Query psy3895
Match_columns 185
No_of_seqs 174 out of 821
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 20:07:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3053|consensus 100.0 3.8E-34 8.3E-39 243.7 6.2 121 63-183 15-137 (293)
2 PHA02862 5L protein; Provision 99.8 3.7E-20 8.1E-25 146.7 3.0 64 68-143 2-65 (156)
3 PHA02825 LAP/PHD finger-like p 99.8 2.1E-19 4.7E-24 144.3 4.3 59 63-132 3-61 (162)
4 smart00744 RINGv The RING-vari 99.7 7E-18 1.5E-22 111.6 3.7 49 70-126 1-49 (49)
5 PF12906 RINGv: RING-variant d 99.7 7.1E-18 1.5E-22 110.6 2.3 47 71-125 1-47 (47)
6 COG5183 SSM4 Protein involved 99.7 1.2E-16 2.5E-21 153.1 7.4 80 65-152 9-94 (1175)
7 KOG1609|consensus 99.1 1E-10 2.2E-15 100.6 4.4 60 67-132 77-136 (323)
8 PF11793 FANCL_C: FANCL C-term 98.1 1.8E-06 4E-11 60.8 2.2 63 68-133 2-69 (70)
9 PF13639 zf-RING_2: Ring finge 98.0 2.6E-06 5.5E-11 54.1 1.9 44 69-126 1-44 (44)
10 PF12861 zf-Apc11: Anaphase-pr 97.7 6.1E-05 1.3E-09 55.3 4.5 57 67-132 20-84 (85)
11 PHA02929 N1R/p28-like protein; 97.6 8.4E-05 1.8E-09 63.9 4.1 57 66-135 172-232 (238)
12 KOG4628|consensus 97.5 8E-05 1.7E-09 67.1 3.5 50 69-131 230-279 (348)
13 COG5540 RING-finger-containing 97.1 0.00038 8.3E-09 61.9 3.5 55 63-130 318-372 (374)
14 PF12678 zf-rbx1: RING-H2 zinc 97.1 0.00049 1.1E-08 48.6 3.4 46 68-126 19-73 (73)
15 PLN03208 E3 ubiquitin-protein 97.1 0.00059 1.3E-08 57.0 4.0 57 66-131 16-80 (193)
16 PF13920 zf-C3HC4_3: Zinc fing 97.1 0.00034 7.5E-09 45.5 2.0 46 68-130 2-48 (50)
17 COG5243 HRD1 HRD ubiquitin lig 96.9 0.0011 2.5E-08 60.4 4.8 56 65-133 284-348 (491)
18 PHA02926 zinc finger-like prot 96.9 0.0011 2.5E-08 56.6 4.2 63 66-135 168-235 (242)
19 cd00162 RING RING-finger (Real 96.9 0.0012 2.6E-08 40.1 3.2 45 70-129 1-45 (45)
20 smart00184 RING Ring finger. E 96.3 0.0057 1.2E-07 35.6 3.2 39 71-125 1-39 (39)
21 KOG1645|consensus 96.2 0.0036 7.8E-08 57.6 3.2 56 66-131 2-57 (463)
22 PF00097 zf-C3HC4: Zinc finger 96.2 0.0046 9.9E-08 38.1 2.7 40 71-125 1-41 (41)
23 KOG1493|consensus 96.1 0.0024 5.1E-08 46.3 1.1 54 70-132 22-83 (84)
24 KOG0823|consensus 96.1 0.0098 2.1E-07 50.9 4.9 54 65-132 44-97 (230)
25 KOG0802|consensus 95.7 0.0091 2E-07 56.5 3.3 53 65-130 288-341 (543)
26 TIGR00599 rad18 DNA repair pro 95.7 0.018 3.9E-07 53.0 5.1 53 63-132 21-73 (397)
27 KOG0828|consensus 95.6 0.0075 1.6E-07 56.9 2.5 53 65-129 568-633 (636)
28 PF13923 zf-C3HC4_2: Zinc fing 95.3 0.011 2.5E-07 36.4 1.8 38 71-125 1-39 (39)
29 smart00504 Ubox Modified RING 95.1 0.041 8.9E-07 36.5 4.3 46 69-131 2-47 (63)
30 PF14634 zf-RING_5: zinc-RING 94.4 0.042 9.2E-07 34.7 2.7 44 70-127 1-44 (44)
31 PF14569 zf-UDP: Zinc-binding 94.3 0.043 9.4E-07 39.8 2.8 58 65-132 6-64 (80)
32 KOG0827|consensus 93.3 0.061 1.3E-06 49.5 2.6 48 69-126 5-52 (465)
33 PLN02189 cellulose synthase 93.2 0.07 1.5E-06 54.2 3.0 56 66-131 32-88 (1040)
34 KOG0804|consensus 93.1 0.037 8.1E-07 51.6 0.9 49 67-130 174-222 (493)
35 KOG0317|consensus 93.0 0.13 2.8E-06 45.5 4.2 50 65-131 236-285 (293)
36 COG5219 Uncharacterized conser 92.9 0.04 8.7E-07 55.7 1.0 55 67-131 1468-1524(1525)
37 PF05883 Baculo_RING: Baculovi 92.9 0.084 1.8E-06 41.9 2.6 70 68-147 26-100 (134)
38 PF14570 zf-RING_4: RING/Ubox 92.6 0.097 2.1E-06 34.6 2.2 48 71-130 1-48 (48)
39 PLN02195 cellulose synthase A 92.4 0.13 2.9E-06 52.0 3.9 55 66-130 4-59 (977)
40 KOG1734|consensus 92.3 0.11 2.5E-06 45.8 2.8 95 65-170 221-326 (328)
41 PLN02638 cellulose synthase A 92.1 0.13 2.9E-06 52.5 3.5 56 65-130 14-70 (1079)
42 PLN02436 cellulose synthase A 92.0 0.12 2.6E-06 52.7 3.0 55 66-130 34-89 (1094)
43 KOG4445|consensus 91.9 0.073 1.6E-06 47.6 1.2 60 67-132 114-188 (368)
44 COG5194 APC11 Component of SCF 91.7 0.26 5.7E-06 36.0 3.7 29 97-133 56-84 (88)
45 PF13445 zf-RING_UBOX: RING-ty 90.4 0.21 4.6E-06 31.9 2.0 43 71-123 1-43 (43)
46 KOG2930|consensus 90.4 0.23 5.1E-06 38.0 2.5 29 97-133 83-111 (114)
47 PLN02400 cellulose synthase 90.1 0.19 4.1E-06 51.4 2.4 56 66-131 34-90 (1085)
48 KOG0287|consensus 88.7 0.29 6.2E-06 44.6 2.2 50 65-131 20-69 (442)
49 PF10272 Tmpp129: Putative tra 88.4 0.55 1.2E-05 42.8 3.9 43 86-131 305-352 (358)
50 PLN02915 cellulose synthase A 87.0 0.47 1E-05 48.5 2.7 57 65-131 12-69 (1044)
51 KOG0320|consensus 86.9 0.93 2E-05 37.8 4.0 49 67-130 130-178 (187)
52 PF15227 zf-C3HC4_4: zinc fing 85.6 0.44 9.5E-06 30.1 1.1 42 71-125 1-42 (42)
53 KOG0825|consensus 84.6 0.35 7.6E-06 48.3 0.5 28 97-132 146-173 (1134)
54 PF07800 DUF1644: Protein of u 84.4 2 4.4E-05 35.1 4.7 59 67-130 1-91 (162)
55 PF04564 U-box: U-box domain; 84.0 1.1 2.5E-05 31.1 2.8 64 68-149 4-67 (73)
56 KOG4265|consensus 83.7 1.4 3E-05 40.1 3.8 49 66-130 288-336 (349)
57 TIGR00570 cdk7 CDK-activating 83.6 1.2 2.7E-05 39.8 3.5 53 68-132 3-56 (309)
58 KOG3970|consensus 82.9 2.6 5.5E-05 36.7 5.0 71 63-140 45-115 (299)
59 KOG1785|consensus 82.6 0.51 1.1E-05 44.0 0.7 52 64-130 365-416 (563)
60 KOG1428|consensus 75.7 3.7 8E-05 44.2 4.3 78 65-148 3483-3564(3738)
61 KOG1039|consensus 73.5 3.1 6.8E-05 37.8 3.0 64 66-135 159-226 (344)
62 KOG3268|consensus 73.3 4.6 0.0001 33.9 3.7 64 65-133 162-231 (234)
63 COG5574 PEX10 RING-finger-cont 71.6 3.8 8.3E-05 36.0 2.9 49 66-130 213-262 (271)
64 COG5175 MOT2 Transcriptional r 71.5 3.1 6.8E-05 38.1 2.4 54 66-131 12-65 (480)
65 PF09889 DUF2116: Uncharacteri 71.3 18 0.00038 24.8 5.6 14 119-132 3-16 (59)
66 PF00628 PHD: PHD-finger; Int 70.9 1.5 3.3E-05 27.9 0.2 48 70-126 1-49 (51)
67 KOG2177|consensus 68.7 2.4 5.3E-05 34.2 1.1 46 65-127 10-55 (386)
68 KOG2164|consensus 67.6 4.4 9.4E-05 38.6 2.6 52 68-131 186-237 (513)
69 COG5432 RAD18 RING-finger-cont 66.8 5.4 0.00012 35.9 2.9 51 66-133 23-73 (391)
70 PF10367 Vps39_2: Vacuolar sor 63.8 2.8 6E-05 30.2 0.5 33 67-106 77-109 (109)
71 PF05290 Baculo_IE-1: Baculovi 63.4 5.9 0.00013 31.6 2.2 56 67-132 79-134 (140)
72 KOG4323|consensus 63.1 7.5 0.00016 36.7 3.2 63 66-132 166-228 (464)
73 KOG3899|consensus 60.3 6.6 0.00014 35.3 2.3 42 88-132 321-367 (381)
74 KOG1814|consensus 60.1 8 0.00017 36.1 2.8 57 68-130 184-240 (445)
75 COG5236 Uncharacterized conser 55.0 26 0.00055 32.5 5.1 56 62-132 55-110 (493)
76 KOG1952|consensus 53.9 15 0.00033 37.2 3.8 60 65-130 188-247 (950)
77 KOG0955|consensus 49.1 12 0.00026 38.8 2.2 37 65-105 216-252 (1051)
78 PF13717 zinc_ribbon_4: zinc-r 48.9 8.3 0.00018 23.5 0.7 13 120-132 3-15 (36)
79 PF08746 zf-RING-like: RING-li 48.8 10 0.00023 24.0 1.2 21 99-125 23-43 (43)
80 KOG2034|consensus 47.4 9.8 0.00021 38.6 1.3 38 66-110 815-852 (911)
81 KOG0956|consensus 44.2 15 0.00033 36.6 2.1 66 65-130 114-182 (900)
82 PF13719 zinc_ribbon_5: zinc-r 44.0 11 0.00024 23.0 0.8 14 120-133 3-16 (37)
83 PF09813 Coiled-coil_56: Coile 44.0 18 0.00038 27.4 2.0 11 175-185 67-78 (100)
84 KOG4692|consensus 43.7 18 0.00038 33.6 2.3 49 65-130 419-467 (489)
85 PF02891 zf-MIZ: MIZ/SP-RING z 43.1 17 0.00036 23.7 1.5 38 85-128 11-50 (50)
86 KOG1973|consensus 41.9 21 0.00046 31.1 2.4 41 83-130 229-270 (274)
87 PF04423 Rad50_zn_hook: Rad50 41.6 23 0.00049 23.1 2.0 26 103-132 8-33 (54)
88 KOG1002|consensus 40.2 17 0.00037 35.3 1.7 57 64-132 532-588 (791)
89 PF14353 CpXC: CpXC protein 38.2 21 0.00046 27.0 1.7 19 116-134 35-53 (128)
90 PF13465 zf-H2C2_2: Zinc-finge 37.3 16 0.00035 20.3 0.7 14 117-130 12-25 (26)
91 PF13894 zf-C2H2_4: C2H2-type 36.2 16 0.00034 18.7 0.5 11 121-131 2-12 (24)
92 PF09788 Tmemb_55A: Transmembr 35.7 42 0.00091 29.4 3.3 13 120-132 158-170 (256)
93 PF06170 DUF983: Protein of un 34.4 54 0.0012 23.9 3.3 21 119-139 8-28 (86)
94 PF10571 UPF0547: Uncharacteri 32.9 20 0.00044 20.4 0.6 13 118-130 13-25 (26)
95 COG4640 Predicted membrane pro 32.8 45 0.00097 31.3 3.1 16 117-132 13-28 (465)
96 TIGR02098 MJ0042_CXXC MJ0042 f 32.3 24 0.00053 21.1 1.0 13 120-132 3-15 (38)
97 PF15353 HECA: Headcase protei 31.3 30 0.00065 26.5 1.5 20 89-111 37-56 (107)
98 PF00096 zf-C2H2: Zinc finger, 30.5 20 0.00044 18.7 0.3 11 121-131 2-12 (23)
99 KOG2068|consensus 29.8 68 0.0015 29.1 3.7 56 66-134 247-302 (327)
100 KOG0978|consensus 29.4 27 0.00059 34.7 1.2 54 62-131 637-690 (698)
101 PF09986 DUF2225: Uncharacteri 28.7 30 0.00066 29.0 1.3 15 118-132 4-18 (214)
102 smart00249 PHD PHD zinc finger 28.0 38 0.00083 19.9 1.3 46 70-125 1-47 (47)
103 KOG0956|consensus 27.8 36 0.00079 34.1 1.7 61 68-130 5-73 (900)
104 PF08274 PhnA_Zn_Ribbon: PhnA 27.3 27 0.00058 20.7 0.5 13 120-132 3-15 (30)
105 PRK05978 hypothetical protein; 26.7 98 0.0021 24.9 3.8 16 119-134 52-67 (148)
106 PF04532 DUF587: Protein of un 26.6 18 0.00038 30.8 -0.5 29 74-102 93-121 (215)
107 KOG1941|consensus 26.1 22 0.00048 33.3 -0.0 51 65-126 362-412 (518)
108 KOG1100|consensus 25.6 41 0.0009 28.3 1.5 43 67-130 157-200 (207)
109 PF05191 ADK_lid: Adenylate ki 25.4 28 0.00061 21.3 0.3 14 120-133 2-15 (36)
110 PHA03375 hypothetical protein; 24.7 22 0.00048 35.5 -0.3 28 74-101 99-126 (844)
111 PRK13743 conjugal transfer pro 24.2 87 0.0019 25.0 3.0 15 96-110 58-72 (141)
112 PF14446 Prok-RING_1: Prokaryo 23.6 40 0.00086 22.8 0.8 15 117-131 19-33 (54)
113 PF10497 zf-4CXXC_R1: Zinc-fin 23.3 1.1E+02 0.0023 23.0 3.3 59 64-127 3-69 (105)
114 PF07503 zf-HYPF: HypF finger; 22.9 53 0.0011 20.1 1.2 31 102-132 4-34 (35)
115 COG4068 Uncharacterized protei 22.8 2.5E+02 0.0054 19.5 4.6 15 118-132 7-21 (64)
116 KOG2114|consensus 22.6 50 0.0011 33.7 1.7 45 69-132 841-885 (933)
117 KOG4684|consensus 22.6 1.4E+02 0.0029 26.0 4.1 13 120-132 171-183 (275)
118 KOG0801|consensus 22.3 45 0.00097 27.7 1.1 28 65-93 174-201 (205)
119 KOG1940|consensus 22.2 52 0.0011 29.2 1.5 44 71-127 161-204 (276)
120 PF03884 DUF329: Domain of unk 21.6 30 0.00066 23.5 -0.0 12 120-131 3-14 (57)
121 PF05210 Sprouty: Sprouty prot 21.5 63 0.0014 24.8 1.7 18 88-110 60-77 (108)
122 PF01299 Lamp: Lysosome-associ 21.5 81 0.0018 27.6 2.6 34 151-184 270-305 (306)
123 KOG0802|consensus 21.5 39 0.00085 32.1 0.7 47 65-132 476-522 (543)
124 PF15446 zf-PHD-like: PHD/FYVE 21.3 55 0.0012 27.1 1.4 32 70-104 1-32 (175)
125 PF13913 zf-C2HC_2: zinc-finge 21.1 49 0.0011 18.4 0.8 12 120-131 3-14 (25)
126 PF07227 DUF1423: Protein of u 20.9 57 0.0012 30.8 1.6 59 69-131 129-195 (446)
No 1
>KOG3053|consensus
Probab=100.00 E-value=3.8e-34 Score=243.72 Aligned_cols=121 Identities=56% Similarity=1.220 Sum_probs=114.4
Q ss_pred cCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCccchHHHH
Q psy3895 63 ERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPYRGLLVSL 142 (185)
Q Consensus 63 ~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~~~~~~~l 142 (185)
+..+.++.|||||.+++|+....|++||+|+||+||||++||.+|+.+|+.+|......|+||+++|.+++|+..++...
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~~~~~ 94 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGPFDRV 94 (293)
T ss_pred CccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccChHHHH
Confidence 44677899999999998876667999999999999999999999999999888889999999999999999999999999
Q ss_pred HHHHHhhhhhhhhHHHHHHHHhHHHHHHHHHhhhhhe--eccc
Q psy3895 143 LDTIDTAVYKLCPFVAAGVVLGSMYWCAVTYGAVTVM--VHHK 183 (185)
Q Consensus 143 l~~~~~~~~~~~p~i~~~~l~~~~y~~a~~yG~~~i~--~G~~ 183 (185)
+++++....+++||++.+++++.+||.|++|||.+++ +|++
T Consensus 95 Le~~d~~i~r~cp~l~~g~~v~~iYWsAVtyGA~T~lQv~G~~ 137 (293)
T KOG3053|consen 95 LERLDILIFRLCPFLAAGIFVGSIYWSAVTYGAVTVLQVVGQE 137 (293)
T ss_pred HHHhhhHHhhcChHHHHHHHhheeehhhhhhcceeeeehhhhH
Confidence 9999999999999999999999999999999999999 8886
No 2
>PHA02862 5L protein; Provisional
Probab=99.79 E-value=3.7e-20 Score=146.67 Aligned_cols=64 Identities=27% Similarity=0.550 Sum_probs=53.3
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCccchHHHHH
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPYRGLLVSLL 143 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~~~~~~~ll 143 (185)
...||||+++++++ ++||+|+||++|||++||++|++. +++..||+|+++|.+. +...|+....
T Consensus 2 ~diCWIC~~~~~e~-----~~PC~C~GS~K~VHq~CL~~WIn~------S~k~~CeLCkteY~Ik-~~yKpf~kW~ 65 (156)
T PHA02862 2 SDICWICNDVCDER-----NNFCGCNEEYKVVHIKCMQLWINY------SKKKECNLCKTKYNIK-KTYVSFKKWN 65 (156)
T ss_pred CCEEEEecCcCCCC-----cccccccCcchhHHHHHHHHHHhc------CCCcCccCCCCeEEEE-EccccHHHhh
Confidence 47899999987542 699999999999999999999976 4679999999999986 4445666554
No 3
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.77 E-value=2.1e-19 Score=144.30 Aligned_cols=59 Identities=32% Similarity=0.777 Sum_probs=51.6
Q ss_pred cCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 63 ERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 63 ~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
+.++.++.||||+++.. ++.+||+|+||++|||++||++|+..+ +...||+|+++|++.
T Consensus 3 ~~s~~~~~CRIC~~~~~-----~~~~PC~CkGs~k~VH~sCL~rWi~~s------~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 3 DVSLMDKCCWICKDEYD-----VVTNYCNCKNENKIVHKECLEEWINTS------KNKSCKICNGPYNIK 61 (162)
T ss_pred CcCCCCCeeEecCCCCC-----CccCCcccCCCchHHHHHHHHHHHhcC------CCCcccccCCeEEEE
Confidence 34677899999998742 467999999999999999999999974 568999999999997
No 4
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=99.71 E-value=7e-18 Score=111.55 Aligned_cols=49 Identities=39% Similarity=1.001 Sum_probs=42.5
Q ss_pred eeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCC
Q psy3895 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126 (185)
Q Consensus 70 ~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck 126 (185)
+||||++.++ ++++|++||+|+||++|||++||++|+..+ ...+||+|+
T Consensus 1 ~CrIC~~~~~--~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~------~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGD--EGDPLVSPCRCKGSLKYVHQECLERWINES------GNKTCEICK 49 (49)
T ss_pred CccCCCCCCC--CCCeeEeccccCCchhHHHHHHHHHHHHHc------CCCcCCCCC
Confidence 5999999333 367999999999999999999999999985 346999996
No 5
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.69 E-value=7.1e-18 Score=110.61 Aligned_cols=47 Identities=40% Similarity=1.096 Sum_probs=37.0
Q ss_pred eeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCC
Q psy3895 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125 (185)
Q Consensus 71 CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~C 125 (185)
||||+++++++ .+|++||.|+||++|||++||++|+..+ +..+|++|
T Consensus 1 CrIC~~~~~~~--~~li~pC~C~Gs~~~vH~~CL~~W~~~~------~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEED--EPLISPCRCKGSMKYVHRSCLERWIRES------GNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSS--S-EE-SSS-SSCCGSEECCHHHHHHHHH------T-SB-TTT
T ss_pred CeEeCCcCCCC--CceecccccCCCcchhHHHHHHHHHHhc------CCCcCCCC
Confidence 89999998764 3899999999999999999999999985 45779998
No 6
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.66 E-value=1.2e-16 Score=153.13 Aligned_cols=80 Identities=23% Similarity=0.554 Sum_probs=64.7
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee------cCccch
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV------YPYRGL 138 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~------~p~~~~ 138 (185)
.++.+.||||..++.+ ++||.+||+|+||+||+|++||..|+.. +++.+|++|+++|+++ +|+.-|
T Consensus 9 N~d~~~CRICr~e~~~--d~pLfhPCKC~GSIkYiH~eCL~eW~~~------s~~~kCdiChy~~~Fk~IY~e~mP~~IP 80 (1175)
T COG5183 9 NEDKRSCRICRTEDIR--DDPLFHPCKCSGSIKYIHRECLMEWMEC------SGTKKCDICHYEYKFKDIYKEDMPQIIP 80 (1175)
T ss_pred CccchhceeecCCCCC--CCcCcccccccchhHHHHHHHHHHHHhc------CCCcceeeecceeeeeeecccCCCcccc
Confidence 4556999999998765 5799999999999999999999999996 4789999999999986 466666
Q ss_pred HHHHHHHHHhhhhh
Q psy3895 139 LVSLLDTIDTAVYK 152 (185)
Q Consensus 139 ~~~ll~~~~~~~~~ 152 (185)
+.-++.++......
T Consensus 81 fsiL~rk~a~t~~~ 94 (1175)
T COG5183 81 FSILIRKVADTGWK 94 (1175)
T ss_pred eehhHHHHHHHHHH
Confidence 66555555444333
No 7
>KOG1609|consensus
Probab=99.07 E-value=1e-10 Score=100.58 Aligned_cols=60 Identities=28% Similarity=0.834 Sum_probs=51.4
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
++..||||..+..+....+++.||.|+|+.++||+.||.+|+..+ ....|++|+..|...
T Consensus 77 ~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~------~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 77 SGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIK------GNITCEICKSFFINV 136 (323)
T ss_pred CCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccc------cCeeeecccccceec
Confidence 368999999987653122799999999999999999999999975 569999999999875
No 8
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.09 E-value=1.8e-06 Score=60.77 Aligned_cols=63 Identities=22% Similarity=0.439 Sum_probs=30.8
Q ss_pred CCeeeEecccccCCCC--CceeeccCCCCCCccccHHHHHHHHHHhccCCC---CCCccccCCCcceeeec
Q psy3895 68 LKYCWVCFATHEDDRN--ALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNA---FTQVACPQCNTKYFIVY 133 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~--~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~---~~~~~Ce~Ck~~y~i~~ 133 (185)
+..|.||++...+++. ..+-....|. +.+|..||.+|+....+.+. ...-.||.|+.++.+.+
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~---~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~~ 69 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCG---KKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWSF 69 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT-------B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccC---CHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEec
Confidence 4679999987542211 2333446787 78999999999998765322 12247999999998753
No 9
>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=98.03 E-value=2.6e-06 Score=54.14 Aligned_cols=44 Identities=27% Similarity=0.854 Sum_probs=32.6
Q ss_pred CeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCC
Q psy3895 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126 (185)
Q Consensus 69 ~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck 126 (185)
..|-||+++..++ +.....| |. +.+|.+||.+|+..+ .+||+|+
T Consensus 1 d~C~IC~~~~~~~-~~~~~l~--C~---H~fh~~Ci~~~~~~~--------~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDG-EKVVKLP--CG---HVFHRSCIKEWLKRN--------NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTT-SCEEEET--TS---EEEEHHHHHHHHHHS--------SB-TTTH
T ss_pred CCCcCCChhhcCC-CeEEEcc--CC---CeeCHHHHHHHHHhC--------CcCCccC
Confidence 3699999988652 3445555 54 899999999999873 4999995
No 10
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.69 E-value=6.1e-05 Score=55.30 Aligned_cols=57 Identities=18% Similarity=0.486 Sum_probs=42.2
Q ss_pred CCCeeeEecccccCC--------CCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 67 DLKYCWVCFATHEDD--------RNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~--------~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
+...|-||+...+.. .+-|++- +.|+ +.+|..||.+|+... .....||+|+.++.+.
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~-g~C~---H~FH~hCI~kWl~~~-----~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVW-GKCS---HNFHMHCILKWLSTQ-----SSKGQCPMCRQPWKFK 84 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceee-ccCc---cHHHHHHHHHHHccc-----cCCCCCCCcCCeeeeC
Confidence 367888888766421 1335553 5787 889999999999974 2357999999999874
No 11
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.55 E-value=8.4e-05 Score=63.89 Aligned_cols=57 Identities=23% Similarity=0.480 Sum_probs=40.9
Q ss_pred CCCCeeeEecccccCCCC--C--ceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCc
Q psy3895 66 VDLKYCWVCFATHEDDRN--A--LWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPY 135 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~--~--~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~ 135 (185)
.....|-||++...+.+. . ..+.||. +.+|..||.+|+.. ...||+|+.++....+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~-----H~FC~~CI~~Wl~~--------~~tCPlCR~~~~~v~~~ 232 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCN-----HVFCIECIDIWKKE--------KNTCPVCRTPFISVIKS 232 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCC-----CcccHHHHHHHHhc--------CCCCCCCCCEeeEEeee
Confidence 346899999997543211 1 2344554 78999999999874 36899999999876543
No 12
>KOG4628|consensus
Probab=97.50 E-value=8e-05 Score=67.11 Aligned_cols=50 Identities=24% Similarity=0.723 Sum_probs=39.8
Q ss_pred CeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 69 ~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
..|-||+++..+. +.--+-||+ +.+|..|++.||... ...||+||....-
T Consensus 230 ~~CaIClEdY~~G-dklRiLPC~-----H~FH~~CIDpWL~~~-------r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKG-DKLRILPCS-----HKFHVNCIDPWLTQT-------RTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccC-CeeeEecCC-----CchhhccchhhHhhc-------CccCCCCCCcCCC
Confidence 6999999999763 233447777 669999999999873 4779999997764
No 13
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.14 E-value=0.00038 Score=61.92 Aligned_cols=55 Identities=24% Similarity=0.547 Sum_probs=43.3
Q ss_pred cCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 63 ERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 63 ~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
.+.+.+-.|-||++...- .+.-.+.||+ +-+|..|+.+|+.. -..+||.|+++..
T Consensus 318 ~ea~~GveCaICms~fiK-~d~~~vlPC~-----H~FH~~Cv~kW~~~-------y~~~CPvCrt~iP 372 (374)
T COG5540 318 VEADKGVECAICMSNFIK-NDRLRVLPCD-----HRFHVGCVDKWLLG-------YSNKCPVCRTAIP 372 (374)
T ss_pred HhcCCCceEEEEhhhhcc-cceEEEeccC-----ceechhHHHHHHhh-------hcccCCccCCCCC
Confidence 345667899999998753 2346789988 55999999999985 3589999999763
No 14
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=97.13 E-value=0.00049 Score=48.62 Aligned_cols=46 Identities=28% Similarity=0.763 Sum_probs=30.6
Q ss_pred CCeeeEecccccCC-------C-CCcee-eccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCC
Q psy3895 68 LKYCWVCFATHEDD-------R-NALWV-QPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126 (185)
Q Consensus 68 ~~~CrIC~~~~~~~-------~-~~~li-~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck 126 (185)
...|-||++.-.+. . ..++. .+ |. +.+|..||.+|+.. ...||+|+
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~--C~---H~FH~~Ci~~Wl~~--------~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGP--CG---HIFHFHCISQWLKQ--------NNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEET--TS---EEEEHHHHHHHHTT--------SSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecc--cC---CCEEHHHHHHHHhc--------CCcCCCCC
Confidence 34599999876332 1 12222 34 44 89999999999975 24999996
No 15
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.09 E-value=0.00059 Score=57.03 Aligned_cols=57 Identities=16% Similarity=0.352 Sum_probs=41.6
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccC--------CCCCCccccCCCcceee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKG--------NAFTQVACPQCNTKYFI 131 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~--------~~~~~~~Ce~Ck~~y~i 131 (185)
++...|.||++... .+.+.+|. +.++..||.+|+...... +..+...||+|+.++..
T Consensus 16 ~~~~~CpICld~~~----dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCNICLDQVR----DPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCccCCCcCC----CcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 34678999998753 46888765 779999999998753210 12345799999999853
No 16
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.07 E-value=0.00034 Score=45.46 Aligned_cols=46 Identities=22% Similarity=0.571 Sum_probs=36.3
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCCcc-ccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTSKW-VHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~-VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
...|.||++... ...+.||. +. +-..|+.+|+.. ..+||+|+.++.
T Consensus 2 ~~~C~iC~~~~~----~~~~~pCg-----H~~~C~~C~~~~~~~--------~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPR----DVVLLPCG-----HLCFCEECAERLLKR--------KKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBS----SEEEETTC-----EEEEEHHHHHHHHHT--------TSBBTTTTBB-S
T ss_pred cCCCccCCccCC----ceEEeCCC-----ChHHHHHHhHHhccc--------CCCCCcCChhhc
Confidence 468999999753 47889986 56 999999999983 589999999875
No 17
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.0011 Score=60.38 Aligned_cols=56 Identities=21% Similarity=0.554 Sum_probs=40.9
Q ss_pred CCCCCeeeEecccc-cCC--------CCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeec
Q psy3895 65 SVDLKYCWVCFATH-EDD--------RNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVY 133 (185)
Q Consensus 65 ~~~~~~CrIC~~~~-~~~--------~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~ 133 (185)
.++.+.|-||.++- ..+ ...|-.-||- +..|..||+.|+..+ .+||+|+.+..+..
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCG-----HilHl~CLknW~ERq--------QTCPICr~p~ifd~ 348 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCG-----HILHLHCLKNWLERQ--------QTCPICRRPVIFDQ 348 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCccccccc-----ceeeHHHHHHHHHhc--------cCCCcccCcccccc
Confidence 56789999999883 221 1123345665 779999999999864 78999999976653
No 18
>PHA02926 zinc finger-like protein; Provisional
Probab=96.90 E-value=0.0011 Score=56.61 Aligned_cols=63 Identities=21% Similarity=0.449 Sum_probs=45.2
Q ss_pred CCCCeeeEecccccC-----CCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCc
Q psy3895 66 VDLKYCWVCFATHED-----DRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPY 135 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~-----~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~ 135 (185)
..+..|-||++.--+ +..-.++.+|. +.+...|+.+|...+.. ......||+|+..+.+..|.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~Cn-----HsFCl~CIr~Wr~~r~~--~~~~rsCPiCR~~f~~I~pS 235 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCN-----HIFCITCINIWHRTRRE--TGASDNCPICRTRFRNITMS 235 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCC-----chHHHHHHHHHHHhccc--cCcCCcCCCCcceeeeeccc
Confidence 346899999986422 11124667776 66999999999997531 12457899999999987664
No 19
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=96.89 E-value=0.0012 Score=40.09 Aligned_cols=45 Identities=22% Similarity=0.765 Sum_probs=32.5
Q ss_pred eeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcce
Q psy3895 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKY 129 (185)
Q Consensus 70 ~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y 129 (185)
.|.||++...+ ...+.||. +.+|..||.+|+.. ....||+|+..+
T Consensus 1 ~C~iC~~~~~~---~~~~~~C~-----H~~c~~C~~~~~~~-------~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFRE---PVVLLPCG-----HVFCRSCIDKWLKS-------GKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhC---ceEecCCC-----ChhcHHHHHHHHHh-------CcCCCCCCCCcC
Confidence 48899887622 23445565 56999999999986 247899999753
No 20
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=96.27 E-value=0.0057 Score=35.63 Aligned_cols=39 Identities=26% Similarity=0.798 Sum_probs=29.3
Q ss_pred eeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCC
Q psy3895 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125 (185)
Q Consensus 71 CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~C 125 (185)
|.||++.. ....+.||. +.+|..|+.+|+.. ...+||+|
T Consensus 1 C~iC~~~~----~~~~~~~C~-----H~~c~~C~~~~~~~-------~~~~CP~C 39 (39)
T smart00184 1 CPICLEEL----KDPVVLPCG-----HTFCRSCIRKWLKS-------GNNTCPIC 39 (39)
T ss_pred CCcCccCC----CCcEEecCC-----ChHHHHHHHHHHHh-------CcCCCCCC
Confidence 67898873 346777866 55999999999982 24678887
No 21
>KOG1645|consensus
Probab=96.24 E-value=0.0036 Score=57.60 Aligned_cols=56 Identities=23% Similarity=0.489 Sum_probs=46.8
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
+.+.+|.||+++.+...+..+++| .|. +.+..+|+++|+- + .....||+|+.+-..
T Consensus 2 d~g~tcpiclds~~~~g~hr~vsl-~cg---hlFgs~cie~wl~-k-----~~~~~cp~c~~katk 57 (463)
T KOG1645|consen 2 DCGTTCPICLDSYTTAGNHRIVSL-QCG---HLFGSQCIEKWLG-K-----KTKMQCPLCSGKATK 57 (463)
T ss_pred CccccCceeeeeeeecCceEEeee-ccc---ccccHHHHHHHHh-h-----hhhhhCcccCChhHH
Confidence 457899999999987667889998 887 8899999999995 3 356999999987654
No 22
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=96.23 E-value=0.0046 Score=38.13 Aligned_cols=40 Identities=33% Similarity=0.884 Sum_probs=31.7
Q ss_pred eeEecccccCCCCCce-eeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCC
Q psy3895 71 CWVCFATHEDDRNALW-VQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125 (185)
Q Consensus 71 CrIC~~~~~~~~~~~l-i~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~C 125 (185)
|.||++...+ +. +.||. +.++..||.+|+.. .....||+|
T Consensus 1 C~iC~~~~~~----~~~~~~C~-----H~fC~~C~~~~~~~------~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFED----PVILLPCG-----HSFCRDCLRKWLEN------SGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSS----EEEETTTS-----EEEEHHHHHHHHHH------TSSSBTTTT
T ss_pred CCcCCccccC----CCEEecCC-----CcchHHHHHHHHHh------cCCccCCcC
Confidence 7789987643 34 78877 67999999999997 246789988
No 23
>KOG1493|consensus
Probab=96.11 E-value=0.0024 Score=46.27 Aligned_cols=54 Identities=20% Similarity=0.555 Sum_probs=41.0
Q ss_pred eeeEecccccCC--------CCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 70 YCWVCFATHEDD--------RNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 70 ~CrIC~~~~~~~--------~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
.|-||....+.. ++-||+-- .|. +.+|.-|+.+|++.+. ....||+|+..|.+.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C~---h~fh~hCI~~wl~~~t-----sq~~CPmcRq~~~~~ 83 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWG-YCL---HAFHAHCILKWLNTPT-----SQGQCPMCRQTWQFK 83 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHH-HHH---HHHHHHHHHHHhcCcc-----ccccCCcchheeEec
Confidence 899998766421 24466644 565 8899999999999863 458999999999874
No 24
>KOG0823|consensus
Probab=96.08 E-value=0.0098 Score=50.92 Aligned_cols=54 Identities=22% Similarity=0.501 Sum_probs=44.3
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
+...-.|-|||+...| |.+++|- +.+==.||-+|+... .....||+||......
T Consensus 44 ~~~~FdCNICLd~akd----PVvTlCG-----HLFCWpClyqWl~~~-----~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKD----PVVTLCG-----HLFCWPCLYQWLQTR-----PNSKECPVCKAEVSID 97 (230)
T ss_pred CCCceeeeeeccccCC----CEEeecc-----cceehHHHHHHHhhc-----CCCeeCCccccccccc
Confidence 4566899999998754 8999886 677789999999985 4568899999998753
No 25
>KOG0802|consensus
Probab=95.67 E-value=0.0091 Score=56.51 Aligned_cols=53 Identities=23% Similarity=0.678 Sum_probs=39.8
Q ss_pred CCCCCeeeEecccccCCC-CCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 65 SVDLKYCWVCFATHEDDR-NALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~-~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
......|.||.+.-...+ ..+-+-||. +.+|..||++|+..+ ..||.|+..+.
T Consensus 288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~er~--------qtCP~CR~~~~ 341 (543)
T KOG0802|consen 288 ALSDELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFERQ--------QTCPTCRTVLY 341 (543)
T ss_pred hhcCCeeeeechhhccccccccceeecc-----cchHHHHHHHHHHHh--------CcCCcchhhhh
Confidence 345789999998765421 115566666 779999999999974 78999999443
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.65 E-value=0.018 Score=52.96 Aligned_cols=53 Identities=17% Similarity=0.342 Sum_probs=41.1
Q ss_pred cCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 63 ERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 63 ~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
..-+....|.||++... .+.+.||. +.+...|+.+|+.. ...||+|+..+...
T Consensus 21 ~~Le~~l~C~IC~d~~~----~PvitpCg-----H~FCs~CI~~~l~~--------~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFD----VPVLTSCS-----HTFCSLCIRRCLSN--------QPKCPLCRAEDQES 73 (397)
T ss_pred cccccccCCCcCchhhh----CccCCCCC-----CchhHHHHHHHHhC--------CCCCCCCCCccccc
Confidence 34456789999998764 36778876 66999999999965 24899999998753
No 27
>KOG0828|consensus
Probab=95.64 E-value=0.0075 Score=56.86 Aligned_cols=53 Identities=26% Similarity=0.742 Sum_probs=39.7
Q ss_pred CCCCCeeeEeccccc-----CC--------CCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcce
Q psy3895 65 SVDLKYCWVCFATHE-----DD--------RNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKY 129 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~-----~~--------~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y 129 (185)
.+....|-||...-+ .+ ..+-+++||. +..|..||++|++. .+..||.|+.+.
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~-----HifH~~CL~~WMd~-------ykl~CPvCR~pL 633 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCH-----HIFHRQCLLQWMDT-------YKLICPVCRCPL 633 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchH-----HHHHHHHHHHHHhh-------hcccCCccCCCC
Confidence 345678999986542 11 1346778998 78999999999985 248999999875
No 28
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=95.30 E-value=0.011 Score=36.36 Aligned_cols=38 Identities=24% Similarity=0.772 Sum_probs=27.7
Q ss_pred eeEecccccCCCCCc-eeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCC
Q psy3895 71 CWVCFATHEDDRNAL-WVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125 (185)
Q Consensus 71 CrIC~~~~~~~~~~~-li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~C 125 (185)
|.||++... ++ .+.||. +.+..+|+.+|+.. ..+||+|
T Consensus 1 C~iC~~~~~----~~~~~~~CG-----H~fC~~C~~~~~~~--------~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR----DPVVVTPCG-----HSFCKECIEKYLEK--------NPKCPVC 39 (39)
T ss_dssp ETTTTSB-S----SEEEECTTS-----EEEEHHHHHHHHHC--------TSB-TTT
T ss_pred CCCCCCccc----CcCEECCCC-----CchhHHHHHHHHHC--------cCCCcCC
Confidence 678988654 36 456665 78999999999986 2789987
No 29
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=95.14 E-value=0.041 Score=36.52 Aligned_cols=46 Identities=9% Similarity=0.165 Sum_probs=36.5
Q ss_pred CeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 69 ~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
-.|.||++.-. +|.+.||. +.+-+.|+.+|+.. ...||+|+.++..
T Consensus 2 ~~Cpi~~~~~~----~Pv~~~~G-----~v~~~~~i~~~~~~--------~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMK----DPVILPSG-----QTYERRAIEKWLLS--------HGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCC----CCEECCCC-----CEEeHHHHHHHHHH--------CCCCCCCcCCCCh
Confidence 36899988753 47888763 78999999999976 2589999998853
No 30
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=94.40 E-value=0.042 Score=34.75 Aligned_cols=44 Identities=23% Similarity=0.593 Sum_probs=34.5
Q ss_pred eeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCc
Q psy3895 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 127 (185)
Q Consensus 70 ~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~ 127 (185)
.|-||++...++ ..+++.+|. +.+...|+.++. .+...||+|+.
T Consensus 1 ~C~~C~~~~~~~-~~~~l~~Cg-----H~~C~~C~~~~~--------~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEE-RRPRLTSCG-----HIFCEKCLKKLK--------GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCC-CCeEEcccC-----CHHHHHHHHhhc--------CCCCCCcCCCC
Confidence 378999888432 468899886 779999998888 14689999984
No 31
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=94.28 E-value=0.043 Score=39.75 Aligned_cols=58 Identities=24% Similarity=0.417 Sum_probs=25.0
Q ss_pred CCCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
.....+|.||-+.-.-..++.+.-.|. |. --|=+.|...=+++ ....|++||++|+-.
T Consensus 6 ~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~---fPvCr~CyEYErke-------g~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 6 NLNGQICQICGDDVGLTENGEVFVACHECA---FPVCRPCYEYERKE-------GNQVCPQCKTRYKRH 64 (80)
T ss_dssp --SS-B-SSS--B--B-SSSSB--S-SSS--------HHHHHHHHHT-------S-SB-TTT--B----
T ss_pred hcCCcccccccCccccCCCCCEEEEEcccC---CccchhHHHHHhhc-------CcccccccCCCcccc
Confidence 346789999988664333455565576 65 56889998877765 568999999999853
No 32
>KOG0827|consensus
Probab=93.29 E-value=0.061 Score=49.55 Aligned_cols=48 Identities=23% Similarity=0.715 Sum_probs=32.3
Q ss_pred CeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCC
Q psy3895 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126 (185)
Q Consensus 69 ~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck 126 (185)
..|.||-+....+.+-.-|+- |. +.+|..||.+|..-.. .+..||||+
T Consensus 5 A~C~Ic~d~~p~~~~l~~i~~--cG---hifh~~cl~qwfe~~P-----s~R~cpic~ 52 (465)
T KOG0827|consen 5 AECHICIDGRPNDHELGPIGT--CG---HIFHTTCLTQWFEGDP-----SNRGCPICQ 52 (465)
T ss_pred ceeeEeccCCccccccccccc--hh---hHHHHHHHHHHHccCC-----ccCCCCcee
Confidence 579999444322222222333 55 7899999999998753 237999999
No 33
>PLN02189 cellulose synthase
Probab=93.16 E-value=0.07 Score=54.25 Aligned_cols=56 Identities=25% Similarity=0.399 Sum_probs=42.0
Q ss_pred CCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
-....|+||-++-.-+.++.+.-+|. |. --|=+.|.+.=+++ ....||+||++|+-
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~---fpvCr~Cyeyer~e-------g~q~CpqCkt~Y~r 88 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECG---FPVCRPCYEYERRE-------GTQNCPQCKTRYKR 88 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCC---Cccccchhhhhhhc-------CCccCcccCCchhh
Confidence 34579999998765444566777898 86 56888998554443 57899999999983
No 34
>KOG0804|consensus
Probab=93.09 E-value=0.037 Score=51.59 Aligned_cols=49 Identities=27% Similarity=0.630 Sum_probs=36.9
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
+.++|.+|++.-+++-++.+..+|. +-+|..||.+|=. ..||+|++--.
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~-----Hsfh~~cl~~w~~----------~scpvcR~~q~ 222 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCN-----HSFHCSCLMKWWD----------SSCPVCRYCQS 222 (493)
T ss_pred cCCCcchhHhhcCccccceeeeecc-----cccchHHHhhccc----------CcChhhhhhcC
Confidence 4689999998766554556667776 4599999999964 57999987544
No 35
>KOG0317|consensus
Probab=93.04 E-value=0.13 Score=45.51 Aligned_cols=50 Identities=24% Similarity=0.612 Sum_probs=39.8
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
.+..+.|-+|++.-. +|=-.||- +.+==.|+..|..++ ..||+|+.++..
T Consensus 236 ~~a~~kC~LCLe~~~----~pSaTpCG-----HiFCWsCI~~w~~ek--------~eCPlCR~~~~p 285 (293)
T KOG0317|consen 236 PEATRKCSLCLENRS----NPSATPCG-----HIFCWSCILEWCSEK--------AECPLCREKFQP 285 (293)
T ss_pred CCCCCceEEEecCCC----CCCcCcCc-----chHHHHHHHHHHccc--------cCCCcccccCCC
Confidence 345689999999864 35567876 678889999999885 459999998864
No 36
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.95 E-value=0.04 Score=55.67 Aligned_cols=55 Identities=24% Similarity=0.713 Sum_probs=38.0
Q ss_pred CCCeeeEeccccc-CCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 67 DLKYCWVCFATHE-DDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 67 ~~~~CrIC~~~~~-~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
....|-||+.--. -|..-|= .-|. |+ .-+|..||-+|..++ +...||+|+.++.+
T Consensus 1468 G~eECaICYsvL~~vdr~lPs-krC~TCk---nKFH~~CLyKWf~Ss------~~s~CPlCRseitf 1524 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPS-KRCATCK---NKFHTRCLYKWFASS------ARSNCPLCRSEITF 1524 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCc-cccchhh---hhhhHHHHHHHHHhc------CCCCCCcccccccc
Confidence 4578999986432 1111121 2233 55 679999999999985 56899999988765
No 37
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=92.89 E-value=0.084 Score=41.87 Aligned_cols=70 Identities=23% Similarity=0.513 Sum_probs=40.9
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCC---ccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCcc--chHHHH
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTS---KWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPYR--GLLVSL 142 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~---k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~~--~~~~~l 142 (185)
...|+||++.-.+ .++-..-+| .|.. +.+|.+|++||..+..+. +-+.. -.|.+.+|.. ..-..+
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~--~g~lnLEkmfc~~C~~rw~~~~~rD-PfnR~------I~y~F~fPf~~~~ec~~~ 95 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTD--GGTLNLEKMFCADCDKRWRRERNRD-PFNRN------IKYWFNFPFKNLEECKSF 95 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEec--CCeehHHHHHHHHHHHHHHhhccCC-Ccccc------eEEEEeCCCCCHHHHHHH
Confidence 5789999997765 234444444 3433 679999999996554321 11111 2566777652 234455
Q ss_pred HHHHH
Q psy3895 143 LDTID 147 (185)
Q Consensus 143 l~~~~ 147 (185)
++...
T Consensus 96 L~~~~ 100 (134)
T PF05883_consen 96 LEKSK 100 (134)
T ss_pred HHhcc
Confidence 55443
No 38
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=92.63 E-value=0.097 Score=34.57 Aligned_cols=48 Identities=25% Similarity=0.499 Sum_probs=22.9
Q ss_pred eeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 71 CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
|.+|.+.-+. ...-+.||.|. ++-|+.=|...+. ...-.||-||.+|.
T Consensus 1 cp~C~e~~d~--~d~~~~PC~Cg------f~IC~~C~~~i~~----~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 1 CPLCDEELDE--TDKDFYPCECG------FQICRFCYHDILE----NEGGRCPGCREPYK 48 (48)
T ss_dssp -TTTS-B--C--CCTT--SSTTS----------HHHHHHHTT----SS-SB-TTT--B--
T ss_pred CCCccccccc--CCCccccCcCC------CcHHHHHHHHHHh----ccCCCCCCCCCCCC
Confidence 5567665522 34568999995 7788877877753 24689999999984
No 39
>PLN02195 cellulose synthase A
Probab=92.43 E-value=0.13 Score=51.95 Aligned_cols=55 Identities=25% Similarity=0.401 Sum_probs=39.6
Q ss_pred CCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
.....|+||-+.-.-+.++.+.-.|. |. --|=+.|.+-=+++ ....|||||++|+
T Consensus 4 ~~~~~c~~cgd~~~~~~~g~~fvaC~eC~---~pvCrpCyeyer~e-------g~q~CpqCkt~Yk 59 (977)
T PLN02195 4 SGAPICATCGEEVGVDSNGEAFVACHECS---YPLCKACLEYEIKE-------GRKVCLRCGGPYD 59 (977)
T ss_pred CCCccceecccccCcCCCCCeEEEeccCC---Cccccchhhhhhhc-------CCccCCccCCccc
Confidence 35679999988665444455555576 65 55888998554443 5799999999999
No 40
>KOG1734|consensus
Probab=92.29 E-value=0.11 Score=45.80 Aligned_cols=95 Identities=20% Similarity=0.247 Sum_probs=56.0
Q ss_pred CCCCCeeeEecccccC--CCCC--ceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeec-Cc--c-
Q psy3895 65 SVDLKYCWVCFATHED--DRNA--LWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVY-PY--R- 136 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~--~~~~--~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~-p~--~- 136 (185)
..+...|-||-..-.. +.++ .=+.-=.|. +.+|+.|++-|..- .++..||-||.+..+.. ++ +
T Consensus 221 hl~d~vCaVCg~~~~~s~~eegvienty~LsCn---HvFHEfCIrGWciv------GKkqtCPYCKekVdl~rmfsnpWe 291 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCN---HVFHEFCIRGWCIV------GKKQTCPYCKEKVDLKRMFSNPWE 291 (328)
T ss_pred CCCcchhHhhcchheeecchhhhhhhheeeecc---cchHHHhhhhheee------cCCCCCchHHHHhhHhhhccCccc
Confidence 3556788898543211 1011 011223455 78999999999876 36799999999988652 11 1
Q ss_pred ---chHHHHHHHHHhhhhhhhhHHHHHHHHhHHHHHH
Q psy3895 137 ---GLLVSLLDTIDTAVYKLCPFVAAGVVLGSMYWCA 170 (185)
Q Consensus 137 ---~~~~~ll~~~~~~~~~~~p~i~~~~l~~~~y~~a 170 (185)
-....+++.++.+ -+-..++++++.|..||..
T Consensus 292 kph~~yg~LldwlRyl--Vawqpvi~~iVqgin~~lg 326 (328)
T KOG1734|consen 292 KPHVWYGQLLDWLRYL--VAWQPVIITIVQGINYYLG 326 (328)
T ss_pred cchhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhc
Confidence 1233556655432 2234556667777777653
No 41
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=92.12 E-value=0.13 Score=52.45 Aligned_cols=56 Identities=23% Similarity=0.389 Sum_probs=40.3
Q ss_pred CCCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
.-.+..|+||-++-.-..++.+.-.|. |. --|=+.|.+-=+++ ....|||||++|+
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~---FPVCrpCYEYEr~e-------G~q~CPqCktrYk 70 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACDVCA---FPVCRPCYEYERKD-------GNQSCPQCKTKYK 70 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEeccCC---Cccccchhhhhhhc-------CCccCCccCCchh
Confidence 345679999998765444455555676 65 55888998554443 5799999999998
No 42
>PLN02436 cellulose synthase A
Probab=91.98 E-value=0.12 Score=52.73 Aligned_cols=55 Identities=27% Similarity=0.431 Sum_probs=41.2
Q ss_pred CCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
-....|+||-++-.-..++.+.-.|. |. --|=+.|.+.=+++ ....||+||++|+
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~---fpvCr~Cyeyer~e-------g~~~Cpqckt~Y~ 89 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECA---FPVCRPCYEYERRE-------GNQACPQCKTRYK 89 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCC---Cccccchhhhhhhc-------CCccCcccCCchh
Confidence 34579999998764434556777798 86 55888998544443 5789999999998
No 43
>KOG4445|consensus
Probab=91.86 E-value=0.073 Score=47.60 Aligned_cols=60 Identities=27% Similarity=0.572 Sum_probs=43.0
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccC---------------CCCCCccccCCCcceee
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKG---------------NAFTQVACPQCNTKYFI 131 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~---------------~~~~~~~Ce~Ck~~y~i 131 (185)
...+|-||+-+..+. ..--+.||- +|.|-.||.|.|.+...+ ...-...|++|+.++.+
T Consensus 114 p~gqCvICLygfa~~-~~ft~T~C~-----Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 114 PNGQCVICLYGFASS-PAFTVTACD-----HYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCceEEEEEeecCC-CceeeehhH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 357899998877653 234567776 999999999999875321 01123679999999987
Q ss_pred e
Q psy3895 132 V 132 (185)
Q Consensus 132 ~ 132 (185)
.
T Consensus 188 e 188 (368)
T KOG4445|consen 188 E 188 (368)
T ss_pred c
Confidence 5
No 44
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=91.73 E-value=0.26 Score=36.04 Aligned_cols=29 Identities=28% Similarity=0.706 Sum_probs=25.7
Q ss_pred ccccHHHHHHHHHHhccCCCCCCccccCCCcceeeec
Q psy3895 97 KWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVY 133 (185)
Q Consensus 97 k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~ 133 (185)
+.+|.-|+.|||..+ -.||+++.+|.+..
T Consensus 56 HaFH~HCI~rWL~Tk--------~~CPld~q~w~~~~ 84 (88)
T COG5194 56 HAFHDHCIYRWLDTK--------GVCPLDRQTWVLAD 84 (88)
T ss_pred hHHHHHHHHHHHhhC--------CCCCCCCceeEEec
Confidence 779999999999974 78999999998864
No 45
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=90.45 E-value=0.21 Score=31.94 Aligned_cols=43 Identities=23% Similarity=0.566 Sum_probs=23.1
Q ss_pred eeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCcccc
Q psy3895 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACP 123 (185)
Q Consensus 71 CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce 123 (185)
|.||++ ..++.+.|.+-||. +.+=++||+++..... ....+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CG-----H~~c~~cl~~l~~~~~----~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCG-----HVFCKDCLQKLSKKSD----RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS------EEEHHHHHHHHHH-S-----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCc-----cHHHHHHHHHHHhcCC----CCeeeCc
Confidence 778988 54444668889865 6699999999999642 2456775
No 46
>KOG2930|consensus
Probab=90.44 E-value=0.23 Score=37.95 Aligned_cols=29 Identities=24% Similarity=0.677 Sum_probs=25.4
Q ss_pred ccccHHHHHHHHHHhccCCCCCCccccCCCcceeeec
Q psy3895 97 KWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVY 133 (185)
Q Consensus 97 k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~ 133 (185)
+-+|.-|+.|||+.+ ..||+|..++.+..
T Consensus 83 HaFH~hCisrWlktr--------~vCPLdn~eW~~qr 111 (114)
T KOG2930|consen 83 HAFHFHCISRWLKTR--------NVCPLDNKEWVFQR 111 (114)
T ss_pred hHHHHHHHHHHHhhc--------CcCCCcCcceeEee
Confidence 779999999999874 78999999998753
No 47
>PLN02400 cellulose synthase
Probab=90.14 E-value=0.19 Score=51.41 Aligned_cols=56 Identities=21% Similarity=0.362 Sum_probs=38.7
Q ss_pred CCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
-.+..|+||-++-.-..++.+.-.|. |. --|=+.|.+.=++ .....|||||++|+-
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~FVAC~eCa---FPVCRpCYEYERk-------eGnq~CPQCkTrYkR 90 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVFVACNECA---FPVCRPCYEYERK-------DGTQCCPQCKTRYRR 90 (1085)
T ss_pred cCCceeeecccccCcCCCCCEEEEEccCC---Cccccchhheecc-------cCCccCcccCCcccc
Confidence 35679999998764433455555576 65 4577788743333 367999999999983
No 48
>KOG0287|consensus
Probab=88.69 E-value=0.29 Score=44.64 Aligned_cols=50 Identities=22% Similarity=0.551 Sum_probs=40.1
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
-++--.|-||++-.. -|+|.||. +-+-.-|+...+.. ...||.|..+++=
T Consensus 20 lD~lLRC~IC~eyf~----ip~itpCs-----HtfCSlCIR~~L~~--------~p~CP~C~~~~~E 69 (442)
T KOG0287|consen 20 LDDLLRCGICFEYFN----IPMITPCS-----HTFCSLCIRKFLSY--------KPQCPTCCVTVTE 69 (442)
T ss_pred hHHHHHHhHHHHHhc----Cceecccc-----chHHHHHHHHHhcc--------CCCCCceecccch
Confidence 345678999999874 58999965 45778899988876 4789999998874
No 49
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=88.45 E-value=0.55 Score=42.81 Aligned_cols=43 Identities=28% Similarity=0.743 Sum_probs=33.6
Q ss_pred eeeccCCCCCCccccHHHHHHHHHHhccCC-----CCCCccccCCCcceee
Q psy3895 86 WVQPCLCRGTSKWVHQACLNRWIDEKQKGN-----AFTQVACPQCNTKYFI 131 (185)
Q Consensus 86 li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~-----~~~~~~Ce~Ck~~y~i 131 (185)
=-.+|.|+ -.-=.+||-+|..++|... .+++..||.|+++|=+
T Consensus 305 ~C~~C~CR---PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 305 PCQQCYCR---PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred CCcccccc---chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 34578887 5567899999999998532 2578999999999865
No 50
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=87.02 E-value=0.47 Score=48.50 Aligned_cols=57 Identities=32% Similarity=0.487 Sum_probs=40.3
Q ss_pred CCCCCeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
.-+...|+||-++-.-+.++.+.-.|. |. --|=+.|..-=+++ ....||+||++|+-
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~---fpvCr~cyeye~~~-------g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCG---FPVCKPCYEYERSE-------GNQCCPQCNTRYKR 69 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCC---Cccccchhhhhhhc-------CCccCCccCCchhh
Confidence 346789999998765444455555576 65 45788998544433 57899999999983
No 51
>KOG0320|consensus
Probab=86.85 E-value=0.93 Score=37.75 Aligned_cols=49 Identities=18% Similarity=0.482 Sum_probs=36.3
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
.--.|.||++..++. .+ + -=+|. +.+=..|++.-+.. ..+||+|+.++.
T Consensus 130 ~~~~CPiCl~~~sek--~~-v-sTkCG---HvFC~~Cik~alk~--------~~~CP~C~kkIt 178 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEK--VP-V-STKCG---HVFCSQCIKDALKN--------TNKCPTCRKKIT 178 (187)
T ss_pred cccCCCceecchhhc--cc-c-ccccc---hhHHHHHHHHHHHh--------CCCCCCcccccc
Confidence 347899999988652 22 2 23676 88889999888864 589999998543
No 52
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=85.59 E-value=0.44 Score=30.06 Aligned_cols=42 Identities=26% Similarity=0.630 Sum_probs=27.4
Q ss_pred eeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCC
Q psy3895 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQC 125 (185)
Q Consensus 71 CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~C 125 (185)
|.||++--. +|..-+|. +.+=+.||.+|..... .....||+|
T Consensus 1 CpiC~~~~~----~Pv~l~CG-----H~FC~~Cl~~~~~~~~----~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK----DPVSLPCG-----HSFCRSCLERLWKEPS----GSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S----SEEE-SSS-----SEEEHHHHHHHHCCSS----SST---SSS
T ss_pred CCccchhhC----CccccCCc-----CHHHHHHHHHHHHccC----CcCCCCcCC
Confidence 778988764 47777776 5688999999987642 223789988
No 53
>KOG0825|consensus
Probab=84.63 E-value=0.35 Score=48.25 Aligned_cols=28 Identities=18% Similarity=0.502 Sum_probs=22.7
Q ss_pred ccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 97 KWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 97 k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
+|+|..||..|-.. ..+|++|+..|--+
T Consensus 146 H~FC~~Ci~sWsR~--------aqTCPiDR~EF~~v 173 (1134)
T KOG0825|consen 146 HYFCEECVGSWSRC--------AQTCPVDRGEFGEV 173 (1134)
T ss_pred cccHHHHhhhhhhh--------cccCchhhhhhhee
Confidence 67889999888765 47899999999643
No 54
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=84.35 E-value=2 Score=35.07 Aligned_cols=59 Identities=24% Similarity=0.617 Sum_probs=39.5
Q ss_pred CCCeeeEecccccCCCCCcee---------eccCCCCCCccccHHHHHHHHHHhccCC----------------------
Q psy3895 67 DLKYCWVCFATHEDDRNALWV---------QPCLCRGTSKWVHQACLNRWIDEKQKGN---------------------- 115 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li---------~PC~C~GS~k~VH~~CL~~Wi~~~~~~~---------------------- 115 (185)
+...|.||++-.- +.-|+ .|=-|. +.|-|..||.|..+...+..
T Consensus 1 ed~~CpICme~PH---NAVLLlCSS~~kgcRpymc~--Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (162)
T PF07800_consen 1 EDVTCPICMEHPH---NAVLLLCSSHEKGCRPYMCD--TSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSES 75 (162)
T ss_pred CCccCceeccCCC---ceEEEEeccccCCccccccC--CccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccc
Confidence 3568999998652 22222 333366 47999999999988765411
Q ss_pred -CCCCccccCCCccee
Q psy3895 116 -AFTQVACPQCNTKYF 130 (185)
Q Consensus 116 -~~~~~~Ce~Ck~~y~ 130 (185)
......||+|+-+..
T Consensus 76 ~~~~~L~CPLCRG~V~ 91 (162)
T PF07800_consen 76 QEQPELACPLCRGEVK 91 (162)
T ss_pred cccccccCccccCcee
Confidence 123689999998765
No 55
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=84.00 E-value=1.1 Score=31.13 Aligned_cols=64 Identities=11% Similarity=0.034 Sum_probs=40.2
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCccchHHHHHHHHH
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPYRGLLVSLLDTID 147 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~~~~~~~ll~~~~ 147 (185)
.-.|-|+++--. +|.+.|+. +.+=+.|+.+|+.. ....||+|+.++... ..-+-..+.+.++
T Consensus 4 ~f~CpIt~~lM~----dPVi~~~G-----~tyer~~I~~~l~~-------~~~~~P~t~~~l~~~--~l~pn~~Lk~~I~ 65 (73)
T PF04564_consen 4 EFLCPITGELMR----DPVILPSG-----HTYERSAIERWLEQ-------NGGTDPFTRQPLSES--DLIPNRALKSAIE 65 (73)
T ss_dssp GGB-TTTSSB-S----SEEEETTS-----EEEEHHHHHHHHCT-------TSSB-TTT-SB-SGG--GSEE-HHHHHHHH
T ss_pred ccCCcCcCcHhh----CceeCCcC-----CEEcHHHHHHHHHc-------CCCCCCCCCCcCCcc--cceECHHHHHHHH
Confidence 456788877653 48888854 67999999999986 358999999887653 2234445555554
Q ss_pred hh
Q psy3895 148 TA 149 (185)
Q Consensus 148 ~~ 149 (185)
.+
T Consensus 66 ~~ 67 (73)
T PF04564_consen 66 EW 67 (73)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 56
>KOG4265|consensus
Probab=83.71 E-value=1.4 Score=40.13 Aligned_cols=49 Identities=22% Similarity=0.436 Sum_probs=34.9
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
+.++.|=||+++..+ -++-||+- -..=..|-+.-+- ....||+|+.++.
T Consensus 288 ~~gkeCVIClse~rd----t~vLPCRH----LCLCs~Ca~~Lr~--------q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSESRD----TVVLPCRH----LCLCSGCAKSLRY--------QTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecCCcc----eEEecchh----hehhHhHHHHHHH--------hhcCCCccccchH
Confidence 558999999998754 58888872 1244567665552 2468999999875
No 57
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.61 E-value=1.2 Score=39.79 Aligned_cols=53 Identities=21% Similarity=0.364 Sum_probs=36.9
Q ss_pred CCeeeEecccccCCCCC-ceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 68 LKYCWVCFATHEDDRNA-LWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~-~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
...|.||..+.--.++. -++++|- +-+=.+|+.+.+.. ....||+|+..++..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CG-----H~~C~sCv~~l~~~-------~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCG-----HTLCESCVDLLFVR-------GSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCC-----CcccHHHHHHHhcC-------CCCCCCCCCCccchh
Confidence 46899999875433222 3677664 55888999996532 246899999988753
No 58
>KOG3970|consensus
Probab=82.93 E-value=2.6 Score=36.66 Aligned_cols=71 Identities=20% Similarity=0.320 Sum_probs=46.6
Q ss_pred cCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCccchHH
Q psy3895 63 ERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPYRGLLV 140 (185)
Q Consensus 63 ~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~~~~~~ 140 (185)
.|++-...|+.|-..-.+.+.-.|+ |= +.+|=.||..|...-...-......||-|..++-.......|+.
T Consensus 45 ~DsDY~pNC~LC~t~La~gdt~RLv----Cy---hlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva 115 (299)
T KOG3970|consen 45 QDSDYNPNCRLCNTPLASGDTTRLV----CY---HLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVA 115 (299)
T ss_pred hhcCCCCCCceeCCccccCcceeeh----hh---hhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhH
Confidence 3556678899997655442233444 32 88999999999987654333456899999998743333333433
No 59
>KOG1785|consensus
Probab=82.57 E-value=0.51 Score=43.96 Aligned_cols=52 Identities=23% Similarity=0.658 Sum_probs=40.3
Q ss_pred CCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 64 RSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 64 ~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
+...-..|.||-+.+.+ .-|.||- +..-..||..|..+. ....||.|+.+++
T Consensus 365 MgsTFeLCKICaendKd----vkIEPCG-----HLlCt~CLa~WQ~sd------~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 365 MGSTFELCKICAENDKD----VKIEPCG-----HLLCTSCLAAWQDSD------EGQTCPFCRCEIK 416 (563)
T ss_pred ccchHHHHHHhhccCCC----ccccccc-----chHHHHHHHhhcccC------CCCCCCceeeEec
Confidence 33445789999887643 5688986 667789999999874 3588999999886
No 60
>KOG1428|consensus
Probab=75.70 E-value=3.7 Score=44.25 Aligned_cols=78 Identities=21% Similarity=0.423 Sum_probs=50.1
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCC--CCCccccCCCcceeee-c-CccchHH
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNA--FTQVACPQCNTKYFIV-Y-PYRGLLV 140 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~--~~~~~Ce~Ck~~y~i~-~-p~~~~~~ 140 (185)
.+..+.|-|||.+.-. ..|-|+ -.|. +.+|..|..+=+...-.+.. ...+.||+|+.++.-. . .-.+|+.
T Consensus 3483 QD~DDmCmICFTE~L~--AAP~Iq-L~C~---HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~~LkDLldPiK 3556 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALS--AAPAIQ-LDCS---HIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIVLKDLLDPIK 3556 (3738)
T ss_pred cccCceEEEEehhhhC--CCccee-cCCc---cchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhHHHHHHHHHHH
Confidence 3456899999987532 234443 2465 89999999887766543221 3568999999998732 1 2235565
Q ss_pred HHHHHHHh
Q psy3895 141 SLLDTIDT 148 (185)
Q Consensus 141 ~ll~~~~~ 148 (185)
.+.+.+.+
T Consensus 3557 el~edV~~ 3564 (3738)
T KOG1428|consen 3557 ELYEDVRR 3564 (3738)
T ss_pred HHHHHHHH
Confidence 66555543
No 61
>KOG1039|consensus
Probab=73.51 E-value=3.1 Score=37.76 Aligned_cols=64 Identities=22% Similarity=0.424 Sum_probs=43.2
Q ss_pred CCCCeeeEecccccCCCC----CceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecCc
Q psy3895 66 VDLKYCWVCFATHEDDRN----ALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYPY 135 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~----~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p~ 135 (185)
..+..|=||++.-.+... ...+.+|. +..=..|+..|....+- +..-...||+|+..-.++.|.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~-----H~~Cl~Cir~wr~~~q~-~~~~sksCP~CRv~s~~v~pS 226 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCN-----HSFCLNCIRKWRQATQF-ESKTSKSCPFCRVPSSFVNPS 226 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcc-----hhhhhcHhHhhhhhhcc-ccccccCCCcccCcccccccc
Confidence 347899999998765320 11123354 55778999999977542 222358999999998887655
No 62
>KOG3268|consensus
Probab=73.32 E-value=4.6 Score=33.94 Aligned_cols=64 Identities=27% Similarity=0.552 Sum_probs=39.7
Q ss_pred CCCCCeeeEecccccCCCCCceeecc---CCCCCCccccHHHHHHHHHHhccCCC---CCCccccCCCcceeeec
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPC---LCRGTSKWVHQACLNRWIDEKQKGNA---FTQVACPQCNTKYFIVY 133 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC---~C~GS~k~VH~~CL~~Wi~~~~~~~~---~~~~~Ce~Ck~~y~i~~ 133 (185)
+++..-|-||+.-.-+. +.+ -.-| .|. +-+|+-||-.|+..-...+. .-.-.||-|..+..+.+
T Consensus 162 dd~~~~cgicyayqldG-Tip-DqtCdN~qCg---kpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm 231 (234)
T KOG3268|consen 162 DDELGACGICYAYQLDG-TIP-DQTCDNIQCG---KPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM 231 (234)
T ss_pred chhhhcccceeeeecCC-ccc-cccccccccC---CcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence 44566788887432211 000 1122 354 77999999999987644322 22368999999988764
No 63
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.60 E-value=3.8 Score=36.04 Aligned_cols=49 Identities=24% Similarity=0.614 Sum_probs=37.8
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHH-HHHHhccCCCCCCccccCCCccee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNR-WIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~-Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
.....|-||++..+ .+.-.||. +.+=-.||.. |-.. +...||+|+++-.
T Consensus 213 ~~d~kC~lC~e~~~----~ps~t~Cg-----HlFC~~Cl~~~~t~~-------k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPE----VPSCTPCG-----HLFCLSCLLISWTKK-------KYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccC----Cccccccc-----chhhHHHHHHHHHhh-------ccccCchhhhhcc
Confidence 44688999999764 46677765 7788899998 8776 3577999998754
No 64
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=71.48 E-value=3.1 Score=38.15 Aligned_cols=54 Identities=26% Similarity=0.514 Sum_probs=36.9
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
++++.|..|.+.-+. ...-..||.|. . +-|--=|-.-++. -.-.||-|+..|.-
T Consensus 12 deed~cplcie~mdi--tdknf~pc~cg---y---~ic~fc~~~irq~----lngrcpacrr~y~d 65 (480)
T COG5175 12 DEEDYCPLCIEPMDI--TDKNFFPCPCG---Y---QICQFCYNNIRQN----LNGRCPACRRKYDD 65 (480)
T ss_pred cccccCccccccccc--ccCCcccCCcc---c---HHHHHHHHHHHhh----ccCCChHhhhhccc
Confidence 445669999987654 34567899996 3 4454446555442 34789999999863
No 65
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=71.34 E-value=18 Score=24.80 Aligned_cols=14 Identities=21% Similarity=0.422 Sum_probs=11.3
Q ss_pred CccccCCCcceeee
Q psy3895 119 QVACPQCNTKYFIV 132 (185)
Q Consensus 119 ~~~Ce~Ck~~y~i~ 132 (185)
..+|+.|+.+....
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 57899999988754
No 66
>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=70.87 E-value=1.5 Score=27.89 Aligned_cols=48 Identities=29% Similarity=0.738 Sum_probs=28.1
Q ss_pred eeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhccCCCCCCccccCCC
Q psy3895 70 YCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126 (185)
Q Consensus 70 ~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck 126 (185)
.|.||..... ++.|+. |. |. .++|..|+.-=+..... ......|+.|.
T Consensus 1 ~C~vC~~~~~---~~~~i~-C~~C~---~~~H~~C~~~~~~~~~~--~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDD---DGDMIQ-CDSCN---RWYHQECVGPPEKAEEI--PSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCT---TSSEEE-BSTTS---CEEETTTSTSSHSHHSH--HSSSBSSHHHH
T ss_pred eCcCCCCcCC---CCCeEE-cCCCC---hhhCcccCCCChhhccC--CCCcEECcCCc
Confidence 4778887332 456775 54 55 99999998533322110 12267777765
No 67
>KOG2177|consensus
Probab=68.75 E-value=2.4 Score=34.20 Aligned_cols=46 Identities=24% Similarity=0.548 Sum_probs=36.4
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCc
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 127 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~ 127 (185)
.++.-.|.||++...+ +.+.||. +.+=..||..+.. ....||.|+.
T Consensus 10 ~~~~~~C~iC~~~~~~----p~~l~C~-----H~~c~~C~~~~~~--------~~~~Cp~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFRE----PVLLPCG-----HNFCRACLTRSWE--------GPLSCPVCRP 55 (386)
T ss_pred ccccccChhhHHHhhc----Ccccccc-----chHhHHHHHHhcC--------CCcCCcccCC
Confidence 4577899999998864 3777777 5577889988887 2499999995
No 68
>KOG2164|consensus
Probab=67.56 E-value=4.4 Score=38.63 Aligned_cols=52 Identities=13% Similarity=0.338 Sum_probs=38.4
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
...|.|||+...- +...- |. +++=-.||.+.+.... -....+||+|...+.+
T Consensus 186 ~~~CPICL~~~~~----p~~t~--CG---HiFC~~CiLqy~~~s~---~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSV----PVRTN--CG---HIFCGPCILQYWNYSA---IKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCc----ccccc--cC---ceeeHHHHHHHHhhhc---ccCCccCCchhhhccc
Confidence 7899999997642 33332 55 7888899988777642 1356899999998876
No 69
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=66.82 E-value=5.4 Score=35.91 Aligned_cols=51 Identities=18% Similarity=0.336 Sum_probs=39.5
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeec
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVY 133 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~ 133 (185)
+.-..|+||.+--. -|++.||. +-+-.-|+++.+.. .-.||+|.+++....
T Consensus 23 Ds~lrC~IC~~~i~----ip~~TtCg-----HtFCslCIR~hL~~--------qp~CP~Cr~~~~esr 73 (391)
T COG5432 23 DSMLRCRICDCRIS----IPCETTCG-----HTFCSLCIRRHLGT--------QPFCPVCREDPCESR 73 (391)
T ss_pred hhHHHhhhhhheee----cceecccc-----cchhHHHHHHHhcC--------CCCCccccccHHhhh
Confidence 34578999988753 47888887 44778899888875 478999999998764
No 70
>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=63.79 E-value=2.8 Score=30.19 Aligned_cols=33 Identities=30% Similarity=0.588 Sum_probs=22.8
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHH
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNR 106 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~ 106 (185)
+...|.+|...-.. +.-.+-||. +.||..|++|
T Consensus 77 ~~~~C~vC~k~l~~--~~f~~~p~~-----~v~H~~C~~r 109 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN--SVFVVFPCG-----HVVHYSCIKR 109 (109)
T ss_pred CCCCccCcCCcCCC--ceEEEeCCC-----eEEecccccC
Confidence 45779999886643 223456654 7899999864
No 71
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=63.45 E-value=5.9 Score=31.62 Aligned_cols=56 Identities=23% Similarity=0.462 Sum_probs=42.1
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
.--.|-||.+...| ..++.|=.|-|= ..-..=|..-|--.. -..+||.||+.|+-.
T Consensus 79 ~lYeCnIC~etS~e---e~FLKPneCCgY-~iCn~Cya~LWK~~~------~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 79 KLYECNICKETSAE---ERFLKPNECCGY-SICNACYANLWKFCN------LYPVCPVCKTSFKSS 134 (140)
T ss_pred CceeccCcccccch---hhcCCcccccch-HHHHHHHHHHHHHcc------cCCCCCccccccccc
Confidence 66799999998765 479999888872 444445566676653 458999999999854
No 72
>KOG4323|consensus
Probab=63.08 E-value=7.5 Score=36.71 Aligned_cols=63 Identities=29% Similarity=0.494 Sum_probs=47.5
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
....+|-+|+.+.... .+.++.=|+|. .|+|+.|-+=-+.....+.......|..|...-...
T Consensus 166 ~~n~qc~vC~~g~~~~-~NrmlqC~~C~---~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~ 228 (464)
T KOG4323|consen 166 KVNLQCSVCYCGGPGA-GNRMLQCDKCR---QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKV 228 (464)
T ss_pred cccceeeeeecCCcCc-cceeeeecccc---cHHHHHhccCCCCHhhccCccceEeehhhccchhhc
Confidence 3356699999876654 45899988898 999999987666665544556779999998876543
No 73
>KOG3899|consensus
Probab=60.30 E-value=6.6 Score=35.35 Aligned_cols=42 Identities=24% Similarity=0.613 Sum_probs=31.7
Q ss_pred eccCCCCCCccccHHHHHHHHHHhccCC-----CCCCccccCCCcceeee
Q psy3895 88 QPCLCRGTSKWVHQACLNRWIDEKQKGN-----AFTQVACPQCNTKYFIV 132 (185)
Q Consensus 88 ~PC~C~GS~k~VH~~CL~~Wi~~~~~~~-----~~~~~~Ce~Ck~~y~i~ 132 (185)
+-|-|+ ..--.+||.+|....+..- ..++.+||.|+++|-+.
T Consensus 321 ~nc~cr---p~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~ 367 (381)
T KOG3899|consen 321 ENCICR---PLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR 367 (381)
T ss_pred cccccc---cHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence 335677 6677899999999876421 35678999999999764
No 74
>KOG1814|consensus
Probab=60.14 E-value=8 Score=36.13 Aligned_cols=57 Identities=18% Similarity=0.463 Sum_probs=44.2
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
--.|-||++..... ..-...||. ++.=+.||+.......+.+..+..+||.++.+=.
T Consensus 184 lf~C~ICf~e~~G~-~c~~~lpC~-----Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~ 240 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQ-HCFKFLPCS-----HVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSV 240 (445)
T ss_pred cccceeeehhhcCc-ceeeecccc-----hHHHHHHHHHHHHHhhhcceeeeecCCCCCCccc
Confidence 36899999986431 123457877 8888999999998887777788899999987654
No 75
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=55.05 E-value=26 Score=32.47 Aligned_cols=56 Identities=23% Similarity=0.402 Sum_probs=37.9
Q ss_pred ecCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 62 IERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 62 ~~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
++.+++...|.||-.+.+- .-+.||.-+ .-+.|-.|-..- .....|++|+++..-+
T Consensus 55 ddtDEen~~C~ICA~~~TY----s~~~PC~H~-----~CH~Ca~RlRAL------Y~~K~C~~CrTE~e~V 110 (493)
T COG5236 55 DDTDEENMNCQICAGSTTY----SARYPCGHQ-----ICHACAVRLRAL------YMQKGCPLCRTETEAV 110 (493)
T ss_pred cccccccceeEEecCCceE----EEeccCCch-----HHHHHHHHHHHH------HhccCCCccccccceE
Confidence 4557788999999887643 357888733 444555444433 3568999999988643
No 76
>KOG1952|consensus
Probab=53.87 E-value=15 Score=37.20 Aligned_cols=60 Identities=20% Similarity=0.525 Sum_probs=42.6
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
+++...|-||++.-... ...| + |+ ---+.+|..|+++|-....+. ....+.||-|++.+.
T Consensus 188 ~~~~yeCmIC~e~I~~t-~~~W-S-C~--sCYhVFHl~CI~~WArs~ek~-~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRT-APVW-S-CK--SCYHVFHLNCIKKWARSSEKT-GQDGWRCPACQSVSK 247 (950)
T ss_pred hcCceEEEEeeeecccc-CCce-e-cc--hhhhhhhHHHHHHHHHHhhhc-cCccccCCcccchhc
Confidence 45568999999876532 2233 2 33 234899999999999885443 346799999997776
No 77
>KOG0955|consensus
Probab=49.06 E-value=12 Score=38.80 Aligned_cols=37 Identities=22% Similarity=0.411 Sum_probs=26.1
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHH
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLN 105 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~ 105 (185)
.++...|-||++.+... ...|--|. |-..+||++|.-
T Consensus 216 ~~~D~~C~iC~~~~~~n--~n~ivfCD--~Cnl~VHq~Cyg 252 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGECQN--SNVIVFCD--GCNLAVHQECYG 252 (1051)
T ss_pred cCCCccceeecccccCC--CceEEEcC--CCcchhhhhccC
Confidence 36678999999988652 33444354 334999999986
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.94 E-value=8.3 Score=23.53 Aligned_cols=13 Identities=46% Similarity=1.139 Sum_probs=11.8
Q ss_pred ccccCCCcceeee
Q psy3895 120 VACPQCNTKYFIV 132 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~ 132 (185)
+.||.|+++|.+.
T Consensus 3 i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 3 ITCPNCQAKYEID 15 (36)
T ss_pred EECCCCCCEEeCC
Confidence 6899999999986
No 79
>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=48.77 E-value=10 Score=23.97 Aligned_cols=21 Identities=24% Similarity=1.024 Sum_probs=14.1
Q ss_pred ccHHHHHHHHHHhccCCCCCCccccCC
Q psy3895 99 VHQACLNRWIDEKQKGNAFTQVACPQC 125 (185)
Q Consensus 99 VH~~CL~~Wi~~~~~~~~~~~~~Ce~C 125 (185)
+|..|+++++... ...+||.|
T Consensus 23 ~H~~C~~~y~r~~------~~~~CP~C 43 (43)
T PF08746_consen 23 LHDDCFKKYFRHR------SNPKCPNC 43 (43)
T ss_dssp E-HHHHHHHTTT-------SS-B-TTT
T ss_pred HHHHHHHHHHhcC------CCCCCcCC
Confidence 9999999999874 23489987
No 80
>KOG2034|consensus
Probab=47.36 E-value=9.8 Score=38.60 Aligned_cols=38 Identities=24% Similarity=0.365 Sum_probs=27.4
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHH
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDE 110 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~ 110 (185)
+....|++|-..--. ..-.+-||. +.+|.+||.+-+..
T Consensus 815 ep~d~C~~C~~~ll~--~pF~vf~Cg-----H~FH~~Cl~~~v~~ 852 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI--KPFYVFPCG-----HCFHRDCLIRHVLS 852 (911)
T ss_pred cCccchHHhcchhhc--Ccceeeecc-----chHHHHHHHHHHHc
Confidence 346899999765432 234678887 56999999987764
No 81
>KOG0956|consensus
Probab=44.17 E-value=15 Score=36.60 Aligned_cols=66 Identities=18% Similarity=0.284 Sum_probs=41.0
Q ss_pred CCCCCeeeEecccccCCCC-CceeeccCCCCCCccccHHHHHHHHH-HhccCC-CCCCccccCCCccee
Q psy3895 65 SVDLKYCWVCFATHEDDRN-ALWVQPCLCRGTSKWVHQACLNRWID-EKQKGN-AFTQVACPQCNTKYF 130 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~-~~li~PC~C~GS~k~VH~~CL~~Wi~-~~~~~~-~~~~~~Ce~Ck~~y~ 130 (185)
+...+.|.||.+...+... .--..-|+=.|-.+-+|-.|-++-=. -...++ .....+|--||+.|.
T Consensus 114 dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hfs 182 (900)
T KOG0956|consen 114 DRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFS 182 (900)
T ss_pred hhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHH
Confidence 5567999999998655311 11223455334448899999866411 111112 346689999999986
No 82
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=44.05 E-value=11 Score=22.97 Aligned_cols=14 Identities=29% Similarity=0.982 Sum_probs=12.2
Q ss_pred ccccCCCcceeeec
Q psy3895 120 VACPQCNTKYFIVY 133 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~~ 133 (185)
+.||.|++.|++..
T Consensus 3 i~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD 16 (37)
T ss_pred EECCCCCceEEcCH
Confidence 68999999999863
No 83
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=43.97 E-value=18 Score=27.43 Aligned_cols=11 Identities=45% Similarity=0.751 Sum_probs=7.4
Q ss_pred hhhhe-ecccCC
Q psy3895 175 AVTVM-VHHKDF 185 (185)
Q Consensus 175 ~~~i~-~G~~~~ 185 (185)
+|+|. +++|+|
T Consensus 67 ~YTi~sV~Qe~F 78 (100)
T PF09813_consen 67 AYTIYSVKQEDF 78 (100)
T ss_pred hheeeeechhhh
Confidence 34566 888776
No 84
>KOG4692|consensus
Probab=43.72 E-value=18 Score=33.57 Aligned_cols=49 Identities=20% Similarity=0.455 Sum_probs=36.3
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
+-++..|.||+.+. -+..+.||+-+ --..|+.+-+.. ...|=.||+...
T Consensus 419 ~sEd~lCpICyA~p----i~Avf~PC~H~-----SC~~CI~qHlmN--------~k~CFfCktTv~ 467 (489)
T KOG4692|consen 419 DSEDNLCPICYAGP----INAVFAPCSHR-----SCYGCITQHLMN--------CKRCFFCKTTVI 467 (489)
T ss_pred CcccccCcceeccc----chhhccCCCCc-----hHHHHHHHHHhc--------CCeeeEecceee
Confidence 45678999999985 35789999843 445677666654 478999998876
No 85
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=43.10 E-value=17 Score=23.70 Aligned_cols=38 Identities=24% Similarity=0.532 Sum_probs=16.8
Q ss_pred ceeeccCCCCCCccccHHH--HHHHHHHhccCCCCCCccccCCCcc
Q psy3895 85 LWVQPCLCRGTSKWVHQAC--LNRWIDEKQKGNAFTQVACPQCNTK 128 (185)
Q Consensus 85 ~li~PC~C~GS~k~VH~~C--L~~Wi~~~~~~~~~~~~~Ce~Ck~~ 128 (185)
++..|.+=. .-.|.+| |..||....+ .....||+|+.+
T Consensus 11 ~i~~P~Rg~---~C~H~~CFDl~~fl~~~~~---~~~W~CPiC~~~ 50 (50)
T PF02891_consen 11 RIRIPVRGK---NCKHLQCFDLESFLESNQR---TPKWKCPICNKP 50 (50)
T ss_dssp B-SSEEEET---T--SS--EEHHHHHHHHHH---S---B-TTT---
T ss_pred EEEeCccCC---cCcccceECHHHHHHHhhc---cCCeECcCCcCc
Confidence 445565522 5578899 4568887654 345999999864
No 86
>KOG1973|consensus
Probab=41.89 E-value=21 Score=31.10 Aligned_cols=41 Identities=22% Similarity=0.541 Sum_probs=29.1
Q ss_pred CCceeeccCCCCCC-ccccHHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 83 NALWVQPCLCRGTS-KWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 83 ~~~li~PC~C~GS~-k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
.+.+|. |.|.+-- .|+|-.|.- ...-+.+.+.|+.|+..-.
T Consensus 229 yg~Mi~-CDn~~C~~eWFH~~CVG------L~~~PkgkWyC~~C~~~~~ 270 (274)
T KOG1973|consen 229 YGKMIG-CDNPGCPIEWFHFTCVG------LKTKPKGKWYCPRCKAENK 270 (274)
T ss_pred cccccc-cCCCCCCcceEEEeccc------cccCCCCcccchhhhhhhh
Confidence 356887 8887766 999999961 1122456699999987644
No 87
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=41.61 E-value=23 Score=23.09 Aligned_cols=26 Identities=23% Similarity=0.492 Sum_probs=13.1
Q ss_pred HHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 103 CLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 103 CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
-+.+++..-.. ....||+|+.+|.-.
T Consensus 8 ~~~k~i~~l~~----~~~~CPlC~r~l~~e 33 (54)
T PF04423_consen 8 ELKKYIEELKE----AKGCCPLCGRPLDEE 33 (54)
T ss_dssp HHHHHHHHHTT-----SEE-TTT--EE-HH
T ss_pred HHHHHHHHHhc----CCCcCCCCCCCCCHH
Confidence 35666666421 223999999998743
No 88
>KOG1002|consensus
Probab=40.17 E-value=17 Score=35.33 Aligned_cols=57 Identities=19% Similarity=0.438 Sum_probs=43.7
Q ss_pred CCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 64 RSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 64 ~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
+..++..|-+|.+..++ +..+-|. +.+-+-|+..++..-.. .....||.|.....+.
T Consensus 532 enk~~~~C~lc~d~aed----~i~s~Ch-----H~FCrlCi~eyv~~f~~---~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAED----YIESSCH-----HKFCRLCIKEYVESFME---NNNVTCPVCHIGLSID 588 (791)
T ss_pred cccCceeecccCChhhh----hHhhhhh-----HHHHHHHHHHHHHhhhc---ccCCCCcccccccccc
Confidence 34567899999988654 6788776 44788999999887532 2349999999998875
No 89
>PF14353 CpXC: CpXC protein
Probab=38.18 E-value=21 Score=27.04 Aligned_cols=19 Identities=32% Similarity=0.948 Sum_probs=15.3
Q ss_pred CCCCccccCCCcceeeecC
Q psy3895 116 AFTQVACPQCNTKYFIVYP 134 (185)
Q Consensus 116 ~~~~~~Ce~Ck~~y~i~~p 134 (185)
.....+||.|++.+.+.+|
T Consensus 35 ~l~~~~CP~Cg~~~~~~~p 53 (128)
T PF14353_consen 35 SLFSFTCPSCGHKFRLEYP 53 (128)
T ss_pred CcCEEECCCCCCceecCCC
Confidence 4567999999999988643
No 90
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=37.33 E-value=16 Score=20.34 Aligned_cols=14 Identities=21% Similarity=0.626 Sum_probs=11.7
Q ss_pred CCCccccCCCccee
Q psy3895 117 FTQVACPQCNTKYF 130 (185)
Q Consensus 117 ~~~~~Ce~Ck~~y~ 130 (185)
.+...|++|+..|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 56799999998874
No 91
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=36.23 E-value=16 Score=18.67 Aligned_cols=11 Identities=27% Similarity=0.884 Sum_probs=7.1
Q ss_pred cccCCCcceee
Q psy3895 121 ACPQCNTKYFI 131 (185)
Q Consensus 121 ~Ce~Ck~~y~i 131 (185)
.|++|+..|.-
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 69999998863
No 92
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=35.72 E-value=42 Score=29.44 Aligned_cols=13 Identities=23% Similarity=0.835 Sum_probs=8.6
Q ss_pred ccccCCCcceeee
Q psy3895 120 VACPQCNTKYFIV 132 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~ 132 (185)
..|..|+..|.+.
T Consensus 158 v~CghC~~~Fl~~ 170 (256)
T PF09788_consen 158 VICGHCSNTFLFN 170 (256)
T ss_pred EECCCCCCcEecc
Confidence 5677777776654
No 93
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=34.43 E-value=54 Score=23.85 Aligned_cols=21 Identities=24% Similarity=0.480 Sum_probs=16.0
Q ss_pred CccccCCCcceeeecCccchH
Q psy3895 119 QVACPQCNTKYFIVYPYRGLL 139 (185)
Q Consensus 119 ~~~Ce~Ck~~y~i~~p~~~~~ 139 (185)
..+|+.|+..|......-.|.
T Consensus 8 ~~~C~~CG~d~~~~~adDgPA 28 (86)
T PF06170_consen 8 APRCPHCGLDYSHARADDGPA 28 (86)
T ss_pred CCcccccCCccccCCcCccch
Confidence 478999999999876554443
No 94
>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=32.94 E-value=20 Score=20.45 Aligned_cols=13 Identities=23% Similarity=0.751 Sum_probs=9.9
Q ss_pred CCccccCCCccee
Q psy3895 118 TQVACPQCNTKYF 130 (185)
Q Consensus 118 ~~~~Ce~Ck~~y~ 130 (185)
....||.|++.|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 4578999988774
No 95
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.83 E-value=45 Score=31.29 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=12.2
Q ss_pred CCCccccCCCcceeee
Q psy3895 117 FTQVACPQCNTKYFIV 132 (185)
Q Consensus 117 ~~~~~Ce~Ck~~y~i~ 132 (185)
.....|++|++++.-.
T Consensus 13 Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 13 EDDVQCTQCGHKFTSR 28 (465)
T ss_pred cccccccccCCcCCch
Confidence 3456699999998754
No 96
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=32.33 E-value=24 Score=21.07 Aligned_cols=13 Identities=38% Similarity=1.178 Sum_probs=11.6
Q ss_pred ccccCCCcceeee
Q psy3895 120 VACPQCNTKYFIV 132 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~ 132 (185)
..||.|++.|.+.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 6899999999986
No 97
>PF15353 HECA: Headcase protein family homologue
Probab=31.25 E-value=30 Score=26.51 Aligned_cols=20 Identities=25% Similarity=0.898 Sum_probs=15.5
Q ss_pred ccCCCCCCccccHHHHHHHHHHh
Q psy3895 89 PCLCRGTSKWVHQACLNRWIDEK 111 (185)
Q Consensus 89 PC~C~GS~k~VH~~CL~~Wi~~~ 111 (185)
.|... .|+|.+|++.|=..-
T Consensus 37 ~Cp~~---~~MH~~CF~~wE~~i 56 (107)
T PF15353_consen 37 SCPFG---QYMHRECFEKWEDSI 56 (107)
T ss_pred CCCCC---CchHHHHHHHHHHHH
Confidence 36663 899999999996653
No 98
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=30.49 E-value=20 Score=18.69 Aligned_cols=11 Identities=27% Similarity=0.890 Sum_probs=9.2
Q ss_pred cccCCCcceee
Q psy3895 121 ACPQCNTKYFI 131 (185)
Q Consensus 121 ~Ce~Ck~~y~i 131 (185)
.|+.|+..|.-
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 69999998864
No 99
>KOG2068|consensus
Probab=29.78 E-value=68 Score=29.12 Aligned_cols=56 Identities=18% Similarity=0.314 Sum_probs=36.9
Q ss_pred CCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeeecC
Q psy3895 66 VDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIVYP 134 (185)
Q Consensus 66 ~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~~p 134 (185)
.-...|.||.+.... +....-||.|. .-.+..|+.. . ......|+.|+.+|.....
T Consensus 247 ~v~~s~p~~~~~~~~--~d~~~lP~~~~---~~~~l~~~~t---~-----~~~~~~~~~~rk~~~~~t~ 302 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDL--TDSNFLPCPCG---FRLCLFCHKT---I-----SDGDGRCPGCRKPYERNTK 302 (327)
T ss_pred ccCCCCCCCCCcccc--ccccccccccc---ccchhhhhhc---c-----cccCCCCCccCCccccCcc
Confidence 445899999987632 34567899997 2244444422 1 1346899999999876543
No 100
>KOG0978|consensus
Probab=29.35 E-value=27 Score=34.71 Aligned_cols=54 Identities=20% Similarity=0.509 Sum_probs=39.2
Q ss_pred ecCCCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceee
Q psy3895 62 IERSVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFI 131 (185)
Q Consensus 62 ~~~~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i 131 (185)
+..=..--.|..|.+.+- +..|. +|- +.+=..|++.-+..+ ..+||.|++.|-.
T Consensus 637 lk~yK~~LkCs~Cn~R~K----d~vI~--kC~---H~FC~~Cvq~r~etR-------qRKCP~Cn~aFga 690 (698)
T KOG0978|consen 637 LKEYKELLKCSVCNTRWK----DAVIT--KCG---HVFCEECVQTRYETR-------QRKCPKCNAAFGA 690 (698)
T ss_pred HHHHHhceeCCCccCchh----hHHHH--hcc---hHHHHHHHHHHHHHh-------cCCCCCCCCCCCc
Confidence 333344578999996553 34666 453 778889999988875 5899999999964
No 101
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=28.74 E-value=30 Score=28.98 Aligned_cols=15 Identities=20% Similarity=0.791 Sum_probs=13.0
Q ss_pred CCccccCCCcceeee
Q psy3895 118 TQVACPQCNTKYFIV 132 (185)
Q Consensus 118 ~~~~Ce~Ck~~y~i~ 132 (185)
+..+||+|+..|...
T Consensus 4 k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 4 KKITCPVCGKEFKTK 18 (214)
T ss_pred CceECCCCCCeeeee
Confidence 578999999999865
No 102
>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 KOG0956|consensus
Probab=27.78 E-value=36 Score=34.07 Aligned_cols=61 Identities=28% Similarity=0.394 Sum_probs=38.6
Q ss_pred CCeeeEecccccCCCCCceeeccCCCCCCccccHHHHH-------HHHHHhcc-CCCCCCccccCCCccee
Q psy3895 68 LKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLN-------RWIDEKQK-GNAFTQVACPQCNTKYF 130 (185)
Q Consensus 68 ~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~-------~Wi~~~~~-~~~~~~~~Ce~Ck~~y~ 130 (185)
.--|-+|-++..- .++|||. |.=-+-.--|||.|-- -|+=.|-. ...-....||+|-+++-
T Consensus 5 VGGCCVCSDErGW-aeNPLVY-CDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdG 73 (900)
T KOG0956|consen 5 VGGCCVCSDERGW-AENPLVY-CDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDG 73 (900)
T ss_pred ccceeeecCcCCC-ccCceee-ecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCccc
Confidence 3458899876644 3688986 6522223779999953 26544321 11234589999998874
No 104
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=27.27 E-value=27 Score=20.72 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=4.0
Q ss_pred ccccCCCcceeee
Q psy3895 120 VACPQCNTKYFIV 132 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~ 132 (185)
-+||+|+..|...
T Consensus 3 p~Cp~C~se~~y~ 15 (30)
T PF08274_consen 3 PKCPLCGSEYTYE 15 (30)
T ss_dssp ---TTT-----EE
T ss_pred CCCCCCCCcceec
Confidence 4799999999864
No 105
>PRK05978 hypothetical protein; Provisional
Probab=26.65 E-value=98 Score=24.88 Aligned_cols=16 Identities=13% Similarity=0.333 Sum_probs=13.5
Q ss_pred CccccCCCcceeeecC
Q psy3895 119 QVACPQCNTKYFIVYP 134 (185)
Q Consensus 119 ~~~Ce~Ck~~y~i~~p 134 (185)
..+|+.|+.+|.....
T Consensus 52 ~~~C~~CG~~~~~~~a 67 (148)
T PRK05978 52 VDHCAACGEDFTHHRA 67 (148)
T ss_pred CCCccccCCccccCCc
Confidence 4799999999998743
No 106
>PF04532 DUF587: Protein of unknown function (DUF587); InterPro: IPR007618 This domain is found at the N-termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N-terminal to the UL87 (IPR004285 from INTERPRO), which has no known function.
Probab=26.64 E-value=18 Score=30.78 Aligned_cols=29 Identities=28% Similarity=0.554 Sum_probs=19.1
Q ss_pred ecccccCCCCCceeeccCCCCCCccccHH
Q psy3895 74 CFATHEDDRNALWVQPCLCRGTSKWVHQA 102 (185)
Q Consensus 74 C~~~~~~~~~~~li~PC~C~GS~k~VH~~ 102 (185)
|+.++-+-.+.--..|+.|.|.+.|||+.
T Consensus 93 CyCdeWd~~eyl~~~~~~C~GP~LYVhr~ 121 (215)
T PF04532_consen 93 CYCDEWDTNEYLAECAYFCRGPLLYVHRK 121 (215)
T ss_pred eeecceehhhHHhhCCcccCCceEEEEcc
Confidence 66554332112234788999999999993
No 107
>KOG1941|consensus
Probab=26.07 E-value=22 Score=33.32 Aligned_cols=51 Identities=22% Similarity=0.475 Sum_probs=35.9
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCC
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCN 126 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck 126 (185)
++.+-.|-.|-+.-...+ .. ...=+|. +.+|..||...+.. +....||-|+
T Consensus 362 ~e~~L~Cg~CGe~~Glk~-e~-LqALpCs---HIfH~rCl~e~L~~------n~~rsCP~Cr 412 (518)
T KOG1941|consen 362 EETELYCGLCGESIGLKN-ER-LQALPCS---HIFHLRCLQEILEN------NGTRSCPNCR 412 (518)
T ss_pred HHHhhhhhhhhhhhcCCc-cc-ccccchh---HHHHHHHHHHHHHh------CCCCCCccHH
Confidence 445678999977654422 22 2333454 88999999999854 4679999999
No 108
>KOG1100|consensus
Probab=25.60 E-value=41 Score=28.27 Aligned_cols=43 Identities=19% Similarity=0.475 Sum_probs=26.5
Q ss_pred CCCeeeEecccccCCCCCceeeccCCCCCCcccc-HHHHHHHHHHhccCCCCCCccccCCCccee
Q psy3895 67 DLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVH-QACLNRWIDEKQKGNAFTQVACPQCNTKYF 130 (185)
Q Consensus 67 ~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH-~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~ 130 (185)
....||.|...+. .-++.||+- ++| ..| ..+...||+|+..-.
T Consensus 157 ~~~~Cr~C~~~~~----~VlllPCrH-----l~lC~~C------------~~~~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 157 RMRSCRKCGEREA----TVLLLPCRH-----LCLCGIC------------DESLRICPICRSPKT 200 (207)
T ss_pred ccccceecCcCCc----eEEeecccc-----eEecccc------------cccCccCCCCcChhh
Confidence 3445999998763 478899871 111 122 112577999997543
No 109
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=25.36 E-value=28 Score=21.30 Aligned_cols=14 Identities=36% Similarity=1.006 Sum_probs=11.9
Q ss_pred ccccCCCcceeeec
Q psy3895 120 VACPQCNTKYFIVY 133 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~~ 133 (185)
..|+.|+..|++.+
T Consensus 2 r~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 2 RICPKCGRIYHIEF 15 (36)
T ss_dssp EEETTTTEEEETTT
T ss_pred cCcCCCCCcccccc
Confidence 46999999999865
No 110
>PHA03375 hypothetical protein; Provisional
Probab=24.70 E-value=22 Score=35.50 Aligned_cols=28 Identities=29% Similarity=0.654 Sum_probs=19.8
Q ss_pred ecccccCCCCCceeeccCCCCCCccccH
Q psy3895 74 CFATHEDDRNALWVQPCLCRGTSKWVHQ 101 (185)
Q Consensus 74 C~~~~~~~~~~~li~PC~C~GS~k~VH~ 101 (185)
|+.++.+..+.--..+|.|.|.+.|||+
T Consensus 99 CycdeWd~~eyl~~~~~~C~gP~LYvhr 126 (844)
T PHA03375 99 CYCDEWDVNEYLAKTACNCRGPLLYIHR 126 (844)
T ss_pred ccccchhhhhhhhhcccccCCceEEEEe
Confidence 6665544222233489999999999999
No 111
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=24.18 E-value=87 Score=24.95 Aligned_cols=15 Identities=20% Similarity=0.733 Sum_probs=10.9
Q ss_pred CccccHHHHHHHHHH
Q psy3895 96 SKWVHQACLNRWIDE 110 (185)
Q Consensus 96 ~k~VH~~CL~~Wi~~ 110 (185)
|+.+-..|+..|..+
T Consensus 58 M~~iFd~CIDsWkAd 72 (141)
T PRK13743 58 MHSIFDACIDSWKAD 72 (141)
T ss_pred HHHHHHHHHHhhhcC
Confidence 355667888888875
No 112
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.60 E-value=40 Score=22.76 Aligned_cols=15 Identities=33% Similarity=0.780 Sum_probs=11.5
Q ss_pred CCCccccCCCcceee
Q psy3895 117 FTQVACPQCNTKYFI 131 (185)
Q Consensus 117 ~~~~~Ce~Ck~~y~i 131 (185)
.....|+.|+++|.-
T Consensus 19 dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 19 DDIVVCPECGAPYHR 33 (54)
T ss_pred CCEEECCCCCCcccH
Confidence 355889999998873
No 113
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=23.30 E-value=1.1e+02 Score=22.99 Aligned_cols=59 Identities=27% Similarity=0.491 Sum_probs=38.9
Q ss_pred CCCCCCeeeEecccccCCCCCceeecc-------CCCCCCccccHHHHHHHHHHhccC-CCCCCccccCCCc
Q psy3895 64 RSVDLKYCWVCFATHEDDRNALWVQPC-------LCRGTSKWVHQACLNRWIDEKQKG-NAFTQVACPQCNT 127 (185)
Q Consensus 64 ~~~~~~~CrIC~~~~~~~~~~~li~PC-------~C~GS~k~VH~~CL~~Wi~~~~~~-~~~~~~~Ce~Ck~ 127 (185)
|+..+..|..|.....+ ....| .|.+....+=..||.++..+.... .......||-|+-
T Consensus 3 d~~~g~~CHqCrqKt~~-----~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTLD-----FKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cCCCCCCchhhcCCCCC-----CceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 45567889999876543 22345 454445667789999998875421 1245689998876
No 114
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=22.88 E-value=53 Score=20.05 Aligned_cols=31 Identities=23% Similarity=0.754 Sum_probs=16.1
Q ss_pred HHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 102 ACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 102 ~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
+|++...+-..++-....+.|+.|+-+|.+.
T Consensus 4 ~C~~Ey~~p~~RR~~~~~isC~~CGPr~~i~ 34 (35)
T PF07503_consen 4 DCLKEYFDPSNRRFHYQFISCTNCGPRYSII 34 (35)
T ss_dssp HHHHHHCSTTSTTTT-TT--BTTCC-SCCCE
T ss_pred HHHHHHcCCCCCcccCcCccCCCCCCCEEEe
Confidence 5665544333222334678999999988764
No 115
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.80 E-value=2.5e+02 Score=19.47 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=11.9
Q ss_pred CCccccCCCcceeee
Q psy3895 118 TQVACPQCNTKYFIV 132 (185)
Q Consensus 118 ~~~~Ce~Ck~~y~i~ 132 (185)
...+|..|++.+...
T Consensus 7 PH~HC~VCg~aIp~d 21 (64)
T COG4068 7 PHRHCVVCGKAIPPD 21 (64)
T ss_pred CCccccccCCcCCCc
Confidence 357899999998653
No 116
>KOG2114|consensus
Probab=22.59 E-value=50 Score=33.70 Aligned_cols=45 Identities=31% Similarity=0.543 Sum_probs=34.8
Q ss_pred CeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 69 KYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 69 ~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
..|-+|-..- +-|.|+- .|. +-+|+.|+. .+..+||-|+.+++-.
T Consensus 841 skCs~C~~~L----dlP~VhF-~Cg---HsyHqhC~e-----------~~~~~CP~C~~e~~~~ 885 (933)
T KOG2114|consen 841 SKCSACEGTL----DLPFVHF-LCG---HSYHQHCLE-----------DKEDKCPKCLPELRGV 885 (933)
T ss_pred eeecccCCcc----ccceeee-ecc---cHHHHHhhc-----------cCcccCCccchhhhhh
Confidence 4799997654 3578885 787 889999996 2468999999988754
No 117
>KOG4684|consensus
Probab=22.59 E-value=1.4e+02 Score=26.04 Aligned_cols=13 Identities=31% Similarity=0.904 Sum_probs=10.2
Q ss_pred ccccCCCcceeee
Q psy3895 120 VACPQCNTKYFIV 132 (185)
Q Consensus 120 ~~Ce~Ck~~y~i~ 132 (185)
.+|--|+..|.+.
T Consensus 171 V~CgHC~~tFLfn 183 (275)
T KOG4684|consen 171 VKCGHCNETFLFN 183 (275)
T ss_pred EEecCccceeehh
Confidence 5788888888764
No 118
>KOG0801|consensus
Probab=22.35 E-value=45 Score=27.73 Aligned_cols=28 Identities=29% Similarity=0.638 Sum_probs=20.0
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCC
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCR 93 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~ 93 (185)
.++.-.|-||+++-+.. +..-.-||.|-
T Consensus 174 ~ddkGECvICLEdL~~G-dtIARLPCLCI 201 (205)
T KOG0801|consen 174 KDDKGECVICLEDLEAG-DTIARLPCLCI 201 (205)
T ss_pred cccCCcEEEEhhhccCC-CceeccceEEE
Confidence 34567899999987652 34556899995
No 119
>KOG1940|consensus
Probab=22.21 E-value=52 Score=29.15 Aligned_cols=44 Identities=23% Similarity=0.446 Sum_probs=28.3
Q ss_pred eeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCc
Q psy3895 71 CWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNT 127 (185)
Q Consensus 71 CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~ 127 (185)
|.||.+.-... .+....=+|. ++.|..|++.-+.+ . ..||+|+.
T Consensus 161 cPic~e~l~~s--~~~~~~~~Cg---H~~h~~cf~e~~~~-------~-y~CP~C~~ 204 (276)
T KOG1940|consen 161 CPICKEYLFLS--FEDAGVLKCG---HYMHSRCFEEMICE-------G-YTCPICSK 204 (276)
T ss_pred CchhHHHhccc--cccCCccCcc---cchHHHHHHHHhcc-------C-CCCCcccc
Confidence 77776644332 2344444555 88997776655543 3 99999998
No 120
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=21.65 E-value=30 Score=23.49 Aligned_cols=12 Identities=33% Similarity=0.689 Sum_probs=7.1
Q ss_pred ccccCCCcceee
Q psy3895 120 VACPQCNTKYFI 131 (185)
Q Consensus 120 ~~Ce~Ck~~y~i 131 (185)
..||+|+.+...
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 689999999987
No 121
>PF05210 Sprouty: Sprouty protein (Spry); InterPro: IPR007875 Sprouty (Spry) and Spred (Sprouty related EVH1 domain) proteins have been identified as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases [1,2]. These proteins share a conserved, C-terminal cysteine-rich region, the SPR domain. This domain has been defined as a novel cytosol to membrane translocation domain [, , , ]. It has been found to be a PtdIns(4,5)P2-binding domain that targets the proteins to a cellular localization that maximizes their inhibitory potential [, ]. It also mediates homodimer formation of these proteins [, ]. The SPR domain can occur in association with the WH1 domain (see IPR000697 from INTERPRO) (located in the N-terminal part of the proteins) in the Spred proteins.; GO: 0007275 multicellular organismal development, 0009966 regulation of signal transduction, 0016020 membrane
Probab=21.51 E-value=63 Score=24.77 Aligned_cols=18 Identities=33% Similarity=1.019 Sum_probs=15.3
Q ss_pred eccCCCCCCccccHHHHHHHHHH
Q psy3895 88 QPCLCRGTSKWVHQACLNRWIDE 110 (185)
Q Consensus 88 ~PC~C~GS~k~VH~~CL~~Wi~~ 110 (185)
+||.|.. +..|..||..-
T Consensus 60 ~PCSC~~-----~~~c~~RW~~L 77 (108)
T PF05210_consen 60 HPCSCDT-----PSRCCARWLAL 77 (108)
T ss_pred CccccCC-----ccchHHHHHHH
Confidence 5999984 89999999875
No 122
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=21.50 E-value=81 Score=27.58 Aligned_cols=34 Identities=12% Similarity=0.137 Sum_probs=22.7
Q ss_pred hhhhhHHHHHHHHhHHHHHHHHHhhhhhe--ecccC
Q psy3895 151 YKLCPFVAAGVVLGSMYWCAVTYGAVTVM--VHHKD 184 (185)
Q Consensus 151 ~~~~p~i~~~~l~~~~y~~a~~yG~~~i~--~G~~~ 184 (185)
..+.|+++.++|++++.++.++|...=-+ .||..
T Consensus 270 ~~~vPIaVG~~La~lvlivLiaYli~Rrr~~~gYq~ 305 (306)
T PF01299_consen 270 SDLVPIAVGAALAGLVLIVLIAYLIGRRRSRAGYQS 305 (306)
T ss_pred cchHHHHHHHHHHHHHHHHHHhheeEeccccccccc
Confidence 55677777777788777777777654333 55553
No 123
>KOG0802|consensus
Probab=21.49 E-value=39 Score=32.12 Aligned_cols=47 Identities=26% Similarity=0.667 Sum_probs=34.5
Q ss_pred CCCCCeeeEecccccCCCCCceeeccCCCCCCccccHHHHHHHHHHhccCCCCCCccccCCCcceeee
Q psy3895 65 SVDLKYCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACLNRWIDEKQKGNAFTQVACPQCNTKYFIV 132 (185)
Q Consensus 65 ~~~~~~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL~~Wi~~~~~~~~~~~~~Ce~Ck~~y~i~ 132 (185)
.+....|+||+... . .-+.||. |..||..|...+ ..||+|.......
T Consensus 476 ~~~~~~~~~~~~~~-~----~~~~~~~--------~~~~l~~~~~~~--------~~~pl~~~~~~~~ 522 (543)
T KOG0802|consen 476 REPNDVCAICYQEM-S----ARITPCS--------HALCLRKWLYVQ--------EVCPLCHTYMKED 522 (543)
T ss_pred hcccCcchHHHHHH-H----hcccccc--------chhHHHhhhhhc--------cccCCCchhhhcc
Confidence 34568899999876 1 2345555 999999999863 7899998766654
No 124
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=21.28 E-value=55 Score=27.14 Aligned_cols=32 Identities=34% Similarity=0.592 Sum_probs=22.2
Q ss_pred eeeEecccccCCCCCceeeccCCCCCCccccHHHH
Q psy3895 70 YCWVCFATHEDDRNALWVQPCLCRGTSKWVHQACL 104 (185)
Q Consensus 70 ~CrIC~~~~~~~~~~~li~PC~C~GS~k~VH~~CL 104 (185)
.|..|.....+...++||- |.|-..-+|+.||
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~---CQGCs~sYHk~CL 32 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVY---CQGCSSSYHKACL 32 (175)
T ss_pred CcccccCCCCCccCCCeEE---cCccChHHHhhhc
Confidence 4788876443333578886 5555677999998
No 125
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.12 E-value=49 Score=18.38 Aligned_cols=12 Identities=42% Similarity=0.977 Sum_probs=10.1
Q ss_pred ccccCCCcceee
Q psy3895 120 VACPQCNTKYFI 131 (185)
Q Consensus 120 ~~Ce~Ck~~y~i 131 (185)
..|+.|+..|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 689999999953
No 126
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=20.88 E-value=57 Score=30.80 Aligned_cols=59 Identities=20% Similarity=0.504 Sum_probs=34.9
Q ss_pred CeeeEecccccCCCCCceeeccC-CCCCCccccHHHHHHHHHHhcc---CC----CCCCccccCCCcceee
Q psy3895 69 KYCWVCFATHEDDRNALWVQPCL-CRGTSKWVHQACLNRWIDEKQK---GN----AFTQVACPQCNTKYFI 131 (185)
Q Consensus 69 ~~CrIC~~~~~~~~~~~li~PC~-C~GS~k~VH~~CL~~Wi~~~~~---~~----~~~~~~Ce~Ck~~y~i 131 (185)
=.|.||..-+.+..+-.||. |. |. +|.|.+|-.+=-..... .+ ......|--|+..-.+
T Consensus 129 C~C~iC~kfD~~~n~~~Wi~-Cd~Cg---H~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seL 195 (446)
T PF07227_consen 129 CMCCICSKFDDNKNTCSWIG-CDVCG---HWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSEL 195 (446)
T ss_pred CCccccCCcccCCCCeeEEe-ccCCC---ceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhH
Confidence 36778865332223446776 65 44 99999997654332211 11 1235789999987654
Done!