Query 029308
Match_columns 195
No_of_seqs 135 out of 398
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 10:49:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15227 zf-C3HC4_4: zinc fing 99.2 1.5E-11 3.2E-16 80.9 2.1 34 1-34 7-42 (42)
2 smart00504 Ubox Modified RING 98.9 4.1E-10 8.8E-15 76.1 2.5 50 2-53 11-62 (63)
3 TIGR00599 rad18 DNA repair pro 98.7 4.4E-09 9.5E-14 97.4 2.7 53 2-56 36-90 (397)
4 PF00097 zf-C3HC4: Zinc finger 98.7 7.9E-09 1.7E-13 65.4 1.8 33 2-34 8-41 (41)
5 PF13639 zf-RING_2: Ring finge 98.7 6.4E-09 1.4E-13 67.3 0.9 31 3-35 14-44 (44)
6 KOG2177 Predicted E3 ubiquitin 98.6 1.2E-08 2.6E-13 79.3 1.9 51 2-54 23-73 (386)
7 PLN03208 E3 ubiquitin-protein 98.6 2.1E-08 4.6E-13 85.6 3.2 39 2-40 28-80 (193)
8 PF04564 U-box: U-box domain; 98.6 2E-08 4.3E-13 71.9 1.2 56 2-58 14-71 (73)
9 PF13923 zf-C3HC4_2: Zinc fing 98.5 3.2E-08 7E-13 62.9 1.6 29 4-34 10-39 (39)
10 cd00162 RING RING-finger (Real 98.5 1.2E-07 2.6E-12 58.0 2.6 31 7-38 15-45 (45)
11 PF13920 zf-C3HC4_3: Zinc fing 98.4 8.6E-08 1.9E-12 63.6 1.6 35 4-40 14-49 (50)
12 KOG0287 Postreplication repair 98.4 8.7E-08 1.9E-12 88.9 1.4 55 2-58 33-89 (442)
13 PF14835 zf-RING_6: zf-RING of 98.4 6.5E-08 1.4E-12 70.6 0.4 47 1-51 16-65 (65)
14 smart00184 RING Ring finger. E 98.4 2.2E-07 4.7E-12 54.9 2.2 31 3-34 9-39 (39)
15 PF14634 zf-RING_5: zinc-RING 98.3 3E-07 6.5E-12 60.1 2.3 32 3-36 13-44 (44)
16 KOG0823 Predicted E3 ubiquitin 98.1 9.6E-07 2.1E-11 77.4 2.2 37 4-40 59-96 (230)
17 COG5432 RAD18 RING-finger-cont 98.1 2.9E-06 6.2E-11 77.9 4.0 51 3-55 36-88 (391)
18 PF12678 zf-rbx1: RING-H2 zinc 98.0 2.6E-06 5.7E-11 61.4 1.7 28 6-35 46-73 (73)
19 PF13445 zf-RING_UBOX: RING-ty 98.0 2.5E-06 5.3E-11 57.0 0.8 28 5-32 14-43 (43)
20 TIGR00570 cdk7 CDK-activating 97.9 6.7E-06 1.4E-10 74.6 3.2 31 9-40 25-55 (309)
21 KOG2164 Predicted E3 ubiquitin 97.7 1.4E-05 3E-10 76.7 2.2 36 5-40 199-237 (513)
22 PF12861 zf-Apc11: Anaphase-pr 97.6 3.3E-05 7.1E-10 58.9 2.0 35 6-40 48-83 (85)
23 KOG1039 Predicted E3 ubiquitin 97.4 7.3E-05 1.6E-09 68.7 2.5 37 7-43 184-225 (344)
24 KOG0824 Predicted E3 ubiquitin 97.4 5.6E-05 1.2E-09 69.1 1.8 35 5-40 20-54 (324)
25 KOG0825 PHD Zn-finger protein 97.4 6E-05 1.3E-09 76.2 1.6 53 7-61 141-195 (1134)
26 KOG4159 Predicted E3 ubiquitin 97.2 0.00019 4.1E-09 67.0 2.3 39 2-42 94-132 (398)
27 KOG0802 E3 ubiquitin ligase [P 97.1 0.0002 4.4E-09 67.8 1.3 33 5-39 309-341 (543)
28 KOG0827 Predicted E3 ubiquitin 96.9 0.00053 1.1E-08 65.0 2.3 53 8-63 23-77 (465)
29 KOG4628 Predicted E3 ubiquitin 96.9 0.00042 9.1E-09 64.0 1.5 37 3-40 243-279 (348)
30 COG5243 HRD1 HRD ubiquitin lig 96.8 0.00082 1.8E-08 63.7 2.5 33 5-39 313-345 (491)
31 KOG2660 Locus-specific chromos 96.6 0.00048 1E-08 63.4 -0.1 49 3-53 27-77 (331)
32 KOG4739 Uncharacterized protei 96.5 0.00084 1.8E-08 59.2 0.4 43 6-52 19-61 (233)
33 KOG1734 Predicted RING-contain 96.3 0.0012 2.7E-08 60.2 0.3 33 7-39 249-281 (328)
34 KOG0311 Predicted E3 ubiquitin 96.2 0.001 2.2E-08 62.2 -0.6 34 6-40 58-91 (381)
35 COG5194 APC11 Component of SCF 95.9 0.0043 9.2E-08 47.8 1.8 30 9-40 53-82 (88)
36 KOG0297 TNF receptor-associate 95.7 0.005 1.1E-07 56.8 1.5 36 3-40 32-68 (391)
37 PF11789 zf-Nse: Zinc-finger o 95.6 0.0044 9.4E-08 43.5 0.5 32 2-33 21-53 (57)
38 KOG2930 SCF ubiquitin ligase, 95.4 0.0084 1.8E-07 48.1 1.8 29 9-39 80-108 (114)
39 PF14447 Prok-RING_4: Prokaryo 95.3 0.0076 1.7E-07 43.0 1.0 33 4-40 19-51 (55)
40 KOG1493 Anaphase-promoting com 95.3 0.0053 1.1E-07 47.0 0.1 32 9-40 50-82 (84)
41 KOG1785 Tyrosine kinase negati 95.1 0.01 2.2E-07 57.0 1.5 35 6-40 383-417 (563)
42 smart00744 RINGv The RING-vari 94.4 0.027 5.8E-07 38.2 1.9 33 3-35 12-49 (49)
43 PF04641 Rtf2: Rtf2 RING-finge 94.3 0.027 5.8E-07 49.0 2.2 31 7-40 132-162 (260)
44 KOG1002 Nucleotide excision re 94.2 0.02 4.3E-07 56.7 1.3 36 5-40 549-587 (791)
45 KOG1813 Predicted E3 ubiquitin 93.8 0.019 4.1E-07 52.7 0.2 36 3-40 252-287 (313)
46 KOG1001 Helicase-like transcri 93.7 0.025 5.3E-07 56.1 0.9 38 3-40 464-501 (674)
47 KOG0804 Cytoplasmic Zn-finger 93.7 0.025 5.5E-07 54.4 0.9 30 6-39 193-222 (493)
48 KOG1645 RING-finger-containing 92.9 0.049 1.1E-06 52.2 1.4 35 6-40 23-57 (463)
49 PHA03096 p28-like protein; Pro 92.8 0.056 1.2E-06 48.6 1.7 34 6-39 200-234 (284)
50 KOG4185 Predicted E3 ubiquitin 91.9 0.098 2.1E-06 45.2 2.0 33 5-38 22-54 (296)
51 PF14570 zf-RING_4: RING/Ubox 91.9 0.13 2.9E-06 35.6 2.2 32 7-39 17-48 (48)
52 KOG4172 Predicted E3 ubiquitin 91.8 0.046 1E-06 39.7 -0.1 34 6-40 21-55 (62)
53 COG5222 Uncharacterized conser 91.7 0.094 2E-06 49.1 1.7 47 4-57 286-333 (427)
54 KOG2932 E3 ubiquitin ligase in 90.9 0.1 2.2E-06 48.8 1.2 30 7-40 106-135 (389)
55 PF11793 FANCL_C: FANCL C-term 89.9 0.063 1.4E-06 38.6 -0.8 32 8-39 26-66 (70)
56 PHA02825 LAP/PHD finger-like p 89.5 0.32 7E-06 41.2 2.9 52 15-66 35-93 (162)
57 KOG1812 Predicted E3 ubiquitin 89.4 0.23 4.9E-06 46.1 2.1 59 7-66 165-234 (384)
58 KOG1814 Predicted E3 ubiquitin 88.4 0.21 4.6E-06 47.9 1.2 34 6-39 201-240 (445)
59 PHA02862 5L protein; Provision 88.3 0.26 5.6E-06 41.6 1.5 25 16-40 30-54 (156)
60 KOG1941 Acetylcholine receptor 87.6 0.23 5.1E-06 47.8 1.0 32 8-39 385-416 (518)
61 KOG3161 Predicted E3 ubiquitin 87.5 0.32 7E-06 49.2 1.9 29 4-37 27-55 (861)
62 PF05290 Baculo_IE-1: Baculovi 85.3 0.67 1.5E-05 38.6 2.4 33 9-41 101-134 (140)
63 KOG3039 Uncharacterized conser 83.5 0.82 1.8E-05 41.8 2.3 34 5-40 238-271 (303)
64 PF06844 DUF1244: Protein of u 78.2 1.1 2.3E-05 33.4 1.0 11 13-23 11-21 (68)
65 KOG0298 DEAD box-containing he 77.5 0.73 1.6E-05 49.4 -0.0 34 4-39 1166-1199(1394)
66 KOG0825 PHD Zn-finger protein 75.8 0.92 2E-05 47.1 0.2 34 9-42 120-157 (1134)
67 PF03854 zf-P11: P-11 zinc fin 75.7 1.3 2.8E-05 31.3 0.8 28 11-40 20-47 (50)
68 PF11238 DUF3039: Protein of u 75.1 0.53 1.1E-05 34.1 -1.3 35 1-40 22-56 (58)
69 KOG3800 Predicted E3 ubiquitin 75.0 2.7 5.9E-05 38.8 2.9 50 9-62 22-71 (300)
70 COG5236 Uncharacterized conser 74.5 1.9 4.1E-05 41.3 1.9 34 6-40 75-109 (493)
71 smart00647 IBR In Between Ring 74.1 0.93 2E-05 30.1 -0.2 14 9-22 45-58 (64)
72 KOG1815 Predicted E3 ubiquitin 72.4 1.4 3.1E-05 41.1 0.5 20 3-22 177-196 (444)
73 PF14812 PBP1_TM: Transmembran 72.1 1.2 2.7E-05 33.9 0.0 12 94-105 45-56 (81)
74 KOG4362 Transcriptional regula 69.8 1.4 3.1E-05 44.4 -0.1 35 4-39 33-69 (684)
75 KOG1428 Inhibitor of type V ad 69.3 1.5 3.2E-05 48.7 -0.1 36 5-40 3502-3545(3738)
76 cd00350 rubredoxin_like Rubred 67.6 4.3 9.4E-05 25.3 1.8 14 27-40 16-29 (33)
77 KOG4367 Predicted Zn-finger pr 63.4 4 8.6E-05 40.4 1.5 21 2-22 14-34 (699)
78 cd00729 rubredoxin_SM Rubredox 62.6 5.8 0.00013 25.1 1.7 11 29-39 19-29 (34)
79 KOG3113 Uncharacterized conser 62.4 8.8 0.00019 35.3 3.4 31 6-40 129-159 (293)
80 PF12906 RINGv: RING-variant d 59.4 3.8 8.2E-05 27.4 0.5 19 16-34 29-47 (47)
81 PF04423 Rad50_zn_hook: Rad50 58.7 3 6.5E-05 28.2 -0.1 11 30-40 22-32 (54)
82 smart00734 ZnF_Rad18 Rad18-lik 58.6 2.9 6.4E-05 25.2 -0.2 21 29-49 2-22 (26)
83 COG3492 Uncharacterized protei 58.5 4.4 9.6E-05 32.2 0.8 11 13-23 42-52 (104)
84 PF14569 zf-UDP: Zinc-binding 58.4 7.3 0.00016 29.9 1.9 32 9-41 33-64 (80)
85 COG2816 NPY1 NTP pyrophosphohy 57.9 2.4 5.2E-05 38.6 -0.9 57 11-73 110-169 (279)
86 PF01485 IBR: IBR domain; Int 56.7 1.6 3.6E-05 28.8 -1.7 17 6-22 41-58 (64)
87 PLN02195 cellulose synthase A 54.9 7.3 0.00016 41.0 1.8 30 9-39 30-59 (977)
88 PLN02638 cellulose synthase A 54.7 7.3 0.00016 41.4 1.8 31 9-40 41-71 (1079)
89 PF07972 Flavodoxin_NdrI: NrdI 54.6 2.7 5.9E-05 33.6 -1.0 22 108-130 78-99 (122)
90 PF10571 UPF0547: Uncharacteri 54.5 4.2 9E-05 24.7 0.0 23 15-39 3-25 (26)
91 KOG1815 Predicted E3 ubiquitin 54.2 6.3 0.00014 36.9 1.1 20 4-23 83-102 (444)
92 PLN02189 cellulose synthase 53.3 8.3 0.00018 40.8 1.9 31 9-40 58-88 (1040)
93 PF08746 zf-RING-like: RING-li 53.1 11 0.00023 25.0 1.8 26 9-34 18-43 (43)
94 PLN02436 cellulose synthase A 52.7 7.5 0.00016 41.3 1.5 31 9-40 60-90 (1094)
95 KOG4185 Predicted E3 ubiquitin 51.6 5.6 0.00012 34.4 0.4 27 10-37 239-265 (296)
96 PF09538 FYDLN_acid: Protein o 51.4 6.8 0.00015 30.8 0.8 10 30-39 28-37 (108)
97 PLN02915 cellulose synthase A 50.7 8.4 0.00018 40.8 1.5 31 9-40 39-69 (1044)
98 PF13240 zinc_ribbon_2: zinc-r 50.3 3.6 7.8E-05 24.2 -0.7 23 14-38 1-23 (23)
99 PF09723 Zn-ribbon_8: Zinc rib 50.1 5.1 0.00011 26.1 -0.1 26 8-36 9-34 (42)
100 KOG2114 Vacuolar assembly/sort 47.7 8.3 0.00018 40.3 0.9 27 6-37 855-881 (933)
101 PLN02400 cellulose synthase 45.5 12 0.00026 39.8 1.7 31 9-40 60-90 (1085)
102 KOG1812 Predicted E3 ubiquitin 45.2 8.7 0.00019 35.8 0.6 27 7-35 326-352 (384)
103 KOG3053 Uncharacterized conser 45.1 9.4 0.0002 35.2 0.8 30 14-43 51-86 (293)
104 PF02891 zf-MIZ: MIZ/SP-RING z 45.0 16 0.00034 24.8 1.7 29 8-37 19-50 (50)
105 PF06524 NOA36: NOA36 protein; 42.6 21 0.00046 33.1 2.6 39 2-40 180-221 (314)
106 COG4640 Predicted membrane pro 41.8 6.9 0.00015 37.9 -0.6 39 13-53 2-42 (465)
107 PF14353 CpXC: CpXC protein 41.4 9.7 0.00021 29.4 0.2 12 29-40 2-13 (128)
108 PF07975 C1_4: TFIIH C1-like d 40.6 25 0.00054 24.6 2.2 18 30-47 23-43 (51)
109 TIGR02605 CxxC_CxxC_SSSS putat 38.3 14 0.00031 24.3 0.6 27 8-39 9-38 (52)
110 cd00065 FYVE FYVE domain; Zinc 38.3 14 0.00031 24.3 0.7 16 8-23 22-37 (57)
111 KOG3002 Zn finger protein [Gen 36.9 14 0.00031 33.6 0.6 41 10-56 67-107 (299)
112 PF10013 DUF2256: Uncharacteri 36.3 19 0.00042 24.6 1.0 11 29-39 9-19 (42)
113 COG3813 Uncharacterized protei 36.0 24 0.00052 27.1 1.6 26 11-40 28-53 (84)
114 KOG1609 Protein involved in mR 34.9 22 0.00047 30.2 1.4 26 15-40 110-135 (323)
115 PTZ00364 dipeptidyl-peptidase 34.8 16 0.00034 36.0 0.6 12 114-125 432-443 (548)
116 PF15556 Zwint: ZW10 interacto 34.8 47 0.001 30.0 3.5 23 164-186 112-143 (252)
117 PF05883 Baculo_RING: Baculovi 34.7 15 0.00033 30.4 0.4 12 12-23 55-66 (134)
118 PF09986 DUF2225: Uncharacteri 34.6 17 0.00037 31.0 0.7 12 29-40 6-17 (214)
119 PF04710 Pellino: Pellino; In 34.3 13 0.00029 35.8 0.0 32 6-40 305-340 (416)
120 PRK00564 hypA hydrogenase nick 33.1 16 0.00035 28.6 0.3 29 11-39 70-99 (117)
121 PF10497 zf-4CXXC_R1: Zinc-fin 32.9 44 0.00095 26.0 2.7 29 11-39 37-72 (105)
122 KOG1356 Putative transcription 32.7 12 0.00027 38.9 -0.5 33 8-40 247-283 (889)
123 cd02620 Peptidase_C1A_Cathepsi 32.3 18 0.00039 30.6 0.5 12 114-125 211-222 (236)
124 TIGR02300 FYDLN_acid conserved 32.1 18 0.00038 29.9 0.4 27 14-40 11-38 (129)
125 cd02698 Peptidase_C1A_Cathepsi 32.0 18 0.00039 30.6 0.5 12 114-125 206-217 (239)
126 cd02248 Peptidase_C1A Peptidas 31.9 18 0.00039 28.9 0.4 11 114-124 185-195 (210)
127 PF07191 zinc-ribbons_6: zinc- 31.9 5.8 0.00013 29.6 -2.2 35 5-42 10-44 (70)
128 KOG3970 Predicted E3 ubiquitin 31.2 34 0.00074 31.4 2.0 36 3-38 63-104 (299)
129 PRK01343 zinc-binding protein; 30.8 29 0.00063 25.0 1.2 11 29-39 10-20 (57)
130 PF06906 DUF1272: Protein of u 30.6 39 0.00085 24.5 1.9 24 13-40 30-53 (57)
131 PF09237 GAGA: GAGA factor; I 30.5 13 0.00029 26.6 -0.5 13 28-40 24-36 (54)
132 PF14311 DUF4379: Domain of un 30.4 25 0.00054 23.7 0.9 11 30-40 30-40 (55)
133 PRK12380 hydrogenase nickel in 30.2 14 0.00031 28.8 -0.5 26 13-38 71-96 (113)
134 TIGR00100 hypA hydrogenase nic 30.0 14 0.0003 28.8 -0.5 27 13-39 71-97 (115)
135 KOG1952 Transcription factor N 29.9 27 0.00058 36.8 1.3 31 9-39 212-247 (950)
136 COG4338 Uncharacterized protei 29.8 17 0.00036 26.0 -0.1 12 29-40 13-24 (54)
137 PRK02551 flavoprotein NrdI; Pr 29.8 8.7 0.00019 31.8 -1.8 28 107-135 99-126 (154)
138 PF14169 YdjO: Cold-inducible 29.5 29 0.00063 25.1 1.1 14 27-40 38-51 (59)
139 PF01155 HypA: Hydrogenase exp 29.5 7.4 0.00016 30.1 -2.1 27 13-39 71-97 (113)
140 PF01363 FYVE: FYVE zinc finge 29.1 23 0.00049 24.4 0.5 20 22-41 3-22 (69)
141 PF00096 zf-C2H2: Zinc finger, 29.0 16 0.00035 19.9 -0.2 11 30-40 2-12 (23)
142 cd02621 Peptidase_C1A_Cathepsi 28.9 22 0.00049 29.9 0.5 13 113-125 214-226 (243)
143 PF00112 Peptidase_C1: Papain 27.8 24 0.00051 27.9 0.4 13 113-125 191-203 (219)
144 COG4647 AcxC Acetone carboxyla 27.6 23 0.00049 30.0 0.3 9 8-16 73-81 (165)
145 PF13894 zf-C2H2_4: C2H2-type 27.5 23 0.0005 18.6 0.2 11 30-40 2-12 (24)
146 smart00645 Pept_C1 Papain fami 27.4 23 0.0005 28.6 0.3 12 114-125 147-158 (174)
147 PF05605 zf-Di19: Drought indu 26.6 41 0.00089 22.5 1.4 12 28-39 2-13 (54)
148 PTZ00203 cathepsin L protease; 26.5 25 0.00054 32.3 0.4 12 113-124 312-323 (348)
149 KOG2231 Predicted E3 ubiquitin 26.4 41 0.0009 34.2 1.9 34 7-40 15-53 (669)
150 KOG3039 Uncharacterized conser 26.2 40 0.00087 31.2 1.6 19 4-22 55-73 (303)
151 PF10083 DUF2321: Uncharacteri 26.1 40 0.00087 28.7 1.5 25 11-40 27-51 (158)
152 KOG1543 Cysteine proteinase Ca 26.1 28 0.0006 31.6 0.6 13 113-125 295-307 (325)
153 PF14369 zf-RING_3: zinc-finge 25.7 21 0.00045 22.9 -0.2 28 12-39 2-32 (35)
154 PF13913 zf-C2HC_2: zinc-finge 25.1 33 0.00071 20.2 0.6 12 29-40 3-14 (25)
155 PF11693 DUF2990: Protein of u 24.3 35 0.00075 25.3 0.7 18 83-103 14-31 (64)
156 KOG2907 RNA polymerase I trans 23.8 28 0.0006 28.4 0.1 47 11-57 6-55 (116)
157 PF08882 Acetone_carb_G: Aceto 23.6 32 0.0007 27.8 0.5 11 6-16 25-35 (112)
158 PRK14559 putative protein seri 22.7 39 0.00085 33.9 1.0 25 11-39 14-38 (645)
159 PF15337 Vasculin: Vascular pr 22.6 54 0.0012 26.0 1.5 34 93-130 35-68 (97)
160 PTZ00200 cysteine proteinase; 22.6 32 0.0007 32.9 0.3 13 113-125 414-426 (448)
161 PF00301 Rubredoxin: Rubredoxi 21.8 57 0.0012 22.3 1.3 13 25-37 31-43 (47)
162 PF09297 zf-NADH-PPase: NADH p 21.7 24 0.00051 21.6 -0.5 27 11-37 2-30 (32)
163 KOG1940 Zn-finger protein [Gen 21.5 38 0.00082 30.9 0.6 47 4-52 174-220 (276)
164 cd02619 Peptidase_C1 C1 Peptid 21.5 37 0.00081 26.8 0.5 13 114-126 200-212 (223)
165 PF13248 zf-ribbon_3: zinc-rib 21.4 22 0.00048 21.0 -0.7 9 29-37 17-25 (26)
166 COG1885 Uncharacterized protei 21.4 38 0.00082 27.5 0.5 26 28-53 49-76 (115)
167 cd00730 rubredoxin Rubredoxin; 21.3 63 0.0014 22.3 1.5 15 26-40 32-46 (50)
168 PF04216 FdhE: Protein involve 20.6 28 0.0006 30.6 -0.5 28 11-40 196-223 (290)
169 PLN02248 cellulose synthase-li 20.4 67 0.0015 34.7 2.1 32 7-40 147-178 (1135)
170 COG4357 Zinc finger domain con 20.4 68 0.0015 25.7 1.7 18 23-40 75-92 (105)
171 PRK11595 DNA utilization prote 20.3 80 0.0017 26.8 2.2 25 13-39 21-45 (227)
172 PF13465 zf-H2C2_2: Zinc-finge 20.2 29 0.00064 20.2 -0.3 11 29-39 15-25 (26)
173 PF10161 DDDD: Putative mitoch 20.1 41 0.00089 25.7 0.4 15 80-95 63-77 (79)
No 1
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.15 E-value=1.5e-11 Score=80.87 Aligned_cols=34 Identities=21% Similarity=0.406 Sum_probs=25.2
Q ss_pred CCCCCCcCCCCCcccHHhHHhhhccCCC--CCCCCC
Q 029308 1 MLGQDSSPGNGSCKSATCILRWASYVRN--PTCPQC 34 (195)
Q Consensus 1 ~~~QpVtl~CGHsFC~~CI~rW~e~kq~--~sCP~C 34 (195)
+|.+||+++|||+||..||.+||+.... ..||+|
T Consensus 7 ~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 7 LFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp B-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred hhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 4789999999999999999998875444 479998
No 2
>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=98.95 E-value=4.1e-10 Score=76.05 Aligned_cols=50 Identities=18% Similarity=0.269 Sum_probs=41.5
Q ss_pred CCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc--Cccccccccchhh
Q 029308 2 LGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF--LHVHRSLDGSISD 53 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~--l~vNr~LdG~ved 53 (195)
+..||+++|||+||+.||.+|+.. ..+||+|+.+++. +.+|..|.+.+++
T Consensus 11 ~~~Pv~~~~G~v~~~~~i~~~~~~--~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 11 MKDPVILPSGQTYERRAIEKWLLS--HGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred CCCCEECCCCCEEeHHHHHHHHHH--CCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 456899999999999999999765 3689999999974 7788877776654
No 3
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.74 E-value=4.4e-09 Score=97.43 Aligned_cols=53 Identities=17% Similarity=0.275 Sum_probs=45.7
Q ss_pred CCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc--Cccccccccchhhhhh
Q 029308 2 LGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF--LHVHRSLDGSISDYMF 56 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~--l~vNr~LdG~vedy~~ 56 (195)
+..||+++|||.||..||..|+... ..||+|+.++.. +..|..|.++|+.|..
T Consensus 36 ~~~PvitpCgH~FCs~CI~~~l~~~--~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~~~ 90 (397)
T TIGR00599 36 FDVPVLTSCSHTFCSLCIRRCLSNQ--PKCPLCRAEDQESKLRSNWLVSEIVESFKN 90 (397)
T ss_pred hhCccCCCCCCchhHHHHHHHHhCC--CCCCCCCCccccccCccchHHHHHHHHHHH
Confidence 5678999999999999999987653 579999999875 7889999999988764
No 4
>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=98.68 E-value=7.9e-09 Score=65.36 Aligned_cols=33 Identities=18% Similarity=0.487 Sum_probs=27.5
Q ss_pred CCCCC-cCCCCCcccHHhHHhhhccCCCCCCCCC
Q 029308 2 LGQDS-SPGNGSCKSATCILRWASYVRNPTCPQC 34 (195)
Q Consensus 2 ~~QpV-tl~CGHsFC~~CI~rW~e~kq~~sCP~C 34 (195)
+.+++ +++|||.||..||.+|++......||+|
T Consensus 8 ~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 8 FEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp CSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred ccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 34566 8999999999999999875555789998
No 5
>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=98.66 E-value=6.4e-09 Score=67.28 Aligned_cols=31 Identities=23% Similarity=0.542 Sum_probs=25.7
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCC
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCK 35 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK 35 (195)
..++.++|||.||..||.+|.... .+||+||
T Consensus 14 ~~~~~l~C~H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 14 EKVVKLPCGHVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp SCEEEETTSEEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CeEEEccCCCeeCHHHHHHHHHhC--CcCCccC
Confidence 356788999999999999998664 6999996
No 6
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.63 E-value=1.2e-08 Score=79.32 Aligned_cols=51 Identities=18% Similarity=0.267 Sum_probs=38.0
Q ss_pred CCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCccccccccchhhh
Q 029308 2 LGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSISDY 54 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~vedy 54 (195)
|.+|++++|||+||..||..+|. ....||.|+.+...+..|..|.++++.+
T Consensus 23 ~~~p~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr~~~~~~~~n~~l~~~~~~~ 73 (386)
T KOG2177|consen 23 FREPVLLPCGHNFCRACLTRSWE--GPLSCPVCRPPSRNLRPNVLLANLVERL 73 (386)
T ss_pred hhcCccccccchHhHHHHHHhcC--CCcCCcccCCchhccCccHHHHHHHHHH
Confidence 56789999999999999999776 4468999996333455566666555444
No 7
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.62 E-value=2.1e-08 Score=85.58 Aligned_cols=39 Identities=23% Similarity=0.438 Sum_probs=31.9
Q ss_pred CCCCCcCCCCCcccHHhHHhhhcc--------------CCCCCCCCCCCCCCc
Q 029308 2 LGQDSSPGNGSCKSATCILRWASY--------------VRNPTCPQCKHPFEF 40 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~--------------kq~~sCP~CK~pFs~ 40 (195)
+..||++.|||.||..||.+|... +....||+||.+++.
T Consensus 28 ~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 28 VRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 457899999999999999999632 123589999999985
No 8
>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=98.56 E-value=2e-08 Score=71.90 Aligned_cols=56 Identities=21% Similarity=0.341 Sum_probs=44.6
Q ss_pred CCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc--Cccccccccchhhhhhhh
Q 029308 2 LGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF--LHVHRSLDGSISDYMFEE 58 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~--l~vNr~LdG~vedy~~Ee 58 (195)
+-+||.++|||+|++.||.+|... ...+||+|+.+++. +.+|..|...|+.|..++
T Consensus 14 M~dPVi~~~G~tyer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~~~~~ 71 (73)
T PF04564_consen 14 MRDPVILPSGHTYERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRALKSAIEEWCAEN 71 (73)
T ss_dssp -SSEEEETTSEEEEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHHHHHHHHHHHHC
T ss_pred hhCceeCCcCCEEcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHHHHHHHHHHHHc
Confidence 467999999999999999999765 34799999999986 899999999999987664
No 9
>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=98.54 E-value=3.2e-08 Score=62.93 Aligned_cols=29 Identities=28% Similarity=0.629 Sum_probs=24.0
Q ss_pred CC-CcCCCCCcccHHhHHhhhccCCCCCCCCC
Q 029308 4 QD-SSPGNGSCKSATCILRWASYVRNPTCPQC 34 (195)
Q Consensus 4 Qp-Vtl~CGHsFC~~CI~rW~e~kq~~sCP~C 34 (195)
+| +.++|||+||..||.+|.+. ...||+|
T Consensus 10 ~~~~~~~CGH~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 10 DPVVVTPCGHSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp SEEEECTTSEEEEHHHHHHHHHC--TSB-TTT
T ss_pred CcCEECCCCCchhHHHHHHHHHC--cCCCcCC
Confidence 46 68999999999999999665 3799998
No 10
>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=98.46 E-value=1.2e-07 Score=58.04 Aligned_cols=31 Identities=29% Similarity=0.679 Sum_probs=24.9
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCC
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPF 38 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pF 38 (195)
+.+|||.||..|+..|... ....||+|+..+
T Consensus 15 ~~~C~H~~c~~C~~~~~~~-~~~~Cp~C~~~~ 45 (45)
T cd00162 15 LLPCGHVFCRSCIDKWLKS-GKNTCPLCRTPI 45 (45)
T ss_pred ecCCCChhcHHHHHHHHHh-CcCCCCCCCCcC
Confidence 3449999999999999765 346899999864
No 11
>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=98.43 E-value=8.6e-08 Score=63.64 Aligned_cols=35 Identities=26% Similarity=0.464 Sum_probs=29.0
Q ss_pred CCCcCCCCCc-ccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 4 QDSSPGNGSC-KSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 4 QpVtl~CGHs-FC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.++.++|||. ||..|+.+|+. ....||+|+++++.
T Consensus 14 ~~~~~pCgH~~~C~~C~~~~~~--~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 14 DVVLLPCGHLCFCEECAERLLK--RKKKCPICRQPIES 49 (50)
T ss_dssp SEEEETTCEEEEEHHHHHHHHH--TTSBBTTTTBB-SE
T ss_pred ceEEeCCCChHHHHHHhHHhcc--cCCCCCcCChhhcC
Confidence 4678899999 99999999976 34789999999863
No 12
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.40 E-value=8.7e-08 Score=88.92 Aligned_cols=55 Identities=24% Similarity=0.410 Sum_probs=48.1
Q ss_pred CCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc--Cccccccccchhhhhhhh
Q 029308 2 LGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF--LHVHRSLDGSISDYMFEE 58 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~--l~vNr~LdG~vedy~~Ee 58 (195)
|-=|++++|||.||..||.++..++ +.||.|..+|.. |..|+.|+.+|+.|.|--
T Consensus 33 f~ip~itpCsHtfCSlCIR~~L~~~--p~CP~C~~~~~Es~Lr~n~il~Eiv~S~~~~R 89 (442)
T KOG0287|consen 33 FNIPMITPCSHTFCSLCIRKFLSYK--PQCPTCCVTVTESDLRNNRILDEIVKSLNFAR 89 (442)
T ss_pred hcCceeccccchHHHHHHHHHhccC--CCCCceecccchhhhhhhhHHHHHHHHHHHHH
Confidence 4458999999999999999986655 789999999996 889999999999888764
No 13
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.40 E-value=6.5e-08 Score=70.59 Aligned_cols=47 Identities=26% Similarity=0.473 Sum_probs=24.6
Q ss_pred CCCCCC-cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC--cCccccccccch
Q 029308 1 MLGQDS-SPGNGSCKSATCILRWASYVRNPTCPQCKHPFE--FLHVHRSLDGSI 51 (195)
Q Consensus 1 ~~~QpV-tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs--~l~vNr~LdG~v 51 (195)
++.+|| +-.|.|+||..||..-.. ..||+|..|-- .+.+|+.|+++|
T Consensus 16 ~l~~pv~l~~CeH~fCs~Ci~~~~~----~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 16 ILKEPVCLGGCEHIFCSSCIRDCIG----SECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp --SS-B---SSS--B-TTTGGGGTT----TB-SSS--B-S-SS----HHHHHHH
T ss_pred HhcCCceeccCccHHHHHHhHHhcC----CCCCCcCChHHHHHHHhhhhhhccC
Confidence 467888 489999999999987422 35999999984 599999998864
No 14
>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=98.37 E-value=2.2e-07 Score=54.92 Aligned_cols=31 Identities=29% Similarity=0.605 Sum_probs=25.5
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCC
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQC 34 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~C 34 (195)
..++.++|||.||..||..|.. .....||.|
T Consensus 9 ~~~~~~~C~H~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 9 KDPVVLPCGHTFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcEEecCCChHHHHHHHHHHH-hCcCCCCCC
Confidence 3577899999999999999976 234579998
No 15
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.33 E-value=3e-07 Score=60.08 Aligned_cols=32 Identities=16% Similarity=0.447 Sum_probs=26.8
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCC
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCKH 36 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~ 36 (195)
.++++++|||+||..||.++. .....||+|++
T Consensus 13 ~~~~l~~CgH~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 13 RRPRLTSCGHIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CCeEEcccCCHHHHHHHHhhc--CCCCCCcCCCC
Confidence 468899999999999999984 33468999985
No 16
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=9.6e-07 Score=77.39 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=31.3
Q ss_pred CCCcCCCCCcccHHhHHhhhccCCC-CCCCCCCCCCCc
Q 029308 4 QDSSPGNGSCKSATCILRWASYVRN-PTCPQCKHPFEF 40 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW~e~kq~-~sCP~CK~pFs~ 40 (195)
+||...|||-||.-||-+|.....+ ..||+||...+.
T Consensus 59 dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 59 DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCEEeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 5899999999999999999764333 478999999985
No 17
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.09 E-value=2.9e-06 Score=77.89 Aligned_cols=51 Identities=18% Similarity=0.187 Sum_probs=37.5
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc--Cccccccccchhhhh
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF--LHVHRSLDGSISDYM 55 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~--l~vNr~LdG~vedy~ 55 (195)
.=|+..+|||.||..||.+..... +.||+|+.+|.+ +.-+..+.-+++.|.
T Consensus 36 ~ip~~TtCgHtFCslCIR~hL~~q--p~CP~Cr~~~~esrlr~~s~~~ei~es~~ 88 (391)
T COG5432 36 SIPCETTCGHTFCSLCIRRHLGTQ--PFCPVCREDPCESRLRGSSGSREINESHA 88 (391)
T ss_pred ecceecccccchhHHHHHHHhcCC--CCCccccccHHhhhcccchhHHHHHHhhh
Confidence 457889999999999999975433 789999999986 444444444444443
No 18
>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=98.00 E-value=2.6e-06 Score=61.41 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=22.6
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCC
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCK 35 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK 35 (195)
+...|||.|...||.+|.+.. .+||+||
T Consensus 46 ~~~~C~H~FH~~Ci~~Wl~~~--~~CP~CR 73 (73)
T PF12678_consen 46 VWGPCGHIFHFHCISQWLKQN--NTCPLCR 73 (73)
T ss_dssp EEETTSEEEEHHHHHHHHTTS--SB-TTSS
T ss_pred EecccCCCEEHHHHHHHHhcC--CcCCCCC
Confidence 345899999999999997654 5999997
No 19
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.96 E-value=2.5e-06 Score=57.04 Aligned_cols=28 Identities=14% Similarity=0.273 Sum_probs=18.7
Q ss_pred CCcCCCCCcccHHhHHhhhccC--CCCCCC
Q 029308 5 DSSPGNGSCKSATCILRWASYV--RNPTCP 32 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~k--q~~sCP 32 (195)
|+.|+|||+||..||.++++.. ....||
T Consensus 14 P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 14 PMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 7889999999999999987643 345787
No 20
>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=97.92 E-value=6.7e-06 Score=74.63 Aligned_cols=31 Identities=19% Similarity=0.451 Sum_probs=25.6
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+|||+||.+||...|.. ....||+|+.++..
T Consensus 25 ~CGH~~C~sCv~~l~~~-~~~~CP~C~~~lrk 55 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVR-GSGSCPECDTPLRK 55 (309)
T ss_pred CCCCcccHHHHHHHhcC-CCCCCCCCCCccch
Confidence 69999999999995443 33589999999885
No 21
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.74 E-value=1.4e-05 Score=76.73 Aligned_cols=36 Identities=22% Similarity=0.544 Sum_probs=28.6
Q ss_pred CCcCCCCCcccHHhHHhhhcc---CCCCCCCCCCCCCCc
Q 029308 5 DSSPGNGSCKSATCILRWASY---VRNPTCPQCKHPFEF 40 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~---kq~~sCP~CK~pFs~ 40 (195)
|+...|||.||..||+++|.. +....||+|+..+..
T Consensus 199 p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 199 PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 567789999999999996643 333479999988874
No 22
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=97.60 E-value=3.3e-05 Score=58.88 Aligned_cols=35 Identities=29% Similarity=0.676 Sum_probs=27.9
Q ss_pred CcCCCCCcccHHhHHhhhccC-CCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWASYV-RNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~k-q~~sCP~CK~pFs~ 40 (195)
|.-.|+|+|-..||.+|.+.. .+..||+||++|..
T Consensus 48 v~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 48 VWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred eeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 334799999999999997643 34689999999863
No 23
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=7.3e-05 Score=68.67 Aligned_cols=37 Identities=24% Similarity=0.661 Sum_probs=30.3
Q ss_pred cCCCCCcccHHhHHhhhccCC-----CCCCCCCCCCCCcCcc
Q 029308 7 SPGNGSCKSATCILRWASYVR-----NPTCPQCKHPFEFLHV 43 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq-----~~sCP~CK~pFs~l~v 43 (195)
.++|.|.||..||.+|....+ ...||+||.+...+.+
T Consensus 184 lpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~p 225 (344)
T KOG1039|consen 184 LPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNP 225 (344)
T ss_pred CCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccc
Confidence 478999999999999975544 4689999998886544
No 24
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.44 E-value=5.6e-05 Score=69.11 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=28.5
Q ss_pred CCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 5 DSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
||.+.|+|.||+-||.--. .....+||+|+.||.+
T Consensus 20 Pv~l~C~HkFCyiCiKGsy-~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 20 PVNLYCFHKFCYICIKGSY-KNDKKTCAVCRFPIDS 54 (324)
T ss_pred Cccccccchhhhhhhcchh-hcCCCCCceecCCCCc
Confidence 7999999999999999821 1223589999999996
No 25
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.41 E-value=6e-05 Score=76.17 Aligned_cols=53 Identities=21% Similarity=0.263 Sum_probs=40.8
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCcccccccc--chhhhhhhhhhH
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDG--SISDYMFEESVC 61 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG--~vedy~~EeSvc 61 (195)
-+.|+|.||..||..|.... .+||+|+..|..+.|--...+ .+..+++||+--
T Consensus 141 ~k~c~H~FC~~Ci~sWsR~a--qTCPiDR~EF~~v~V~eS~~~~~~vR~lP~EEs~~ 195 (1134)
T KOG0825|consen 141 EKHTAHYFCEECVGSWSRCA--QTCPVDRGEFGEVKVLESTGIEANVRCLPSEESEN 195 (1134)
T ss_pred ccccccccHHHHhhhhhhhc--ccCchhhhhhheeeeeccccccceeEecchhhhhh
Confidence 47899999999999997665 589999999998655444433 556788887743
No 26
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00019 Score=67.04 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=31.9
Q ss_pred CCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCc
Q 029308 2 LGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFLH 42 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~ 42 (195)
|=-||+++|||+||..||.+-.. +.+.||.|+.++..+.
T Consensus 94 l~~pv~tpcghs~c~~Cl~r~ld--~~~~cp~Cr~~l~e~~ 132 (398)
T KOG4159|consen 94 LYPPVVTPCGHSFCLECLDRSLD--QETECPLCRDELVELP 132 (398)
T ss_pred cCCCccccccccccHHHHHHHhc--cCCCCcccccccccch
Confidence 34588999999999999999433 4478999999998643
No 27
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.07 E-value=0.0002 Score=67.79 Aligned_cols=33 Identities=21% Similarity=0.506 Sum_probs=28.5
Q ss_pred CCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 5 DSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
+--++|||.||..|+.+|.+.+ .+||.||..+.
T Consensus 309 ~~rL~C~Hifh~~CL~~W~er~--qtCP~CR~~~~ 341 (543)
T KOG0802|consen 309 PKRLPCGHIFHDSCLRSWFERQ--QTCPTCRTVLY 341 (543)
T ss_pred cceeecccchHHHHHHHHHHHh--CcCCcchhhhh
Confidence 5668999999999999998875 68999999544
No 28
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00053 Score=64.95 Aligned_cols=53 Identities=32% Similarity=0.483 Sum_probs=37.7
Q ss_pred CC-CCCcccHHhHHhhhccCCC-CCCCCCCCCCCcCccccccccchhhhhhhhhhHHH
Q 029308 8 PG-NGSCKSATCILRWASYVRN-PTCPQCKHPFEFLHVHRSLDGSISDYMFEESVCLL 63 (195)
Q Consensus 8 l~-CGHsFC~~CI~rW~e~kq~-~sCP~CK~pFs~l~vNr~LdG~vedy~~EeSvcLL 63 (195)
|+ |||.|--.|+.+|-+.... ..||+|+-......+. ..+..|..+||++.|+
T Consensus 23 i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~---N~~~~d~vvEe~~Vld 77 (465)
T KOG0827|consen 23 IGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA---NPSTVDHVVEESVVLD 77 (465)
T ss_pred ccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee---chhhhhhhhccchhhh
Confidence 55 9999999999999876544 3799999555442221 2445677778887764
No 29
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.87 E-value=0.00042 Score=63.99 Aligned_cols=37 Identities=19% Similarity=0.338 Sum_probs=29.5
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+.-..|+|.|.|-..||-.|.... ...||+||.....
T Consensus 243 dklRiLPC~H~FH~~CIDpWL~~~-r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 243 DKLRILPCSHKFHVNCIDPWLTQT-RTFCPVCKRDIRT 279 (348)
T ss_pred CeeeEecCCCchhhccchhhHhhc-CccCCCCCCcCCC
Confidence 345679999999999999997654 3579999996553
No 30
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=96.76 E-value=0.00082 Score=63.66 Aligned_cols=33 Identities=24% Similarity=0.573 Sum_probs=28.6
Q ss_pred CCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 5 DSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
|--++|||.|-..|+..|.+.+ .+||+||.|.-
T Consensus 313 pKrLpCGHilHl~CLknW~ERq--QTCPICr~p~i 345 (491)
T COG5243 313 PKRLPCGHILHLHCLKNWLERQ--QTCPICRRPVI 345 (491)
T ss_pred cccccccceeeHHHHHHHHHhc--cCCCcccCccc
Confidence 4568999999999999998876 58999999943
No 31
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.62 E-value=0.00048 Score=63.37 Aligned_cols=49 Identities=14% Similarity=0.287 Sum_probs=35.0
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcC--ccccccccchhh
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFL--HVHRSLDGSISD 53 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l--~vNr~LdG~ved 53 (195)
|--.++.|-|+||++||.+..+. +.+||.|....-.. ..|-..|..+++
T Consensus 27 DATTI~eCLHTFCkSCivk~l~~--~~~CP~C~i~ih~t~pl~ni~~Drtlqd 77 (331)
T KOG2660|consen 27 DATTITECLHTFCKSCIVKYLEE--SKYCPTCDIVIHKTHPLLNIRSDRTLQD 77 (331)
T ss_pred cchhHHHHHHHHHHHHHHHHHHH--hccCCccceeccCccccccCCcchHHHH
Confidence 33456789999999999997655 47999999877652 344445555544
No 32
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=96.46 E-value=0.00084 Score=59.17 Aligned_cols=43 Identities=21% Similarity=0.407 Sum_probs=31.6
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCccccccccchh
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSIS 52 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~ve 52 (195)
-.+.|+|+||-.|...- -+..||+||++...+..+..|-..|.
T Consensus 19 ~LTaC~HvfC~~C~k~~----~~~~C~lCkk~ir~i~l~~slp~~ik 61 (233)
T KOG4739|consen 19 FLTACRHVFCEPCLKAS----SPDVCPLCKKSIRIIQLNRSLPTDIK 61 (233)
T ss_pred eeeechhhhhhhhcccC----CccccccccceeeeeecccccchhHH
Confidence 35789999999998763 12389999999776666666554443
No 33
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.26 E-value=0.0012 Score=60.19 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=27.9
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
.++|+|+|--.||.-|.-.-...+||.||+...
T Consensus 249 ~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 249 KLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred eeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 589999999999999975434469999999876
No 34
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.19 E-value=0.001 Score=62.17 Aligned_cols=34 Identities=18% Similarity=0.285 Sum_probs=27.0
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.+..|+|-||+.||.+- -...+++||-||+..-.
T Consensus 58 ttkeClhrfc~~ci~~a-~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 58 TTKECLHRFCFDCIWKA-LRSGNNECPTCRKKLVS 91 (381)
T ss_pred ccHHHHHHHHHHHHHHH-HHhcCCCCchHHhhccc
Confidence 46789999999999983 23355799999998763
No 35
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=95.92 E-value=0.0043 Score=47.79 Aligned_cols=30 Identities=20% Similarity=0.468 Sum_probs=25.9
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.|.|.|-..||.+|...+ ..||+|+++|..
T Consensus 53 ~CnHaFH~HCI~rWL~Tk--~~CPld~q~w~~ 82 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTK--GVCPLDRQTWVL 82 (88)
T ss_pred ecchHHHHHHHHHHHhhC--CCCCCCCceeEE
Confidence 599999999999996654 689999999863
No 36
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=95.67 E-value=0.005 Score=56.75 Aligned_cols=36 Identities=22% Similarity=0.425 Sum_probs=29.4
Q ss_pred CCCCc-CCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 3 GQDSS-PGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 3 ~QpVt-l~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
-+|+. ..|||.||..||..|-.. ...||.|..+...
T Consensus 32 ~~p~~~~~cgh~fC~~C~~~~~~~--~~~cp~~~~~~~~ 68 (391)
T KOG0297|consen 32 RDPVQTTTCGHRFCAGCLLESLSN--HQKCPVCRQELTQ 68 (391)
T ss_pred cCCCCCCCCCCcccccccchhhcc--CcCCcccccccch
Confidence 45777 599999999999999554 4789999887663
No 37
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.55 E-value=0.0044 Score=43.46 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=20.8
Q ss_pred CCCCCc-CCCCCcccHHhHHhhhccCCCCCCCC
Q 029308 2 LGQDSS-PGNGSCKSATCILRWASYVRNPTCPQ 33 (195)
Q Consensus 2 ~~QpVt-l~CGHsFC~~CI~rW~e~kq~~sCP~ 33 (195)
|-+||. ..|||.|.+..|.+|........||+
T Consensus 21 ~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 21 FEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred hhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 345655 59999999999999964444458999
No 38
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=95.42 E-value=0.0084 Score=48.06 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=24.4
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
.|.|.|-+.||.+|.+.. ..||+|.++-.
T Consensus 80 ~CNHaFH~hCisrWlktr--~vCPLdn~eW~ 108 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR--NVCPLDNKEWV 108 (114)
T ss_pred ecchHHHHHHHHHHHhhc--CcCCCcCccee
Confidence 599999999999996544 68999988754
No 39
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=95.28 E-value=0.0076 Score=42.95 Aligned_cols=33 Identities=30% Similarity=0.581 Sum_probs=26.4
Q ss_pred CCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 4 QDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
..+.++|||.-|..|---+ +-+-||.|.++|..
T Consensus 19 ~~~~~pCgH~I~~~~f~~~----rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 19 KGTVLPCGHLICDNCFPGE----RYNGCPFCGTPFEF 51 (55)
T ss_pred ccccccccceeeccccChh----hccCCCCCCCcccC
Confidence 3578999999999996554 23579999999985
No 40
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=95.25 E-value=0.0053 Score=46.96 Aligned_cols=32 Identities=28% Similarity=0.689 Sum_probs=24.9
Q ss_pred CCCCcccHHhHHhhhccCCC-CCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRN-PTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~-~sCP~CK~pFs~ 40 (195)
-|-|.|=..||.+|-..+.+ -.||+||+.|..
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 48899999999999543222 379999998863
No 41
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=95.06 E-value=0.01 Score=57.02 Aligned_cols=35 Identities=20% Similarity=0.483 Sum_probs=29.2
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
-+-+|||..|..|+..|....+..+||.||-.+..
T Consensus 383 kIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 383 KIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred ccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 35689999999999999655556799999988774
No 42
>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=94.42 E-value=0.027 Score=38.20 Aligned_cols=33 Identities=27% Similarity=0.530 Sum_probs=26.9
Q ss_pred CCCCcCCCC-----CcccHHhHHhhhccCCCCCCCCCC
Q 029308 3 GQDSSPGNG-----SCKSATCILRWASYVRNPTCPQCK 35 (195)
Q Consensus 3 ~QpVtl~CG-----HsFC~~CI~rW~e~kq~~sCP~CK 35 (195)
+.+...+|. |.|=..|+.+|.....+.+||+|+
T Consensus 12 ~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 12 GDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 456667885 899999999998766667999996
No 43
>PF04641 Rtf2: Rtf2 RING-finger
Probab=94.33 E-value=0.027 Score=48.99 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=26.0
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
..+|||+|+..+|.+-. ....||+|..+|..
T Consensus 132 l~~cG~V~s~~alke~k---~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 132 LRPCGCVFSEKALKELK---KSKKCPVCGKPFTE 162 (260)
T ss_pred EcCCCCEeeHHHHHhhc---ccccccccCCcccc
Confidence 45999999999999962 23579999999996
No 44
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=94.25 E-value=0.02 Score=56.68 Aligned_cols=36 Identities=19% Similarity=0.301 Sum_probs=28.0
Q ss_pred CCcCCCCCcccHHhHHhhhc---cCCCCCCCCCCCCCCc
Q 029308 5 DSSPGNGSCKSATCILRWAS---YVRNPTCPQCKHPFEF 40 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e---~kq~~sCP~CK~pFs~ 40 (195)
++..+|-|.||+.||..+-. ...+.+||.|-.+.+.
T Consensus 549 ~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi 587 (791)
T KOG1002|consen 549 YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI 587 (791)
T ss_pred hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence 45678999999999988632 2334699999998874
No 45
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.77 E-value=0.019 Score=52.71 Aligned_cols=36 Identities=17% Similarity=0.266 Sum_probs=29.0
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
=.||...|||.||..|-++- ++....|++|.+....
T Consensus 252 ~~pVvt~c~h~fc~~ca~~~--~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 252 YRPVVTKCGHYFCEVCALKP--YQKGEKCYVCSQQTHG 287 (313)
T ss_pred ccchhhcCCceeehhhhccc--cccCCcceeccccccc
Confidence 35899999999999999883 3334689999987764
No 46
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=93.73 E-value=0.025 Score=56.14 Aligned_cols=38 Identities=16% Similarity=0.280 Sum_probs=30.9
Q ss_pred CCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 3 GQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+-++...|||.||..|+..-.+..+...||+|+.....
T Consensus 464 ~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~ 501 (674)
T KOG1001|consen 464 DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKE 501 (674)
T ss_pred ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence 34688999999999999996666555589999987764
No 47
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=93.69 E-value=0.025 Score=54.44 Aligned_cols=30 Identities=17% Similarity=0.515 Sum_probs=25.5
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
+++.|.|+|=-.|+.+||. .+||+||..-+
T Consensus 193 ~t~~c~Hsfh~~cl~~w~~----~scpvcR~~q~ 222 (493)
T KOG0804|consen 193 LTILCNHSFHCSCLMKWWD----SSCPVCRYCQS 222 (493)
T ss_pred eeeecccccchHHHhhccc----CcChhhhhhcC
Confidence 6899999999999999953 57999997544
No 48
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.85 E-value=0.049 Score=52.15 Aligned_cols=35 Identities=23% Similarity=0.418 Sum_probs=28.6
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
|++.|||-|=..||.+|..++....||+|+..-..
T Consensus 23 vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katk 57 (463)
T KOG1645|consen 23 VSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATK 57 (463)
T ss_pred eeecccccccHHHHHHHHhhhhhhhCcccCChhHH
Confidence 68999999999999999754334589999977654
No 49
>PHA03096 p28-like protein; Provisional
Probab=92.81 E-value=0.056 Score=48.64 Aligned_cols=34 Identities=15% Similarity=0.085 Sum_probs=23.1
Q ss_pred CcCCCCCcccHHhHHhhhccCC-CCCCCCCCCCCC
Q 029308 6 SSPGNGSCKSATCILRWASYVR-NPTCPQCKHPFE 39 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq-~~sCP~CK~pFs 39 (195)
...+|.|.||..||..|..... ..+||.|+..-+
T Consensus 200 il~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~ 234 (284)
T PHA03096 200 ILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNT 234 (284)
T ss_pred ccccCCcHHHHHHHHHHHHhhhhcccCccccchhh
Confidence 4568999999999999965322 235555554433
No 50
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.93 E-value=0.098 Score=45.21 Aligned_cols=33 Identities=15% Similarity=0.312 Sum_probs=25.5
Q ss_pred CCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCC
Q 029308 5 DSSPGNGSCKSATCILRWASYVRNPTCPQCKHPF 38 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pF 38 (195)
|-.+.|||+||..|+.+-... ....||-||.+-
T Consensus 22 p~~l~c~h~~c~~c~~~l~~~-~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 22 PRVLKCGHTICQNCASKLLGN-SRILCPFCRETT 54 (296)
T ss_pred CcccccCceehHhHHHHHhcC-ceeeccCCCCcc
Confidence 445779999999999996333 234799999985
No 51
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=91.90 E-value=0.13 Score=35.60 Aligned_cols=32 Identities=19% Similarity=0.423 Sum_probs=16.3
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
.-.||+..|+.|-.+-.+ ..+..||-||++++
T Consensus 17 PC~Cgf~IC~~C~~~i~~-~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 17 PCECGFQICRFCYHDILE-NEGGRCPGCREPYK 48 (48)
T ss_dssp SSTTS----HHHHHHHTT-SS-SB-TTT--B--
T ss_pred cCcCCCcHHHHHHHHHHh-ccCCCCCCCCCCCC
Confidence 357999999999888432 23468999999874
No 52
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.78 E-value=0.046 Score=39.74 Aligned_cols=34 Identities=24% Similarity=0.382 Sum_probs=25.6
Q ss_pred CcCCCCCc-ccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 6 SSPGNGSC-KSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHs-FC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
|.--|||. .|+.|-.+-|+. ..-.||+||+|...
T Consensus 21 VlYtCGHMCmCy~Cg~rl~~~-~~g~CPiCRapi~d 55 (62)
T KOG4172|consen 21 VLYTCGHMCMCYACGLRLKKA-LHGCCPICRAPIKD 55 (62)
T ss_pred HHHHcchHHhHHHHHHHHHHc-cCCcCcchhhHHHH
Confidence 44569996 799999984443 23589999999764
No 53
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.71 E-value=0.094 Score=49.09 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=30.8
Q ss_pred CCCcC-CCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCccccccccchhhhhhh
Q 029308 4 QDSSP-GNGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSISDYMFE 57 (195)
Q Consensus 4 QpVtl-~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~vedy~~E 57 (195)
||+-. .|||.||..||..-. ......||.|-..= ..|++..-|+..+
T Consensus 286 np~kT~cC~~~fc~eci~~al-~dsDf~CpnC~rkd------vlld~l~pD~dk~ 333 (427)
T COG5222 286 NPMKTPCCGHTFCDECIGTAL-LDSDFKCPNCSRKD------VLLDGLTPDIDKK 333 (427)
T ss_pred CcccCccccchHHHHHHhhhh-hhccccCCCccccc------chhhccCccHHHH
Confidence 45544 899999999999832 22336899997531 2356666555444
No 54
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=90.94 E-value=0.1 Score=48.81 Aligned_cols=30 Identities=13% Similarity=0.205 Sum_probs=24.4
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+|+|-|.||..|-..- ....||.|-.++..
T Consensus 106 mIPCkHvFCl~CAr~~----~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 106 MIPCKHVFCLECARSD----SDKICPLCDDRVQR 135 (389)
T ss_pred ccccchhhhhhhhhcC----ccccCcCcccHHHH
Confidence 6999999999997653 23589999988774
No 55
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=89.94 E-value=0.063 Score=38.60 Aligned_cols=32 Identities=28% Similarity=0.692 Sum_probs=16.9
Q ss_pred CCCCCcccHHhHHhhhcc----CC--CC---CCCCCCCCCC
Q 029308 8 PGNGSCKSATCILRWASY----VR--NP---TCPQCKHPFE 39 (195)
Q Consensus 8 l~CGHsFC~~CI~rW~e~----kq--~~---sCP~CK~pFs 39 (195)
..|++.|-..||.+|... .+ .+ .||.|+++++
T Consensus 26 ~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 26 PSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred cccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 379999999999999532 11 11 5999999875
No 56
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=89.53 E-value=0.32 Score=41.24 Aligned_cols=52 Identities=17% Similarity=0.512 Sum_probs=34.5
Q ss_pred cHHhHHhhhccCCCCCCCCCCCCCCcCccccccccc------hhh-hhhhhhhHHHhhh
Q 029308 15 SATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGS------ISD-YMFEESVCLLLRA 66 (195)
Q Consensus 15 C~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~------ved-y~~EeSvcLL~Ra 66 (195)
-.+|+.+|....++..||+|+.+|........|..- +++ -.+--+.||++=.
T Consensus 35 H~sCL~rWi~~s~~~~CeiC~~~Y~i~~~~kpl~~W~~~~~dc~~~~l~~~llcl~~~~ 93 (162)
T PHA02825 35 HKECLEEWINTSKNKSCKICNGPYNIKKNYKKCTKWRCSFRDCHDSAIVNSLLCLIVGG 93 (162)
T ss_pred HHHHHHHHHhcCCCCcccccCCeEEEEEecCCCccccccCcchhhHHHHHHHHHHHHhh
Confidence 578999998877778999999999853333333221 122 4455567877654
No 57
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.42 E-value=0.23 Score=46.11 Aligned_cols=59 Identities=19% Similarity=0.234 Sum_probs=38.5
Q ss_pred cCCCCCcccHHhHHhhhccC----CCCCCC--CCCCCCCc-----CccccccccchhhhhhhhhhHHHhhh
Q 029308 7 SPGNGSCKSATCILRWASYV----RNPTCP--QCKHPFEF-----LHVHRSLDGSISDYMFEESVCLLLRA 66 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~k----q~~sCP--~CK~pFs~-----l~vNr~LdG~vedy~~EeSvcLL~Ra 66 (195)
+..|+|.||..|+.+..+.+ ..+.|| .|...++. +.++ .|.-+.+.++.++++-.+.|-
T Consensus 165 ~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~llt~-kl~e~~e~~~~e~~i~~~~~~ 234 (384)
T KOG1812|consen 165 VLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRKLLTP-KLREMWEQRLKEEVIPSLDRV 234 (384)
T ss_pred HhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhhhcCH-HHHHHHHHHHHHHhhhhhhcc
Confidence 57899999999999865432 124676 47777774 3232 444555667777776655553
No 58
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.43 E-value=0.21 Score=47.87 Aligned_cols=34 Identities=12% Similarity=0.116 Sum_probs=24.4
Q ss_pred CcCCCCCcccHHhHHhhhcc--CC----CCCCCCCCCCCC
Q 029308 6 SSPGNGSCKSATCILRWASY--VR----NPTCPQCKHPFE 39 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~--kq----~~sCP~CK~pFs 39 (195)
+-++|+|.||..|+..+-+. ++ ...||.|+-+-.
T Consensus 201 ~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~ 240 (445)
T KOG1814|consen 201 KFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSV 240 (445)
T ss_pred eecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCccc
Confidence 45899999999999996431 11 236998875544
No 59
>PHA02862 5L protein; Provisional
Probab=88.31 E-value=0.26 Score=41.58 Aligned_cols=25 Identities=24% Similarity=0.842 Sum_probs=22.0
Q ss_pred HHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 16 ATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 16 ~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
..|+.+|-...++..||+|+.+|..
T Consensus 30 q~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 30 IKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred HHHHHHHHhcCCCcCccCCCCeEEE
Confidence 6899999877777899999999984
No 60
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=87.64 E-value=0.23 Score=47.78 Aligned_cols=32 Identities=13% Similarity=0.258 Sum_probs=26.9
Q ss_pred CCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 8 PGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 8 l~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
++|.|.|-..|+....+.....+||.|++-.+
T Consensus 385 LpCsHIfH~rCl~e~L~~n~~rsCP~CrklrS 416 (518)
T KOG1941|consen 385 LPCSHIFHLRCLQEILENNGTRSCPNCRKLRS 416 (518)
T ss_pred cchhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence 89999999999999877766679999995443
No 61
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.50 E-value=0.32 Score=49.23 Aligned_cols=29 Identities=24% Similarity=0.424 Sum_probs=23.4
Q ss_pred CCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCC
Q 029308 4 QDSSPGNGSCKSATCILRWASYVRNPTCPQCKHP 37 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~p 37 (195)
.||++.|||..|..|+..- .+.+|| |+..
T Consensus 27 ~Pvsl~cghtic~~c~~~l----yn~scp-~~~D 55 (861)
T KOG3161|consen 27 EPVSLQCGHTICGHCVQLL----YNASCP-TKRD 55 (861)
T ss_pred CcccccccchHHHHHHHhH----hhccCC-CCcc
Confidence 5899999999999999985 235799 6543
No 62
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=85.34 E-value=0.67 Score=38.57 Aligned_cols=33 Identities=24% Similarity=0.482 Sum_probs=26.5
Q ss_pred CCCCcccHHhHHhhhcc-CCCCCCCCCCCCCCcC
Q 029308 9 GNGSCKSATCILRWASY-VRNPTCPQCKHPFEFL 41 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~-kq~~sCP~CK~pFs~l 41 (195)
-||-+-|..|-..-|+. .--+.||+||++|...
T Consensus 101 CCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss 134 (140)
T PF05290_consen 101 CCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS 134 (140)
T ss_pred ccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence 59999999999995553 2336899999999864
No 63
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=83.51 E-value=0.82 Score=41.83 Aligned_cols=34 Identities=12% Similarity=0.255 Sum_probs=28.2
Q ss_pred CCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 5 DSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+|.-+|||+||..|+.+... ..-.||+|..|...
T Consensus 238 a~Lr~sg~Vv~~ecvEklir--~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 238 AVLRPSGHVVTKECVEKLIR--KDMVDPVTDKPLKD 271 (303)
T ss_pred EEeccCCcEeeHHHHHHhcc--ccccccCCCCcCcc
Confidence 45678999999999999733 33689999999996
No 64
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=78.24 E-value=1.1 Score=33.45 Aligned_cols=11 Identities=18% Similarity=0.655 Sum_probs=7.9
Q ss_pred cccHHhHHhhh
Q 029308 13 CKSATCILRWA 23 (195)
Q Consensus 13 sFC~~CI~rW~ 23 (195)
-||+.|+.+|.
T Consensus 11 gFCRNCLskWy 21 (68)
T PF06844_consen 11 GFCRNCLSKWY 21 (68)
T ss_dssp S--HHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 49999999995
No 65
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=77.51 E-value=0.73 Score=49.39 Aligned_cols=34 Identities=26% Similarity=0.447 Sum_probs=28.1
Q ss_pred CCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 4 QDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
|--+..|||.||..|+.-|..+. ..||.|+..+.
T Consensus 1166 ~~~I~~cgh~~c~~c~~~~l~~~--s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1166 QGGIAGCGHEPCCRCDELWLYAS--SRCPICKSIKG 1199 (1394)
T ss_pred cCCeeeechhHhhhHHHHHHHHh--ccCcchhhhhh
Confidence 55678999999999999996554 68999996554
No 66
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=75.76 E-value=0.92 Score=47.09 Aligned_cols=34 Identities=6% Similarity=0.121 Sum_probs=26.4
Q ss_pred CCCCcccHHhHHhhhccC----CCCCCCCCCCCCCcCc
Q 029308 9 GNGSCKSATCILRWASYV----RNPTCPQCKHPFEFLH 42 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~k----q~~sCP~CK~pFs~l~ 42 (195)
.|+|+||..||+.|.... ....||.|++-|..+.
T Consensus 120 ~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs 157 (1134)
T KOG0825|consen 120 THVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS 157 (1134)
T ss_pred hhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhh
Confidence 499999999999997432 1247999999888643
No 67
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=75.73 E-value=1.3 Score=31.26 Aligned_cols=28 Identities=21% Similarity=0.486 Sum_probs=19.2
Q ss_pred CCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 11 GSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.|.-|..|+..-... +..||+|+++.+.
T Consensus 20 dHYLCl~CLt~ml~~--s~~C~iC~~~LPt 47 (50)
T PF03854_consen 20 DHYLCLNCLTLMLSR--SDRCPICGKPLPT 47 (50)
T ss_dssp S-EEEHHHHHHT-SS--SSEETTTTEE---
T ss_pred chhHHHHHHHHHhcc--ccCCCcccCcCcc
Confidence 599999999996433 3689999998764
No 68
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=75.10 E-value=0.53 Score=34.05 Aligned_cols=35 Identities=23% Similarity=0.421 Sum_probs=23.1
Q ss_pred CCCCCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 1 MLGQDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 1 ~~~QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+.|+||..=||-.| +-. ...+..+.||.||.-+..
T Consensus 22 v~G~pVvALCGk~w----vp~-rdp~~~PVCP~Ck~iye~ 56 (58)
T PF11238_consen 22 VMGTPVVALCGKVW----VPT-RDPKPFPVCPECKEIYES 56 (58)
T ss_pred hcCceeEeeeCcee----CCC-CCCCCCCCCcCHHHHHHh
Confidence 45888988898766 222 122234689999987654
No 69
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=74.96 E-value=2.7 Score=38.77 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=34.4
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCccccccccchhhhhhhhhhHH
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSISDYMFEESVCL 62 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~vedy~~EeSvcL 62 (195)
+|||.-|-+|.-.--.. ++..||.|..+.-....+ -..++|-+++.++-+
T Consensus 22 ~C~H~lCEsCvd~iF~~-g~~~CpeC~~iLRk~nfr---~q~fED~~vekEv~i 71 (300)
T KOG3800|consen 22 ECGHRLCESCVDRIFSL-GPAQCPECMVILRKNNFR---VQTFEDPTVEKEVDI 71 (300)
T ss_pred cccchHHHHHHHHHHhc-CCCCCCcccchhhhcccc---hhhcchhHHHHHHHH
Confidence 89999999999994333 345899999876642222 224577777766544
No 70
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.53 E-value=1.9 Score=41.33 Aligned_cols=34 Identities=24% Similarity=0.507 Sum_probs=26.1
Q ss_pred CcCCCCCcccHHhHHhhhc-cCCCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWAS-YVRNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e-~kq~~sCP~CK~pFs~ 40 (195)
..++|+|..|..|-.+-.- +. ...||.||..-..
T Consensus 75 ~~~PC~H~~CH~Ca~RlRALY~-~K~C~~CrTE~e~ 109 (493)
T COG5236 75 ARYPCGHQICHACAVRLRALYM-QKGCPLCRTETEA 109 (493)
T ss_pred EeccCCchHHHHHHHHHHHHHh-ccCCCccccccce
Confidence 3579999999999998432 32 2589999988764
No 71
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=74.14 E-value=0.93 Score=30.10 Aligned_cols=14 Identities=21% Similarity=0.472 Sum_probs=11.4
Q ss_pred CCCCcccHHhHHhh
Q 029308 9 GNGSCKSATCILRW 22 (195)
Q Consensus 9 ~CGHsFC~~CI~rW 22 (195)
.|||.||..|-..|
T Consensus 45 ~C~~~fC~~C~~~~ 58 (64)
T smart00647 45 KCGFSFCFRCKVPW 58 (64)
T ss_pred CCCCeECCCCCCcC
Confidence 67888888888777
No 72
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.36 E-value=1.4 Score=41.07 Aligned_cols=20 Identities=15% Similarity=0.046 Sum_probs=16.9
Q ss_pred CCCCcCCCCCcccHHhHHhh
Q 029308 3 GQDSSPGNGSCKSATCILRW 22 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW 22 (195)
+.+|.-.|||.||+.|...|
T Consensus 177 ~~~v~C~~g~~FC~~C~~~~ 196 (444)
T KOG1815|consen 177 SVEVDCGCGHEFCFACGEES 196 (444)
T ss_pred ccceeCCCCchhHhhccccc
Confidence 35678899999999998776
No 73
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=72.06 E-value=1.2 Score=33.91 Aligned_cols=12 Identities=25% Similarity=0.313 Sum_probs=0.0
Q ss_pred cchhhhHHhhCC
Q 029308 94 EDDLDEVYFRSS 105 (195)
Q Consensus 94 ~d~~~e~y~~~~ 105 (195)
+|+++|.+|..-
T Consensus 45 dDdeeee~m~rK 56 (81)
T PF14812_consen 45 DDDEEEEPMPRK 56 (81)
T ss_dssp ------------
T ss_pred cchhhccccccc
Confidence 344678888764
No 74
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=69.83 E-value=1.4 Score=44.38 Aligned_cols=35 Identities=17% Similarity=0.208 Sum_probs=27.2
Q ss_pred CCCcCCCCCcccHHhHHh--hhccCCCCCCCCCCCCCC
Q 029308 4 QDSSPGNGSCKSATCILR--WASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~r--W~e~kq~~sCP~CK~pFs 39 (195)
.|+++.|.|.||..|+.. ||.. ....||+|+....
T Consensus 33 ~p~~~kc~~~~l~~~~n~~f~~~~-~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 33 EPSLLKCDHIFLKFCLNKLFESKK-GPKQCALCKSDIE 69 (684)
T ss_pred ccchhhhhHHHHhhhhhceeeccC-ccccchhhhhhhh
Confidence 468899999999999998 4333 2468999996555
No 75
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=69.34 E-value=1.5 Score=48.74 Aligned_cols=36 Identities=19% Similarity=0.348 Sum_probs=25.7
Q ss_pred CCcCCCCCcccHHhHHh-----hhccCC---CCCCCCCCCCCCc
Q 029308 5 DSSPGNGSCKSATCILR-----WASYVR---NPTCPQCKHPFEF 40 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~r-----W~e~kq---~~sCP~CK~pFs~ 40 (195)
.+.++|||.|-..|..+ |....- --+||+|+.++..
T Consensus 3502 ~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3502 AIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred ceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 35689999999999765 522110 0279999999886
No 76
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=67.60 E-value=4.3 Score=25.26 Aligned_cols=14 Identities=29% Similarity=0.581 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCCc
Q 029308 27 RNPTCPQCKHPFEF 40 (195)
Q Consensus 27 q~~sCP~CK~pFs~ 40 (195)
.+..||+|..+-..
T Consensus 16 ~~~~CP~Cg~~~~~ 29 (33)
T cd00350 16 APWVCPVCGAPKDK 29 (33)
T ss_pred CCCcCcCCCCcHHH
Confidence 34589999986543
No 77
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=63.39 E-value=4 Score=40.36 Aligned_cols=21 Identities=5% Similarity=-0.084 Sum_probs=18.8
Q ss_pred CCCCCcCCCCCcccHHhHHhh
Q 029308 2 LGQDSSPGNGSCKSATCILRW 22 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~rW 22 (195)
+-+|++++|||+.|..|-..-
T Consensus 14 ~~epiil~c~h~lc~~ca~~~ 34 (699)
T KOG4367|consen 14 YREPIILPCSHNLCQACARNI 34 (699)
T ss_pred ccCceEeecccHHHHHHHHhh
Confidence 568999999999999999874
No 78
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=62.60 E-value=5.8 Score=25.13 Aligned_cols=11 Identities=45% Similarity=1.038 Sum_probs=8.7
Q ss_pred CCCCCCCCCCC
Q 029308 29 PTCPQCKHPFE 39 (195)
Q Consensus 29 ~sCP~CK~pFs 39 (195)
..||+|.++-.
T Consensus 19 ~~CP~Cg~~~~ 29 (34)
T cd00729 19 EKCPICGAPKE 29 (34)
T ss_pred CcCcCCCCchH
Confidence 48999998744
No 79
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.41 E-value=8.8 Score=35.31 Aligned_cols=31 Identities=13% Similarity=0.260 Sum_probs=24.3
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
+.-+|||+|-..=+.+. ....|++|.++|..
T Consensus 129 ~l~~CGcV~SerAlKei----kas~C~~C~a~y~~ 159 (293)
T KOG3113|consen 129 ALRCCGCVFSERALKEI----KASVCHVCGAAYQE 159 (293)
T ss_pred EEeccceeccHHHHHHh----hhccccccCCcccc
Confidence 35689999987776664 23689999999995
No 80
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=59.35 E-value=3.8 Score=27.44 Aligned_cols=19 Identities=32% Similarity=0.863 Sum_probs=13.7
Q ss_pred HHhHHhhhccCCCCCCCCC
Q 029308 16 ATCILRWASYVRNPTCPQC 34 (195)
Q Consensus 16 ~~CI~rW~e~kq~~sCP~C 34 (195)
..|+.+|...+.+..|++|
T Consensus 29 ~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 29 RSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp CCHHHHHHHHHT-SB-TTT
T ss_pred HHHHHHHHHhcCCCcCCCC
Confidence 4699999876666789998
No 81
>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=58.70 E-value=3 Score=28.20 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=6.3
Q ss_pred CCCCCCCCCCc
Q 029308 30 TCPQCKHPFEF 40 (195)
Q Consensus 30 sCP~CK~pFs~ 40 (195)
.||+|..+|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 79999999995
No 82
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=58.60 E-value=2.9 Score=25.16 Aligned_cols=21 Identities=24% Similarity=0.444 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCcCcccccccc
Q 029308 29 PTCPQCKHPFEFLHVHRSLDG 49 (195)
Q Consensus 29 ~sCP~CK~pFs~l~vNr~LdG 49 (195)
..||+|.+.++...+|.-||.
T Consensus 2 v~CPiC~~~v~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREVPENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcccHHHHHHHHHH
Confidence 369999999876666666663
No 83
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.49 E-value=4.4 Score=32.19 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=9.8
Q ss_pred cccHHhHHhhh
Q 029308 13 CKSATCILRWA 23 (195)
Q Consensus 13 sFC~~CI~rW~ 23 (195)
-||+.|+..|.
T Consensus 42 gFCRNCLs~Wy 52 (104)
T COG3492 42 GFCRNCLSNWY 52 (104)
T ss_pred HHHHHHHHHHH
Confidence 49999999995
No 84
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=58.44 E-value=7.3 Score=29.88 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=12.8
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCcC
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEFL 41 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l 41 (195)
.|+--.|+.|..-=. ...+..||+|+.+|..+
T Consensus 33 eC~fPvCr~CyEYEr-keg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 33 ECAFPVCRPCYEYER-KEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp SS-----HHHHHHHH-HTS-SB-TTT--B----
T ss_pred ccCCccchhHHHHHh-hcCcccccccCCCcccc
Confidence 577788999987521 22345899999988853
No 85
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=57.93 E-value=2.4 Score=38.64 Aligned_cols=57 Identities=16% Similarity=0.165 Sum_probs=32.6
Q ss_pred CCcccHHhHHhhhc--cCCCCCCCCCCCCCCc-CccccccccchhhhhhhhhhHHHhhhccccccc
Q 029308 11 GSCKSATCILRWAS--YVRNPTCPQCKHPFEF-LHVHRSLDGSISDYMFEESVCLLLRATWFKPLI 73 (195)
Q Consensus 11 GHsFC~~CI~rW~e--~kq~~sCP~CK~pFs~-l~vNr~LdG~vedy~~EeSvcLL~Ra~wf~~~~ 73 (195)
.|-||-.|-.+--. ..-...||.|++.+-. +-|--. +-.-.-++ +||+.+.++| +..
T Consensus 110 ~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~fPR~dP~vI----v~v~~~~~-ilLa~~~~h~-~g~ 169 (279)
T COG2816 110 SHRFCGRCGTKTYPREGGWARVCPKCGHEHFPRIDPCVI----VAVIRGDE-ILLARHPRHF-PGM 169 (279)
T ss_pred hCcCCCCCCCcCccccCceeeeCCCCCCccCCCCCCeEE----EEEecCCc-eeecCCCCCC-Ccc
Confidence 58999999888311 1112479999987653 222100 01111122 7888888888 433
No 86
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=56.65 E-value=1.6 Score=28.80 Aligned_cols=17 Identities=18% Similarity=0.221 Sum_probs=14.1
Q ss_pred CcCC-CCCcccHHhHHhh
Q 029308 6 SSPG-NGSCKSATCILRW 22 (195)
Q Consensus 6 Vtl~-CGHsFC~~CI~rW 22 (195)
|+=+ |++.||..|-..|
T Consensus 41 ~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 41 VTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp CCTTSCCSEECSSSTSES
T ss_pred eECCCCCCcCccccCccc
Confidence 3444 9999999999888
No 87
>PLN02195 cellulose synthase A
Probab=54.89 E-value=7.3 Score=40.99 Aligned_cols=30 Identities=13% Similarity=0.421 Sum_probs=22.0
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
.||---|+.|- .+-....+..|||||+++.
T Consensus 30 eC~~pvCrpCy-eyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 30 ECSYPLCKACL-EYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred cCCCccccchh-hhhhhcCCccCCccCCccc
Confidence 47777899998 4422334458999999998
No 88
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=54.71 E-value=7.3 Score=41.35 Aligned_cols=31 Identities=23% Similarity=0.434 Sum_probs=21.8
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.||---|+.|- .+-....+..|||||+++..
T Consensus 41 eC~FPVCrpCY-EYEr~eG~q~CPqCktrYkr 71 (1079)
T PLN02638 41 VCAFPVCRPCY-EYERKDGNQSCPQCKTKYKR 71 (1079)
T ss_pred cCCCccccchh-hhhhhcCCccCCccCCchhh
Confidence 46666899998 43223344589999999984
No 89
>PF07972 Flavodoxin_NdrI: NrdI Flavodoxin like ; InterPro: IPR004465 Ribonucleotide reductases (RNRs) are enzymes that provide the precursors of DNA synthesis. The three characterised classes of RNRs differ by their metal cofactor and their stable organic radical. Class Ib RNR is encoded in four different genes: nrdH, nrdI, nrdE and nrdF []. The exact function of NrdI within the ribonucleotide reductases has not yet been fully characterised.; PDB: 1RLJ_A 3N39_C 3N3B_D 3N3A_C 2XOE_A 2XOD_A 2X2P_A 2X2O_A.
Probab=54.64 E-value=2.7 Score=33.60 Aligned_cols=22 Identities=36% Similarity=0.616 Sum_probs=17.1
Q ss_pred eeeccccccCCCccccccccccc
Q 029308 108 LRIGNRRWGDNGYVRAGRQEARP 130 (195)
Q Consensus 108 ~~ignrr~g~ngyvr~gr~~arp 130 (195)
+-=|||-||++ |..+|+..|.=
T Consensus 78 igSGNrNfg~~-f~~aa~~ia~k 99 (122)
T PF07972_consen 78 IGSGNRNFGDN-FCLAADKIAEK 99 (122)
T ss_dssp EEEE-GGGGGG-TTHHHHHHHHH
T ss_pred EecCCcHHHHH-HHHHHHHHHHH
Confidence 44799999999 99999877643
No 90
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=54.46 E-value=4.2 Score=24.73 Aligned_cols=23 Identities=26% Similarity=0.554 Sum_probs=13.6
Q ss_pred cHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 15 SATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 15 C~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
|-.|-..+.... ..||.|...|.
T Consensus 3 CP~C~~~V~~~~--~~Cp~CG~~F~ 25 (26)
T PF10571_consen 3 CPECGAEVPESA--KFCPHCGYDFE 25 (26)
T ss_pred CCCCcCCchhhc--CcCCCCCCCCc
Confidence 444544543322 47888888875
No 91
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.18 E-value=6.3 Score=36.88 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=17.2
Q ss_pred CCCcCCCCCcccHHhHHhhh
Q 029308 4 QDSSPGNGSCKSATCILRWA 23 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW~ 23 (195)
..+.+.|||.||..|+..+-
T Consensus 83 ~~~~~~c~H~~c~~cw~~yl 102 (444)
T KOG1815|consen 83 EIIGLGCGHPFCPPCWTGYL 102 (444)
T ss_pred hhhhcCCCcHHHHHHHHHHh
Confidence 35678999999999999864
No 92
>PLN02189 cellulose synthase
Probab=53.33 E-value=8.3 Score=40.83 Aligned_cols=31 Identities=23% Similarity=0.394 Sum_probs=22.3
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.||---|+.|..- -....+..||+||+++..
T Consensus 58 ~C~fpvCr~Cyey-er~eg~q~CpqCkt~Y~r 88 (1040)
T PLN02189 58 ECGFPVCRPCYEY-ERREGTQNCPQCKTRYKR 88 (1040)
T ss_pred cCCCccccchhhh-hhhcCCccCcccCCchhh
Confidence 3777799999843 223344689999999983
No 93
>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=53.14 E-value=11 Score=24.96 Aligned_cols=26 Identities=23% Similarity=0.590 Sum_probs=15.4
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCC
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQC 34 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~C 34 (195)
+|+=.+=..|+.+++....++.||.|
T Consensus 18 ~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 18 DCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 57777888899997766555589998
No 94
>PLN02436 cellulose synthase A
Probab=52.71 E-value=7.5 Score=41.34 Aligned_cols=31 Identities=23% Similarity=0.428 Sum_probs=22.4
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.||---|+.|.. +-....+..||+||+++..
T Consensus 60 ~C~fpvCr~Cye-yer~eg~~~Cpqckt~Y~r 90 (1094)
T PLN02436 60 ECAFPVCRPCYE-YERREGNQACPQCKTRYKR 90 (1094)
T ss_pred cCCCccccchhh-hhhhcCCccCcccCCchhh
Confidence 377779999994 3223344689999999984
No 95
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.62 E-value=5.6 Score=34.42 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=21.7
Q ss_pred CCCcccHHhHHhhhccCCCCCCCCCCCC
Q 029308 10 NGSCKSATCILRWASYVRNPTCPQCKHP 37 (195)
Q Consensus 10 CGHsFC~~CI~rW~e~kq~~sCP~CK~p 37 (195)
|||.-|..||..-..... ..||.|+..
T Consensus 239 c~htlc~~c~~~~l~~~~-~~cp~~~~~ 265 (296)
T KOG4185|consen 239 EGHTLCKECIDTILLQAG-IKCPFCTWS 265 (296)
T ss_pred HHHHHHhcchHHHHHHhh-hcCCcccce
Confidence 999999999999533322 689999976
No 96
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=51.36 E-value=6.8 Score=30.84 Aligned_cols=10 Identities=40% Similarity=1.221 Sum_probs=5.2
Q ss_pred CCCCCCCCCC
Q 029308 30 TCPQCKHPFE 39 (195)
Q Consensus 30 sCP~CK~pFs 39 (195)
.||.|.+.|.
T Consensus 28 vCP~CG~~~~ 37 (108)
T PF09538_consen 28 VCPKCGTEFP 37 (108)
T ss_pred cCCCCCCccC
Confidence 4555555554
No 97
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=50.70 E-value=8.4 Score=40.79 Aligned_cols=31 Identities=23% Similarity=0.464 Sum_probs=21.9
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.||---|+.|. .+-....+..||+||+++..
T Consensus 39 eC~fpvCr~cy-eye~~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 39 VCGFPVCKPCY-EYERSEGNQCCPQCNTRYKR 69 (1044)
T ss_pred cCCCccccchh-hhhhhcCCccCCccCCchhh
Confidence 46666899998 44223344689999999883
No 98
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.26 E-value=3.6 Score=24.19 Aligned_cols=23 Identities=22% Similarity=0.528 Sum_probs=12.4
Q ss_pred ccHHhHHhhhccCCCCCCCCCCCCC
Q 029308 14 KSATCILRWASYVRNPTCPQCKHPF 38 (195)
Q Consensus 14 FC~~CI~rW~e~kq~~sCP~CK~pF 38 (195)
||..|=.+-. .....||.|.+++
T Consensus 1 ~Cp~CG~~~~--~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIE--DDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCC--CcCcchhhhCCcC
Confidence 4444544431 2235788888764
No 99
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=50.13 E-value=5.1 Score=26.14 Aligned_cols=26 Identities=15% Similarity=0.244 Sum_probs=16.0
Q ss_pred CCCCCcccHHhHHhhhccCCCCCCCCCCC
Q 029308 8 PGNGSCKSATCILRWASYVRNPTCPQCKH 36 (195)
Q Consensus 8 l~CGHsFC~~CI~rW~e~kq~~sCP~CK~ 36 (195)
..|||.|=.. ..-++ .....||.|+.
T Consensus 9 ~~Cg~~fe~~--~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 9 EECGHEFEVL--QSISE-DDPVPCPECGS 34 (42)
T ss_pred CCCCCEEEEE--EEcCC-CCCCcCCCCCC
Confidence 3689888542 12222 23458999998
No 100
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.66 E-value=8.3 Score=40.30 Aligned_cols=27 Identities=19% Similarity=0.434 Sum_probs=21.7
Q ss_pred CcCCCCCcccHHhHHhhhccCCCCCCCCCCCC
Q 029308 6 SSPGNGSCKSATCILRWASYVRNPTCPQCKHP 37 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~p 37 (195)
|...|||+|-..|... ....||-|+..
T Consensus 855 VhF~CgHsyHqhC~e~-----~~~~CP~C~~e 881 (933)
T KOG2114|consen 855 VHFLCGHSYHQHCLED-----KEDKCPKCLPE 881 (933)
T ss_pred eeeecccHHHHHhhcc-----CcccCCccchh
Confidence 5678999999999983 22579999983
No 101
>PLN02400 cellulose synthase
Probab=45.50 E-value=12 Score=39.83 Aligned_cols=31 Identities=19% Similarity=0.392 Sum_probs=21.3
Q ss_pred CCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 9 GNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.|+---|+.|- .+-....+..|||||+.+..
T Consensus 60 eCaFPVCRpCY-EYERkeGnq~CPQCkTrYkR 90 (1085)
T PLN02400 60 ECAFPVCRPCY-EYERKDGTQCCPQCKTRYRR 90 (1085)
T ss_pred cCCCccccchh-heecccCCccCcccCCcccc
Confidence 46666899998 33222334589999999983
No 102
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.19 E-value=8.7 Score=35.81 Aligned_cols=27 Identities=19% Similarity=0.296 Sum_probs=17.8
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCC
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCK 35 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK 35 (195)
+-.|||-||..|-..|-... ..|..|-
T Consensus 326 ~CrC~~~fcy~C~~~~~~~~--~~~~~~~ 352 (384)
T KOG1812|consen 326 TCRCGHQFCYMCGGDWKTHN--GECYECC 352 (384)
T ss_pred EeeccccchhhcCcchhhCC--ccccCcc
Confidence 34499999999998884333 3454443
No 103
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.12 E-value=9.4 Score=35.16 Aligned_cols=30 Identities=23% Similarity=0.720 Sum_probs=20.7
Q ss_pred ccHHhHHhhhccCC------CCCCCCCCCCCCcCcc
Q 029308 14 KSATCILRWASYVR------NPTCPQCKHPFEFLHV 43 (195)
Q Consensus 14 FC~~CI~rW~e~kq------~~sCP~CK~pFs~l~v 43 (195)
.-.+||.+|-..++ ..+||||.+.+....+
T Consensus 51 VHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P 86 (293)
T KOG3053|consen 51 VHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFP 86 (293)
T ss_pred HHHHHHHHHHhHHhcCCCCceeechhhcchheeecc
Confidence 34689999964322 1379999999886333
No 104
>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=45.03 E-value=16 Score=24.80 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=10.5
Q ss_pred CCCCCcccHHhHHhh---hccCCCCCCCCCCCC
Q 029308 8 PGNGSCKSATCILRW---ASYVRNPTCPQCKHP 37 (195)
Q Consensus 8 l~CGHsFC~~CI~rW---~e~kq~~sCP~CK~p 37 (195)
..|-|.-|++ +..| ........||+|.++
T Consensus 19 ~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 19 KNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp TT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred CcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 5789998865 3333 233333579999875
No 105
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=42.61 E-value=21 Score=33.07 Aligned_cols=39 Identities=23% Similarity=0.313 Sum_probs=28.4
Q ss_pred CCCCCcCCCCCcccHHhHHh--h-hccCCCCCCCCCCCCCCc
Q 029308 2 LGQDSSPGNGSCKSATCILR--W-ASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 2 ~~QpVtl~CGHsFC~~CI~r--W-~e~kq~~sCP~CK~pFs~ 40 (195)
+||-+-|.|--.||-.=+.+ . .+...++.||-|..+.+.
T Consensus 180 lGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~e 221 (314)
T PF06524_consen 180 LGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQE 221 (314)
T ss_pred ccchhhhheeeeehhhhhhhcccccccCCCCCCCCCCCcccc
Confidence 67888888888898877776 1 122334689999988774
No 106
>COG4640 Predicted membrane protein [Function unknown]
Probab=41.79 E-value=6.9 Score=37.92 Aligned_cols=39 Identities=23% Similarity=0.360 Sum_probs=26.4
Q ss_pred cccHHhHHhhhccCCCCCCCCCCCCCCc--Cccccccccchhh
Q 029308 13 CKSATCILRWASYVRNPTCPQCKHPFEF--LHVHRSLDGSISD 53 (195)
Q Consensus 13 sFC~~CI~rW~e~kq~~sCP~CK~pFs~--l~vNr~LdG~ved 53 (195)
-||..|=.+=.+ ....||+|.++|.. .+-|+.++..++.
T Consensus 2 ~fC~kcG~qk~E--d~~qC~qCG~~~t~~~sqan~~tn~i~~t 42 (465)
T COG4640 2 KFCPKCGSQKAE--DDVQCTQCGHKFTSRQSQANKSTNEIIQT 42 (465)
T ss_pred Cccccccccccc--ccccccccCCcCCchhhhhhHHHHHHHHh
Confidence 488888755323 22469999999996 5566666666543
No 107
>PF14353 CpXC: CpXC protein
Probab=41.38 E-value=9.7 Score=29.36 Aligned_cols=12 Identities=67% Similarity=1.489 Sum_probs=8.8
Q ss_pred CCCCCCCCCCCc
Q 029308 29 PTCPQCKHPFEF 40 (195)
Q Consensus 29 ~sCP~CK~pFs~ 40 (195)
.+||.|.++|..
T Consensus 2 itCP~C~~~~~~ 13 (128)
T PF14353_consen 2 ITCPHCGHEFEF 13 (128)
T ss_pred cCCCCCCCeeEE
Confidence 368888888774
No 108
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=40.55 E-value=25 Score=24.59 Aligned_cols=18 Identities=39% Similarity=1.052 Sum_probs=6.9
Q ss_pred CCCCCCCCCCc---Ccccccc
Q 029308 30 TCPQCKHPFEF---LHVHRSL 47 (195)
Q Consensus 30 sCP~CK~pFs~---l~vNr~L 47 (195)
.||.|+..|-. +.++-+|
T Consensus 23 ~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 23 RCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp --TTTT--B-HHHHHTTTTTS
T ss_pred ECCCCCCccccCcChhhhccc
Confidence 56666666663 4444444
No 109
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=38.29 E-value=14 Score=24.26 Aligned_cols=27 Identities=19% Similarity=0.304 Sum_probs=15.5
Q ss_pred CCCCCcccHHhHHhhhcc--CCCCCCCCCCC-CCC
Q 029308 8 PGNGSCKSATCILRWASY--VRNPTCPQCKH-PFE 39 (195)
Q Consensus 8 l~CGHsFC~~CI~rW~e~--kq~~sCP~CK~-pFs 39 (195)
..|||.|= .|... .....||.|.. ...
T Consensus 9 ~~Cg~~fe-----~~~~~~~~~~~~CP~Cg~~~~~ 38 (52)
T TIGR02605 9 TACGHRFE-----VLQKMSDDPLATCPECGGEKLR 38 (52)
T ss_pred CCCCCEeE-----EEEecCCCCCCCCCCCCCCcee
Confidence 36788772 24221 12347999997 443
No 110
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=38.29 E-value=14 Score=24.27 Aligned_cols=16 Identities=13% Similarity=0.138 Sum_probs=13.6
Q ss_pred CCCCCcccHHhHHhhh
Q 029308 8 PGNGSCKSATCILRWA 23 (195)
Q Consensus 8 l~CGHsFC~~CI~rW~ 23 (195)
-.||+.||..|.....
T Consensus 22 r~Cg~~~C~~C~~~~~ 37 (57)
T cd00065 22 RNCGRIFCSKCSSNRI 37 (57)
T ss_pred CcCcCCcChHHcCCee
Confidence 4799999999998753
No 111
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=36.85 E-value=14 Score=33.64 Aligned_cols=41 Identities=20% Similarity=0.527 Sum_probs=29.1
Q ss_pred CCCcccHHhHHhhhccCCCCCCCCCCCCCCcCccccccccchhhhhh
Q 029308 10 NGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSISDYMF 56 (195)
Q Consensus 10 CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~vedy~~ 56 (195)
-||.-|.+|=.+- .+.||.|+.++..+ .++.++.+++...+
T Consensus 67 nGHlaCssC~~~~-----~~~CP~Cr~~~g~~-R~~amEkV~e~~~v 107 (299)
T KOG3002|consen 67 NGHLACSSCRTKV-----SNKCPTCRLPIGNI-RCRAMEKVAEAVLV 107 (299)
T ss_pred CCcEehhhhhhhh-----cccCCccccccccH-HHHHHHHHHHhcee
Confidence 4899999998753 25799999999953 44555555554443
No 112
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=36.29 E-value=19 Score=24.59 Aligned_cols=11 Identities=45% Similarity=1.268 Sum_probs=10.1
Q ss_pred CCCCCCCCCCC
Q 029308 29 PTCPQCKHPFE 39 (195)
Q Consensus 29 ~sCP~CK~pFs 39 (195)
..||+|..||+
T Consensus 9 K~C~~C~rpf~ 19 (42)
T PF10013_consen 9 KICPVCGRPFT 19 (42)
T ss_pred CcCcccCCcch
Confidence 48999999998
No 113
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.98 E-value=24 Score=27.12 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=19.8
Q ss_pred CCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 11 GSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
-|.||..|...-.. -.||.|.-.+..
T Consensus 28 EcTFCadCae~~l~----g~CPnCGGelv~ 53 (84)
T COG3813 28 ECTFCADCAENRLH----GLCPNCGGELVA 53 (84)
T ss_pred eeehhHhHHHHhhc----CcCCCCCchhhc
Confidence 47899999986322 379999988774
No 114
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=34.93 E-value=22 Score=30.24 Aligned_cols=26 Identities=35% Similarity=0.645 Sum_probs=22.3
Q ss_pred cHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 15 SATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 15 C~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
=..|+.+|...+++..|.+|...+..
T Consensus 110 H~~cl~~W~~~~~~~~CeiC~~~~~~ 135 (323)
T KOG1609|consen 110 HRSCLEKWFSIKGNITCEICKSFFIN 135 (323)
T ss_pred HHHHHHhhhccccCeeeeccccccee
Confidence 46799999887788899999998884
No 115
>PTZ00364 dipeptidyl-peptidase I precursor; Provisional
Probab=34.82 E-value=16 Score=36.03 Aligned_cols=12 Identities=33% Similarity=0.747 Sum_probs=10.1
Q ss_pred cccCCCcccccc
Q 029308 114 RWGDNGYVRAGR 125 (195)
Q Consensus 114 r~g~ngyvr~gr 125 (195)
.||+|||+|-=|
T Consensus 432 ~WGE~GYfRI~R 443 (548)
T PTZ00364 432 SWCDGGTRKIAR 443 (548)
T ss_pred CcccCCeEEEEc
Confidence 899999997644
No 116
>PF15556 Zwint: ZW10 interactor
Probab=34.79 E-value=47 Score=29.99 Aligned_cols=23 Identities=48% Similarity=0.534 Sum_probs=14.4
Q ss_pred HHhHHHHHHHHH---------HHHHHHHHHhc
Q 029308 164 ALKREAADKAAA---------SKHQQHLARLG 186 (195)
Q Consensus 164 a~kreaa~k~~~---------~kh~~~l~~~g 186 (195)
|.|++|.+|+-+ +||.+||.+..
T Consensus 112 aKKqva~eK~r~AQkqwqlqQeK~LQ~Lae~s 143 (252)
T PF15556_consen 112 AKKQVAMEKLRAAQKQWQLQQEKHLQHLAEVS 143 (252)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666666544 57888887643
No 117
>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=34.70 E-value=15 Score=30.37 Aligned_cols=12 Identities=33% Similarity=0.620 Sum_probs=11.1
Q ss_pred CcccHHhHHhhh
Q 029308 12 SCKSATCILRWA 23 (195)
Q Consensus 12 HsFC~~CI~rW~ 23 (195)
|.||..|+.+|.
T Consensus 55 kmfc~~C~~rw~ 66 (134)
T PF05883_consen 55 KMFCADCDKRWR 66 (134)
T ss_pred HHHHHHHHHHHH
Confidence 899999999994
No 118
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=34.56 E-value=17 Score=31.05 Aligned_cols=12 Identities=42% Similarity=0.944 Sum_probs=10.7
Q ss_pred CCCCCCCCCCCc
Q 029308 29 PTCPQCKHPFEF 40 (195)
Q Consensus 29 ~sCP~CK~pFs~ 40 (195)
.+||+|.+.|..
T Consensus 6 ~~CPvC~~~F~~ 17 (214)
T PF09986_consen 6 ITCPVCGKEFKT 17 (214)
T ss_pred eECCCCCCeeee
Confidence 589999999995
No 119
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=34.33 E-value=13 Score=35.76 Aligned_cols=32 Identities=22% Similarity=0.478 Sum_probs=0.0
Q ss_pred CcCCCCCcccHHhHHhhhccC----CCCCCCCCCCCCCc
Q 029308 6 SSPGNGSCKSATCILRWASYV----RNPTCPQCKHPFEF 40 (195)
Q Consensus 6 Vtl~CGHsFC~~CI~rW~e~k----q~~sCP~CK~pFs~ 40 (195)
|-+.|||++=. -.|-... ...+||+|+.+-+.
T Consensus 305 VYl~CGHVhG~---h~Wg~~~~~~~~~r~CPlCr~~g~~ 340 (416)
T PF04710_consen 305 VYLNCGHVHGY---HNWGQDSDRDPRSRTCPLCRQVGPY 340 (416)
T ss_dssp ---------------------------------------
T ss_pred eeccccceeee---cccccccccccccccCCCccccCCc
Confidence 55899998822 2363211 13489999988765
No 120
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.06 E-value=16 Score=28.63 Aligned_cols=29 Identities=10% Similarity=0.233 Sum_probs=18.0
Q ss_pred CCcccHHhHHhhhccCCCC-CCCCCCCCCC
Q 029308 11 GSCKSATCILRWASYVRNP-TCPQCKHPFE 39 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq~~-sCP~CK~pFs 39 (195)
...+|..|=..|....... .||.|..+..
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKNV 99 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCce
Confidence 3467888886663322223 4999997654
No 121
>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=32.89 E-value=44 Score=25.97 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=20.5
Q ss_pred CCcccHHhHHhhhcc-------CCCCCCCCCCCCCC
Q 029308 11 GSCKSATCILRWASY-------VRNPTCPQCKHPFE 39 (195)
Q Consensus 11 GHsFC~~CI~rW~e~-------kq~~sCP~CK~pFs 39 (195)
.=.||..||..+... ..+..||.|+...+
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCn 72 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICN 72 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeC
Confidence 667999999985321 12246999998665
No 122
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=32.72 E-value=12 Score=38.94 Aligned_cols=33 Identities=15% Similarity=0.196 Sum_probs=22.2
Q ss_pred CCCCCcccHHhHHhhh----ccCCCCCCCCCCCCCCc
Q 029308 8 PGNGSCKSATCILRWA----SYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 8 l~CGHsFC~~CI~rW~----e~kq~~sCP~CK~pFs~ 40 (195)
..|||-||..|+..|- .....-.|+.|+..+..
T Consensus 247 ~~C~~~~Cl~C~r~~~p~~~~~e~a~k~~~~~~~C~~ 283 (889)
T KOG1356|consen 247 PRCGFGVCLDCYRKWYPRLSKEEVAEKCEFSWLKCNK 283 (889)
T ss_pred cccCCeeeecchhhccccchHhHhhhhhhHHHHhcCC
Confidence 4699999999999993 11111257777666653
No 123
>cd02620 Peptidase_C1A_CathepsinB Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane
Probab=32.35 E-value=18 Score=30.59 Aligned_cols=12 Identities=58% Similarity=1.268 Sum_probs=9.9
Q ss_pred cccCCCcccccc
Q 029308 114 RWGDNGYVRAGR 125 (195)
Q Consensus 114 r~g~ngyvr~gr 125 (195)
.||++||+|--|
T Consensus 211 ~WGe~Gy~ri~~ 222 (236)
T cd02620 211 DWGENGYFRILR 222 (236)
T ss_pred CCCCCcEEEEEc
Confidence 799999998643
No 124
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=32.09 E-value=18 Score=29.93 Aligned_cols=27 Identities=11% Similarity=0.073 Sum_probs=15.1
Q ss_pred ccHHhHHhhhcc-CCCCCCCCCCCCCCc
Q 029308 14 KSATCILRWASY-VRNPTCPQCKHPFEF 40 (195)
Q Consensus 14 FC~~CI~rW~e~-kq~~sCP~CK~pFs~ 40 (195)
-|.+|-.++... +.+..||.|...|..
T Consensus 11 ~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 11 ICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred cCCCcCccccccCCCCccCCCcCCccCc
Confidence 356666664433 233467777777654
No 125
>cd02698 Peptidase_C1A_CathepsinX Cathepsin X; the only papain-like lysosomal cysteine peptidase exhibiting carboxymonopeptidase activity. It can also act as a carboxydipeptidase, like cathepsin B, but has been shown to preferentially cleave substrates through a monopeptidyl carboxypeptidase pathway. The propeptide region of cathepsin X, the shortest among papain-like peptidases, is covalently attached to the active site cysteine in the inactive form of the enzyme. Little is known about the biological function of cathepsin X. Some studies point to a role in early tumorigenesis. A more recent study indicates that cathepsin X expression is restricted to immune cells suggesting a role in phagocytosis and the regulation of the immune response.
Probab=31.97 E-value=18 Score=30.60 Aligned_cols=12 Identities=33% Similarity=0.947 Sum_probs=9.7
Q ss_pred cccCCCcccccc
Q 029308 114 RWGDNGYVRAGR 125 (195)
Q Consensus 114 r~g~ngyvr~gr 125 (195)
-||++||++--|
T Consensus 206 ~WGe~Gy~~i~r 217 (239)
T cd02698 206 PWGERGWFRIVT 217 (239)
T ss_pred ccCcCceEEEEc
Confidence 699999997643
No 126
>cd02248 Peptidase_C1A Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates the P2 sidechain of the substrate (the second residue away from the scissile bond). Most members of the papain subfamily are endopeptidases. Some exceptions to this rule can be explained by specific details of the catalytic domains like the occluding loop in cathepsin B which confers an additional carboxydipeptidyl activity and the mini-chain of cathepsin H resulting in an N-terminal exopeptidase activity. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds. Parasitic CPs act extracellularly to help invade tissues and cells, to h
Probab=31.89 E-value=18 Score=28.95 Aligned_cols=11 Identities=45% Similarity=1.392 Sum_probs=9.1
Q ss_pred cccCCCccccc
Q 029308 114 RWGDNGYVRAG 124 (195)
Q Consensus 114 r~g~ngyvr~g 124 (195)
.||+|||++--
T Consensus 185 ~WG~~Gy~~i~ 195 (210)
T cd02248 185 SWGEKGYIRIA 195 (210)
T ss_pred ccccCcEEEEE
Confidence 69999998753
No 127
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=31.87 E-value=5.8 Score=29.57 Aligned_cols=35 Identities=23% Similarity=0.556 Sum_probs=20.6
Q ss_pred CCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCc
Q 029308 5 DSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFLH 42 (195)
Q Consensus 5 pVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~ 42 (195)
+....=||.+|..|-..+... ..||.|.++...|.
T Consensus 10 ~L~~~~~~~~C~~C~~~~~~~---a~CPdC~~~Le~Lk 44 (70)
T PF07191_consen 10 ELEWQGGHYHCEACQKDYKKE---AFCPDCGQPLEVLK 44 (70)
T ss_dssp BEEEETTEEEETTT--EEEEE---EE-TTT-SB-EEEE
T ss_pred ccEEeCCEEECccccccceec---ccCCCcccHHHHHH
Confidence 333333899999999986322 58999999988643
No 128
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.19 E-value=34 Score=31.36 Aligned_cols=36 Identities=17% Similarity=0.274 Sum_probs=27.3
Q ss_pred CCCCcCCCCCcccHHhHHhhhccC------CCCCCCCCCCCC
Q 029308 3 GQDSSPGNGSCKSATCILRWASYV------RNPTCPQCKHPF 38 (195)
Q Consensus 3 ~QpVtl~CGHsFC~~CI~rW~e~k------q~~sCP~CK~pF 38 (195)
|+-+-+.|=|.|-..|+..|+-.- ....||-|-.++
T Consensus 63 gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 63 GDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 556778999999999999996421 123799998764
No 129
>PRK01343 zinc-binding protein; Provisional
Probab=30.79 E-value=29 Score=24.96 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=9.5
Q ss_pred CCCCCCCCCCC
Q 029308 29 PTCPQCKHPFE 39 (195)
Q Consensus 29 ~sCP~CK~pFs 39 (195)
..||+|++++.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 47999999986
No 130
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=30.59 E-value=39 Score=24.50 Aligned_cols=24 Identities=25% Similarity=0.440 Sum_probs=18.6
Q ss_pred cccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 13 CKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 13 sFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.||..|...-. ...||.|.-.|..
T Consensus 30 TFC~~C~e~~l----~~~CPNCgGelv~ 53 (57)
T PF06906_consen 30 TFCADCAETML----NGVCPNCGGELVR 53 (57)
T ss_pred cccHHHHHHHh----cCcCcCCCCcccc
Confidence 69999998852 2579999987764
No 131
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=30.52 E-value=13 Score=26.64 Aligned_cols=13 Identities=31% Similarity=0.659 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCCc
Q 029308 28 NPTCPQCKHPFEF 40 (195)
Q Consensus 28 ~~sCP~CK~pFs~ 40 (195)
+.+||+|...++.
T Consensus 24 PatCP~C~a~~~~ 36 (54)
T PF09237_consen 24 PATCPICGAVIRQ 36 (54)
T ss_dssp -EE-TTT--EESS
T ss_pred CCCCCcchhhccc
Confidence 3489999998874
No 132
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.40 E-value=25 Score=23.66 Aligned_cols=11 Identities=36% Similarity=1.183 Sum_probs=6.5
Q ss_pred CCCCCCCCCCc
Q 029308 30 TCPQCKHPFEF 40 (195)
Q Consensus 30 sCP~CK~pFs~ 40 (195)
.||.|.+.+..
T Consensus 30 ~C~~Cgh~w~~ 40 (55)
T PF14311_consen 30 KCPKCGHEWKA 40 (55)
T ss_pred ECCCCCCeeEc
Confidence 36666665554
No 133
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.22 E-value=14 Score=28.77 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=14.9
Q ss_pred cccHHhHHhhhccCCCCCCCCCCCCC
Q 029308 13 CKSATCILRWASYVRNPTCPQCKHPF 38 (195)
Q Consensus 13 sFC~~CI~rW~e~kq~~sCP~CK~pF 38 (195)
.+|..|=..|........||.|..+-
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHGER 96 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCCCC
Confidence 35666665553222224699999653
No 134
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=30.01 E-value=14 Score=28.83 Aligned_cols=27 Identities=19% Similarity=0.498 Sum_probs=16.6
Q ss_pred cccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 13 CKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 13 sFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
.+|..|=..|........||.|+.+..
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCPKCHGIML 97 (115)
T ss_pred EEcccCCCEEecCCcCccCcCCcCCCc
Confidence 567777755533222346999997654
No 135
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=29.90 E-value=27 Score=36.76 Aligned_cols=31 Identities=23% Similarity=0.471 Sum_probs=23.0
Q ss_pred CCCCcccHHhHHhhhccCC-----CCCCCCCCCCCC
Q 029308 9 GNGSCKSATCILRWASYVR-----NPTCPQCKHPFE 39 (195)
Q Consensus 9 ~CGHsFC~~CI~rW~e~kq-----~~sCP~CK~pFs 39 (195)
.|=|+|=..||.+|+...+ ...||.|.....
T Consensus 212 sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 212 SCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred hhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 4889999999999975322 236999995444
No 136
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.83 E-value=17 Score=26.02 Aligned_cols=12 Identities=42% Similarity=1.342 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCc
Q 029308 29 PTCPQCKHPFEF 40 (195)
Q Consensus 29 ~sCP~CK~pFs~ 40 (195)
..||+|..||+-
T Consensus 13 KICpvCqRPFsW 24 (54)
T COG4338 13 KICPVCQRPFSW 24 (54)
T ss_pred hhhhhhcCchHH
Confidence 379999999983
No 137
>PRK02551 flavoprotein NrdI; Provisional
Probab=29.76 E-value=8.7 Score=31.84 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=22.8
Q ss_pred ceeeccccccCCCcccccccccccccCCC
Q 029308 107 SLRIGNRRWGDNGYVRAGRQEARPVCRPN 135 (195)
Q Consensus 107 ~~~ignrr~g~ngyvr~gr~~arpv~~~~ 135 (195)
-+-.|||-||++ |..+|+..|+=-.+|-
T Consensus 99 VigsGNrNfg~~-F~~aa~~ia~~~~vP~ 126 (154)
T PRK02551 99 IIGSGNRNFNNQ-YCLTAKQYAKRFGFPM 126 (154)
T ss_pred EEeecccHHHHH-HHHHHHHHHHHcCCCE
Confidence 455899999999 9999998888666554
No 138
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=29.49 E-value=29 Score=25.10 Aligned_cols=14 Identities=43% Similarity=1.080 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCCc
Q 029308 27 RNPTCPQCKHPFEF 40 (195)
Q Consensus 27 q~~sCP~CK~pFs~ 40 (195)
+.+.||+|+.+...
T Consensus 38 ~~p~CPlC~s~M~~ 51 (59)
T PF14169_consen 38 EEPVCPLCKSPMVS 51 (59)
T ss_pred CCccCCCcCCcccc
Confidence 44789999988764
No 139
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=29.47 E-value=7.4 Score=30.13 Aligned_cols=27 Identities=19% Similarity=0.448 Sum_probs=14.4
Q ss_pred cccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 13 CKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 13 sFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
.+|..|=..|.-......||.|..+.-
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCGSPDV 97 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSSSS-E
T ss_pred EECCCCCCEEecCCCCCCCcCCcCCCc
Confidence 356667666642222246999998743
No 140
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=29.14 E-value=23 Score=24.36 Aligned_cols=20 Identities=20% Similarity=0.678 Sum_probs=9.4
Q ss_pred hhccCCCCCCCCCCCCCCcC
Q 029308 22 WASYVRNPTCPQCKHPFEFL 41 (195)
Q Consensus 22 W~e~kq~~sCP~CK~pFs~l 41 (195)
|-...+...|++|.++|+.+
T Consensus 3 W~~d~~~~~C~~C~~~F~~~ 22 (69)
T PF01363_consen 3 WVPDSEASNCMICGKKFSLF 22 (69)
T ss_dssp SSSGGG-SB-TTT--B-BSS
T ss_pred cCCCCCCCcCcCcCCcCCCc
Confidence 54344456899999999753
No 141
>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=29.02 E-value=16 Score=19.94 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=9.5
Q ss_pred CCCCCCCCCCc
Q 029308 30 TCPQCKHPFEF 40 (195)
Q Consensus 30 sCP~CK~pFs~ 40 (195)
.||.|.+.|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 59999999985
No 142
>cd02621 Peptidase_C1A_CathepsinC Cathepsin C; also known as Dipeptidyl Peptidase I (DPPI), an atypical papain-like cysteine peptidase with chloride dependency and dipeptidyl aminopeptidase activity, resulting from its tetrameric structure which limits substrate access. Each subunit of the tetramer is composed of three peptides: the heavy and light chains, which together adopts the papain fold and forms the catalytic domain; and the residual propeptide region, which forms a beta barrel and points towards the substrate's N-terminus. The subunit composition is the result of the unique characteristic of procathepsin C maturation involving the cleavage of the catalytic domain and the non-autocatalytic excision of an activation peptide within its propeptide region. By removing N-terminal dipeptide extensions, cathepsin C activates granule serine peptidases (granzymes) involved in cell-mediated apoptosis, inflammation and tissue remodelling. Loss-of-function mutations in cathepsin C are assoc
Probab=28.89 E-value=22 Score=29.91 Aligned_cols=13 Identities=38% Similarity=1.127 Sum_probs=10.4
Q ss_pred ccccCCCcccccc
Q 029308 113 RRWGDNGYVRAGR 125 (195)
Q Consensus 113 rr~g~ngyvr~gr 125 (195)
--||++||++--|
T Consensus 214 ~~WGe~Gy~~i~~ 226 (243)
T cd02621 214 SSWGEKGYFKIRR 226 (243)
T ss_pred CCCCcCCeEEEec
Confidence 4799999998644
No 143
>PF00112 Peptidase_C1: Papain family cysteine protease This is family C1 in the peptidase classification. ; InterPro: IPR000668 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins belong to the peptidase family C1, sub-family C1A (papain family, clan CA). It includes proteins classed as non-peptidase homologs. These are have either been shown experimentally to lack peptidase activity or lack one or more of the active site residues. The papain family has a wide variety of activities, including broad-range (papain) and narrow-range endo-peptidases, aminopeptidases, dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity []. Members of the papain family are widespread, found in baculovirus [], eubacteria, yeast, and practically all protozoa, plants and mammals []. The proteins are typically lysosomal or secreted, and proteolytic cleavage of the propeptide is required for enzyme activation, although bleomycin hydrolase is cytosolic in fungi and mammals []. Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions. The propeptide regions serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme, the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association, and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate []. The catalytic residues of papain are Cys-25 and His-159, other important residues being Gln-19, which helps form the 'oxyanion hole', and Asn-175, which orientates the imidazole ring of His-159. ; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MOR_B 3HHI_B 1S4V_A 3F75_A 1MEG_A 1PCI_C 1PPO_A 3HD3_B 1F29_A 1EWL_A ....
Probab=27.82 E-value=24 Score=27.90 Aligned_cols=13 Identities=54% Similarity=1.173 Sum_probs=10.5
Q ss_pred ccccCCCcccccc
Q 029308 113 RRWGDNGYVRAGR 125 (195)
Q Consensus 113 rr~g~ngyvr~gr 125 (195)
..||++||++--+
T Consensus 191 ~~WG~~Gy~~i~~ 203 (219)
T PF00112_consen 191 TDWGDNGYFRISY 203 (219)
T ss_dssp TTSTBTTEEEEES
T ss_pred CccCCCeEEEEee
Confidence 6799999987654
No 144
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.61 E-value=23 Score=30.01 Aligned_cols=9 Identities=11% Similarity=-0.086 Sum_probs=7.7
Q ss_pred CCCCCcccH
Q 029308 8 PGNGSCKSA 16 (195)
Q Consensus 8 l~CGHsFC~ 16 (195)
-.|||+||.
T Consensus 73 cecghsf~d 81 (165)
T COG4647 73 CECGHSFGD 81 (165)
T ss_pred EeccccccC
Confidence 479999996
No 145
>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=27.50 E-value=23 Score=18.63 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=7.3
Q ss_pred CCCCCCCCCCc
Q 029308 30 TCPQCKHPFEF 40 (195)
Q Consensus 30 sCP~CK~pFs~ 40 (195)
.||+|...|..
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 49999998875
No 146
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=27.42 E-value=23 Score=28.58 Aligned_cols=12 Identities=58% Similarity=1.403 Sum_probs=9.7
Q ss_pred cccCCCcccccc
Q 029308 114 RWGDNGYVRAGR 125 (195)
Q Consensus 114 r~g~ngyvr~gr 125 (195)
.||++||++--|
T Consensus 147 ~WG~~G~~~i~~ 158 (174)
T smart00645 147 DWGENGYFRIAR 158 (174)
T ss_pred CcccCeEEEEEc
Confidence 599999998643
No 147
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=26.57 E-value=41 Score=22.53 Aligned_cols=12 Identities=42% Similarity=0.933 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCC
Q 029308 28 NPTCPQCKHPFE 39 (195)
Q Consensus 28 ~~sCP~CK~pFs 39 (195)
...||.|.+.|+
T Consensus 2 ~f~CP~C~~~~~ 13 (54)
T PF05605_consen 2 SFTCPYCGKGFS 13 (54)
T ss_pred CcCCCCCCCccC
Confidence 357999998666
No 148
>PTZ00203 cathepsin L protease; Provisional
Probab=26.53 E-value=25 Score=32.29 Aligned_cols=12 Identities=50% Similarity=1.273 Sum_probs=10.0
Q ss_pred ccccCCCccccc
Q 029308 113 RRWGDNGYVRAG 124 (195)
Q Consensus 113 rr~g~ngyvr~g 124 (195)
--||++||++--
T Consensus 312 ~~WGe~GY~ri~ 323 (348)
T PTZ00203 312 EDWGEKGYVRVT 323 (348)
T ss_pred CCcCcCceEEEE
Confidence 479999999864
No 149
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.44 E-value=41 Score=34.23 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=25.2
Q ss_pred cCCCCC-cccHHhHHhhhccCC----CCCCCCCCCCCCc
Q 029308 7 SPGNGS-CKSATCILRWASYVR----NPTCPQCKHPFEF 40 (195)
Q Consensus 7 tl~CGH-sFC~~CI~rW~e~kq----~~sCP~CK~pFs~ 40 (195)
.-+||| .-|.+|..+...... ...||+|+..+..
T Consensus 15 ~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~ 53 (669)
T KOG2231|consen 15 RGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVET 53 (669)
T ss_pred cccccccccchhhhhhhhhhcccccccccCcccccceee
Confidence 357999 999999999643333 3478999986653
No 150
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.21 E-value=40 Score=31.16 Aligned_cols=19 Identities=16% Similarity=0.191 Sum_probs=17.1
Q ss_pred CCCcCCCCCcccHHhHHhh
Q 029308 4 QDSSPGNGSCKSATCILRW 22 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW 22 (195)
.||+.+=||.||+.||+++
T Consensus 55 dPvit~~GylfdrEaILe~ 73 (303)
T KOG3039|consen 55 DPVITPDGYLFDREAILEY 73 (303)
T ss_pred CCccCCCCeeeeHHHHHHH
Confidence 5788889999999999985
No 151
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.13 E-value=40 Score=28.74 Aligned_cols=25 Identities=20% Similarity=0.470 Sum_probs=19.8
Q ss_pred CCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 11 GSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.+.||..|=.+- . ..||.|..+...
T Consensus 27 ~~~fC~kCG~~t--I---~~Cp~C~~~IrG 51 (158)
T PF10083_consen 27 REKFCSKCGAKT--I---TSCPNCSTPIRG 51 (158)
T ss_pred HHHHHHHhhHHH--H---HHCcCCCCCCCC
Confidence 357999998874 2 369999999885
No 152
>KOG1543 consensus Cysteine proteinase Cathepsin L [Posttranslational modification, protein turnover, chaperones]
Probab=26.13 E-value=28 Score=31.60 Aligned_cols=13 Identities=46% Similarity=1.214 Sum_probs=10.5
Q ss_pred ccccCCCcccccc
Q 029308 113 RRWGDNGYVRAGR 125 (195)
Q Consensus 113 rr~g~ngyvr~gr 125 (195)
.-||++||+|-=|
T Consensus 295 ~~WGe~Gy~ri~r 307 (325)
T KOG1543|consen 295 TDWGEKGYFRIAR 307 (325)
T ss_pred CCcccCceEEEec
Confidence 4799999998644
No 153
>PF14369 zf-RING_3: zinc-finger
Probab=25.74 E-value=21 Score=22.87 Aligned_cols=28 Identities=18% Similarity=0.286 Sum_probs=17.2
Q ss_pred CcccHHhHHhhhc--cCCC-CCCCCCCCCCC
Q 029308 12 SCKSATCILRWAS--YVRN-PTCPQCKHPFE 39 (195)
Q Consensus 12 HsFC~~CI~rW~e--~kq~-~sCP~CK~pFs 39 (195)
..||..|-....- .... ..||.|...|-
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFv 32 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFV 32 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCCcEe
Confidence 4578888765321 1222 35999997764
No 154
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=25.13 E-value=33 Score=20.25 Aligned_cols=12 Identities=33% Similarity=0.833 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCc
Q 029308 29 PTCPQCKHPFEF 40 (195)
Q Consensus 29 ~sCP~CK~pFs~ 40 (195)
..||.|...|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 369999999974
No 155
>PF11693 DUF2990: Protein of unknown function (DUF2990); InterPro: IPR021706 This family of proteins represents a fungal protein with unknown function.
Probab=24.25 E-value=35 Score=25.29 Aligned_cols=18 Identities=39% Similarity=0.702 Sum_probs=12.3
Q ss_pred ccccccCCCCccchhhhHHhh
Q 029308 83 DLEDDYSYEDEEDDLDEVYFR 103 (195)
Q Consensus 83 ~~~~~y~y~~~~d~~~e~y~~ 103 (195)
=++|.|+|+|| +.|+|=+
T Consensus 14 ~fd~~Yd~S~d---laeFy~r 31 (64)
T PF11693_consen 14 FFDNVYDYSDD---LAEFYGR 31 (64)
T ss_pred hhhccccCCHH---HHHHHHH
Confidence 35677888665 8887744
No 156
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=23.78 E-value=28 Score=28.39 Aligned_cols=47 Identities=13% Similarity=0.055 Sum_probs=26.2
Q ss_pred CCcccHHhHHhhh--ccCCCCCCCCCCCCCCc-Cccccccccchhhhhhh
Q 029308 11 GSCKSATCILRWA--SYVRNPTCPQCKHPFEF-LHVHRSLDGSISDYMFE 57 (195)
Q Consensus 11 GHsFC~~CI~rW~--e~kq~~sCP~CK~pFs~-l~vNr~LdG~vedy~~E 57 (195)
.-.||..|=.-.- ..+....|++|+..++. ...+......+..+.+.
T Consensus 6 ~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~ 55 (116)
T KOG2907|consen 6 DLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFT 55 (116)
T ss_pred CcchhhhhhhhcccccccCceEeccccccCCHHHhCCeeEEEEEeecccc
Confidence 3469999965421 12222359999999985 33344444444333333
No 157
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=23.60 E-value=32 Score=27.84 Aligned_cols=11 Identities=9% Similarity=-0.173 Sum_probs=8.7
Q ss_pred CcCCCCCcccH
Q 029308 6 SSPGNGSCKSA 16 (195)
Q Consensus 6 Vtl~CGHsFC~ 16 (195)
|.-.|||.||.
T Consensus 25 vkc~CGh~f~d 35 (112)
T PF08882_consen 25 VKCDCGHEFCD 35 (112)
T ss_pred eeccCCCeecC
Confidence 44579999996
No 158
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.74 E-value=39 Score=33.92 Aligned_cols=25 Identities=20% Similarity=0.429 Sum_probs=13.8
Q ss_pred CCcccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 11 GSCKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
|+.||..|=..- ....||.|.+...
T Consensus 14 ~akFC~~CG~~l----~~~~Cp~CG~~~~ 38 (645)
T PRK14559 14 NNRFCQKCGTSL----THKPCPQCGTEVP 38 (645)
T ss_pred CCccccccCCCC----CCCcCCCCCCCCC
Confidence 345999995442 1134666665533
No 159
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=22.59 E-value=54 Score=26.02 Aligned_cols=34 Identities=26% Similarity=0.511 Sum_probs=21.4
Q ss_pred ccchhhhHHhhCCCceeeccccccCCCccccccccccc
Q 029308 93 EEDDLDEVYFRSSSSLRIGNRRWGDNGYVRAGRQEARP 130 (195)
Q Consensus 93 ~~d~~~e~y~~~~~~~~ignrr~g~ngyvr~gr~~arp 130 (195)
-+|++-|+.+..- - +.---+|.|||... |.-.-+
T Consensus 35 TEDElkEF~~kse-Q--lrrNGf~kngfl~~-rs~slf 68 (97)
T PF15337_consen 35 TEDELKEFQVKSE-Q--LRRNGFGKNGFLQS-RSLSLF 68 (97)
T ss_pred cHHHHHHHHHHHH-H--HHHccccccchhhh-hhhhcc
Confidence 3677999988852 2 22334777888777 665533
No 160
>PTZ00200 cysteine proteinase; Provisional
Probab=22.59 E-value=32 Score=32.89 Aligned_cols=13 Identities=54% Similarity=1.285 Sum_probs=10.6
Q ss_pred ccccCCCcccccc
Q 029308 113 RRWGDNGYVRAGR 125 (195)
Q Consensus 113 rr~g~ngyvr~gr 125 (195)
..||++||++--|
T Consensus 414 ~~WGe~GY~ri~r 426 (448)
T PTZ00200 414 TDWGENGYMRLER 426 (448)
T ss_pred CCcccCeeEEEEe
Confidence 4799999998654
No 161
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=21.79 E-value=57 Score=22.27 Aligned_cols=13 Identities=31% Similarity=0.767 Sum_probs=7.3
Q ss_pred cCCCCCCCCCCCC
Q 029308 25 YVRNPTCPQCKHP 37 (195)
Q Consensus 25 ~kq~~sCP~CK~p 37 (195)
......||+|..+
T Consensus 31 Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 31 LPDDWVCPVCGAP 43 (47)
T ss_dssp S-TT-B-TTTSSB
T ss_pred CCCCCcCcCCCCc
Confidence 3344589999876
No 162
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.67 E-value=24 Score=21.58 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=12.5
Q ss_pred CCcccHHhHHhhhccCC--CCCCCCCCCC
Q 029308 11 GSCKSATCILRWASYVR--NPTCPQCKHP 37 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq--~~sCP~CK~p 37 (195)
.|-||-.|=..-..... ...||.|...
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence 37788888776211111 1368888754
No 163
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=21.53 E-value=38 Score=30.93 Aligned_cols=47 Identities=23% Similarity=0.454 Sum_probs=30.5
Q ss_pred CCCcCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCcCccccccccchh
Q 029308 4 QDSSPGNGSCKSATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSIS 52 (195)
Q Consensus 4 QpVtl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~l~vNr~LdG~ve 52 (195)
-|..++|||.-=..|....-. ...+||+|.++-......+.|+..|.
T Consensus 174 ~~~~~~CgH~~h~~cf~e~~~--~~y~CP~C~~~~d~~~~~~~~d~~l~ 220 (276)
T KOG1940|consen 174 DAGVLKCGHYMHSRCFEEMIC--EGYTCPICSKPGDMSHYFRKLDKELA 220 (276)
T ss_pred cCCccCcccchHHHHHHHHhc--cCCCCCcccchHHHHHHHHHHHHHHh
Confidence 356789999988888887532 22789999993222334444544443
No 164
>cd02619 Peptidase_C1 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel str
Probab=21.47 E-value=37 Score=26.77 Aligned_cols=13 Identities=54% Similarity=1.135 Sum_probs=10.1
Q ss_pred cccCCCccccccc
Q 029308 114 RWGDNGYVRAGRQ 126 (195)
Q Consensus 114 r~g~ngyvr~gr~ 126 (195)
-||++||++--+.
T Consensus 200 ~wg~~Gy~~i~~~ 212 (223)
T cd02619 200 DWGDNGYGRISYE 212 (223)
T ss_pred ccccCCEEEEehh
Confidence 7999999975443
No 165
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=21.43 E-value=22 Score=21.02 Aligned_cols=9 Identities=33% Similarity=0.962 Sum_probs=5.9
Q ss_pred CCCCCCCCC
Q 029308 29 PTCPQCKHP 37 (195)
Q Consensus 29 ~sCP~CK~p 37 (195)
..||.|.++
T Consensus 17 ~fC~~CG~~ 25 (26)
T PF13248_consen 17 KFCPNCGAK 25 (26)
T ss_pred ccChhhCCC
Confidence 467777665
No 166
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.43 E-value=38 Score=27.53 Aligned_cols=26 Identities=35% Similarity=0.760 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCCc--Cccccccccchhh
Q 029308 28 NPTCPQCKHPFEF--LHVHRSLDGSISD 53 (195)
Q Consensus 28 ~~sCP~CK~pFs~--l~vNr~LdG~ved 53 (195)
...||.|..+|.. +--|..|=|.+=.
T Consensus 49 ~t~CP~Cg~~~e~~fvva~~aLVgl~l~ 76 (115)
T COG1885 49 STSCPKCGEPFESAFVVANTALVGLILS 76 (115)
T ss_pred cccCCCCCCccceeEEEecceeEEEEEE
Confidence 3579999999996 4456667676533
No 167
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=21.32 E-value=63 Score=22.26 Aligned_cols=15 Identities=20% Similarity=0.348 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCCc
Q 029308 26 VRNPTCPQCKHPFEF 40 (195)
Q Consensus 26 kq~~sCP~CK~pFs~ 40 (195)
.....||+|..+-+.
T Consensus 32 p~~w~CP~C~a~K~~ 46 (50)
T cd00730 32 PDDWVCPVCGAGKDD 46 (50)
T ss_pred CCCCCCCCCCCcHHH
Confidence 334589999987543
No 168
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.56 E-value=28 Score=30.61 Aligned_cols=28 Identities=21% Similarity=0.520 Sum_probs=14.6
Q ss_pred CCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 11 GSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 11 GHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
-|.+|..|=..| ... ...||.|...-..
T Consensus 196 R~L~Cs~C~t~W-~~~-R~~Cp~Cg~~~~~ 223 (290)
T PF04216_consen 196 RYLHCSLCGTEW-RFV-RIKCPYCGNTDHE 223 (290)
T ss_dssp EEEEETTT--EE-E---TTS-TTT---SS-
T ss_pred EEEEcCCCCCee-eec-CCCCcCCCCCCCc
Confidence 367899999998 333 2589999987553
No 169
>PLN02248 cellulose synthase-like protein
Probab=20.39 E-value=67 Score=34.69 Aligned_cols=32 Identities=22% Similarity=0.503 Sum_probs=25.3
Q ss_pred cCCCCCcccHHhHHhhhccCCCCCCCCCCCCCCc
Q 029308 7 SPGNGSCKSATCILRWASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 7 tl~CGHsFC~~CI~rW~e~kq~~sCP~CK~pFs~ 40 (195)
.-.|++..|++|-..--. ..-.||-||.++..
T Consensus 147 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~ 178 (1135)
T PLN02248 147 PCECGFKICRDCYIDAVK--SGGICPGCKEPYKV 178 (1135)
T ss_pred cccccchhHHhHhhhhhh--cCCCCCCCcccccc
Confidence 457999999999998422 23589999999963
No 170
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=20.38 E-value=68 Score=25.73 Aligned_cols=18 Identities=39% Similarity=0.840 Sum_probs=13.5
Q ss_pred hccCCCCCCCCCCCCCCc
Q 029308 23 ASYVRNPTCPQCKHPFEF 40 (195)
Q Consensus 23 ~e~kq~~sCP~CK~pFs~ 40 (195)
.++.....||.|..||..
T Consensus 75 ~EY~~~~~Cp~C~spFNp 92 (105)
T COG4357 75 AEYGMCGSCPYCQSPFNP 92 (105)
T ss_pred HHHhhcCCCCCcCCCCCc
Confidence 455445689999999985
No 171
>PRK11595 DNA utilization protein GntX; Provisional
Probab=20.34 E-value=80 Score=26.77 Aligned_cols=25 Identities=24% Similarity=0.535 Sum_probs=18.1
Q ss_pred cccHHhHHhhhccCCCCCCCCCCCCCC
Q 029308 13 CKSATCILRWASYVRNPTCPQCKHPFE 39 (195)
Q Consensus 13 sFC~~CI~rW~e~kq~~sCP~CK~pFs 39 (195)
..|..|...+--. .+.||.|..+..
T Consensus 21 ~lC~~C~~~l~~~--~~~C~~Cg~~~~ 45 (227)
T PRK11595 21 GICSVCSRALRTL--KTCCPQCGLPAT 45 (227)
T ss_pred cccHHHHhhCCcc--cCcCccCCCcCC
Confidence 4799999986322 257999998753
No 172
>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=20.22 E-value=29 Score=20.25 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=9.3
Q ss_pred CCCCCCCCCCC
Q 029308 29 PTCPQCKHPFE 39 (195)
Q Consensus 29 ~sCP~CK~pFs 39 (195)
..||+|.+.|.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 47999999885
No 173
>PF10161 DDDD: Putative mitochondrial precursor protein; InterPro: IPR018782 This entry represents a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. These proteins have been putatively designated as mitochondrial precursor proteins but this has not been confirmed.
Probab=20.07 E-value=41 Score=25.71 Aligned_cols=15 Identities=20% Similarity=0.428 Sum_probs=7.2
Q ss_pred cccccccccCCCCccc
Q 029308 80 VQDDLEDDYSYEDEED 95 (195)
Q Consensus 80 ~~~~~~~~y~y~~~~d 95 (195)
+.||.|. |..|||||
T Consensus 63 fLEe~di-FvP~DDDD 77 (79)
T PF10161_consen 63 FLEENDI-FVPEDDDD 77 (79)
T ss_pred HHHHhcc-cCCCcCCC
Confidence 4555555 44444433
Done!