 Sum_probs=28.8
Q ss_pred CcccccccccCCCCceEeeCCCCCcchhhhccc
Q 040047 21 NEYSCSACELIISGSAYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 21 ~~~~C~~C~~~~~g~~Y~C~~C~f~lH~~Ca~~ 53 (240)
...+|+.|..+++-.+++|..|+|-+|+.|+..
T Consensus 188 ~~~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~ 220 (678)
T KOG0193|consen 188 PLAFCDSCCNKFLFTGFRCQTCGYKFHQSCSPR 220 (678)
T ss_pred chhhhhhhcchhhhcccccCCCCCccccccCCC
Confidence 678899887777767899999999999999975
No 65
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=79.79 E-value=1.6 Score=26.06 Aligned_cols=28 Identities=29% Similarity=0.606 Sum_probs=20.9
Q ss_pred ecccccccccCCcceeEEeCCCCeeeecc
Q 040047 141 VCDICHKQLDQKCFWSYNCFACNFHAHVS 169 (240)
Q Consensus 141 ~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~ 169 (240)
.|.+|.+..... ...|.|..|+..++..
T Consensus 2 rC~vC~~~k~rk-~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 2 RCKVCSKKKRRK-DTRYMCSKCDVPLCVE 29 (32)
T ss_pred CCeECCcCCccc-eeEEEccCCCCcccCC
Confidence 477888865443 4799999999887763
No 66
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=78.34 E-value=0.98 Score=44.64 Aligned_cols=94 Identities=17% Similarity=0.167 Sum_probs=60.0
Q ss_pred CccccccCCCCCceeEEcCCCCcccccccccCCcee---------eeCCCceeeEEeecCCccCCCCccceecccccccc
Q 040047 79 NFLCNACGEPGSAFSFCCPLCDFDLHVQCAFLPEIL---------IHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQL 149 (240)
Q Consensus 79 ~~~Cd~C~~~~~g~~Y~C~~C~f~lH~~Ca~lP~~i---------~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~ 149 (240)
...|..|..........|..|+..+|..|...-.+. .+..|.+.-..++.+. .......|.+|.+.+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~s~~~~~~~~~~~~~~~k~~~~~~~~~~----~~~~~~~c~~c~~~c 119 (634)
T KOG1169|consen 44 QMVCCVCLWSEMAPSVDCDVDGGVSHEECVSGAASDCPLLVLLGFENQRHKTDGDHVWRPK----HLWKPAYCFVCPKSC 119 (634)
T ss_pred hhhhhhhhhcccccccceeccccchhhhhhcccccchHHHHHHHhhhhhhhccCceeccCC----CCCCCceEEeccccc
Confidence 448999988555567889999999999998653321 1222322112222221 113567888888876
Q ss_pred cCCc---ceeEEeCCCCeeeecccccCccc
Q 040047 150 DQKC---FWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 150 ~~~~---~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
.... .-.+.|.+|++.+|..|......
T Consensus 120 ~~~~~~~~~g~~C~~C~~~vh~~C~~~~~~ 149 (634)
T KOG1169|consen 120 GSCGVGIKQGLCCDWCGRTVHERCVRRADP 149 (634)
T ss_pred cchhhcccCceeeccccchHHHHHHhhcCc
Confidence 4320 23599999999999999765543
No 67
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=77.87 E-value=1.7 Score=29.19 Aligned_cols=33 Identities=24% Similarity=0.471 Sum_probs=29.2
Q ss_pred CCccccccCCCC--CceeEEcCCCCcccccccccC
Q 040047 78 GNFLCNACGEPG--SAFSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~--~g~~Y~C~~C~f~lH~~Ca~l 110 (240)
....|.+||+.+ ......|.+|+--.|..|...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 357899999999 578999999999999999854
No 68
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=77.52 E-value=0.81 Score=42.38 Aligned_cols=34 Identities=29% Similarity=0.722 Sum_probs=30.3
Q ss_pred CcccccccccCCCCc---eEeeCCCCCcchhhhcccc
Q 040047 21 NEYSCSACELIISGS---AYGCWECKFFLHEQCGNAS 54 (240)
Q Consensus 21 ~~~~C~~C~~~~~g~---~Y~C~~C~f~lH~~Ca~~p 54 (240)
....|..|...|||. +|+|..|.+.+|++|-.+.
T Consensus 140 rr~~c~ic~d~iwglgrqgyrcinckl~vhkkch~~v 176 (593)
T KOG0695|consen 140 RRAYCGICSDRIWGLGRQGYRCINCKLLVHKKCHGLV 176 (593)
T ss_pred cceeeeechhhhhhcccccceeecceeehhhhhcccc
Confidence 678999999999986 6999999999999998753
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.45 E-value=2.8 Score=32.48 Aligned_cols=32 Identities=22% Similarity=0.676 Sum_probs=25.1
Q ss_pred CccccccCCCCC------------ceeEEcCCCCcccccccccC
Q 040047 79 NFLCNACGEPGS------------AFSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 79 ~~~Cd~C~~~~~------------g~~Y~C~~C~f~lH~~Ca~l 110 (240)
...|-+|...+. ..+|.|..|.-+++..|-..
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~f 98 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVF 98 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchh
Confidence 457999988542 34799999999999998653
No 70
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=77.16 E-value=1.5 Score=43.68 Aligned_cols=90 Identities=23% Similarity=0.417 Sum_probs=64.1
Q ss_pred CCcccccccccCCCCceEeeCCCCCc------------chhhhccccccccCC-CCCCcceEEeeccCCCCCCccccccC
Q 040047 20 GNEYSCSACELIISGSAYGCWECKFF------------LHEQCGNASRAMQHT-SHPMHHLTLVPTTTYSAGNFLCNACG 86 (240)
Q Consensus 20 ~~~~~C~~C~~~~~g~~Y~C~~C~f~------------lH~~Ca~~p~~i~h~-~Hp~H~L~l~~~~~~~~~~~~Cd~C~ 86 (240)
..+|+|.-|...---.+++|..|-|. -|.-||.+-++++.. .|-.-|..|...|. +.-...|-+|.
T Consensus 46 tGpWfCrKCesqeraarvrCeLCP~kdGALKkTDn~GWAHVVCALYIPEVrFgNV~TMEPIiLq~VP~-dRfnKtCYIC~ 124 (900)
T KOG0956|consen 46 TGPWFCRKCESQERAARVRCELCPHKDGALKKTDNGGWAHVVCALYIPEVRFGNVHTMEPIILQDVPH-DRFNKTCYICN 124 (900)
T ss_pred CCchhhhhhhhhhhhccceeecccCcccceecccCCCceEEEEEeeccceeecccccccceeeccCch-hhhcceeeeec
Confidence 48899999977644558999999653 588899976666643 45445666665553 23467899998
Q ss_pred CCC------CceeEEcCC--CCcccccccccC
Q 040047 87 EPG------SAFSFCCPL--CDFDLHVQCAFL 110 (240)
Q Consensus 87 ~~~------~g~~Y~C~~--C~f~lH~~Ca~l 110 (240)
+.+ .|--..|.. |.-.+|..||..
T Consensus 125 E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~ 156 (900)
T KOG0956|consen 125 EEGRPNKAAKGACMTCNKSGCKQAFHVTCAQR 156 (900)
T ss_pred ccCCccccccccceecccccchhhhhhhHhhh
Confidence 875 245566764 888899999964
No 71
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=77.11 E-value=1.4 Score=40.19 Aligned_cols=89 Identities=26% Similarity=0.513 Sum_probs=49.3
Q ss_pred CCcccccccccCCCCceEeeCCCCCcc------hhhhcccc---ccccCCCCCCcceEE---eeccCCCCCCccccccCC
Q 040047 20 GNEYSCSACELIISGSAYGCWECKFFL------HEQCGNAS---RAMQHTSHPMHHLTL---VPTTTYSAGNFLCNACGE 87 (240)
Q Consensus 20 ~~~~~C~~C~~~~~g~~Y~C~~C~f~l------H~~Ca~~p---~~i~h~~Hp~H~L~l---~~~~~~~~~~~~Cd~C~~ 87 (240)
+.+..| +|-..+.|.+|.|.+|.--+ +..|...- ..+.-.+|.--||+- ++...+ .+...|-+|+.
T Consensus 261 ~~ps~C-~CH~~~~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~-~~~~~Cf~C~~ 338 (378)
T KOG2807|consen 261 DTPSFC-ACHSELSGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEY-NGSRFCFACQG 338 (378)
T ss_pred cCcchh-eeccccccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhcccccc-CCCcceeeecc
Confidence 345555 35566677789999886433 33333211 111112221113332 111121 24566999944
Q ss_pred -CCCceeEEcCCCCcccccccccC
Q 040047 88 -PGSAFSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 88 -~~~g~~Y~C~~C~f~lH~~Ca~l 110 (240)
...+.+|+|..|.-.++..|-.+
T Consensus 339 ~~~~~~~y~C~~Ck~~FCldCDv~ 362 (378)
T KOG2807|consen 339 ELLSSGRYRCESCKNVFCLDCDVF 362 (378)
T ss_pred ccCCCCcEEchhccceeeccchHH
Confidence 44578999999998888888643
No 72
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=76.50 E-value=2.3 Score=28.66 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=30.6
Q ss_pred CcccccccccCC--CCceEeeCCCCCcchhhhcccccc
Q 040047 21 NEYSCSACELII--SGSAYGCWECKFFLHEQCGNASRA 56 (240)
Q Consensus 21 ~~~~C~~C~~~~--~g~~Y~C~~C~f~lH~~Ca~~p~~ 56 (240)
....|..|++++ .+..-.|..|+--.|..|.+....
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~ 41 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGG 41 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCc
Confidence 568999999998 556899999999999999985433
No 73
>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=75.37 E-value=1.5 Score=29.14 Aligned_cols=30 Identities=27% Similarity=0.566 Sum_probs=18.4
Q ss_pred cccccccCCCC--------ceEeeCCCCCcchhhhccc
Q 040047 24 SCSACELIISG--------SAYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 24 ~C~~C~~~~~g--------~~Y~C~~C~f~lH~~Ca~~ 53 (240)
.|.||..++.. .+|+|..|.-+++..|--+
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~f 38 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVF 38 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHHHT
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcChh
Confidence 37889887744 4799999998888888664
No 74
>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 KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=73.51 E-value=0.24 Score=46.51 Aligned_cols=32 Identities=22% Similarity=0.333 Sum_probs=24.8
Q ss_pred CcccccccccCCCCceEeeCCCCCcchhhhcc
Q 040047 21 NEYSCSACELIISGSAYGCWECKFFLHEQCGN 52 (240)
Q Consensus 21 ~~~~C~~C~~~~~g~~Y~C~~C~f~lH~~Ca~ 52 (240)
...+|-+|.+.|+|..-.|.-=|-.+|..|+.
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFt 304 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFT 304 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhccccee
Confidence 44599999999998877777666777777765
No 76
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=73.43 E-value=2 Score=40.47 Aligned_cols=33 Identities=33% Similarity=0.784 Sum_probs=29.2
Q ss_pred CCccccccCCCCCcee-EEcCCC-CcccccccccC
Q 040047 78 GNFLCNACGEPGSAFS-FCCPLC-DFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~~g~~-Y~C~~C-~f~lH~~Ca~l 110 (240)
+.+.|+.|...+.+.. .+|.+| +||||..|...
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~ 47 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSV 47 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhc
Confidence 5789999999998765 999999 69999999865
No 77
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=71.92 E-value=1.3 Score=40.67 Aligned_cols=33 Identities=30% Similarity=0.653 Sum_probs=29.5
Q ss_pred Cccccccc-ccCCCCceEeeCCC-CCcchhhhccc
Q 040047 21 NEYSCSAC-ELIISGSAYGCWEC-KFFLHEQCGNA 53 (240)
Q Consensus 21 ~~~~C~~C-~~~~~g~~Y~C~~C-~f~lH~~Ca~~ 53 (240)
-+..|+.| .+++-|++|+|..| ++.++..|.-.
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwr 273 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWR 273 (434)
T ss_pred CCccCcceecccccchhhhHhhcCCccccchhhcc
Confidence 67899999 66788999999999 89999999864
No 78
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=71.86 E-value=3.7 Score=43.09 Aligned_cols=133 Identities=19% Similarity=0.254 Sum_probs=77.5
Q ss_pred CCcccccccccCCC---CceEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCCCce----
Q 040047 20 GNEYSCSACELIIS---GSAYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPGSAF---- 92 (240)
Q Consensus 20 ~~~~~C~~C~~~~~---g~~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~g~---- 92 (240)
+..-.|..|.+--. ...-.|..||..+|..|...|. . ..+.|.|--|...-.+.
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~-----i--------------peg~WlCr~Cl~s~~~~v~c~ 277 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPF-----I--------------PEGQWLCRRCLQSPQRPVRCL 277 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCCCcchhhhhccCCCC-----C--------------CCCcEeehhhccCcCcccceE
Confidence 47789999977542 3468999999999999998321 1 12445555554432222
Q ss_pred -------eEEcCCCCcccccccccCCceeeeCCCceeeEEeecCCccCCCCccceecccccccccCCcceeEEeC--CCC
Q 040047 93 -------SFCCPLCDFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQLDQKCFWSYNCF--ACN 163 (240)
Q Consensus 93 -------~Y~C~~C~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~~~~~~~Y~C~--~C~ 163 (240)
.|.=+.=+-..|..||.+-..+.. .+.+.+..+..-..+ +.....+.|-+|..... +..-+|. .|.
T Consensus 278 ~cp~~~gAFkqt~dgrw~Hv~caiwipev~F-~nt~~~E~I~~i~~i-~~aRwkL~cy~cK~~~~---gaciqcs~~~c~ 352 (1051)
T KOG0955|consen 278 LCPSKGGAFKQTDDGRWAHVVCAIWIPEVSF-ANTVFLEPIDSIENI-PPARWKLTCYICKQKGL---GACIQCSKANCY 352 (1051)
T ss_pred eccCCCCcceeccCCceeeeehhhccccccc-ccchhhccccchhcC-cHhhhhceeeeeccCCC---Ccceecchhhhh
Confidence 222223345689999875333221 111222222211000 00124678999999863 3466776 588
Q ss_pred eeeecccccCccc
Q 040047 164 FHAHVSCTRNRNN 176 (240)
Q Consensus 164 ~~lH~~C~~~~~~ 176 (240)
-.+|+.|+....-
T Consensus 353 ~a~hvtca~~agl 365 (1051)
T KOG0955|consen 353 TAFHVTCARRAGL 365 (1051)
T ss_pred hhhhhhhHhhcCc
Confidence 8999999876554
No 79
>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 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=69.42 E-value=4.2 Score=22.77 Aligned_cols=20 Identities=50% Similarity=1.271 Sum_probs=13.6
Q ss_pred ccccCCCC----CceeEEcCCCCc
Q 040047 82 CNACGEPG----SAFSFCCPLCDF 101 (240)
Q Consensus 82 Cd~C~~~~----~g~~Y~C~~C~f 101 (240)
|..|+..+ .+..|.|..|++
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 55676654 256788888875
No 81
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.49 E-value=2.8 Score=32.44 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=24.6
Q ss_pred cccccccccCCCC------------ceEeeCCCCCcchhhhccc
Q 040047 22 EYSCSACELIISG------------SAYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 22 ~~~C~~C~~~~~g------------~~Y~C~~C~f~lH~~Ca~~ 53 (240)
...|.+|..++.. .+|.|..|.-+++..|--+
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~f 98 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVF 98 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchh
Confidence 3569999886532 3799999998888888763
No 82
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=68.01 E-value=4 Score=37.25 Aligned_cols=46 Identities=17% Similarity=0.418 Sum_probs=35.4
Q ss_pred cceecccccccccCCcceeEEeCCC-CeeeecccccCccccCCCCCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFAC-NFHAHVSCTRNRNNSDSAKPEPN 185 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C-~~~lH~~C~~~~~~~~~~~p~~~ 185 (240)
..+-|++|...+.. ..+-+|.+| +|++++.|........+-.|+.+
T Consensus 4 ~k~hCdvC~~d~T~--~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~ 50 (432)
T COG5114 4 VKIHCDVCFLDMTD--LTFIKCNECPAVDLCLPCFVNGIETGVHSPYHG 50 (432)
T ss_pred ceeeehHHHHhhhc--ceeeeeecccccceehhhhhccccccccCCCCC
Confidence 56889999998864 578899999 99999999887766433344433
No 83
>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=65.56 E-value=2.3 Score=27.04 Aligned_cols=31 Identities=23% Similarity=0.599 Sum_probs=18.6
Q ss_pred cccccccccCCcceeEEeC--CCCeeeecccccCccc
Q 040047 142 CDICHKQLDQKCFWSYNCF--ACNFHAHVSCTRNRNN 176 (240)
Q Consensus 142 C~vC~~~~~~~~~~~Y~C~--~C~~~lH~~C~~~~~~ 176 (240)
|.+|.+.+ .++.+|. .|+..+|..|+.....
T Consensus 1 C~~C~~iv----~~G~~C~~~~C~~r~H~~C~~~y~r 33 (43)
T PF08746_consen 1 CEACKEIV----TQGQRCSNRDCNVRLHDDCFKKYFR 33 (43)
T ss_dssp -TTT-SB-----SSSEE-SS--S--EE-HHHHHHHTT
T ss_pred CcccchhH----eeeccCCCCccCchHHHHHHHHHHh
Confidence 67888876 5789999 6999999999876554
No 84
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=65.35 E-value=4.6 Score=29.87 Aligned_cols=33 Identities=21% Similarity=0.529 Sum_probs=26.8
Q ss_pred CCcccccccccCCCCceEeeCCCCCcchhhhcc
Q 040047 20 GNEYSCSACELIISGSAYGCWECKFFLHEQCGN 52 (240)
Q Consensus 20 ~~~~~C~~C~~~~~g~~Y~C~~C~f~lH~~Ca~ 52 (240)
+....|..|++++....|.=..|+-.+|..|+.
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 366789999999876666666788999999975
No 85
>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=63.67 E-value=1.9 Score=33.46 Aligned_cols=57 Identities=25% Similarity=0.642 Sum_probs=39.1
Q ss_pred CCccccccCCCC---CceeEEcCCCCcccccccccCCceeeeCCCceeeEEeecCCccCCCCccceeccccccccc----
Q 040047 78 GNFLCNACGEPG---SAFSFCCPLCDFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQLD---- 150 (240)
Q Consensus 78 ~~~~Cd~C~~~~---~g~~Y~C~~C~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~---- 150 (240)
+...|..|+... .+..-.|.+|...++..|... .. ....|.|.+|.+.-.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~-----------------~~------~~~~WlC~vC~k~rel~~~ 109 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY-----------------SK------KEPIWLCKVCQKQRELKKK 109 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE-----------------TS------SSCCEEEHHHHHHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc-----------------CC------CCCCEEChhhHHHHHHHHH
Confidence 567999999864 244588999999999999653 11 125799999999532
Q ss_pred CCcceeEE
Q 040047 151 QKCFWSYN 158 (240)
Q Consensus 151 ~~~~~~Y~ 158 (240)
++ .|+|.
T Consensus 110 sG-~Wf~~ 116 (118)
T PF02318_consen 110 SG-EWFYE 116 (118)
T ss_dssp CS-HHHHC
T ss_pred hh-hHHhc
Confidence 33 67763
No 86
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=63.62 E-value=5.3 Score=24.62 Aligned_cols=31 Identities=23% Similarity=0.268 Sum_probs=24.1
Q ss_pred ceecccccccccCCcceeEEeCCCCeeeecccccCc
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNR 174 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~ 174 (240)
...|..+++. ...|+|..|+..++..|+...
T Consensus 3 ~~~C~~H~~~-----~~~~~C~~C~~~~C~~C~~~~ 33 (42)
T PF00643_consen 3 EPKCPEHPEE-----PLSLFCEDCNEPLCSECTVSG 33 (42)
T ss_dssp SSB-SSTTTS-----BEEEEETTTTEEEEHHHHHTS
T ss_pred CccCccCCcc-----ceEEEecCCCCccCccCCCCC
Confidence 3567777764 469999999999999998664
No 87
>PHA00369 H minor spike protein
Probab=62.72 E-value=8.3 Score=33.68 Aligned_cols=20 Identities=35% Similarity=0.556 Sum_probs=16.1
Q ss_pred chhhhHHHHHHHHHHHHHHH
Q 040047 207 TEIEDPVLEAQLELQRLQLE 226 (240)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~ 226 (240)
..++++-+..|.||.+||+.
T Consensus 140 AGm~~ag~~~QKEl~kMQLD 159 (325)
T PHA00369 140 AGMEDAGFNNQKELTKMQLD 159 (325)
T ss_pred ccchhhhhhhHHHHHHHhhc
Confidence 37788888888888888875
No 88
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=62.09 E-value=7.6 Score=28.67 Aligned_cols=31 Identities=32% Similarity=0.780 Sum_probs=22.4
Q ss_pred ceecccccccccCCcceeEEeCCCCeeeeccccc
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTR 172 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~ 172 (240)
...|.+|++.+..+ . +.=-.||-.+|..|+.
T Consensus 78 ~~~C~vC~k~l~~~-~--f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNS-V--FVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCc-e--EEEeCCCeEEeccccc
Confidence 46799999998754 2 2222557889999975
No 89
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=59.10 E-value=5.4 Score=24.39 Aligned_cols=20 Identities=20% Similarity=0.491 Sum_probs=13.8
Q ss_pred eeEEcCCCCcccccccccCC
Q 040047 92 FSFCCPLCDFDLHVQCAFLP 111 (240)
Q Consensus 92 ~~Y~C~~C~f~lH~~Ca~lP 111 (240)
..+.|..|++.+|..|....
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~ 22 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVS 22 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-S
T ss_pred ceEEeCCCCCcCChhhCCcc
Confidence 46789999999999998765
No 90
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=58.71 E-value=2.7 Score=37.76 Aligned_cols=71 Identities=21% Similarity=0.345 Sum_probs=49.3
Q ss_pred eEEcCCCCcccccccccCCceeeeCCCceeeEEeecCCccCCCCccceecccccccccCCcceeEEeCCCCeeeeccccc
Q 040047 93 SFCCPLCDFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTR 172 (240)
Q Consensus 93 ~Y~C~~C~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~ 172 (240)
.-.|..|....|+.|..++..+.. +.-++.... ..-..|.+|+++... .-...|..||-..|.-|+.
T Consensus 279 ~I~C~~C~~~~HP~Ci~M~~elv~------~~KTY~W~C-----~~C~lC~IC~~P~~E--~E~~FCD~CDRG~HT~CVG 345 (381)
T KOG1512|consen 279 WIVCKPCATRPHPYCVAMIPELVG------QYKTYFWKC-----SSCELCRICLGPVIE--SEHLFCDVCDRGPHTLCVG 345 (381)
T ss_pred ceeecccccCCCCcchhcCHHHHh------HHhhcchhh-----cccHhhhccCCcccc--hheeccccccCCCCccccc
Confidence 468999999999999998865431 111121100 134578888887643 3578899999999999998
Q ss_pred Cccc
Q 040047 173 NRNN 176 (240)
Q Consensus 173 ~~~~ 176 (240)
+...
T Consensus 346 L~~l 349 (381)
T KOG1512|consen 346 LQDL 349 (381)
T ss_pred cccc
Confidence 7664
No 91
>PF12773 DZR: Double zinc ribbon
Probab=57.97 E-value=9.2 Score=24.53 Aligned_cols=21 Identities=29% Similarity=0.806 Sum_probs=11.7
Q ss_pred CccccccCCCCCceeEEcCCC
Q 040047 79 NFLCNACGEPGSAFSFCCPLC 99 (240)
Q Consensus 79 ~~~Cd~C~~~~~g~~Y~C~~C 99 (240)
...|..|+..+....-.|..|
T Consensus 29 ~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 29 KKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred CCCCcCCcCCCcCCcCccCcc
Confidence 456666766654444445554
No 92
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=57.83 E-value=4.4 Score=27.81 Aligned_cols=22 Identities=36% Similarity=0.804 Sum_probs=16.7
Q ss_pred ceecccccccccCCcceeEEeCCCCee
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFH 165 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~ 165 (240)
-++|.-|++. +..|+|..|||.
T Consensus 38 I~Rc~~CRk~-----g~~Y~Cp~CGF~ 59 (61)
T COG2888 38 IYRCAKCRKL-----GNPYRCPKCGFE 59 (61)
T ss_pred eehhhhHHHc-----CCceECCCcCcc
Confidence 3567777776 458999999984
No 93
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=56.38 E-value=5.3 Score=27.36 Aligned_cols=21 Identities=43% Similarity=1.028 Sum_probs=16.1
Q ss_pred eecccccccccCCcceeEEeCCCCee
Q 040047 140 YVCDICHKQLDQKCFWSYNCFACNFH 165 (240)
Q Consensus 140 ~~C~vC~~~~~~~~~~~Y~C~~C~~~ 165 (240)
++|.-|++. +..|.|..|||.
T Consensus 37 ~RC~~CRk~-----~~~Y~CP~CGF~ 57 (59)
T PRK14890 37 YRCEKCRKQ-----SNPYTCPKCGFE 57 (59)
T ss_pred eechhHHhc-----CCceECCCCCCc
Confidence 567777776 458999999984
No 94
>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=55.52 E-value=13 Score=25.52 Aligned_cols=38 Identities=24% Similarity=0.398 Sum_probs=23.2
Q ss_pred cceecccccccccCCcceeEEeCCCCeeeecccccCccc
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
....|.+|++..+.- ...+.|..||-.++..|......
T Consensus 8 ~~~~C~~C~~~F~~~-~rrhhCr~CG~~vC~~Cs~~~~~ 45 (69)
T PF01363_consen 8 EASNCMICGKKFSLF-RRRHHCRNCGRVVCSSCSSQRIP 45 (69)
T ss_dssp G-SB-TTT--B-BSS-S-EEE-TTT--EEECCCS-EEEE
T ss_pred CCCcCcCcCCcCCCc-eeeEccCCCCCEECCchhCCEEc
Confidence 567899999998644 67999999999999999876664
No 95
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=55.43 E-value=5.5 Score=28.83 Aligned_cols=33 Identities=21% Similarity=0.579 Sum_probs=15.4
Q ss_pred CCccccccCCCC----Cc-eeEEcCCCCcccccccccC
Q 040047 78 GNFLCNACGEPG----SA-FSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~----~g-~~Y~C~~C~f~lH~~Ca~l 110 (240)
....|.+||..+ .| .+-.|.+|.|-++..|...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEY 45 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEY 45 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHH
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHH
Confidence 467999999976 23 5678999999999999754
No 96
>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=54.13 E-value=7.1 Score=22.15 Aligned_cols=23 Identities=30% Similarity=0.852 Sum_probs=17.5
Q ss_pred cccccCCCCCceeEEcCCCCccc
Q 040047 81 LCNACGEPGSAFSFCCPLCDFDL 103 (240)
Q Consensus 81 ~Cd~C~~~~~g~~Y~C~~C~f~l 103 (240)
.|-.|+..+....-.|..|++++
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 57888888876666788888764
No 97
>KOG0694 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=54.13 E-value=4.2 Score=40.60 Aligned_cols=97 Identities=18% Similarity=0.320 Sum_probs=59.4
Q ss_pred CccccccCCCCCc---eeEEcCCCCcccccccccCCc---eeeeC-C--CceeeE-EeecCCcc--CCCCccceeccccc
Q 040047 79 NFLCNACGEPGSA---FSFCCPLCDFDLHVQCAFLPE---ILIHD-S--HFHSLN-LSYALPAA--HHYESSSYVCDICH 146 (240)
Q Consensus 79 ~~~Cd~C~~~~~g---~~Y~C~~C~f~lH~~Ca~lP~---~i~~~-~--H~H~L~-l~~~~~~~--~~~~~~~~~C~vC~ 146 (240)
...|..|.+-+.| -.|.|..|.+++|..|..+-- ..... . .+-.+. +.+..++. .-......+|+-|+
T Consensus 169 pt~Cs~C~kFi~gL~kqGyQCqvC~~vvHKkCh~kvv~~C~~~~~~n~e~q~~~~~~~~~~Phrf~~~~~q~ptFc~hCG 248 (694)
T KOG0694|consen 169 PTFCSWCQKFIWGLRKQGYQCQVCWRVVHKKCHVKVVTLCDFLDNLNSEPQGFLFEFTFRNPHRFVKLNRQRPTFCDHCG 248 (694)
T ss_pred cchhhhhhhheeccCCCceEEeeeeehHhhhhHHHHHHhccCcCccCcCCccccccccccCCCcchhhhccCccHHHhcc
Confidence 6789999997754 369999999999999985310 00000 0 000001 11111000 00013457899999
Q ss_pred ccccCCcceeEEeCCCCeeeecccccCcc
Q 040047 147 KQLDQKCFWSYNCFACNFHAHVSCTRNRN 175 (240)
Q Consensus 147 ~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~ 175 (240)
............|..|+...|.+|+....
T Consensus 249 s~L~r~~qqGlkCs~Cg~n~H~~c~~~va 277 (694)
T KOG0694|consen 249 SVLYRLRQQGLKCSTCGRNVHNRCVENLA 277 (694)
T ss_pred hhhhhhcccCeeehhhhccccHHHHHhcc
Confidence 97653224688999999999999975444
No 98
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=54.04 E-value=7.6 Score=23.78 Aligned_cols=27 Identities=19% Similarity=0.328 Sum_probs=19.6
Q ss_pred ceecccccccccCCcceeEEeCCCCee
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFH 165 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~ 165 (240)
...|.+|+..........|+|..|+..
T Consensus 8 ~~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCeEeEccCCEEEhhhCceE
Confidence 456999999743222569999999864
No 99
>PF04687 Microvir_H: Microvirus H protein (pilot protein); InterPro: IPR006777 Bacteriophage PhiX174 is one of the simplest viruses, having a single-stranded, closed circular DNA of 5386 nucleotide bases and four capsid proteins, J, F, G and H. A single molecule of H protein is found on each of the 12 spikes on the microvirus shell of the bacteriophage. H is involved in the ejection of the phage DNA, and at least one copy is injected into the hosts periplasmic space along with the ssDNA viral genome []. Part of H is thought to lie outside the shell, where it recognises lipopolysaccharide from virus-sensitive bacterial strains []. Part of H may lie within the capsid, since mutations in H can influence the DNA ejection mechanism by affecting the DNA-protein interactions []. H may span the capsid through the hydrophilic channels formed by G proteins [].; GO: 0016032 viral reproduction, 0019028 viral capsid
Probab=53.58 E-value=15 Score=32.12 Aligned_cols=19 Identities=37% Similarity=0.588 Sum_probs=14.9
Q ss_pred hhhhHHHHHHHHHHHHHHH
Q 040047 208 EIEDPVLEAQLELQRLQLE 226 (240)
Q Consensus 208 ~~~~~~~~~~~~~~~~~~~ 226 (240)
.++++-++.|.||.||||.
T Consensus 125 gm~~ag~~~qkel~kmqld 143 (310)
T PF04687_consen 125 GMEDAGFQNQKELTKMQLD 143 (310)
T ss_pred cccccchhhHHHHHHHhhh
Confidence 6777778888888888875
No 100
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=53.38 E-value=6.1 Score=38.20 Aligned_cols=55 Identities=20% Similarity=0.464 Sum_probs=40.0
Q ss_pred CCccccccCCCCC-ceeEEcCCCCcccccccccCCceeeeCCCceeeEEeecCCccCCCCccceeccccccc
Q 040047 78 GNFLCNACGEPGS-AFSFCCPLCDFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQ 148 (240)
Q Consensus 78 ~~~~Cd~C~~~~~-g~~Y~C~~C~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~ 148 (240)
-.+.|.+|++.-. .+...|..|++..|..|...|.+ -.+.. ....+|.|.-|++.
T Consensus 543 ~~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLT-----------R~Pkk-----~kn~gWqCsECdk~ 598 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLT-----------RLPKK-----NKNFGWQCSECDKN 598 (707)
T ss_pred cceeeeeeccchhhHHHhhcchhhceeeccccCCccc-----------cCccc-----ccCcceeecccccc
Confidence 4789999999764 67789999999999999886633 11111 11357889999664
No 101
>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=53.16 E-value=9 Score=22.45 Aligned_cols=23 Identities=30% Similarity=0.823 Sum_probs=15.3
Q ss_pred ccccccCCCCCceeEEcCCCCccccc
Q 040047 80 FLCNACGEPGSAFSFCCPLCDFDLHV 105 (240)
Q Consensus 80 ~~Cd~C~~~~~g~~Y~C~~C~f~lH~ 105 (240)
..|.+|+. ...|.|..|+..++.
T Consensus 3 ~~C~vC~~---~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN---PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS---EESEE-TTT--EESS
T ss_pred CCCccCcC---CCEEECCCcCCceeC
Confidence 57999997 556999999877653
No 102
>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=52.67 E-value=21 Score=22.31 Aligned_cols=36 Identities=14% Similarity=0.222 Sum_probs=22.4
Q ss_pred ecccccccc---cCCcceeEEeCCCCeeeecccccCcccc
Q 040047 141 VCDICHKQL---DQKCFWSYNCFACNFHAHVSCTRNRNNS 177 (240)
Q Consensus 141 ~C~vC~~~~---~~~~~~~Y~C~~C~~~lH~~C~~~~~~~ 177 (240)
+|..|+... +.. ..-+.|..||..+...=+.....|
T Consensus 2 ~Cp~Cg~~~~~~D~~-~g~~vC~~CG~Vl~e~~i~~~~e~ 40 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPE-RGELVCPNCGLVLEENIIDEGPEW 40 (43)
T ss_dssp SBTTTSSSEEEEETT-TTEEEETTT-BBEE-TTBSCCCSC
T ss_pred CCcCCcCCceEEcCC-CCeEECCCCCCEeecccccCCccc
Confidence 567777752 222 457788888888887766666655
No 103
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=52.17 E-value=7.3 Score=38.63 Aligned_cols=32 Identities=22% Similarity=0.575 Sum_probs=26.0
Q ss_pred CccccccCCCCCceeEEcCCCCcccccccccC
Q 040047 79 NFLCNACGEPGSAFSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 79 ~~~Cd~C~~~~~g~~Y~C~~C~f~lH~~Ca~l 110 (240)
...|+.|...+.--.++|..|+|.+|..|+..
T Consensus 189 ~~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~ 220 (678)
T KOG0193|consen 189 LAFCDSCCNKFLFTGFRCQTCGYKFHQSCSPR 220 (678)
T ss_pred hhhhhhhcchhhhcccccCCCCCccccccCCC
Confidence 56888777776555589999999999999953
No 104
>KOG2996 consensus Rho guanine nucleotide exchange factor VAV3 [Signal transduction mechanisms]
Probab=48.37 E-value=7.2 Score=38.47 Aligned_cols=42 Identities=26% Similarity=0.735 Sum_probs=33.9
Q ss_pred CCCeeeeecCCCcccccccccCCCCc---eEeeCCCCCcchhhhccc
Q 040047 10 HNLRIYQVQHGNEYSCSACELIISGS---AYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 10 H~L~l~~~~~~~~~~C~~C~~~~~g~---~Y~C~~C~f~lH~~Ca~~ 53 (240)
|.+...+.. ....|++|...+-|. +|.|..|+-+.|+.|...
T Consensus 524 H~fqmhtF~--~~tsCkvC~mllrGtfYQGY~C~~c~~~ahkecl~~ 568 (865)
T KOG2996|consen 524 HDFQMHTFK--NTTSCKVCQMLLRGTFYQGYKCEKCGADAHKECLGR 568 (865)
T ss_pred cceEEEecc--CCcchHHHHHHhhhhhhcceeeeeccccHHHHhccC
Confidence 555555543 789999998877664 799999999999999874
No 105
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=47.84 E-value=24 Score=34.92 Aligned_cols=92 Identities=14% Similarity=0.097 Sum_probs=50.6
Q ss_pred ccceecccccccccCC-cceeEEeCCCCeeeecccccCccc---------cCCCCCCCChhhhhhhhhhcCC-CCCCCCc
Q 040047 137 SSSYVCDICHKQLDQK-CFWSYNCFACNFHAHVSCTRNRNN---------SDSAKPEPNSAAYQKEESASGS-SQQNQTE 205 (240)
Q Consensus 137 ~~~~~C~vC~~~~~~~-~~~~Y~C~~C~~~lH~~C~~~~~~---------~~~~~p~~~~~~~~~~~~~~~~-~~~~~~~ 205 (240)
.-+++|.+|+..+++. -.+.=.|..+|.++|..|...... ||.- +++-+...+..-++--. -..|+-.
T Consensus 338 aQ~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~~~svIPARVl~~WDf~-~y~Vs~~a~~~L~~ir~~Pl~~~q~ 416 (580)
T KOG1829|consen 338 AQNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQNDKSVIPARVLHNWDFT-KYPVSNFAKQFLDEIREQPLFNLQD 416 (580)
T ss_pred ccCceecccCCCcccccccchhHhhhhhhhhCchhcccCcccccccceecccCc-ccccchhHHHHHHHHhccchhhhcc
Confidence 3578999999998743 134446777788888888655443 5522 33333222222211111 2333334
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHH
Q 040047 206 RTEIEDPVLEAQLELQRLQLEMQM 229 (240)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~ 229 (240)
.++.+..-.++-.+++++|+.++.
T Consensus 417 ln~~Ly~~~~~L~~v~~lR~qL~~ 440 (580)
T KOG1829|consen 417 LNPDLYSKVKALAEVKELRQQLQH 440 (580)
T ss_pred cChHHHhhhHHHHHHHHHHHHHHH
Confidence 445555555666666666666544
No 106
>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=47.45 E-value=14 Score=25.30 Aligned_cols=33 Identities=21% Similarity=0.334 Sum_probs=19.5
Q ss_pred CCccccccCCCCC--ceeEEcCCCCcccccccccC
Q 040047 78 GNFLCNACGEPGS--AFSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~~--g~~Y~C~~C~f~lH~~Ca~l 110 (240)
....|..|++.+. ...++|..|+-.++..|...
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 4678999999874 56799999999999999853
No 107
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=47.23 E-value=18 Score=27.54 Aligned_cols=35 Identities=20% Similarity=0.479 Sum_probs=22.8
Q ss_pred ceecccccccccCCcceeEEeCCCCeeeecccccCccc
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
.|+|.+|++++..+-.+-|.-. -.+|-.|......
T Consensus 2 kWkC~iCg~~I~~gqlFTF~~k---G~VH~~C~~~~~~ 36 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFTKK---GPVHYECFREKAS 36 (101)
T ss_pred ceEEEecCCeeeecceEEEecC---CcEeHHHHHHHHh
Confidence 4899999999864312333333 4599999765544
No 108
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=46.83 E-value=7 Score=28.28 Aligned_cols=39 Identities=26% Similarity=0.508 Sum_probs=18.9
Q ss_pred CcccccccccCC----CCc-eEeeCCCCCcchhhhccccccccC
Q 040047 21 NEYSCSACELII----SGS-AYGCWECKFFLHEQCGNASRAMQH 59 (240)
Q Consensus 21 ~~~~C~~C~~~~----~g~-~Y~C~~C~f~lH~~Ca~~p~~i~h 59 (240)
..-.|..|+..+ .|. +-.|.+|+|-+++.|.+.-++.-.
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~ 51 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGN 51 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCc
Confidence 467899998875 343 578999999999999997655433
No 109
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=46.52 E-value=3.7 Score=28.05 Aligned_cols=58 Identities=26% Similarity=0.575 Sum_probs=31.6
Q ss_pred ccccccCCCCceEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCC
Q 040047 25 CSACELIISGSAYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEP 88 (240)
Q Consensus 25 C~~C~~~~~g~~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~ 88 (240)
|..|+.. .+..|-|..|++..+..=.. .-...|..-.+|+|.+...+ +...|-.|+..
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~~~~-~Ha~~H~~~~~H~l~v~~~~----~~i~C~~C~~~ 58 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGRYSN-GHALKHYKETGHPLAVSLST----GSIWCYACDDY 58 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETTTST-SHHHHHHHHHT--EEEETTT----TCEEETTTTEE
T ss_pred CCCCCCc-CCceEEeCCCCcccccCCcC-cHHHHhhcccCCeEEEECCC----CeEEEcCCCcE
Confidence 6677766 55679999999888763111 01123333336888876442 35677777654
No 110
>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 KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=44.11 E-value=8.6 Score=34.62 Aligned_cols=82 Identities=20% Similarity=0.242 Sum_probs=53.6
Q ss_pred CcccccccccC----CCCc---eEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCC-Cce
Q 040047 21 NEYSCSACELI----ISGS---AYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPG-SAF 92 (240)
Q Consensus 21 ~~~~C~~C~~~----~~g~---~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~-~g~ 92 (240)
..-.|..|... +.|. ...|..|.-..|..|.+.+..+..-.- --++.- ..=..|.+|+... ..-
T Consensus 257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~K-TY~W~C-------~~C~lC~IC~~P~~E~E 328 (381)
T KOG1512|consen 257 RRNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYK-TYFWKC-------SSCELCRICLGPVIESE 328 (381)
T ss_pred chhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHh-hcchhh-------cccHhhhccCCcccchh
Confidence 44567777542 2232 488999999999999998765432111 001111 1235677887765 466
Q ss_pred eEEcCCCCcccccccccC
Q 040047 93 SFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 93 ~Y~C~~C~f~lH~~Ca~l 110 (240)
...|..||--.|..|..|
T Consensus 329 ~~FCD~CDRG~HT~CVGL 346 (381)
T KOG1512|consen 329 HLFCDVCDRGPHTLCVGL 346 (381)
T ss_pred eeccccccCCCCcccccc
Confidence 788999999999999764
No 112
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=43.88 E-value=12 Score=33.47 Aligned_cols=68 Identities=21% Similarity=0.395 Sum_probs=42.7
Q ss_pred eEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCCC-ceeEEcCCCCcccccccccCC
Q 040047 36 AYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPGS-AFSFCCPLCDFDLHVQCAFLP 111 (240)
Q Consensus 36 ~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~-g~~Y~C~~C~f~lH~~Ca~lP 111 (240)
--.|..|+-.=|.+|..+...|.-..- .-++.-. .=..|++||..-+ .....|.+||--.|.-|...|
T Consensus 246 lvscsdcgrsghpsclqft~nm~~avk-~yrwqci-------eck~csicgtsenddqllfcddcdrgyhmyclspp 314 (336)
T KOG1244|consen 246 LVSCSDCGRSGHPSCLQFTANMIAAVK-TYRWQCI-------ECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPP 314 (336)
T ss_pred hcchhhcCCCCCcchhhhhHHHHHHHH-hheeeee-------ecceeccccCcCCCceeEeecccCCceeeEecCCC
Confidence 367777777777777765443321111 0111111 1356888888654 566889999999999997755
No 113
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=43.52 E-value=12 Score=25.65 Aligned_cols=25 Identities=20% Similarity=0.760 Sum_probs=20.7
Q ss_pred CccccccCCCC---CceeEEcCCCCccc
Q 040047 79 NFLCNACGEPG---SAFSFCCPLCDFDL 103 (240)
Q Consensus 79 ~~~Cd~C~~~~---~g~~Y~C~~C~f~l 103 (240)
-+.|.-|+... .+.+.+|.+|+|.+
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGYRI 47 (62)
T ss_pred EEEeccccccccccCCCcEehhhcchHH
Confidence 57899998865 37899999999865
No 114
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=43.45 E-value=15 Score=34.27 Aligned_cols=38 Identities=21% Similarity=0.448 Sum_probs=29.8
Q ss_pred ceecccccccccCCcceeEEeCCCCeeeecccccCccc
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
...|.+|...+.+-+--.|+|..|..-+|.+|-.....
T Consensus 141 r~~c~ic~d~iwglgrqgyrcinckl~vhkkch~~v~~ 178 (593)
T KOG0695|consen 141 RAYCGICSDRIWGLGRQGYRCINCKLLVHKKCHGLVPL 178 (593)
T ss_pred ceeeeechhhhhhcccccceeecceeehhhhhcccccc
Confidence 46899999886532135899999999999999876553
No 115
>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=43.03 E-value=19 Score=24.69 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=24.1
Q ss_pred cceecccccccccC--CcceeEEeCCCCeeeec
Q 040047 138 SSYVCDICHKQLDQ--KCFWSYNCFACNFHAHV 168 (240)
Q Consensus 138 ~~~~C~vC~~~~~~--~~~~~Y~C~~C~~~lH~ 168 (240)
.+-.|..|+..... + ...|.|..|++..|.
T Consensus 27 TSq~C~~CG~~~~~~~~-~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRS-GRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCcccccccccc-cceEEcCCCCCEECc
Confidence 56789999997654 4 679999999998764
No 116
>KOG1170 consensus Diacylglycerol kinase [Lipid transport and metabolism]
Probab=42.47 E-value=18 Score=37.11 Aligned_cols=97 Identities=15% Similarity=0.209 Sum_probs=53.2
Q ss_pred ccceecccccccccCCc-ceeEEeCCCCeeeecccccCcccc-------CCCCCCCChhhhhhhh-----hhcCC--CCC
Q 040047 137 SSSYVCDICHKQLDQKC-FWSYNCFACNFHAHVSCTRNRNNS-------DSAKPEPNSAAYQKEE-----SASGS--SQQ 201 (240)
Q Consensus 137 ~~~~~C~vC~~~~~~~~-~~~Y~C~~C~~~lH~~C~~~~~~~-------~~~~p~~~~~~~~~~~-----~~~~~--~~~ 201 (240)
.....|.+|.+.+.+.. ..-|+|.+|+-.+|..|......- .+++|--.++.++++. ++.++ -.+
T Consensus 116 pvsskc~vc~k~cgs~~rlqd~rclwc~~~vh~~c~~~~~~~cs~~~~~~svi~ptal~~~~~dg~~v~~~~a~~~~~~s 195 (1099)
T KOG1170|consen 116 PVSSKCSVCEKPCGSVLRLQDYRCLWCGCCVHDTCIGNLARACSLGHSALSVIPPTALKEVTPDGTAVFWEEAYGGPCGS 195 (1099)
T ss_pred CccccccccccccccccccCCcceEeeccEeehhhhhhHHhhcccccccccccChhhhcccCCCcceeehhhhcCCCCCC
Confidence 46789999999875321 568999999999999997544320 1122222222222221 11222 222
Q ss_pred CCCccchhhhHHHHHHHHHHHHHHHHHHHHHH
Q 040047 202 NQTERTEIEDPVLEAQLELQRLQLEMQMAQEL 233 (240)
Q Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 (240)
++....---.--=+.|++++++..++.+++..
T Consensus 196 pllv~insksgd~qg~~~lrkfkq~lnp~qVf 227 (1099)
T KOG1170|consen 196 PLLVFINSKSGDSQGQRFLRKFKQILNPIQVF 227 (1099)
T ss_pred ceeEeecccCCCchhHHHHHhhhhhcCHHHHH
Confidence 21111000111126789999999998777643
No 117
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=42.35 E-value=23 Score=20.67 Aligned_cols=26 Identities=19% Similarity=0.568 Sum_probs=15.5
Q ss_pred ceeccccccccc--CCcceeEEeCCCCee
Q 040047 139 SYVCDICHKQLD--QKCFWSYNCFACNFH 165 (240)
Q Consensus 139 ~~~C~vC~~~~~--~~~~~~Y~C~~C~~~ 165 (240)
...|..|+.+.. .. +|.-+|..|+..
T Consensus 3 ~rfC~~CG~~t~~~~~-g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPG-GWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SS-SS-EEESSSS-E
T ss_pred CcccCcCCccccCCCC-cCEeECCCCcCE
Confidence 357999998753 34 799999999753
No 118
>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=41.95 E-value=12 Score=24.49 Aligned_cols=37 Identities=22% Similarity=0.310 Sum_probs=30.5
Q ss_pred eecccccccccCCcceeEEeCCCCeeeecccccCcccc
Q 040047 140 YVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNNS 177 (240)
Q Consensus 140 ~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~~ 177 (240)
..|..|++..+.. .+.+.|..|+..++..|.......
T Consensus 3 ~~C~~C~~~F~~~-~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLT-RRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCC-ccccccCcCcCCcChHHcCCeeec
Confidence 4688999887654 679999999999999999877653
No 119
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=41.53 E-value=14 Score=20.32 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=16.5
Q ss_pred CccccccCCCCCceeEEcCCCCc
Q 040047 79 NFLCNACGEPGSAFSFCCPLCDF 101 (240)
Q Consensus 79 ~~~Cd~C~~~~~g~~Y~C~~C~f 101 (240)
.+.|.+|.......+..|..|+.
T Consensus 2 ~W~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 2 DWECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cccCCCCCCcChhhhccccccCC
Confidence 57888888766666677777753
No 120
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=41.36 E-value=8.4 Score=35.56 Aligned_cols=32 Identities=25% Similarity=0.692 Sum_probs=27.5
Q ss_pred CCccccccCCC-CCceeEEcCCC-Cccccccccc
Q 040047 78 GNFLCNACGEP-GSAFSFCCPLC-DFDLHVQCAF 109 (240)
Q Consensus 78 ~~~~Cd~C~~~-~~g~~Y~C~~C-~f~lH~~Ca~ 109 (240)
.+..|+.|... +-|++|+|..| ++.+++.|.-
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfw 272 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFW 272 (434)
T ss_pred CCccCcceecccccchhhhHhhcCCccccchhhc
Confidence 46789999765 46999999999 8999999974
No 121
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.48 E-value=20 Score=27.53 Aligned_cols=25 Identities=16% Similarity=0.384 Sum_probs=19.1
Q ss_pred cceecccccccccCCcceeEEeCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACN 163 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~ 163 (240)
...+|..|+...... .+.|.|..|+
T Consensus 69 ~~~~C~~Cg~~~~~~-~~~~~CP~Cg 93 (113)
T PRK12380 69 AQAWCWDCSQVVEIH-QHDAQCPHCH 93 (113)
T ss_pred cEEEcccCCCEEecC-CcCccCcCCC
Confidence 578999999876544 5677788885
No 122
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.39 E-value=24 Score=22.54 Aligned_cols=26 Identities=23% Similarity=0.654 Sum_probs=17.5
Q ss_pred eecccccccccCCcceeEEeCCCCee
Q 040047 140 YVCDICHKQLDQKCFWSYNCFACNFH 165 (240)
Q Consensus 140 ~~C~vC~~~~~~~~~~~Y~C~~C~~~ 165 (240)
+.|.-|+..+.......-+|..|+.-
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCce
Confidence 57888888765322456788888754
No 123
>PLN02436 cellulose synthase A
Probab=39.63 E-value=28 Score=36.79 Aligned_cols=80 Identities=16% Similarity=0.339 Sum_probs=0.0
Q ss_pred cceeccccccccc---CCcceeEEeCCCCeeeecccccCcccc------CCCCCCC---ChhhhhhhhhhcCC-CC----
Q 040047 138 SSYVCDICHKQLD---QKCFWSYNCFACNFHAHVSCTRNRNNS------DSAKPEP---NSAAYQKEESASGS-SQ---- 200 (240)
Q Consensus 138 ~~~~C~vC~~~~~---~~~~~~Y~C~~C~~~lH~~C~~~~~~~------~~~~p~~---~~~~~~~~~~~~~~-~~---- 200 (240)
..-.|.+|+..+. .+ ..+--|.+|+|-+|..|.-.+..- .=..+++ ++..+.++|+|..- -.
T Consensus 35 ~~~iCqICGD~Vg~t~dG-e~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~kgs~~~~~d~ee~~~dd~e~ef 113 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDG-EPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKRIKGSPRVEGDEEEDDIDDLENEF 113 (1094)
T ss_pred CCccccccccccCcCCCC-CEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhccCCCCcCCccccccchhhhhhh
Q ss_pred ---CCCCccchhhhHHHHHHH
Q 040047 201 ---QNQTERTEIEDPVLEAQL 218 (240)
Q Consensus 201 ---~~~~~~~~~~~~~~~~~~ 218 (240)
.+.....++.+.|+..+.
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~ 134 (1094)
T PLN02436 114 DYGNNGLDPEQVAEAMLSSRL 134 (1094)
T ss_pred cCcccccchHHHHHHHhhhhc
No 124
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=38.92 E-value=16 Score=19.51 Aligned_cols=10 Identities=30% Similarity=0.873 Sum_probs=6.2
Q ss_pred EeeCCCCCcc
Q 040047 37 YGCWECKFFL 46 (240)
Q Consensus 37 Y~C~~C~f~l 46 (240)
|+|..|+|.-
T Consensus 1 y~C~~C~y~t 10 (24)
T PF13909_consen 1 YKCPHCSYST 10 (24)
T ss_dssp EE-SSSS-EE
T ss_pred CCCCCCCCcC
Confidence 7888888754
No 125
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=38.88 E-value=25 Score=24.73 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=22.3
Q ss_pred ccccccccCCcceeEEeCCCCe----eeeccccc
Q 040047 143 DICHKQLDQKCFWSYNCFACNF----HAHVSCTR 172 (240)
Q Consensus 143 ~vC~~~~~~~~~~~Y~C~~C~~----~lH~~C~~ 172 (240)
++|+.....+ .+.|+|..|.. .++..|+.
T Consensus 1 ~~C~~~~~~~-~~~y~C~tC~~~~~~~iC~~Cf~ 33 (71)
T smart00396 1 DVCTYKFTGG-EVIYRCKTCGLDPTCVLCSDCFR 33 (71)
T ss_pred CCCCCccCCC-CEEEECcCCCCCCCEeEChHHCC
Confidence 4677776666 78999999963 57888877
No 126
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=38.81 E-value=22 Score=27.57 Aligned_cols=63 Identities=14% Similarity=0.268 Sum_probs=39.4
Q ss_pred cccccccccCCcceeEEeCCCCeeeecccccCccccCCCCCCCChhhhhhhhhhcCCCCCCCCccchhhhHHHHHHHHHH
Q 040047 142 CDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNNSDSAKPEPNSAAYQKEESASGSSQQNQTERTEIEDPVLEAQLELQ 221 (240)
Q Consensus 142 C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (240)
|-+|+..+. -..++|..|+..+--.=...... .-+. +| ..++...+++...|.
T Consensus 1 CPvCg~~l~---vt~l~C~~C~t~i~G~F~l~~~~--------------~L~~-----E~-----~~Fi~~Fi~~rGnlK 53 (113)
T PF09862_consen 1 CPVCGGELV---VTRLKCPSCGTEIEGEFELPWFA--------------RLSP-----EQ-----LEFIKLFIKNRGNLK 53 (113)
T ss_pred CCCCCCceE---EEEEEcCCCCCEEEeeeccchhh--------------cCCH-----HH-----HHHHHHHHHhcCCHH
Confidence 678888765 45889999986553321111111 1111 11 578888888888888
Q ss_pred HHHHHHHHHH
Q 040047 222 RLQLEMQMAQ 231 (240)
Q Consensus 222 ~~~~~~~~~~ 231 (240)
+|+-++.+++
T Consensus 54 e~e~~lgiSY 63 (113)
T PF09862_consen 54 EMEKELGISY 63 (113)
T ss_pred HHHHHHCCCc
Confidence 8888865554
No 127
>PHA00626 hypothetical protein
Probab=38.00 E-value=23 Score=24.03 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=18.2
Q ss_pred ceecccccccccCCcceeEEeCCCCeeeec
Q 040047 139 SYVCDICHKQLDQKCFWSYNCFACNFHAHV 168 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~ 168 (240)
..+|..|.+.. -.|.|..|+|.+=.
T Consensus 11 Ivrcg~cr~~s-----nrYkCkdCGY~ft~ 35 (59)
T PHA00626 11 IAKEKTMRGWS-----DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeeceecccC-----cceEcCCCCCeech
Confidence 45777777752 38999999986543
No 128
>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=37.30 E-value=16 Score=25.85 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=3.8
Q ss_pred ceeccccccc
Q 040047 139 SYVCDICHKQ 148 (240)
Q Consensus 139 ~~~C~vC~~~ 148 (240)
.+.|+.|.+.
T Consensus 17 ~~~C~~C~~~ 26 (70)
T PF07191_consen 17 HYHCEACQKD 26 (70)
T ss_dssp EEEETTT--E
T ss_pred EEECcccccc
Confidence 3455555553
No 129
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=36.59 E-value=7.5 Score=35.40 Aligned_cols=37 Identities=19% Similarity=0.357 Sum_probs=24.6
Q ss_pred cceeccccccccc----------CCcceeEEeCCCCeeeecccccCcc
Q 040047 138 SSYVCDICHKQLD----------QKCFWSYNCFACNFHAHVSCTRNRN 175 (240)
Q Consensus 138 ~~~~C~vC~~~~~----------~~~~~~Y~C~~C~~~lH~~C~~~~~ 175 (240)
.+.-|-+|..+.. .+ ..+|+|..|.-.++..|-....
T Consensus 361 ks~~Cf~CQ~~fp~~~~~~~~~~~s-s~rY~Ce~CK~~FC~dCdvfiH 407 (421)
T COG5151 361 KSTHCFVCQGPFPKPPVSPFDESTS-SGRYQCELCKSTFCSDCDVFIH 407 (421)
T ss_pred CCccceeccCCCCCCCCCccccccc-ccceechhhhhhhhhhhHHHHH
Confidence 3456888887421 12 4699999998777777754433
No 130
>smart00039 CRF corticotropin-releasing factor.
Probab=36.53 E-value=99 Score=19.46 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 040047 212 PVLEAQLELQRLQLEMQMAQELAKMMSSF 240 (240)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (240)
-+|+.-.||++.+.+++-+..+=+++.++
T Consensus 12 ~vLR~~l~~e~a~~~~~qa~~NR~~L~~i 40 (40)
T smart00039 12 DLLRQRLELEKAERRREQAQANRNFLDDV 40 (40)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46788888888888888777777777553
No 131
>PF09487 HrpB2: Bacterial type III secretion protein (HrpB2); InterPro: IPR013391 This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia.
Probab=36.41 E-value=47 Score=25.93 Aligned_cols=31 Identities=19% Similarity=0.298 Sum_probs=26.4
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 040047 206 RTEIEDPVLEAQLELQRLQLEMQMAQELAKM 236 (240)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (240)
-+++....|+.|.|+.-||+.++..--+|+.
T Consensus 75 m~E~~a~si~~~~e~a~~q~dl~akm~vv~S 105 (117)
T PF09487_consen 75 MNEMAAASIRLQYEAASLQFDLQAKMSVVQS 105 (117)
T ss_pred HHHHHHHHHHHHHHHHHhhhhHHHhhhHhhc
Confidence 3588899999999999999999888777763
No 132
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=36.33 E-value=91 Score=25.36 Aligned_cols=34 Identities=15% Similarity=0.350 Sum_probs=18.6
Q ss_pred ecccccccccCCcceeEEeCCCCeeeecccccCcc
Q 040047 141 VCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRN 175 (240)
Q Consensus 141 ~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~ 175 (240)
.|.+||+.+.+. +..-.=..=-+.+|..|+....
T Consensus 2 ~CEiCG~~i~~~-~~~v~iega~l~vC~~C~k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGK-GFKIVIEGSEMTVCGECRKFGK 35 (154)
T ss_pred ccccCCCccCCC-CeEEEEcCeEEehhhhHHhcCC
Confidence 499999987633 2211212224666777774433
No 133
>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=35.79 E-value=17 Score=21.79 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=13.2
Q ss_pred eecccccccccCCcceeEEeCCCC
Q 040047 140 YVCDICHKQLDQKCFWSYNCFACN 163 (240)
Q Consensus 140 ~~C~vC~~~~~~~~~~~Y~C~~C~ 163 (240)
|.|.+|+....+. ..-..|..|+
T Consensus 3 ~~C~~CG~i~~g~-~~p~~CP~Cg 25 (34)
T cd00729 3 WVCPVCGYIHEGE-EAPEKCPICG 25 (34)
T ss_pred EECCCCCCEeECC-cCCCcCcCCC
Confidence 6677777654432 3345666664
No 134
>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=35.57 E-value=19 Score=21.32 Aligned_cols=23 Identities=30% Similarity=0.733 Sum_probs=12.7
Q ss_pred eecccccccccCCcceeEEeCCCC
Q 040047 140 YVCDICHKQLDQKCFWSYNCFACN 163 (240)
Q Consensus 140 ~~C~vC~~~~~~~~~~~Y~C~~C~ 163 (240)
+.|.+|+-..+.. .--+.|..|+
T Consensus 2 ~~C~~CGy~y~~~-~~~~~CP~Cg 24 (33)
T cd00350 2 YVCPVCGYIYDGE-EAPWVCPVCG 24 (33)
T ss_pred EECCCCCCEECCC-cCCCcCcCCC
Confidence 5677777654432 2344666664
No 135
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.34 E-value=19 Score=19.66 Aligned_cols=21 Identities=29% Similarity=0.645 Sum_probs=11.4
Q ss_pred ccccCCCCCceeEEcCCCCcc
Q 040047 82 CNACGEPGSAFSFCCPLCDFD 102 (240)
Q Consensus 82 Cd~C~~~~~g~~Y~C~~C~f~ 102 (240)
|..||..+....=.|..|+..
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCCcCcchhhhCCc
Confidence 566776664333336666543
No 136
>KOG2996 consensus Rho guanine nucleotide exchange factor VAV3 [Signal transduction mechanisms]
Probab=34.90 E-value=13 Score=36.73 Aligned_cols=35 Identities=26% Similarity=0.676 Sum_probs=28.4
Q ss_pred cceecccccccccCCcceeEEeCCCCeeeeccccc
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTR 172 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~ 172 (240)
....|.+|...+.+...-+|+|..|+.++|..|..
T Consensus 533 ~~tsCkvC~mllrGtfYQGY~C~~c~~~ahkecl~ 567 (865)
T KOG2996|consen 533 NTTSCKVCQMLLRGTFYQGYKCEKCGADAHKECLG 567 (865)
T ss_pred CCcchHHHHHHhhhhhhcceeeeeccccHHHHhcc
Confidence 34689999998764424689999999999999964
No 137
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=34.51 E-value=32 Score=21.96 Aligned_cols=27 Identities=22% Similarity=0.506 Sum_probs=17.5
Q ss_pred ecccccccccCCc---ceeEEeCCCCeeee
Q 040047 141 VCDICHKQLDQKC---FWSYNCFACNFHAH 167 (240)
Q Consensus 141 ~C~vC~~~~~~~~---~~~Y~C~~C~~~lH 167 (240)
.|..|+..+.... ...|.|..|++..-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 5777877654320 13788999987544
No 138
>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=33.97 E-value=30 Score=26.65 Aligned_cols=25 Identities=20% Similarity=0.621 Sum_probs=18.3
Q ss_pred cceecccccccccCCcceeEEeCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACN 163 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~ 163 (240)
...+|..|+...... .+.+.|..|+
T Consensus 69 ~~~~C~~Cg~~~~~~-~~~~~CP~Cg 93 (115)
T TIGR00100 69 VECECEDCSEEVSPE-IDLYRCPKCH 93 (115)
T ss_pred cEEEcccCCCEEecC-CcCccCcCCc
Confidence 578999999876544 4566777774
No 139
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=33.72 E-value=22 Score=36.36 Aligned_cols=33 Identities=21% Similarity=0.449 Sum_probs=27.8
Q ss_pred CccccccCCCC-CceeEEcCCCCcc-cccccccCC
Q 040047 79 NFLCNACGEPG-SAFSFCCPLCDFD-LHVQCAFLP 111 (240)
Q Consensus 79 ~~~Cd~C~~~~-~g~~Y~C~~C~f~-lH~~Ca~lP 111 (240)
...|++|+..- ......|.-|++. +|..|...+
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPd 249 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPD 249 (1134)
T ss_pred cccceeeccCChHHhheeecccccceeeccccCcc
Confidence 57899999875 3677899999998 999998754
No 140
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=33.25 E-value=17 Score=36.21 Aligned_cols=83 Identities=24% Similarity=0.479 Sum_probs=55.3
Q ss_pred CccccccCCCCC---ceeEEcCCCCcccccccccCCceeeeCCCceeeEEeecCCccCCCCccceecccccccccCCcce
Q 040047 79 NFLCNACGEPGS---AFSFCCPLCDFDLHVQCAFLPEILIHDSHFHSLNLSYALPAAHHYESSSYVCDICHKQLDQKCFW 155 (240)
Q Consensus 79 ~~~Cd~C~~~~~---g~~Y~C~~C~f~lH~~Ca~lP~~i~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~~~~~~~ 155 (240)
...|-+|+..+. |....|..|+-..|+.|..+- +.+. .|.-.|.- ..-..|.+|++..+. .-
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~--~~~~----~l~~gWrC-------~~crvCe~c~~~gD~--~k 82 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSW--AQHA----VLSGGWRC-------PSCRVCEACGTTGDP--KK 82 (694)
T ss_pred hhhhhhhccccccccCcchhhhhhcccCCcchhhHH--HhHH----HhcCCccc-------CCceeeeeccccCCc--cc
Confidence 456777776553 667889999999999998751 1110 01111211 145688888876654 35
Q ss_pred eEEeCCCCeeeecccccCccc
Q 040047 156 SYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 156 ~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
+..|..|+..+|--|...+..
T Consensus 83 f~~Ck~cDvsyh~yc~~P~~~ 103 (694)
T KOG4443|consen 83 FLLCKRCDVSYHCYCQKPPND 103 (694)
T ss_pred ccccccccccccccccCCccc
Confidence 789999999999999876654
No 141
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.45 E-value=50 Score=28.99 Aligned_cols=29 Identities=31% Similarity=0.573 Sum_probs=24.1
Q ss_pred CCCccccccCCCCCceeEEcCCCCcccccc
Q 040047 77 AGNFLCNACGEPGSAFSFCCPLCDFDLHVQ 106 (240)
Q Consensus 77 ~~~~~Cd~C~~~~~g~~Y~C~~C~f~lH~~ 106 (240)
..+..|..||. ..+-.|.|..|++..|.+
T Consensus 307 ~tS~~C~~cg~-~~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 307 YTSKTCPCCGH-LSGRLFKCPRCGFVHDRD 335 (364)
T ss_pred CCcccccccCC-ccceeEECCCCCCeehhh
Confidence 34689999999 556779999999988776
No 142
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=32.39 E-value=19 Score=31.81 Aligned_cols=38 Identities=18% Similarity=0.825 Sum_probs=26.8
Q ss_pred ceecccccccccC--------Cc-ceeEEeCCCC-------eeeecccccCccc
Q 040047 139 SYVCDICHKQLDQ--------KC-FWSYNCFACN-------FHAHVSCTRNRNN 176 (240)
Q Consensus 139 ~~~C~vC~~~~~~--------~~-~~~Y~C~~C~-------~~lH~~C~~~~~~ 176 (240)
-|.|++|+..+.. ++ +..|.|.+|+ +-.|.+|+.....
T Consensus 3 ~FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sYknH~kCITEaQK 56 (276)
T KOG2186|consen 3 FFTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSYKNHTKCITEAQK 56 (276)
T ss_pred EEehhhhhhhccccchHHHHHhccCCeeEEeecccccccchhhhhhhhcchHHH
Confidence 3789999986431 11 4578999995 4579999986655
No 143
>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=31.87 E-value=16 Score=21.77 Aligned_cols=22 Identities=27% Similarity=0.786 Sum_probs=11.6
Q ss_pred cccccCCCCC---ceeEEcCCCCcc
Q 040047 81 LCNACGEPGS---AFSFCCPLCDFD 102 (240)
Q Consensus 81 ~Cd~C~~~~~---g~~Y~C~~C~f~ 102 (240)
.|..||..+. +..-+|..|++.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCe
Confidence 4666666542 334567777654
No 144
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.46 E-value=36 Score=26.31 Aligned_cols=25 Identities=20% Similarity=0.595 Sum_probs=17.5
Q ss_pred cceecccccccccCCcceeEE-eCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYN-CFACN 163 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~-C~~C~ 163 (240)
..++|..|+...... .+.|. |..|+
T Consensus 70 ~~~~C~~Cg~~~~~~-~~~~~~CP~Cg 95 (117)
T PRK00564 70 VELECKDCSHVFKPN-ALDYGVCEKCH 95 (117)
T ss_pred CEEEhhhCCCccccC-CccCCcCcCCC
Confidence 578999999876543 34453 88885
No 145
>KOG1011 consensus Neurotransmitter release regulator, UNC-13 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.19 E-value=15 Score=36.95 Aligned_cols=43 Identities=28% Similarity=0.641 Sum_probs=36.0
Q ss_pred CCCCeeeeecCCCcccccccccCCCCc---eEeeCCCCCcchhhhccc
Q 040047 9 PHNLRIYQVQHGNEYSCSACELIISGS---AYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 9 ~H~L~l~~~~~~~~~~C~~C~~~~~g~---~Y~C~~C~f~lH~~Ca~~ 53 (240)
||-+..++.+ .+..|--|.-.+||. +.+|.+|..-+|..|-++
T Consensus 172 phnf~~~t~~--tpt~cyecegllwglarqglrctqc~vk~hdkc~el 217 (1283)
T KOG1011|consen 172 PHNFATTTFQ--TPTFCYECEGLLWGLARQGLRCTQCQVKVHDKCREL 217 (1283)
T ss_pred CCceeeeecc--CCchhhhhhhHHHHHhhcccchhhccccHHHHHHHH
Confidence 5776666655 789999998888885 699999999999999764
No 146
>PLN03044 GTP cyclohydrolase I; Provisional
Probab=31.01 E-value=28 Score=29.37 Aligned_cols=19 Identities=21% Similarity=0.435 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 040047 220 LQRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 220 ~~~~~~~~~~~~~~~~~~~ 238 (240)
-+|+|+|++|.+++|+.|.
T Consensus 112 arRlQiQERLT~qIa~~l~ 130 (188)
T PLN03044 112 ARRLQTQERLTRQIADAIV 130 (188)
T ss_pred hcCcHHHHHHHHHHHHHHH
Confidence 3689999999999999874
No 147
>cd00642 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively.
Probab=30.95 E-value=28 Score=29.34 Aligned_cols=18 Identities=22% Similarity=0.519 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 040047 221 QRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~ 238 (240)
+|+|++++|.+++|+.+.
T Consensus 112 rRlQiQERLt~qIa~al~ 129 (185)
T cd00642 112 RRLQVQERLTKQIAVAIQ 129 (185)
T ss_pred cCchHHHHHHHHHHHHHH
Confidence 689999999999999874
No 148
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.30 E-value=27 Score=19.50 Aligned_cols=22 Identities=27% Similarity=0.692 Sum_probs=12.8
Q ss_pred ccccccCCCCCceeEEcCCCCc
Q 040047 80 FLCNACGEPGSAFSFCCPLCDF 101 (240)
Q Consensus 80 ~~Cd~C~~~~~g~~Y~C~~C~f 101 (240)
..|..||..+....=.|..|+-
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 4677777765433333666654
No 149
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.89 E-value=40 Score=25.95 Aligned_cols=25 Identities=16% Similarity=0.481 Sum_probs=18.2
Q ss_pred cceecccccccccCCccee-EEeCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWS-YNCFACN 163 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~-Y~C~~C~ 163 (240)
..++|..|+...... .+. +.|..|+
T Consensus 69 ~~~~C~~Cg~~~~~~-~~~~~~CP~Cg 94 (114)
T PRK03681 69 AECWCETCQQYVTLL-TQRVRRCPQCH 94 (114)
T ss_pred cEEEcccCCCeeecC-CccCCcCcCcC
Confidence 578999999876543 444 6688885
No 150
>TIGR00063 folE GTP cyclohydrolase I. GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects.
Probab=29.76 E-value=30 Score=29.01 Aligned_cols=18 Identities=22% Similarity=0.484 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 040047 221 QRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~ 238 (240)
+|+|++++|.+++|+.|.
T Consensus 107 rRlQiQERlT~qIa~~l~ 124 (180)
T TIGR00063 107 RRPQVQERLTQQIAEALQ 124 (180)
T ss_pred cCchHHHHHHHHHHHHHH
Confidence 689999999999999875
No 151
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.68 E-value=50 Score=19.92 Aligned_cols=11 Identities=36% Similarity=0.579 Sum_probs=7.0
Q ss_pred ceeEEeCCCCe
Q 040047 154 FWSYNCFACNF 164 (240)
Q Consensus 154 ~~~Y~C~~C~~ 164 (240)
-.++.|..|++
T Consensus 20 r~R~vC~~Cg~ 30 (34)
T PF14803_consen 20 RERLVCPACGF 30 (34)
T ss_dssp S-EEEETTTTE
T ss_pred ccceECCCCCC
Confidence 46777777776
No 152
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=29.44 E-value=30 Score=25.84 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=18.0
Q ss_pred CCCCccccccCCCCCceeEEcCCC
Q 040047 76 SAGNFLCNACGEPGSAFSFCCPLC 99 (240)
Q Consensus 76 ~~~~~~Cd~C~~~~~g~~Y~C~~C 99 (240)
.+....|.+|+..+....|.|.+|
T Consensus 52 Gs~q~~ciic~~~gV~d~~yc~ec 75 (110)
T KOG1705|consen 52 GSYQGRCVICGGVGVSDAYYCKEC 75 (110)
T ss_pred ccccCceEEecCCcccchHHHHHH
Confidence 344667888888777778888876
No 153
>PF14379 Myb_CC_LHEQLE: MYB-CC type transfactor, LHEQLE motif
Probab=28.65 E-value=1.4e+02 Score=19.80 Aligned_cols=10 Identities=40% Similarity=0.564 Sum_probs=5.5
Q ss_pred HHHHHHHHHH
Q 040047 212 PVLEAQLELQ 221 (240)
Q Consensus 212 ~~~~~~~~~~ 221 (240)
..|+.|.|++
T Consensus 6 EALr~QmEvQ 15 (51)
T PF14379_consen 6 EALRMQMEVQ 15 (51)
T ss_pred HHHHHHHHHH
Confidence 3455566655
No 154
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.60 E-value=43 Score=20.68 Aligned_cols=23 Identities=17% Similarity=0.611 Sum_probs=14.7
Q ss_pred ccccccCCCCceEeeCCCCCcch
Q 040047 25 CSACELIISGSAYGCWECKFFLH 47 (240)
Q Consensus 25 C~~C~~~~~g~~Y~C~~C~f~lH 47 (240)
|..|++...-..|.|..|+..++
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC 23 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFC 23 (39)
T ss_pred CcccCCcccccCeECCccCCccc
Confidence 56676654333788888875554
No 155
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.26 E-value=41 Score=22.13 Aligned_cols=29 Identities=17% Similarity=0.492 Sum_probs=21.3
Q ss_pred cceeccccccccc-CCcceeEEeCCCCeee
Q 040047 138 SSYVCDICHKQLD-QKCFWSYNCFACNFHA 166 (240)
Q Consensus 138 ~~~~C~vC~~~~~-~~~~~~Y~C~~C~~~l 166 (240)
..+.|.-|++.+. ..-....+|..|++-+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 4578999999875 2115688999998754
No 156
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.05 E-value=51 Score=19.70 Aligned_cols=27 Identities=19% Similarity=0.086 Sum_probs=18.4
Q ss_pred ceecccccccccC-CcceeEEeCCCCee
Q 040047 139 SYVCDICHKQLDQ-KCFWSYNCFACNFH 165 (240)
Q Consensus 139 ~~~C~vC~~~~~~-~~~~~Y~C~~C~~~ 165 (240)
.+.|..|+..+.- +....|.|..|+..
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 4689999987432 11457889888754
No 157
>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=27.94 E-value=47 Score=21.56 Aligned_cols=43 Identities=21% Similarity=0.631 Sum_probs=22.8
Q ss_pred eEeeCCCCCcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCC
Q 040047 36 AYGCWECKFFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEP 88 (240)
Q Consensus 36 ~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~ 88 (240)
.|.|..|++.+...=.+....|. |.=+|.- .| ..+.|-.|+..
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~----pGt~F~~--Lp----~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIP----PGTPFED--LP----DDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-----TT--GGG--S-----TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcC----CCCCHHH--CC----CCCcCcCCCCc
Confidence 48999999888776554333332 2212221 12 37889998864
No 158
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=27.86 E-value=14 Score=21.20 Aligned_cols=23 Identities=26% Similarity=0.592 Sum_probs=14.5
Q ss_pred CCccccccCCCCCceeEEcCCCC
Q 040047 78 GNFLCNACGEPGSAFSFCCPLCD 100 (240)
Q Consensus 78 ~~~~Cd~C~~~~~g~~Y~C~~C~ 100 (240)
+.+.|..|........-+|..|+
T Consensus 3 g~W~C~~C~~~N~~~~~~C~~C~ 25 (30)
T PF00641_consen 3 GDWKCPSCTFMNPASRSKCVACG 25 (30)
T ss_dssp SSEEETTTTEEEESSSSB-TTT-
T ss_pred cCccCCCCcCCchHHhhhhhCcC
Confidence 57788888866555556677764
No 159
>PF00473 CRF: Corticotropin-releasing factor family; InterPro: IPR000187 Corticotropin-releasing factor (CRF), urotensin-I, urocortin and sauvagine form a family of related neuropeptides in vertebrates. The family can be grouped into 2 separate paralogous lineages, with urotensin-I, urocortin and sauvagine in one group and CRF forming the other group. Urocortin and sauvagine appear to represent orthologues of fish urotensin-I in mammals and amphibians, respectively. The peptides have a variety of physiological effects on stress and anxiety, vasoregulation, thermoregulation, growth and metabolism, metamorphosis and reproduction in various species, and are all released as preprohormones []. CRF [] is a hormone found mainly in the paraventricular nucleus of the mammalian hypothalamus that regulates the release of corticotropin (ACTH) from the pituitary gland. From here, CRF is transported to the anterior pituitary, stimulating adrenocorticotropic hormone (ACTH) release via CRF type 1 receptors, thereby activating the hypothalamo-pituitary-adrenocortical axis (HPA) and thus glucocorticoid release. CRF is evolutionary related to a number of other active peptides. Urocortin acts in vitro to stimulate the secretion of adrenocorticotropic hormone. Urotensin is found in the teleost caudal neurosecretory system and may play a role in osmoregulation and as a corticotropin-releasing factor. Urotensin-I is released from the urophysis of fish, and produces ACTH and subsequent cortisol release in vivo. The nonhormonal portion of the prohormone is thought to be the urotensin binding protein (urophysin). Sauvagine (P01144 from SWISSPROT), isolated from frog skin, has a potent hypotensive and diuretic effect.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 3EHU_C 3EHT_B 2RMF_A 3N96_G.
Probab=27.69 E-value=1.5e+02 Score=18.53 Aligned_cols=27 Identities=37% Similarity=0.500 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 040047 212 PVLEAQLELQRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (240)
-+|+...+|++.+..++-++.+=+++-
T Consensus 11 ~vLR~~l~~~~a~~~~~q~~~NR~~L~ 37 (39)
T PF00473_consen 11 HVLRQRLELERAERQMKQAQANRKFLD 37 (39)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 367777777777776666666655554
No 160
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.59 E-value=46 Score=35.12 Aligned_cols=21 Identities=24% Similarity=0.683 Sum_probs=13.5
Q ss_pred eecccccccccCCcceeEEeCCCCee
Q 040047 140 YVCDICHKQLDQKCFWSYNCFACNFH 165 (240)
Q Consensus 140 ~~C~vC~~~~~~~~~~~Y~C~~C~~~ 165 (240)
+.|.-|+.... .|.|..|++.
T Consensus 652 ~fCP~CG~~~~-----~y~CPKCG~E 672 (1121)
T PRK04023 652 YRCPRCGIEVE-----EDECEKCGRE 672 (1121)
T ss_pred eeCccccCcCC-----CCcCCCCCCC
Confidence 56777766532 4667777764
No 161
>PF09392 MxiH: Type III secretion needle MxiH like; InterPro: IPR021123 This entry represents bacterial type III secretion system needle-like proteins. Type III secretion systems are essential virulence determinants for many Gram-negative bacterial pathogens, acting to translocate proteins, usually virulence factors, out across both inner and outer membranes of bacteria and into the cytoplasm of the host cell. These proteins include: Needle proteins, including MxiH, YscF, EscF, PscF, EprI, that form the needle of the injection apparatus. For instance, MxiH is an extracellular alpha helical needle that is required for translocation of effector proteins into host cells, and once inside, the effector proteins subvert normal cell function to aid infection []. YscI (Yop proteins translocation protein I) in Yersinia and HrpB (hypersensitivity response and pathogenicity protein B) in plant pathogens such as Pseudomonas syringae. YscI is involved in the translocation of Yop proteins across the bacterial membrane or in the specific control of this function. ; GO: 0009405 pathogenesis, 0015031 protein transport; PDB: 2UWJ_F 2CA5_B 3J0R_A 2P58_B 3ZQB_B 3ZQE_B 2G0U_A 2LPZ_S 2JOW_A 2X9C_A ....
Probab=26.15 E-value=1.4e+02 Score=21.52 Aligned_cols=28 Identities=25% Similarity=0.491 Sum_probs=21.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 040047 211 DPVLEAQLELQRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (240)
..||+.|.+|.+.-++..+...+++.++
T Consensus 54 ~~ll~~Q~~l~qysl~~~l~sk~v~~~~ 81 (90)
T PF09392_consen 54 EDLLQLQFALSQYSLQVNLQSKLVKKMK 81 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999888776666665543
No 162
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=25.67 E-value=37 Score=31.45 Aligned_cols=62 Identities=24% Similarity=0.443 Sum_probs=29.0
Q ss_pred eEeeCCCC---CcchhhhccccccccCCCCCCcceEEeeccCCCCCCccccccCCCCC-cee---EEcCCCCcccccccc
Q 040047 36 AYGCWECK---FFLHEQCGNASRAMQHTSHPMHHLTLVPTTTYSAGNFLCNACGEPGS-AFS---FCCPLCDFDLHVQCA 108 (240)
Q Consensus 36 ~Y~C~~C~---f~lH~~Ca~~p~~i~h~~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~-g~~---Y~C~~C~f~lH~~Ca 108 (240)
+|.|.+|+ |.....|... +|+|..+... ...|.|..|+.... ..+ -+|..|+-.-=..++
T Consensus 252 av~C~~C~yt~~~~~~~C~~~----------~H~l~~~~a~---KRFFkC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer~~ 318 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEE----------GHPLKWHDAV---KRFFKCKDCGNRTISLERLPKKHCSNCGSSKWERTG 318 (344)
T ss_dssp EEEETTT--EESS--HHHHHT----------T--EEEEEEE----EEEE-T-TS-EEEESSSS--S--TTT-S---EEE-
T ss_pred EEEcCCCCCcccCcchhHHhc----------CCceEEeeee---eeeEECCCCCCeeeecccCCCCCCCcCCcCceeehh
Confidence 69999997 6778888772 5787766542 35789999998642 122 357777654444444
Q ss_pred cC
Q 040047 109 FL 110 (240)
Q Consensus 109 ~l 110 (240)
.+
T Consensus 319 M~ 320 (344)
T PF09332_consen 319 ML 320 (344)
T ss_dssp --
T ss_pred hh
Confidence 33
No 163
>PRK09347 folE GTP cyclohydrolase I; Provisional
Probab=25.57 E-value=37 Score=28.65 Aligned_cols=19 Identities=16% Similarity=0.375 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 040047 220 LQRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 220 ~~~~~~~~~~~~~~~~~~~ 238 (240)
-+|+|++++|.+++|+.+.
T Consensus 114 arRlQiQERlT~qIa~al~ 132 (188)
T PRK09347 114 ARRPQVQERLTAQIADALQ 132 (188)
T ss_pred HcCchhHHHHHHHHHHHHH
Confidence 3689999999999999874
No 164
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=25.56 E-value=46 Score=28.18 Aligned_cols=37 Identities=24% Similarity=0.523 Sum_probs=27.6
Q ss_pred ccceecccccccccC---CcceeEEeCCCCeeeecccccC
Q 040047 137 SSSYVCDICHKQLDQ---KCFWSYNCFACNFHAHVSCTRN 173 (240)
Q Consensus 137 ~~~~~C~vC~~~~~~---~~~~~Y~C~~C~~~lH~~C~~~ 173 (240)
..++.|.+|+..-.. .....++|..|+-..|..|...
T Consensus 150 ~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 150 QKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK 189 (202)
T ss_pred hCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC
Confidence 457899999974110 1025899999999999999875
No 165
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=25.48 E-value=35 Score=28.39 Aligned_cols=35 Identities=29% Similarity=0.489 Sum_probs=24.3
Q ss_pred eccccccccc--CCcceeEEeCCCCeeeecccccCccc
Q 040047 141 VCDICHKQLD--QKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 141 ~C~vC~~~~~--~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
.|++|+...+ .+ +..-+|-.|...+|..|+.....
T Consensus 1 ~C~~C~~~g~~~~k-G~Lv~CQGCs~sYHk~CLG~Rs~ 37 (175)
T PF15446_consen 1 TCDTCGYEGDDRNK-GPLVYCQGCSSSYHKACLGPRSQ 37 (175)
T ss_pred CcccccCCCCCccC-CCeEEcCccChHHHhhhcCCccc
Confidence 4778865433 23 66778888888888888865543
No 166
>PRK12606 GTP cyclohydrolase I; Reviewed
Probab=25.36 E-value=40 Score=28.77 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 040047 220 LQRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 220 ~~~~~~~~~~~~~~~~~~~ 238 (240)
-+|+|++++|.+++|+.+.
T Consensus 126 arRlQvQERLT~qIa~~l~ 144 (201)
T PRK12606 126 ARRLQIQENLTRQIATAVV 144 (201)
T ss_pred hcCchHHHHHHHHHHHHHH
Confidence 3689999999999999875
No 167
>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=25.30 E-value=39 Score=20.82 Aligned_cols=31 Identities=23% Similarity=0.475 Sum_probs=22.8
Q ss_pred ecccccccccCCcceeEEeCCCCeeeecccccC
Q 040047 141 VCDICHKQLDQKCFWSYNCFACNFHAHVSCTRN 173 (240)
Q Consensus 141 ~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~ 173 (240)
.|.+|-..+..+ ....... |+-.+|..|+..
T Consensus 2 ~C~IC~~~~~~~-~~~~~l~-C~H~fh~~Ci~~ 32 (44)
T PF13639_consen 2 ECPICLEEFEDG-EKVVKLP-CGHVFHRSCIKE 32 (44)
T ss_dssp CETTTTCBHHTT-SCEEEET-TSEEEEHHHHHH
T ss_pred CCcCCChhhcCC-CeEEEcc-CCCeeCHHHHHH
Confidence 588888887543 4455555 999999999754
No 168
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=25.12 E-value=33 Score=26.21 Aligned_cols=23 Identities=30% Similarity=0.665 Sum_probs=14.4
Q ss_pred CCCccccccC-CCCCceeEEcCCC
Q 040047 77 AGNFLCNACG-EPGSAFSFCCPLC 99 (240)
Q Consensus 77 ~~~~~Cd~C~-~~~~g~~Y~C~~C 99 (240)
.....|.+|| ..+...+|.|.+|
T Consensus 53 ~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 53 SLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp STTSB-TTTSSSB--EE-EE-HHH
T ss_pred CcCceEEEecCCCCcccceehhhh
Confidence 3567899999 6667889999887
No 169
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=25.00 E-value=80 Score=23.61 Aligned_cols=29 Identities=38% Similarity=0.709 Sum_probs=23.6
Q ss_pred CCccccccCCCC----C--ceeEEcCCCCcccccc
Q 040047 78 GNFLCNACGEPG----S--AFSFCCPLCDFDLHVQ 106 (240)
Q Consensus 78 ~~~~Cd~C~~~~----~--g~~Y~C~~C~f~lH~~ 106 (240)
..|.|..||..+ . +.+=+|..|=..+|..
T Consensus 3 ~~F~C~~CG~~V~p~~~g~~~RNHCP~CL~S~Hvd 37 (92)
T PF12647_consen 3 ESFTCVHCGLTVSPLAAGSAHRNHCPSCLSSLHVD 37 (92)
T ss_pred cccCccccCCCcccCCCCCCccCcCcccccccccC
Confidence 478999999976 2 3567899999888888
No 170
>PF04687 Microvir_H: Microvirus H protein (pilot protein); InterPro: IPR006777 Bacteriophage PhiX174 is one of the simplest viruses, having a single-stranded, closed circular DNA of 5386 nucleotide bases and four capsid proteins, J, F, G and H. A single molecule of H protein is found on each of the 12 spikes on the microvirus shell of the bacteriophage. H is involved in the ejection of the phage DNA, and at least one copy is injected into the hosts periplasmic space along with the ssDNA viral genome []. Part of H is thought to lie outside the shell, where it recognises lipopolysaccharide from virus-sensitive bacterial strains []. Part of H may lie within the capsid, since mutations in H can influence the DNA ejection mechanism by affecting the DNA-protein interactions []. H may span the capsid through the hydrophilic channels formed by G proteins [].; GO: 0016032 viral reproduction, 0019028 viral capsid
Probab=24.93 E-value=85 Score=27.50 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=19.4
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHHH
Q 040047 206 RTEIEDPVLEAQLELQRLQLEMQMA 230 (240)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (240)
+.+++.--|..|.||++||++-+..
T Consensus 134 qkel~kmqldnqkeiakmq~~~~~~ 158 (310)
T PF04687_consen 134 QKELTKMQLDNQKEIAKMQNETQKQ 158 (310)
T ss_pred HHHHHHHhhhhHHHHHHHHhhhhhh
Confidence 4567777788999999999985543
No 171
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=24.81 E-value=55 Score=23.36 Aligned_cols=34 Identities=26% Similarity=0.671 Sum_probs=28.2
Q ss_pred CCcccccccccCCCCceEeeC--CCCCcchhhhcccc
Q 040047 20 GNEYSCSACELIISGSAYGCW--ECKFFLHEQCGNAS 54 (240)
Q Consensus 20 ~~~~~C~~C~~~~~g~~Y~C~--~C~f~lH~~Ca~~p 54 (240)
.....|..|+++ .|..-.|. .|...+|..||...
T Consensus 34 ~~~~~C~~C~~~-~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 34 RRKLKCSICKKK-GGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred HhCCCCcCCCCC-CCeEEEEeCCCCCcEEChHHHccC
Confidence 366899999988 46678887 59999999999864
No 172
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=24.25 E-value=31 Score=34.52 Aligned_cols=77 Identities=27% Similarity=0.537 Sum_probs=51.7
Q ss_pred ccccccccCCCC---ceEeeCCCCCcchhhhccccccccCC--CCCCcceEEeeccCCCCCCccccccCCCCC-ceeEEc
Q 040047 23 YSCSACELIISG---SAYGCWECKFFLHEQCGNASRAMQHT--SHPMHHLTLVPTTTYSAGNFLCNACGEPGS-AFSFCC 96 (240)
Q Consensus 23 ~~C~~C~~~~~g---~~Y~C~~C~f~lH~~Ca~~p~~i~h~--~Hp~H~L~l~~~~~~~~~~~~Cd~C~~~~~-g~~Y~C 96 (240)
..|-.|+-.+.+ ..-.|..|.-..|..|... .++|. ++ -+. -+ .-..|-+|+..+. ..+..|
T Consensus 19 ~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~--~~~~~~l~~---gWr---C~----~crvCe~c~~~gD~~kf~~C 86 (694)
T KOG4443|consen 19 LMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTS--WAQHAVLSG---GWR---CP----SCRVCEACGTTGDPKKFLLC 86 (694)
T ss_pred hhhhhhccccccccCcchhhhhhcccCCcchhhH--HHhHHHhcC---Ccc---cC----CceeeeeccccCCccccccc
Confidence 445555555443 3589999999999999985 23322 11 111 11 2568999996654 566789
Q ss_pred CCCCcccccccccCC
Q 040047 97 PLCDFDLHVQCAFLP 111 (240)
Q Consensus 97 ~~C~f~lH~~Ca~lP 111 (240)
..||..+|..|..-|
T Consensus 87 k~cDvsyh~yc~~P~ 101 (694)
T KOG4443|consen 87 KRCDVSYHCYCQKPP 101 (694)
T ss_pred ccccccccccccCCc
Confidence 999999999998654
No 173
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.05 E-value=53 Score=25.47 Aligned_cols=22 Identities=27% Similarity=0.771 Sum_probs=16.1
Q ss_pred ccccCCCCCceeEEcCCCCccc
Q 040047 82 CNACGEPGSAFSFCCPLCDFDL 103 (240)
Q Consensus 82 Cd~C~~~~~g~~Y~C~~C~f~l 103 (240)
|-+||....-..++|..|+..+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 6778877777778888887443
No 174
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.62 E-value=70 Score=34.00 Aligned_cols=43 Identities=23% Similarity=0.427 Sum_probs=31.7
Q ss_pred CcccccccccCC----CCc-eEeeCCCCCcchhhhccccccccCCCCC
Q 040047 21 NEYSCSACELII----SGS-AYGCWECKFFLHEQCGNASRAMQHTSHP 63 (240)
Q Consensus 21 ~~~~C~~C~~~~----~g~-~Y~C~~C~f~lH~~Ca~~p~~i~h~~Hp 63 (240)
..-.|..|+..+ .|. +-.|.+|+|=+|..|.+..++--...-|
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CP 63 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCP 63 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCC
Confidence 346999998876 343 5899999999999999876544333333
No 175
>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=23.57 E-value=25 Score=26.99 Aligned_cols=25 Identities=16% Similarity=0.623 Sum_probs=16.6
Q ss_pred cceecccccccccCCcceeEEeCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACN 163 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~ 163 (240)
...+|..|+...... ...+.|..|+
T Consensus 69 ~~~~C~~Cg~~~~~~-~~~~~CP~Cg 93 (113)
T PF01155_consen 69 ARARCRDCGHEFEPD-EFDFSCPRCG 93 (113)
T ss_dssp -EEEETTTS-EEECH-HCCHH-SSSS
T ss_pred CcEECCCCCCEEecC-CCCCCCcCCc
Confidence 578999999987654 5567788884
No 176
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=23.34 E-value=51 Score=19.37 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=15.5
Q ss_pred eeEEeCCCCeeeecccccCc
Q 040047 155 WSYNCFACNFHAHVSCTRNR 174 (240)
Q Consensus 155 ~~Y~C~~C~~~lH~~C~~~~ 174 (240)
..|+|..|+..++..|....
T Consensus 11 ~~~fC~~~~~~iC~~C~~~~ 30 (39)
T cd00021 11 LSLFCETDRALLCVDCDLSV 30 (39)
T ss_pred eEEEeCccChhhhhhcChhh
Confidence 46788888888888887554
No 177
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=23.27 E-value=45 Score=34.35 Aligned_cols=33 Identities=21% Similarity=0.566 Sum_probs=28.9
Q ss_pred CCccccccCCCCCceeEEcCCCCcccccccccC
Q 040047 78 GNFLCNACGEPGSAFSFCCPLCDFDLHVQCAFL 110 (240)
Q Consensus 78 ~~~~Cd~C~~~~~g~~Y~C~~C~f~lH~~Ca~l 110 (240)
..-.|+.|........++|..|+|.++..|...
T Consensus 228 ~~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~ 260 (889)
T KOG1356|consen 228 IREMCDRCETTLFNIHWRCPRCGFGVCLDCYRK 260 (889)
T ss_pred cchhhhhhcccccceeEEccccCCeeeecchhh
Confidence 467899999887778899999999999999854
No 178
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=23.05 E-value=47 Score=34.23 Aligned_cols=36 Identities=25% Similarity=0.553 Sum_probs=29.3
Q ss_pred ccceecccccccccCCcceeEEeCCCCeeeecccccCcc
Q 040047 137 SSSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRN 175 (240)
Q Consensus 137 ~~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~ 175 (240)
+..-.|++|.+..- ...++|..|+|.++..|.....
T Consensus 227 g~~~mC~~C~~tlf---n~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 227 GIREMCDRCETTLF---NIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred Ccchhhhhhccccc---ceeEEccccCCeeeecchhhcc
Confidence 35678999999753 4688999999999999986653
No 179
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=22.86 E-value=47 Score=30.42 Aligned_cols=34 Identities=35% Similarity=0.673 Sum_probs=26.3
Q ss_pred cceecccccccccCCcceeEEeCCCCeeeec-ccccCccc
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACNFHAHV-SCTRNRNN 176 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~-~C~~~~~~ 176 (240)
....|.+|+.. ...|.|..|++-++. +|-.....
T Consensus 6 ~~~~C~ic~vq-----~~~YtCPRCn~~YCsl~CYr~h~~ 40 (383)
T KOG4317|consen 6 SFLACGICGVQ-----KREYTCPRCNLLYCSLKCYRNHKH 40 (383)
T ss_pred ceeeccccccc-----cccccCCCCCccceeeeeecCCCc
Confidence 45689999987 447999999988876 78766554
No 180
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.60 E-value=60 Score=20.47 Aligned_cols=26 Identities=19% Similarity=0.557 Sum_probs=16.1
Q ss_pred ceecccccccccCCc-ceeEEeCCCCe
Q 040047 139 SYVCDICHKQLDQKC-FWSYNCFACNF 164 (240)
Q Consensus 139 ~~~C~vC~~~~~~~~-~~~Y~C~~C~~ 164 (240)
.+.|..|+..+.... ....+|..||.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCC
Confidence 467888888653210 22678888864
No 181
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=22.21 E-value=61 Score=33.49 Aligned_cols=31 Identities=26% Similarity=0.452 Sum_probs=26.0
Q ss_pred ccccccccCCCC-------ceEeeCCCCCcchhhhccc
Q 040047 23 YSCSACELIISG-------SAYGCWECKFFLHEQCGNA 53 (240)
Q Consensus 23 ~~C~~C~~~~~g-------~~Y~C~~C~f~lH~~Ca~~ 53 (240)
..|..|+...+- ...+|..|+..+|..|...
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSn 498 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITK 498 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCC
Confidence 679999887632 3699999999999999974
No 182
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.81 E-value=56 Score=28.67 Aligned_cols=30 Identities=23% Similarity=0.619 Sum_probs=24.8
Q ss_pred CCcccccccccCCCCceEeeCCCCCcchhhh
Q 040047 20 GNEYSCSACELIISGSAYGCWECKFFLHEQC 50 (240)
Q Consensus 20 ~~~~~C~~C~~~~~g~~Y~C~~C~f~lH~~C 50 (240)
.....|..|+. .++..|.|..|++..|..=
T Consensus 307 ~tS~~C~~cg~-~~~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 307 YTSKTCPCCGH-LSGRLFKCPRCGFVHDRDV 336 (364)
T ss_pred CCcccccccCC-ccceeEECCCCCCeehhhH
Confidence 35688999999 6677899999999888653
No 183
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=21.69 E-value=83 Score=24.48 Aligned_cols=25 Identities=20% Similarity=0.567 Sum_probs=20.5
Q ss_pred cceecccccccccCCcceeEEeCCCC
Q 040047 138 SSYVCDICHKQLDQKCFWSYNCFACN 163 (240)
Q Consensus 138 ~~~~C~vC~~~~~~~~~~~Y~C~~C~ 163 (240)
...+|--|+..+... .|.|+|..|+
T Consensus 69 ~~~~C~~C~~~~~~e-~~~~~CP~C~ 93 (115)
T COG0375 69 AECWCLDCGQEVELE-ELDYRCPKCG 93 (115)
T ss_pred cEEEeccCCCeecch-hheeECCCCC
Confidence 578999998887655 7888899885
No 184
>PF10166 DUF2368: Uncharacterised conserved protein (DUF2368); InterPro: IPR019319 This family is conserved from nematodes to humans. The function is not known.
Probab=21.63 E-value=90 Score=24.80 Aligned_cols=9 Identities=44% Similarity=0.376 Sum_probs=4.0
Q ss_pred HHHHHHHHH
Q 040047 227 MQMAQELAK 235 (240)
Q Consensus 227 ~~~~~~~~~ 235 (240)
.+||-++|+
T Consensus 37 rq~A~qiA~ 45 (131)
T PF10166_consen 37 RQMAMQIAW 45 (131)
T ss_pred HHHHHHHHH
Confidence 444444443
No 185
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=21.41 E-value=65 Score=22.37 Aligned_cols=31 Identities=16% Similarity=0.384 Sum_probs=17.8
Q ss_pred cccccccCCcceeEEeCCCC----eeeeccc-ccCcc
Q 040047 144 ICHKQLDQKCFWSYNCFACN----FHAHVSC-TRNRN 175 (240)
Q Consensus 144 vC~~~~~~~~~~~Y~C~~C~----~~lH~~C-~~~~~ 175 (240)
.|...+... .+.|+|..|. ..++..| +...-
T Consensus 2 ~C~~~~~~~-q~~y~C~tC~~~~~~~iC~~CF~~~~H 37 (71)
T PF02207_consen 2 KCTYVWTSG-QIFYRCLTCSLDESSGICEECFANSCH 37 (71)
T ss_dssp SS--B--TT--EEEEETTTBSSTT-BBEHHHHCTSGG
T ss_pred cCCCCCcCC-CEEEECccCCCCCCEEEchhhCCCCCc
Confidence 466666555 7899999994 5688888 44433
No 186
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=21.07 E-value=67 Score=34.12 Aligned_cols=40 Identities=25% Similarity=0.311 Sum_probs=30.6
Q ss_pred ccceecccccccccCCcceeEEeCCCCeeeecccccCccc
Q 040047 137 SSSYVCDICHKQLDQKCFWSYNCFACNFHAHVSCTRNRNN 176 (240)
Q Consensus 137 ~~~~~C~vC~~~~~~~~~~~Y~C~~C~~~lH~~C~~~~~~ 176 (240)
.....|.+|...........-.|..|+..+|..|...+.+
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~i 256 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFI 256 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCC
Confidence 3567999999864321157889999999999999885544
No 187
>PHA00369 H minor spike protein
Probab=20.95 E-value=85 Score=27.59 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=19.3
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHHH
Q 040047 206 RTEIEDPVLEAQLELQRLQLEMQMA 230 (240)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (240)
+.++++--|..|.||++||++-+..
T Consensus 150 QKEl~kMQLDnQKeIAkMQ~~~~~~ 174 (325)
T PHA00369 150 QKELTKMQLDNQKEIAKMQNDTQKQ 174 (325)
T ss_pred HHHHHHHhhccHHHHHHHhhhhhhh
Confidence 4566777788999999999985543
No 188
>TIGR03021 pilP_fam type IV pilus biogenesis protein PilP. Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP.
Probab=20.83 E-value=1.1e+02 Score=23.79 Aligned_cols=25 Identities=36% Similarity=0.401 Sum_probs=20.4
Q ss_pred chhhhHHHHHHHHHHHHHHHHHHHH
Q 040047 207 TEIEDPVLEAQLELQRLQLEMQMAQ 231 (240)
Q Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~~~~ 231 (240)
-|..-.++|||.+++++|.|++-+.
T Consensus 10 iQ~et~LleAq~~~akaq~el~~~~ 34 (119)
T TIGR03021 10 LQSETALLEAQLARAKAQNELEEAE 34 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3666789999999999999987644
No 189
>KOG2698 consensus GTP cyclohydrolase I [Coenzyme transport and metabolism]
Probab=20.81 E-value=93 Score=26.85 Aligned_cols=18 Identities=28% Similarity=0.562 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 040047 221 QRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~ 238 (240)
+|||-+.+|.+++|..|+
T Consensus 173 rrLQVQERlTkQIA~a~s 190 (247)
T KOG2698|consen 173 RRLQVQERLTKQIAVALS 190 (247)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 789999999999999886
No 190
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=20.61 E-value=68 Score=19.81 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=8.4
Q ss_pred cccccccccCC
Q 040047 142 CDICHKQLDQK 152 (240)
Q Consensus 142 C~vC~~~~~~~ 152 (240)
||.|++.+.+.
T Consensus 1 Cd~CG~~I~~e 11 (37)
T PF08394_consen 1 CDYCGGEITGE 11 (37)
T ss_pred CCccCCcccCC
Confidence 78899987644
No 191
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.57 E-value=48 Score=17.60 Aligned_cols=11 Identities=45% Similarity=1.295 Sum_probs=7.1
Q ss_pred eeccccccccc
Q 040047 140 YVCDICHKQLD 150 (240)
Q Consensus 140 ~~C~vC~~~~~ 150 (240)
|.|++|++...
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 46777777553
No 192
>PTZ00484 GTP cyclohydrolase I; Provisional
Probab=20.47 E-value=61 Score=28.81 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 040047 221 QRLQLEMQMAQELAKMMS 238 (240)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~ 238 (240)
.|+|++.+|.+++|+.|.
T Consensus 186 rRlQiQERLT~qIAdaL~ 203 (259)
T PTZ00484 186 RRLQVQERLTQQIANALQ 203 (259)
T ss_pred cccHHHHHHHHHHHHHHH
Confidence 579999999999999875
No 193
>TIGR02558 HrpB2 type III secretion protein HrpB2. This family of genes is found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia.
Probab=20.16 E-value=1.3e+02 Score=23.65 Aligned_cols=30 Identities=20% Similarity=0.238 Sum_probs=23.2
Q ss_pred cchhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 040047 206 RTEIEDPVLEAQLELQRLQLEMQMAQELAK 235 (240)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 (240)
-+++-...|+.|.|+.-||+.++..--.+|
T Consensus 82 m~em~a~~m~l~~E~a~~q~dm~akm~Vv~ 111 (124)
T TIGR02558 82 LEEINVETMRLTYEAAATQLDMEAKMSVVN 111 (124)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHHhhhhhh
Confidence 346677789999999999998877655554
Done!