Query 041841
Match_columns 216
No_of_seqs 230 out of 1166
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 11:12:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 99.9 1.4E-27 3.1E-32 209.9 5.8 152 61-216 146-316 (384)
2 KOG1815 Predicted E3 ubiquitin 99.9 1.1E-24 2.3E-29 195.8 9.5 149 61-216 70-236 (444)
3 KOG1814 Predicted E3 ubiquitin 99.9 1.2E-23 2.6E-28 180.6 6.5 153 61-216 184-378 (445)
4 KOG0006 E3 ubiquitin-protein l 99.6 1.9E-16 4.2E-21 132.4 5.9 149 61-216 221-407 (446)
5 smart00647 IBR In Between Ring 99.5 1.3E-14 2.9E-19 96.1 5.6 63 117-179 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.5 8.2E-15 1.8E-19 97.1 1.4 63 117-179 1-64 (64)
7 PF13639 zf-RING_2: Ring finge 98.4 9.1E-08 2E-12 58.5 1.6 35 63-97 2-36 (44)
8 PF00097 zf-C3HC4: Zinc finger 98.3 3.9E-07 8.4E-12 54.7 2.5 39 64-109 1-39 (41)
9 PF13923 zf-C3HC4_2: Zinc fing 98.3 4.8E-07 1E-11 53.9 2.3 32 64-97 1-32 (39)
10 PF13445 zf-RING_UBOX: RING-ty 98.2 1.1E-06 2.3E-11 53.5 3.2 42 64-109 1-43 (43)
11 PF15227 zf-C3HC4_4: zinc fing 98.2 8.2E-07 1.8E-11 53.8 1.5 40 64-109 1-40 (42)
12 PF14634 zf-RING_5: zinc-RING 98.2 1.6E-06 3.6E-11 53.0 2.8 33 63-95 1-33 (44)
13 cd00162 RING RING-finger (Real 97.9 9.9E-06 2.1E-10 48.7 3.2 33 63-97 1-33 (45)
14 smart00184 RING Ring finger. E 97.8 2.4E-05 5.2E-10 45.3 2.8 30 64-96 1-30 (39)
15 PLN03208 E3 ubiquitin-protein 97.7 5.7E-05 1.2E-09 60.4 4.7 34 61-97 18-51 (193)
16 KOG0320 Predicted E3 ubiquitin 97.5 6.1E-05 1.3E-09 59.0 3.0 41 61-109 131-171 (187)
17 PF13920 zf-C3HC4_3: Zinc fing 97.4 0.00014 3.1E-09 45.5 3.2 32 62-96 3-35 (50)
18 PHA02929 N1R/p28-like protein; 97.3 0.00019 4.2E-09 59.5 3.7 36 61-96 174-214 (238)
19 PHA02926 zinc finger-like prot 97.3 0.00023 5E-09 57.8 3.4 48 61-109 170-223 (242)
20 KOG2164 Predicted E3 ubiquitin 97.2 0.00026 5.7E-09 63.7 3.5 44 61-109 186-229 (513)
21 KOG2177 Predicted E3 ubiquitin 97.2 0.00029 6.3E-09 59.0 3.6 100 61-181 13-124 (386)
22 TIGR00570 cdk7 CDK-activating 96.5 0.0059 1.3E-07 52.4 6.0 42 61-109 3-47 (309)
23 TIGR00599 rad18 DNA repair pro 96.4 0.0027 5.9E-08 56.4 3.2 34 61-97 26-59 (397)
24 KOG4628 Predicted E3 ubiquitin 96.3 0.0017 3.6E-08 56.6 1.6 37 62-98 230-266 (348)
25 smart00504 Ubox Modified RING 96.3 0.0056 1.2E-07 39.7 3.6 33 62-97 2-34 (63)
26 PF12678 zf-rbx1: RING-H2 zinc 96.3 0.0029 6.2E-08 42.9 2.1 36 62-97 20-65 (73)
27 KOG0317 Predicted E3 ubiquitin 96.3 0.0032 7E-08 53.0 2.7 36 61-99 239-274 (293)
28 KOG0823 Predicted E3 ubiquitin 96.2 0.0028 6E-08 51.9 2.1 37 61-100 47-83 (230)
29 KOG0006 E3 ubiquitin-protein l 95.8 0.0094 2E-07 51.0 3.7 89 81-175 341-437 (446)
30 KOG0287 Postreplication repair 95.8 0.0044 9.5E-08 53.4 1.7 33 62-97 24-56 (442)
31 COG5540 RING-finger-containing 95.8 0.0063 1.4E-07 51.7 2.4 36 61-96 323-358 (374)
32 COG5574 PEX10 RING-finger-cont 95.4 0.019 4.1E-07 48.0 3.9 31 61-94 215-245 (271)
33 PF13719 zinc_ribbon_5: zinc-r 94.0 0.036 7.9E-07 32.3 1.7 30 134-165 3-35 (37)
34 KOG1814 Predicted E3 ubiquitin 93.9 0.069 1.5E-06 47.3 3.8 86 75-172 292-403 (445)
35 KOG1039 Predicted E3 ubiquitin 93.7 0.04 8.6E-07 48.2 2.1 49 61-109 161-214 (344)
36 COG5432 RAD18 RING-finger-cont 93.7 0.044 9.5E-07 46.4 2.2 33 62-97 26-58 (391)
37 KOG1812 Predicted E3 ubiquitin 93.5 0.039 8.4E-07 49.2 1.7 42 132-178 305-346 (384)
38 KOG1002 Nucleotide excision re 93.5 0.046 1E-06 49.9 2.1 45 60-109 535-579 (791)
39 KOG1815 Predicted E3 ubiquitin 93.2 0.096 2.1E-06 47.6 3.7 91 79-182 181-278 (444)
40 PF14835 zf-RING_6: zf-RING of 92.4 0.024 5.3E-07 37.2 -0.9 30 62-93 8-37 (65)
41 PF11793 FANCL_C: FANCL C-term 92.3 0.1 2.2E-06 35.0 2.0 41 61-101 2-47 (70)
42 PF10571 UPF0547: Uncharacteri 92.3 0.075 1.6E-06 28.5 1.1 23 135-165 2-24 (26)
43 PF13717 zinc_ribbon_4: zinc-r 91.9 0.11 2.5E-06 30.0 1.7 30 134-165 3-35 (36)
44 PF11789 zf-Nse: Zinc-finger o 91.8 0.14 3.1E-06 32.9 2.2 43 61-110 11-53 (57)
45 PF05883 Baculo_RING: Baculovi 91.7 0.072 1.6E-06 40.2 0.8 41 61-101 26-72 (134)
46 PF02150 RNA_POL_M_15KD: RNA p 91.5 0.11 2.3E-06 30.0 1.3 28 134-164 2-29 (35)
47 KOG2879 Predicted E3 ubiquitin 91.5 0.21 4.6E-06 42.1 3.4 45 58-109 236-280 (298)
48 smart00661 RPOL9 RNA polymeras 91.4 0.18 4E-06 31.3 2.4 28 134-163 1-28 (52)
49 KOG0978 E3 ubiquitin ligase in 91.3 0.061 1.3E-06 50.9 0.1 36 61-99 643-678 (698)
50 COG5243 HRD1 HRD ubiquitin lig 90.7 0.22 4.7E-06 43.8 2.8 38 60-97 286-333 (491)
51 KOG0802 E3 ubiquitin ligase [P 89.3 0.23 5E-06 46.3 2.1 37 61-97 291-329 (543)
52 TIGR02098 MJ0042_CXXC MJ0042 f 87.5 0.34 7.4E-06 28.1 1.3 30 134-165 3-35 (38)
53 KOG0297 TNF receptor-associate 86.9 0.4 8.6E-06 42.9 2.0 35 61-97 21-55 (391)
54 KOG4692 Predicted E3 ubiquitin 86.6 0.44 9.5E-06 41.6 2.0 34 61-97 422-455 (489)
55 KOG0824 Predicted E3 ubiquitin 85.6 0.43 9.2E-06 40.8 1.4 34 61-97 7-40 (324)
56 PRK00398 rpoP DNA-directed RNA 85.4 0.9 1.9E-05 27.6 2.5 30 134-167 4-33 (46)
57 smart00744 RINGv The RING-vari 85.4 1 2.2E-05 27.9 2.7 36 63-99 1-41 (49)
58 PF04564 U-box: U-box domain; 85.0 1.2 2.6E-05 29.8 3.2 34 61-97 4-37 (73)
59 TIGR00622 ssl1 transcription f 84.7 0.91 2E-05 33.3 2.6 71 104-176 14-102 (112)
60 PHA03096 p28-like protein; Pro 84.3 0.64 1.4E-05 39.8 1.9 47 62-109 179-230 (284)
61 KOG1645 RING-finger-containing 83.6 1.1 2.4E-05 39.9 3.1 44 61-109 4-49 (463)
62 KOG4739 Uncharacterized protei 83.0 0.54 1.2E-05 38.9 0.9 30 63-93 5-34 (233)
63 KOG2660 Locus-specific chromos 82.6 0.33 7.1E-06 41.9 -0.5 35 61-97 15-49 (331)
64 COG5152 Uncharacterized conser 82.3 0.6 1.3E-05 37.6 0.9 42 61-109 196-237 (259)
65 KOG0827 Predicted E3 ubiquitin 82.1 0.75 1.6E-05 40.7 1.5 41 61-101 4-45 (465)
66 KOG0311 Predicted E3 ubiquitin 82.0 0.21 4.6E-06 43.5 -1.9 33 61-95 43-75 (381)
67 KOG0828 Predicted E3 ubiquitin 81.8 0.78 1.7E-05 41.8 1.5 38 59-96 569-620 (636)
68 PRK14714 DNA polymerase II lar 81.4 1.2 2.6E-05 45.0 2.8 30 133-172 667-701 (1337)
69 KOG4445 Uncharacterized conser 81.4 0.96 2.1E-05 38.7 1.8 40 61-100 115-154 (368)
70 KOG2807 RNA polymerase II tran 81.1 0.57 1.2E-05 40.5 0.4 78 85-176 277-366 (378)
71 KOG0823 Predicted E3 ubiquitin 81.1 0.7 1.5E-05 38.0 0.9 19 153-173 59-77 (230)
72 PF14570 zf-RING_4: RING/Ubox 80.6 1.6 3.5E-05 27.0 2.2 33 64-96 1-34 (48)
73 KOG2906 RNA polymerase III sub 80.6 1.3 2.8E-05 31.5 2.0 28 134-163 2-29 (105)
74 PF13248 zf-ribbon_3: zinc-rib 79.8 0.79 1.7E-05 24.4 0.6 23 134-164 3-25 (26)
75 PF14803 Nudix_N_2: Nudix N-te 79.7 1 2.3E-05 25.7 1.1 29 134-164 1-31 (34)
76 PF12861 zf-Apc11: Anaphase-pr 79.4 2.3 4.9E-05 29.6 2.9 19 80-98 50-68 (85)
77 COG1594 RPB9 DNA-directed RNA 78.6 1.8 3.8E-05 31.8 2.3 30 133-164 2-31 (113)
78 TIGR01206 lysW lysine biosynth 77.5 2.9 6.3E-05 26.5 2.7 30 134-165 3-32 (54)
79 KOG4185 Predicted E3 ubiquitin 76.1 1.7 3.8E-05 37.0 1.9 42 62-109 4-48 (296)
80 KOG1952 Transcription factor N 75.7 2.2 4.8E-05 41.4 2.6 49 61-109 191-240 (950)
81 PF13240 zinc_ribbon_2: zinc-r 75.0 1.4 3E-05 22.8 0.7 22 135-164 1-22 (23)
82 COG2888 Predicted Zn-ribbon RN 73.8 4.5 9.7E-05 26.1 2.9 32 134-169 10-41 (61)
83 PF01428 zf-AN1: AN1-like Zinc 73.3 1.8 3.9E-05 25.9 1.0 38 136-182 1-38 (43)
84 PF09297 zf-NADH-PPase: NADH p 73.2 3.6 7.8E-05 22.8 2.1 28 133-164 3-30 (32)
85 PRK04023 DNA polymerase II lar 73.2 3.2 6.8E-05 41.3 3.0 33 132-174 625-662 (1121)
86 KOG4265 Predicted E3 ubiquitin 72.4 2.8 6.1E-05 36.7 2.3 33 60-95 289-322 (349)
87 PRK00432 30S ribosomal protein 72.3 3.1 6.7E-05 25.9 1.9 27 133-165 20-47 (50)
88 KOG1785 Tyrosine kinase negati 71.3 2 4.2E-05 38.3 1.1 32 62-96 370-401 (563)
89 KOG2034 Vacuolar sorting prote 70.3 3 6.4E-05 40.7 2.1 39 61-100 817-855 (911)
90 PF09538 FYDLN_acid: Protein o 70.1 3 6.5E-05 30.4 1.7 29 133-166 9-37 (108)
91 KOG1001 Helicase-like transcri 70.1 2.2 4.8E-05 40.9 1.2 32 62-97 455-486 (674)
92 KOG3039 Uncharacterized conser 69.9 4 8.7E-05 34.1 2.5 36 61-96 221-257 (303)
93 PF10367 Vps39_2: Vacuolar sor 69.5 2.1 4.7E-05 30.3 0.8 31 61-92 78-108 (109)
94 PF01599 Ribosomal_S27: Riboso 69.1 2.8 6.1E-05 25.8 1.1 29 133-163 18-46 (47)
95 KOG0801 Predicted E3 ubiquitin 67.9 2 4.3E-05 33.6 0.3 29 60-88 176-204 (205)
96 KOG4159 Predicted E3 ubiquitin 67.7 2.9 6.2E-05 37.5 1.4 31 60-93 83-113 (398)
97 PF14445 Prok-RING_2: Prokaryo 67.5 0.76 1.6E-05 28.6 -1.6 38 61-98 7-45 (57)
98 PLN03208 E3 ubiquitin-protein 67.4 0.7 1.5E-05 37.2 -2.3 32 132-173 17-48 (193)
99 KOG1428 Inhibitor of type V ad 66.9 6.5 0.00014 41.0 3.6 49 61-109 3486-3537(3738)
100 PF06844 DUF1244: Protein of u 66.4 5.1 0.00011 26.4 2.0 17 85-101 11-27 (68)
101 KOG0978 E3 ubiquitin ligase in 66.0 2.5 5.3E-05 40.5 0.6 13 159-171 659-671 (698)
102 PF14369 zf-RING_3: zinc-finge 65.7 7.4 0.00016 22.3 2.4 30 133-165 2-31 (35)
103 PF14446 Prok-RING_1: Prokaryo 65.1 7.3 0.00016 24.7 2.5 33 61-93 5-38 (54)
104 KOG4172 Predicted E3 ubiquitin 65.0 2.5 5.4E-05 26.9 0.3 33 61-96 7-40 (62)
105 KOG1734 Predicted RING-contain 65.0 4.5 9.7E-05 34.3 1.9 44 60-109 223-274 (328)
106 KOG3002 Zn finger protein [Gen 64.8 4.2 9.1E-05 35.1 1.8 28 61-92 48-77 (299)
107 PRK00420 hypothetical protein; 63.4 17 0.00037 26.7 4.5 45 113-164 5-49 (112)
108 PF14952 zf-tcix: Putative tre 62.8 4.3 9.3E-05 24.5 1.0 11 205-215 10-20 (44)
109 PHA00626 hypothetical protein 62.7 7.8 0.00017 24.7 2.2 30 135-166 2-34 (59)
110 KOG0804 Cytoplasmic Zn-finger 62.2 4.9 0.00011 36.4 1.7 34 61-94 175-209 (493)
111 PRK14890 putative Zn-ribbon RN 61.5 13 0.00028 24.0 3.1 30 135-168 9-38 (59)
112 PF12773 DZR: Double zinc ribb 61.4 5.9 0.00013 24.1 1.6 27 132-163 11-37 (50)
113 PF07975 C1_4: TFIIH C1-like d 60.6 2.6 5.6E-05 26.4 -0.2 37 140-176 4-42 (51)
114 PF00098 zf-CCHC: Zinc knuckle 59.7 4.8 0.0001 19.4 0.7 16 165-180 2-17 (18)
115 PF09788 Tmemb_55A: Transmembr 59.6 11 0.00023 31.7 3.2 67 62-149 66-139 (256)
116 KOG1941 Acetylcholine receptor 57.6 5.2 0.00011 35.6 1.1 44 61-109 365-409 (518)
117 PF13913 zf-C2HC_2: zinc-finge 57.4 4.7 0.0001 21.1 0.5 11 155-165 2-12 (25)
118 COG2051 RPS27A Ribosomal prote 56.7 7.7 0.00017 25.6 1.5 32 133-167 19-50 (67)
119 PF04641 Rtf2: Rtf2 RING-finge 56.1 12 0.00025 31.6 3.0 36 59-94 111-147 (260)
120 KOG0825 PHD Zn-finger protein 55.9 3.1 6.7E-05 40.2 -0.6 20 81-100 120-139 (1134)
121 smart00834 CxxC_CXXC_SSSS Puta 55.0 9.5 0.00021 22.0 1.7 28 134-163 6-34 (41)
122 PF11023 DUF2614: Protein of u 54.9 8.3 0.00018 28.2 1.6 23 154-176 68-98 (114)
123 PLN00209 ribosomal protein S27 54.8 10 0.00023 26.3 2.0 33 134-169 37-69 (86)
124 PTZ00083 40S ribosomal protein 53.6 11 0.00023 26.2 1.9 35 134-171 36-70 (85)
125 PF14447 Prok-RING_4: Prokaryo 52.8 5.7 0.00012 25.3 0.4 27 63-92 9-35 (55)
126 TIGR01053 LSD1 zinc finger dom 51.9 20 0.00043 19.9 2.5 26 135-164 3-28 (31)
127 TIGR02300 FYDLN_acid conserved 51.4 11 0.00023 28.3 1.7 28 133-165 9-36 (129)
128 PRK14892 putative transcriptio 51.2 14 0.0003 26.5 2.3 51 131-186 19-70 (99)
129 PF13453 zf-TFIIB: Transcripti 50.9 8 0.00017 22.7 0.9 26 135-162 1-26 (41)
130 cd00021 BBOX B-Box-type zinc f 50.8 9.9 0.00022 21.5 1.3 25 154-178 11-35 (39)
131 PF14353 CpXC: CpXC protein 49.8 14 0.00029 27.4 2.2 13 153-165 36-48 (128)
132 TIGR01384 TFS_arch transcripti 49.7 12 0.00026 26.7 1.8 24 135-164 2-25 (104)
133 KOG1813 Predicted E3 ubiquitin 49.6 5.7 0.00012 34.0 0.1 33 61-96 241-273 (313)
134 PRK12495 hypothetical protein; 49.5 26 0.00056 28.8 3.8 14 132-147 41-54 (226)
135 PF00643 zf-B_box: B-box zinc 48.9 3.6 7.9E-05 24.0 -0.9 24 154-177 14-37 (42)
136 COG3492 Uncharacterized protei 48.5 15 0.00032 25.9 2.0 17 85-101 42-58 (104)
137 KOG0826 Predicted E3 ubiquitin 47.7 32 0.00069 30.0 4.3 34 61-96 300-333 (357)
138 PF12906 RINGv: RING-variant d 47.5 16 0.00035 22.2 1.9 33 64-97 1-38 (47)
139 COG1645 Uncharacterized Zn-fin 47.5 13 0.00028 28.1 1.7 24 134-163 29-52 (131)
140 PF03604 DNA_RNApol_7kD: DNA d 47.4 17 0.00037 20.4 1.8 23 140-165 5-27 (32)
141 KOG2807 RNA polymerase II tran 47.0 9.5 0.00021 33.2 1.0 37 62-99 331-367 (378)
142 KOG4275 Predicted E3 ubiquitin 46.5 8.7 0.00019 32.9 0.7 29 62-93 301-330 (350)
143 TIGR03826 YvyF flagellar opero 46.2 26 0.00057 26.6 3.2 73 133-216 3-91 (137)
144 PF14471 DUF4428: Domain of un 45.9 22 0.00049 22.1 2.4 30 63-94 1-30 (51)
145 COG5175 MOT2 Transcriptional r 45.1 38 0.00083 29.8 4.4 32 62-93 15-47 (480)
146 PRK03824 hypA hydrogenase nick 45.0 28 0.0006 26.3 3.2 36 111-148 39-83 (135)
147 PF02318 FYVE_2: FYVE-type zin 44.8 51 0.0011 24.1 4.6 36 132-172 53-88 (118)
148 COG1579 Zn-ribbon protein, pos 44.7 15 0.00033 30.6 1.9 53 110-164 171-230 (239)
149 PF05191 ADK_lid: Adenylate ki 44.5 16 0.00035 21.0 1.4 28 134-163 2-29 (36)
150 KOG3579 Predicted E3 ubiquitin 44.2 13 0.00028 31.8 1.4 44 61-109 268-315 (352)
151 COG1198 PriA Primosomal protei 43.8 18 0.0004 35.1 2.5 58 111-172 405-484 (730)
152 KOG2164 Predicted E3 ubiquitin 43.6 7.5 0.00016 35.7 -0.1 33 160-216 203-235 (513)
153 PF01363 FYVE: FYVE zinc finge 43.2 14 0.0003 24.0 1.2 33 133-171 9-41 (69)
154 cd00065 FYVE FYVE domain; Zinc 43.0 8.8 0.00019 23.9 0.2 36 62-97 3-39 (57)
155 PF10122 Mu-like_Com: Mu-like 42.3 8.9 0.00019 23.9 0.1 30 134-165 5-34 (51)
156 PRK14559 putative protein seri 41.9 16 0.00035 35.0 1.8 31 133-173 15-51 (645)
157 smart00659 RPOLCX RNA polymera 40.7 31 0.00067 20.8 2.3 23 140-165 7-29 (44)
158 TIGR00595 priA primosomal prot 40.4 40 0.00088 31.2 4.2 33 136-172 225-262 (505)
159 PF02591 DUF164: Putative zinc 40.2 32 0.0007 21.5 2.5 19 198-216 38-56 (56)
160 smart00154 ZnF_AN1 AN1-like Zi 40.2 21 0.00046 20.8 1.5 18 155-172 12-29 (39)
161 COG5236 Uncharacterized conser 39.3 35 0.00075 30.1 3.3 30 61-93 61-90 (493)
162 PF07754 DUF1610: Domain of un 39.2 28 0.00061 18.2 1.7 22 140-163 3-24 (24)
163 PF05715 zf-piccolo: Piccolo Z 39.2 15 0.00032 23.7 0.8 37 135-173 4-40 (61)
164 COG2995 PqiA Uncharacterized p 38.6 26 0.00056 31.4 2.4 33 131-165 16-48 (418)
165 COG5151 SSL1 RNA polymerase II 38.5 10 0.00022 32.9 -0.1 70 104-175 321-408 (421)
166 KOG3161 Predicted E3 ubiquitin 38.3 8.5 0.00018 36.5 -0.6 35 62-96 12-47 (861)
167 PF06677 Auto_anti-p27: Sjogre 38.1 81 0.0017 18.7 3.8 24 134-162 18-41 (41)
168 COG5220 TFB3 Cdk activating ki 37.9 12 0.00026 31.2 0.3 43 61-109 10-55 (314)
169 TIGR00686 phnA alkylphosphonat 37.1 24 0.00052 25.7 1.7 25 135-164 4-28 (109)
170 PF08746 zf-RING-like: RING-li 36.6 16 0.00035 21.8 0.6 35 64-98 1-35 (43)
171 KOG2932 E3 ubiquitin ligase in 36.3 15 0.00032 31.8 0.6 30 63-94 92-121 (389)
172 PRK00415 rps27e 30S ribosomal 36.1 32 0.00069 22.2 2.0 32 133-167 11-42 (59)
173 COG5222 Uncharacterized conser 36.1 28 0.00061 30.0 2.2 40 62-109 275-314 (427)
174 KOG2930 SCF ubiquitin ligase, 35.9 21 0.00045 25.8 1.2 19 80-98 79-97 (114)
175 PF08271 TF_Zn_Ribbon: TFIIB z 35.8 21 0.00046 21.0 1.1 26 135-164 2-28 (43)
176 PRK03681 hypA hydrogenase nick 35.7 24 0.00052 25.8 1.6 48 111-163 39-95 (114)
177 PRK12286 rpmF 50S ribosomal pr 35.6 33 0.00072 21.9 2.0 26 129-163 23-48 (57)
178 PF07282 OrfB_Zn_ribbon: Putat 35.5 25 0.00053 22.8 1.5 28 133-164 28-55 (69)
179 smart00336 BBOX B-Box-type zin 35.5 28 0.00061 19.8 1.6 23 155-177 15-37 (42)
180 smart00064 FYVE Protein presen 34.9 27 0.00058 22.6 1.6 34 133-172 10-43 (68)
181 PF08274 PhnA_Zn_Ribbon: PhnA 34.4 20 0.00044 19.8 0.7 26 135-165 4-29 (30)
182 PRK10220 hypothetical protein; 34.2 33 0.00072 25.0 2.0 25 135-164 5-29 (111)
183 TIGR00100 hypA hydrogenase nic 34.2 27 0.00058 25.6 1.6 47 111-163 39-94 (115)
184 COG3357 Predicted transcriptio 33.9 17 0.00038 25.5 0.5 21 140-162 63-83 (97)
185 PF14392 zf-CCHC_4: Zinc knuck 33.7 14 0.0003 22.6 0.0 17 164-180 32-48 (49)
186 TIGR00155 pqiA_fam integral me 32.9 33 0.00072 30.9 2.3 30 133-164 13-42 (403)
187 KOG2817 Predicted E3 ubiquitin 31.9 46 0.00099 29.8 2.9 65 41-110 315-379 (394)
188 PF01667 Ribosomal_S27e: Ribos 31.6 41 0.00089 21.4 1.9 32 134-168 8-39 (55)
189 smart00249 PHD PHD zinc finger 31.4 38 0.00083 19.3 1.8 32 63-94 1-32 (47)
190 PF02148 zf-UBP: Zn-finger in 31.4 58 0.0013 20.8 2.7 24 64-89 1-24 (63)
191 PF09723 Zn-ribbon_8: Zinc rib 31.0 37 0.0008 20.0 1.6 27 135-163 7-34 (42)
192 PRK00464 nrdR transcriptional 30.9 41 0.00088 26.1 2.2 13 155-167 28-40 (154)
193 PRK12380 hydrogenase nickel in 30.9 32 0.0007 25.1 1.6 47 111-163 39-94 (113)
194 KOG4367 Predicted Zn-finger pr 30.7 25 0.00054 31.9 1.1 34 61-97 4-37 (699)
195 COG4306 Uncharacterized protei 30.3 69 0.0015 24.0 3.2 31 111-148 22-52 (160)
196 PF08209 Sgf11: Sgf11 (transcr 30.3 24 0.00052 19.9 0.6 12 205-216 3-14 (33)
197 PF13465 zf-H2C2_2: Zinc-finge 30.0 28 0.00062 18.1 0.9 12 154-165 13-24 (26)
198 PF02748 PyrI_C: Aspartate car 30.0 52 0.0011 20.5 2.2 33 132-165 5-45 (52)
199 PRK15103 paraquat-inducible me 29.8 45 0.00097 30.2 2.6 30 133-164 10-39 (419)
200 COG5219 Uncharacterized conser 29.8 20 0.00043 35.9 0.3 40 61-100 1469-1512(1525)
201 PF00628 PHD: PHD-finger; Int 29.4 30 0.00066 20.8 1.1 33 64-96 2-34 (51)
202 TIGR03037 anthran_nbaC 3-hydro 29.4 16 0.00035 28.5 -0.2 47 161-214 112-159 (159)
203 PF14569 zf-UDP: Zinc-binding 29.3 46 0.001 22.7 1.9 38 61-102 9-50 (80)
204 PF06943 zf-LSD1: LSD1 zinc fi 28.8 73 0.0016 16.8 2.3 22 140-163 3-24 (25)
205 COG5194 APC11 Component of SCF 28.7 30 0.00066 23.8 1.0 18 80-97 52-69 (88)
206 PF00096 zf-C2H2: Zinc finger, 28.6 21 0.00045 17.5 0.2 9 157-165 2-10 (23)
207 KOG4684 Uncharacterized conser 28.2 50 0.0011 27.1 2.3 20 130-149 135-154 (275)
208 PRK09710 lar restriction allev 28.2 69 0.0015 21.0 2.6 32 132-164 5-36 (64)
209 KOG2824 Glutaredoxin-related p 27.8 30 0.00065 29.5 1.0 16 156-171 230-248 (281)
210 KOG0317 Predicted E3 ubiquitin 27.7 10 0.00022 32.3 -1.7 18 156-173 252-269 (293)
211 PF08792 A2L_zn_ribbon: A2L zi 27.6 57 0.0012 18.3 1.9 29 133-165 3-31 (33)
212 PRK13264 3-hydroxyanthranilate 27.6 18 0.00039 28.7 -0.3 48 161-215 118-166 (177)
213 KOG3970 Predicted E3 ubiquitin 27.5 1.1E+02 0.0024 25.4 4.2 47 62-109 51-98 (299)
214 COG1998 RPS31 Ribosomal protei 27.4 42 0.0009 20.9 1.3 28 133-164 19-46 (51)
215 COG1996 RPC10 DNA-directed RNA 27.2 43 0.00093 20.8 1.4 24 140-165 11-34 (49)
216 COG4391 Uncharacterized protei 27.2 34 0.00074 22.2 1.0 31 133-165 24-58 (62)
217 TIGR02605 CxxC_CxxC_SSSS putat 26.7 54 0.0012 19.9 1.9 27 135-163 7-34 (52)
218 PF13834 DUF4193: Domain of un 26.5 35 0.00077 24.4 1.1 29 61-90 70-98 (99)
219 TIGR01031 rpmF_bact ribosomal 26.4 54 0.0012 20.7 1.8 25 130-163 23-47 (55)
220 PRK02935 hypothetical protein; 26.3 55 0.0012 23.7 2.0 10 165-174 88-97 (110)
221 smart00531 TFIIE Transcription 26.1 57 0.0012 24.8 2.3 31 132-164 98-132 (147)
222 PF14169 YdjO: Cold-inducible 25.9 57 0.0012 21.0 1.9 28 135-163 20-47 (59)
223 COG1656 Uncharacterized conser 25.7 66 0.0014 25.2 2.5 16 131-148 95-110 (165)
224 KOG4362 Transcriptional regula 24.2 25 0.00054 33.7 -0.1 42 61-109 21-62 (684)
225 PRK00564 hypA hydrogenase nick 24.1 39 0.00084 24.8 1.0 48 111-163 39-96 (117)
226 COG4416 Com Mu-like prophage p 23.9 34 0.00074 21.6 0.5 8 207-214 25-32 (60)
227 PRK14559 putative protein seri 23.7 63 0.0014 31.1 2.5 40 134-181 2-46 (645)
228 PRK05580 primosome assembly pr 23.3 65 0.0014 31.1 2.5 34 135-172 392-430 (679)
229 PF14319 Zn_Tnp_IS91: Transpos 23.1 1.4E+02 0.0031 21.6 3.8 28 133-172 42-69 (111)
230 PLN03086 PRLI-interacting fact 22.7 58 0.0013 30.7 2.0 32 132-165 432-463 (567)
231 PF01927 Mut7-C: Mut7-C RNAse 22.4 1.3E+02 0.0028 22.8 3.7 53 111-165 66-134 (147)
232 COG4049 Uncharacterized protei 22.3 56 0.0012 20.9 1.2 13 153-165 15-27 (65)
233 PF02891 zf-MIZ: MIZ/SP-RING z 22.0 93 0.002 19.1 2.2 42 63-109 4-45 (50)
234 KOG3799 Rab3 effector RIM1 and 21.9 32 0.00068 26.1 0.1 19 155-173 81-99 (169)
235 PF14354 Lar_restr_allev: Rest 21.5 1.2E+02 0.0026 19.0 2.8 10 132-143 2-11 (61)
236 PF13894 zf-C2H2_4: C2H2-type 21.4 43 0.00093 16.0 0.5 9 157-165 2-10 (24)
237 KOG1940 Zn-finger protein [Gen 21.4 52 0.0011 28.1 1.3 46 61-113 158-204 (276)
238 PF01783 Ribosomal_L32p: Ribos 21.2 77 0.0017 20.0 1.8 24 131-163 24-47 (56)
239 PF04236 Transp_Tc5_C: Tc5 tra 21.0 67 0.0015 21.0 1.5 30 133-171 27-56 (63)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=1.4e-27 Score=209.89 Aligned_cols=152 Identities=34% Similarity=0.839 Sum_probs=126.1
Q ss_pred CCCCcccccCCC-CCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc---------------CCCHHHHHHHHHHHH
Q 041841 61 KRPFSICMEPKS-TNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP---------------IVPKEVSDRWGNALC 124 (216)
Q Consensus 61 ~~~C~IC~~~~~-~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp---------------~l~~~~~~~y~~~~~ 124 (216)
..+|.||+.+.+ ..+++....|+|.||.+||++|++++..+ ...|+|| +|++.+.+.|.+.+.
T Consensus 146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~-~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~ 224 (384)
T KOG1812|consen 146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLS-GTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRLK 224 (384)
T ss_pred cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhcc-CCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHH
Confidence 579999995554 44667678999999999999999999444 4568888 788899999999999
Q ss_pred HhhhcCCCCcccCcCCCCceeecCCC---CCCCceeCCCCchhccccCCCCCCCCCChHhHHHhcccCCChhHHHHHHHH
Q 041841 125 EGVINGAEKFYCPFKDCSALLINDGL---KNMKESKRPYCKRMFCAQCKVPWHAGMRCEKFRKLNKNEKNSEDMELIKLA 201 (216)
Q Consensus 125 ~~~v~~~~~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~fC~~C~~~~H~~~~C~~~~~~~~~e~~~~d~~~~~~~ 201 (216)
+.++...+.+|||+++|...+..... .......|+.||..||..|+.+||++.+|++|++|..++. .|..+.+++
T Consensus 225 e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~--~d~~~~~~l 302 (384)
T KOG1812|consen 225 EEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEY--VDDITLKYL 302 (384)
T ss_pred HHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCccc--ccHHHHHHH
Confidence 99998777669999999998876653 2344567999999999999999999999999999987532 445667777
Q ss_pred hcCCceecCCCCccC
Q 041841 202 EEKKWKRCPHCNYSV 216 (216)
Q Consensus 202 ~~~~~k~CP~C~~~I 216 (216)
+ ++|++||+|+..|
T Consensus 303 a-~~wr~CpkC~~~i 316 (384)
T KOG1812|consen 303 A-KRWRQCPKCKFMI 316 (384)
T ss_pred H-HhcCcCcccceee
Confidence 6 5999999999876
No 2
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=1.1e-24 Score=195.83 Aligned_cols=149 Identities=23% Similarity=0.471 Sum_probs=127.7
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCc-ccccc---------------CCCH-HHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESIT-SIRCP---------------IVPK-EVSDRWGNAL 123 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~-~i~Cp---------------~l~~-~~~~~y~~~~ 123 (216)
..+|.||++..+. . +..+.|+|.||..||..|+..+|.+|.. .|+|| ++++ ++.++|.+++
T Consensus 70 ~~~c~ic~~~~~~-~-~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i 147 (444)
T KOG1815|consen 70 DVQCGICVESYDG-E-IIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYI 147 (444)
T ss_pred cccCCcccCCCcc-h-hhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHH
Confidence 5799999999876 3 4457999999999999999999998633 38888 3444 5899999999
Q ss_pred HHhhhcCCC-CcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCCCCCCChHhHHHhcccCCChhHHHHHHHHh
Q 041841 124 CEGVINGAE-KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPWHAGMRCEKFRKLNKNEKNSEDMELIKLAE 202 (216)
Q Consensus 124 ~~~~v~~~~-~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C~~~~~~~~~e~~~~d~~~~~~~~ 202 (216)
..+|++.+. ++|||+|+|+..+... ......+.|. ||+.|||.|+.+||.|.+|..+..|.++ ..++.+..+||.
T Consensus 148 ~~syve~~~~lkwCP~~~C~~av~~~-~~~~~~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k--~~~~se~~~wi~ 223 (444)
T KOG1815|consen 148 LRSYVEDNVPLKWCPAPGCGLAVKFG-SLESVEVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKK--CRDDSETINWIL 223 (444)
T ss_pred HHHHHhcCCccccCCCCCCCceeecc-CCCccceeCC-CCchhHhhccccccCCCcccchHHHHHh--hhhhhhhhhhhh
Confidence 999998754 8999999999999763 3346779998 8889999999999999999999999988 456777788998
Q ss_pred cCCceecCCCCccC
Q 041841 203 EKKWKRCPHCNYSV 216 (216)
Q Consensus 203 ~~~~k~CP~C~~~I 216 (216)
. ++|+||+|..+|
T Consensus 224 ~-ntk~CP~c~~~i 236 (444)
T KOG1815|consen 224 A-NTKECPKCKVPI 236 (444)
T ss_pred c-cCccCCCcccch
Confidence 6 999999999886
No 3
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.2e-23 Score=180.59 Aligned_cols=153 Identities=24% Similarity=0.527 Sum_probs=125.4
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCC-cccccc---------------CCCHHHHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESI-TSIRCP---------------IVPKEVSDRWGNALC 124 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~-~~i~Cp---------------~l~~~~~~~y~~~~~ 124 (216)
...|.|||++..+...+.+++|+|.||+.|++.|++..|++|+ ..++|| ++..++++||.+++.
T Consensus 184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~l 263 (445)
T KOG1814|consen 184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKLML 263 (445)
T ss_pred cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHH
Confidence 5799999999988777888999999999999999999999995 579999 678999999999999
Q ss_pred Hhhhc-CCCCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCCCCCCChHhH--------HHhcccC------
Q 041841 125 EGVIN-GAEKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPWHAGMRCEKF--------RKLNKNE------ 189 (216)
Q Consensus 125 ~~~v~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C~~~--------~~~~~~e------ 189 (216)
+..++ ..+..|||++.|..++..+. ....+.|.+|+..||+-|+..||....|.-- ..|....
T Consensus 264 qk~l~~msdv~yCPr~~Cq~p~~~d~--~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~e 341 (445)
T KOG1814|consen 264 QKTLELMSDVVYCPRACCQLPVKQDP--GRALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEARKRE 341 (445)
T ss_pred HHHHHhhcccccCChhhccCccccCc--hhhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHH
Confidence 98875 46789999999999985543 3567899999999999999999998888632 2333210
Q ss_pred -----------CChhHHHHHHHHhcCCceecCCCCccC
Q 041841 190 -----------KNSEDMELIKLAEEKKWKRCPHCNYSV 216 (216)
Q Consensus 190 -----------~~~~d~~~~~~~~~~~~k~CP~C~~~I 216 (216)
...+|.+..+|+.. |.|+||+|+++|
T Consensus 342 le~Ryg~rvve~~vn~~lsekwl~~-N~krCP~C~v~I 378 (445)
T KOG1814|consen 342 LEKRYGKRVVEELVNDFLSEKWLES-NSKRCPKCKVVI 378 (445)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHh-cCCCCCccccee
Confidence 01124445578876 999999999986
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.64 E-value=1.9e-16 Score=132.44 Aligned_cols=149 Identities=22% Similarity=0.457 Sum_probs=113.7
Q ss_pred CCCCcccccCCCCCCceeeCCCC--CccchHHHHHHHHHHhhcCCc--------ccccc---------------CCCHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCS--YSYCTDCIVKYVDSKLRESIT--------SIRCP---------------IVPKEV 115 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~--H~fC~~C~~~y~~~~i~~~~~--------~i~Cp---------------~l~~~~ 115 (216)
..+|..|-+..+. +....|+ |..|.+|++.|..+.+.+.++ .+.|| |+..+.
T Consensus 221 ni~C~~Ctdv~~~---vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~agc~~s~i~e~HHF~ilg~e~ 297 (446)
T KOG0006|consen 221 NITCITCTDVRSP---VLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQ 297 (446)
T ss_pred cceeEEecCCccc---eEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccCCCchHHHHhhhhheecchhH
Confidence 4689999875432 3346898 999999999999999987532 23454 789999
Q ss_pred HHHHHHHHHHhhhcCCCCcccCcCCCCceeecCCCCCCCceeCCC-CchhccccCCCCCCCCCChHhHHH--------hc
Q 041841 116 SDRWGNALCEGVINGAEKFYCPFKDCSALLINDGLKNMKESKRPY-CKRMFCAQCKVPWHAGMRCEKFRK--------LN 186 (216)
Q Consensus 116 ~~~y~~~~~~~~v~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~-C~~~fC~~C~~~~H~~~~C~~~~~--------~~ 186 (216)
|++|+++..+.+|...+-+.||+|+|+..+..++ +.++++|+. ||+.||..|++.+|.| .|...-. +.
T Consensus 298 Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as~t~tc~y~ 374 (446)
T KOG0006|consen 298 YNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEASGTTTCAYR 374 (446)
T ss_pred HHHHHHhhhhhheeecCCEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhccc-cceeeeccccccceeee
Confidence 9999999999998777788999999999887765 478899987 9999999999999998 5652211 11
Q ss_pred ccCC----ChhHHHHHHHHhcCCceecCCCCccC
Q 041841 187 KNEK----NSEDMELIKLAEEKKWKRCPHCNYSV 216 (216)
Q Consensus 187 ~~e~----~~~d~~~~~~~~~~~~k~CP~C~~~I 216 (216)
-+++ .+=|.++...|+. .+|+||||+++.
T Consensus 375 vde~~a~~arwd~as~~TIk~-tTkpCPkChvpt 407 (446)
T KOG0006|consen 375 VDERAAEQARWDAASKETIKK-TTKPCPKCHVPT 407 (446)
T ss_pred cChhhhhhhhhhhhhhhhhhh-ccCCCCCccCcc
Confidence 1111 1125556667775 899999999863
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.53 E-value=1.3e-14 Score=96.15 Aligned_cols=63 Identities=32% Similarity=0.752 Sum_probs=54.9
Q ss_pred HHHHHHHHHhhhcC-CCCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCCCCCCCh
Q 041841 117 DRWGNALCEGVING-AEKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPWHAGMRC 179 (216)
Q Consensus 117 ~~y~~~~~~~~v~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 179 (216)
++|.+++.+.+|+. ++++|||+++|+.++..........+.|+.|+..||+.|+.+||.|++|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47999999999976 5689999999999998863234678999889999999999999999988
No 6
>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=99.48 E-value=8.2e-15 Score=97.11 Aligned_cols=63 Identities=27% Similarity=0.672 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhhcC-CCCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCCCCCCCh
Q 041841 117 DRWGNALCEGVING-AEKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPWHAGMRC 179 (216)
Q Consensus 117 ~~y~~~~~~~~v~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 179 (216)
++|.+++++.+++. ++++|||+++|+.++..+.......++|+.|++.||+.|+.+||.|++|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 57888888888864 4578999999999998876544335999999999999999999999988
No 7
>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=98.43 E-value=9.1e-08 Score=58.54 Aligned_cols=35 Identities=20% Similarity=0.417 Sum_probs=29.9
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
+|+||++++...+.+..++|+|.||.+|+..|+..
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh
Confidence 69999999965555556789999999999999976
No 8
>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=98.32 E-value=3.9e-07 Score=54.74 Aligned_cols=39 Identities=33% Similarity=0.870 Sum_probs=30.5
Q ss_pred CcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
|+||++...... .++.|+|.||..|+.+++.. . ..++||
T Consensus 1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~---~--~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLEN---S--GSVKCP 39 (41)
T ss_dssp ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHH---T--SSSBTT
T ss_pred CCcCCccccCCC--EEecCCCcchHHHHHHHHHh---c--CCccCC
Confidence 789999875432 36899999999999999997 2 235676
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=98.28 E-value=4.8e-07 Score=53.87 Aligned_cols=32 Identities=28% Similarity=0.774 Sum_probs=25.9
Q ss_pred CcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
|+||++.... .+..+.|||.||.+||.+|++.
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHC
Confidence 7899987654 3356899999999999999885
No 10
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.25 E-value=1.1e-06 Score=53.53 Aligned_cols=42 Identities=24% Similarity=0.546 Sum_probs=23.1
Q ss_pred CcccccCC-CCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 64 FSICMEPK-STNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 64 C~IC~~~~-~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
|+||.+ + ...+....+.|||.||++|+++.+.... ...++||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899999 5 3344445678999999999999888543 2357887
No 11
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.17 E-value=8.2e-07 Score=53.81 Aligned_cols=40 Identities=20% Similarity=0.517 Sum_probs=25.5
Q ss_pred CcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
|+||++.+.. ...+.|||.||..|+.++....-. ..+.||
T Consensus 1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~---~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSG---SGFSCP 40 (42)
T ss_dssp ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSS---ST---S
T ss_pred CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCC---cCCCCc
Confidence 7899997653 234799999999999998764222 126676
No 12
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.16 E-value=1.6e-06 Score=52.98 Aligned_cols=33 Identities=24% Similarity=0.537 Sum_probs=28.2
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVKYV 95 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~ 95 (216)
+|+||++.+.....+.+++|||.||..|+....
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 589999999555557789999999999998876
No 13
>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=97.94 E-value=9.9e-06 Score=48.66 Aligned_cols=33 Identities=30% Similarity=0.648 Sum_probs=26.6
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
+|+||++.. .+.+.+..|+|.||..|+..+++.
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh
Confidence 589999987 233445679999999999999885
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=97.77 E-value=2.4e-05 Score=45.26 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=24.3
Q ss_pred CcccccCCCCCCceeeCCCCCccchHHHHHHHH
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
|+||++.. . ....+.|+|.||..|+..++.
T Consensus 1 C~iC~~~~--~-~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEEL--K-DPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCC--C-CcEEecCCChHHHHHHHHHHH
Confidence 78999873 2 344578999999999999987
No 15
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.69 E-value=5.7e-05 Score=60.37 Aligned_cols=34 Identities=21% Similarity=0.539 Sum_probs=27.4
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..+|+||++.... ...+.|||.||..|+..|+..
T Consensus 18 ~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~ 51 (193)
T PLN03208 18 DFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYA 51 (193)
T ss_pred ccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHh
Confidence 4689999997642 234689999999999999864
No 16
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=6.1e-05 Score=59.01 Aligned_cols=41 Identities=24% Similarity=0.635 Sum_probs=31.5
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..-|+||++.+.....+. ..|||.||..|++.-+.. ..+||
T Consensus 131 ~~~CPiCl~~~sek~~vs-TkCGHvFC~~Cik~alk~-------~~~CP 171 (187)
T KOG0320|consen 131 TYKCPICLDSVSEKVPVS-TKCGHVFCSQCIKDALKN-------TNKCP 171 (187)
T ss_pred ccCCCceecchhhccccc-cccchhHHHHHHHHHHHh-------CCCCC
Confidence 478999999986544343 689999999999876663 24777
No 17
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.44 E-value=0.00014 Score=45.49 Aligned_cols=32 Identities=19% Similarity=0.595 Sum_probs=25.8
Q ss_pred CCCcccccCCCCCCceeeCCCCCc-cchHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYS-YCTDCIVKYVD 96 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~-fC~~C~~~y~~ 96 (216)
..|.||++... + ..+.+|+|. ||.+|+.+++.
T Consensus 3 ~~C~iC~~~~~--~-~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPR--D-VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBS--S-EEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCC--c-eEEeCCCChHHHHHHhHHhcc
Confidence 57999999743 2 456799999 99999999988
No 18
>PHA02929 N1R/p28-like protein; Provisional
Probab=97.34 E-value=0.00019 Score=59.48 Aligned_cols=36 Identities=25% Similarity=0.582 Sum_probs=28.3
Q ss_pred CCCCcccccCCCCCC-----ceeeCCCCCccchHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNE-----LFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~-----~~~~~~C~H~fC~~C~~~y~~ 96 (216)
..+|+||++.+...+ +..+.+|+|.||.+|+..++.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 479999999864332 234568999999999999986
No 19
>PHA02926 zinc finger-like protein; Provisional
Probab=97.29 E-value=0.00023 Score=57.84 Aligned_cols=48 Identities=21% Similarity=0.532 Sum_probs=34.1
Q ss_pred CCCCcccccCCCC-----CC-ceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKST-----NE-LFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~-----~~-~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..+|+||++..-. .. +-.+.+|+|.||..|++.+...+-..| ..-.||
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~-~~rsCP 223 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG-ASDNCP 223 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC-cCCcCC
Confidence 5799999997521 11 223579999999999999999754223 234688
No 20
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00026 Score=63.75 Aligned_cols=44 Identities=27% Similarity=0.627 Sum_probs=34.9
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
...|+||+++.+... +..|||.||..|+-+|+...... .+.+||
T Consensus 186 ~~~CPICL~~~~~p~---~t~CGHiFC~~CiLqy~~~s~~~--~~~~CP 229 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPV---RTNCGHIFCGPCILQYWNYSAIK--GPCSCP 229 (513)
T ss_pred CCcCCcccCCCCccc---ccccCceeeHHHHHHHHhhhccc--CCccCC
Confidence 468999999876543 45699999999999999998322 357898
No 21
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.23 E-value=0.00029 Score=59.04 Aligned_cols=100 Identities=15% Similarity=0.312 Sum_probs=59.4
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCccccccCCCH--------HHHHHHHHHHHHhhhcC-C
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCPIVPK--------EVSDRWGNALCEGVING-A 131 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp~l~~--------~~~~~y~~~~~~~~v~~-~ 131 (216)
..+|+||++.+... .++.|+|.||+.|+...+. ..+.||.-.+ -................ .
T Consensus 13 ~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~~~~~~~~~ 82 (386)
T KOG2177|consen 13 ELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCPVCRPPSRNLRPNVLLANLVERLRQLRLSRPL 82 (386)
T ss_pred cccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCcccCCchhccCccHHHHHHHHHHHhcCCcccc
Confidence 56899999998765 4679999999999999888 3478883331 11111111111100000 0
Q ss_pred C--CcccCcCCCCceeecCCCCCCCceeCCCCchhccccCC-CCCCCCCChHh
Q 041841 132 E--KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCK-VPWHAGMRCEK 181 (216)
Q Consensus 132 ~--~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~-~~~H~~~~C~~ 181 (216)
. ...|+.. . ....+.|..|+...|..|. ...|.++.-..
T Consensus 83 ~~~~~~c~~~---------~--~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~~ 124 (386)
T KOG2177|consen 83 GSKEELCEKH---------G--EELKLFCEEDEKLLCVLCRESGEHRGHPVLP 124 (386)
T ss_pred cccchhhhhc---------C--CcceEEecccccccCCCCCCcccccCCcccc
Confidence 0 0123211 1 1145779899999999998 66677665443
No 22
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.53 E-value=0.0059 Score=52.39 Aligned_cols=42 Identities=21% Similarity=0.439 Sum_probs=29.5
Q ss_pred CCCCcccccCCCCCCc---eeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNEL---FSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~---~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
...||+|..+...+.- +.. .|||.||..|+...+. .| +..||
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~----~~--~~~CP 47 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFV----RG--SGSCP 47 (309)
T ss_pred CCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhc----CC--CCCCC
Confidence 3579999997543322 222 7999999999999863 22 34677
No 23
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.38 E-value=0.0027 Score=56.44 Aligned_cols=34 Identities=21% Similarity=0.493 Sum_probs=27.8
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
...|+||.+.+... .++.|+|.||..|+..|+..
T Consensus 26 ~l~C~IC~d~~~~P---vitpCgH~FCs~CI~~~l~~ 59 (397)
T TIGR00599 26 SLRCHICKDFFDVP---VLTSCSHTFCSLCIRRCLSN 59 (397)
T ss_pred ccCCCcCchhhhCc---cCCCCCCchhHHHHHHHHhC
Confidence 57999999977432 24799999999999999864
No 24
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.35 E-value=0.0017 Score=56.60 Aligned_cols=37 Identities=22% Similarity=0.501 Sum_probs=34.2
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSK 98 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~ 98 (216)
.+|.||+|++...+.+..|+|+|.|...|...||...
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~ 266 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT 266 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc
Confidence 3899999999988888889999999999999999964
No 25
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=96.30 E-value=0.0056 Score=39.70 Aligned_cols=33 Identities=21% Similarity=0.118 Sum_probs=26.9
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..|+||.+..... ..+.|||.||+.|+.+|+..
T Consensus 2 ~~Cpi~~~~~~~P---v~~~~G~v~~~~~i~~~~~~ 34 (63)
T smart00504 2 FLCPISLEVMKDP---VILPSGQTYERRAIEKWLLS 34 (63)
T ss_pred cCCcCCCCcCCCC---EECCCCCEEeHHHHHHHHHH
Confidence 3699999976532 34689999999999999976
No 26
>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=96.27 E-value=0.0029 Score=42.92 Aligned_cols=36 Identities=19% Similarity=0.408 Sum_probs=26.7
Q ss_pred CCCcccccCCCC----------CCceeeCCCCCccchHHHHHHHHH
Q 041841 62 RPFSICMEPKST----------NELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 62 ~~C~IC~~~~~~----------~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..|.||++.+.. .-.+....|+|.|...|+.++++.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~ 65 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ 65 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc
Confidence 459999998722 122344689999999999999964
No 27
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=96.25 E-value=0.0032 Score=53.03 Aligned_cols=36 Identities=31% Similarity=0.660 Sum_probs=29.6
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHh
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKL 99 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i 99 (216)
..-|.+|++.... .+.++|||.||-.|+..|...+-
T Consensus 239 ~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~ 274 (293)
T KOG0317|consen 239 TRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKA 274 (293)
T ss_pred CCceEEEecCCCC---CCcCcCcchHHHHHHHHHHcccc
Confidence 4689999998743 34579999999999999998754
No 28
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.22 E-value=0.0028 Score=51.86 Aligned_cols=37 Identities=14% Similarity=0.498 Sum_probs=29.5
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhh
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLR 100 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~ 100 (216)
..+|.||+|.... ..+..|||.||-.|+-+|+.+...
T Consensus 47 ~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~ 83 (230)
T KOG0823|consen 47 FFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPN 83 (230)
T ss_pred ceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCC
Confidence 5799999997542 234579999999999999987554
No 29
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=95.84 E-value=0.0094 Score=50.98 Aligned_cols=89 Identities=22% Similarity=0.527 Sum_probs=57.7
Q ss_pred CCCCccchHHHHHHHHHHhhcC---Ccccccc-CCCHH--HHHHHHHHHHHhhhcCCCCcccCcCCCCceeecCCCCCCC
Q 041841 81 FCSYSYCTDCIVKYVDSKLRES---ITSIRCP-IVPKE--VSDRWGNALCEGVINGAEKFYCPFKDCSALLINDGLKNMK 154 (216)
Q Consensus 81 ~C~H~fC~~C~~~y~~~~i~~~---~~~i~Cp-~l~~~--~~~~y~~~~~~~~v~~~~~~~Cp~~~C~~~~~~~~~~~~~ 154 (216)
+|+-.||++|++.|.+-.-..+ ...-.|- -+++. .-.+|..+... .| +...+.|| .|......+++ .-
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~~as~t~tc~y~vde~~a~~arwd~as~~-TI-k~tTkpCP--kChvptErnGG--Cm 414 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVFEASGTTTCAYRVDERAAEQARWDAASKE-TI-KKTTKPCP--KCHVPTERNGG--CM 414 (446)
T ss_pred CchhHhHHHHHhhhccccceeeeccccccceeeecChhhhhhhhhhhhhhh-hh-hhccCCCC--CccCccccCCc--eE
Confidence 5999999999999876543332 1123454 33432 23355544332 22 23356788 79888877654 45
Q ss_pred ceeCCC--CchhccccCCCCCCC
Q 041841 155 ESKRPY--CKRMFCAQCKVPWHA 175 (216)
Q Consensus 155 ~~~C~~--C~~~fC~~C~~~~H~ 175 (216)
.+.|+. ||..+|+.|+.+|-.
T Consensus 415 Hm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 415 HMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred EeecCCCCCCceeEeccCChhhh
Confidence 688975 999999999999854
No 30
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=95.83 E-value=0.0044 Score=53.38 Aligned_cols=33 Identities=30% Similarity=0.588 Sum_probs=27.9
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..|.||++-+... .+.+|+|.||.-|++.|+..
T Consensus 24 LRC~IC~eyf~ip---~itpCsHtfCSlCIR~~L~~ 56 (442)
T KOG0287|consen 24 LRCGICFEYFNIP---MITPCSHTFCSLCIRKFLSY 56 (442)
T ss_pred HHHhHHHHHhcCc---eeccccchHHHHHHHHHhcc
Confidence 5799999987653 24689999999999999985
No 31
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.78 E-value=0.0063 Score=51.69 Aligned_cols=36 Identities=19% Similarity=0.406 Sum_probs=32.2
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
..+|.||++.+...+-+..++|.|.|...|+.+|+.
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~ 358 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL 358 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHh
Confidence 579999999997766677799999999999999987
No 32
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.44 E-value=0.019 Score=47.96 Aligned_cols=31 Identities=19% Similarity=0.465 Sum_probs=25.3
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKY 94 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y 94 (216)
...|.||++.... +..+.|||.||..|+-..
T Consensus 215 d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~ 245 (271)
T COG5574 215 DYKCFLCLEEPEV---PSCTPCGHLFCLSCLLIS 245 (271)
T ss_pred ccceeeeecccCC---cccccccchhhHHHHHHH
Confidence 6789999997543 445789999999999874
No 33
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.01 E-value=0.036 Score=32.34 Aligned_cols=30 Identities=20% Similarity=0.537 Sum_probs=23.4
Q ss_pred cccCcCCCCceeecCCC---CCCCceeCCCCchhc
Q 041841 134 FYCPFKDCSALLINDGL---KNMKESKRPYCKRMF 165 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~f 165 (216)
+.|| .|+..+..++. .....++|+.|+..|
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 4688 89999887753 346689999999876
No 34
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.85 E-value=0.069 Score=47.30 Aligned_cols=86 Identities=21% Similarity=0.557 Sum_probs=57.9
Q ss_pred CceeeCCCCCccchHHHHHHHHHHhhcCCccccccCC--------------C----HHHHHHHHHHHHHhhhc-------
Q 041841 75 ELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCPIV--------------P----KEVSDRWGNALCEGVIN------- 129 (216)
Q Consensus 75 ~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp~l--------------~----~~~~~~y~~~~~~~~v~------- 129 (216)
.+..-..|.-.||..|...|.- + .+|.+- + .++..||.++..+..++
T Consensus 292 ~l~~CskCnFaFCtlCk~t~HG------~--s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekw 363 (445)
T KOG1814|consen 292 ALAICSKCNFAFCTLCKLTWHG------V--SPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKW 363 (445)
T ss_pred hhhhhccCccHHHHHHHHhhcC------C--CcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 3344467888999999988754 1 345511 1 23445676443333221
Q ss_pred -CCCCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCC
Q 041841 130 -GAEKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVP 172 (216)
Q Consensus 130 -~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 172 (216)
..+...|| .|..+|...++ -.++.|..|++.||+.|...
T Consensus 364 l~~N~krCP--~C~v~IEr~eG--CnKM~C~~c~~~fc~~c~~~ 403 (445)
T KOG1814|consen 364 LESNSKRCP--KCKVVIERSEG--CNKMHCTKCGTYFCWICAEL 403 (445)
T ss_pred HHhcCCCCC--cccceeecCCC--ccceeeccccccceeehhhh
Confidence 23467899 89999988654 67899999999999999874
No 35
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.72 E-value=0.04 Score=48.22 Aligned_cols=49 Identities=33% Similarity=0.622 Sum_probs=32.9
Q ss_pred CCCCcccccCCCCCC-----ceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNE-----LFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~-----~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..+|.||++...... +-.+.+|.|.||.+|.+.+=...--+....-.||
T Consensus 161 ~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP 214 (344)
T KOG1039|consen 161 EKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP 214 (344)
T ss_pred cccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC
Confidence 579999999875433 2234789999999999987644322222234577
No 36
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=93.69 E-value=0.044 Score=46.45 Aligned_cols=33 Identities=21% Similarity=0.414 Sum_probs=27.3
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
.-|-||-+-+... ....|||.||.-|++.|+.+
T Consensus 26 lrC~IC~~~i~ip---~~TtCgHtFCslCIR~hL~~ 58 (391)
T COG5432 26 LRCRICDCRISIP---CETTCGHTFCSLCIRRHLGT 58 (391)
T ss_pred HHhhhhhheeecc---eecccccchhHHHHHHHhcC
Confidence 5799999877642 35789999999999999974
No 37
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.49 E-value=0.039 Score=49.19 Aligned_cols=42 Identities=19% Similarity=0.434 Sum_probs=34.4
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCCCCCCC
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPWHAGMR 178 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~ 178 (216)
..+.|| .|...+....+ -..++|. ||+.||..|+.+|+.+..
T Consensus 305 ~wr~Cp--kC~~~ie~~~G--Cnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 305 RWRQCP--KCKFMIELSEG--CNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred hcCcCc--ccceeeeecCC--cceEEee-ccccchhhcCcchhhCCc
Confidence 467899 89999877544 7789999 999999999999965443
No 38
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=93.48 E-value=0.046 Score=49.88 Aligned_cols=45 Identities=24% Similarity=0.702 Sum_probs=34.8
Q ss_pred CCCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 60 RKRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 60 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
+..+|.+|-++.. + +.-.+|.|.||+-|++.|+........ +.||
T Consensus 535 ~~~~C~lc~d~ae--d-~i~s~ChH~FCrlCi~eyv~~f~~~~n--vtCP 579 (791)
T KOG1002|consen 535 GEVECGLCHDPAE--D-YIESSCHHKFCRLCIKEYVESFMENNN--VTCP 579 (791)
T ss_pred CceeecccCChhh--h-hHhhhhhHHHHHHHHHHHHHhhhcccC--CCCc
Confidence 3679999998642 2 334689999999999999998776532 7888
No 39
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.16 E-value=0.096 Score=47.57 Aligned_cols=91 Identities=25% Similarity=0.483 Sum_probs=54.6
Q ss_pred eCCCCCccchHHHHHHHHHHhhcCCccccccCCCHHHHHHHHHHHHHhhhcCCCCcccCcCCCCceeecCCCCCCCceeC
Q 041841 79 IEFCSYSYCTDCIVKYVDSKLRESITSIRCPIVPKEVSDRWGNALCEGVINGAEKFYCPFKDCSALLINDGLKNMKESKR 158 (216)
Q Consensus 79 ~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp~l~~~~~~~y~~~~~~~~v~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C 158 (216)
.-.|+|.||..|. .+...|..|+.....+...-........+ ..+...|| .|...+..+++ ...+.|
T Consensus 181 ~C~~g~~FC~~C~--------~~~H~p~~C~~~~~wl~k~~~~se~~~wi-~~ntk~CP--~c~~~iek~~g--c~~~~~ 247 (444)
T KOG1815|consen 181 DCGCGHEFCFACG--------EESHSPVSCPGAKKWLKKCRDDSETINWI-LANTKECP--KCKVPIEKDGG--CNHMTC 247 (444)
T ss_pred eCCCCchhHhhcc--------ccccCCCcccchHHHHHhhhhhhhhhhhh-hccCccCC--CcccchhccCC--cccccc
Confidence 4689999999883 23345778985444333222211111111 23345588 79888877654 344566
Q ss_pred CC--CchhccccCCCCC--CC---CCChHhH
Q 041841 159 PY--CKRMFCAQCKVPW--HA---GMRCEKF 182 (216)
Q Consensus 159 ~~--C~~~fC~~C~~~~--H~---~~~C~~~ 182 (216)
.. |++.||..|...| |. +..|..+
T Consensus 248 ~~~~c~~~FCw~Cl~~~~~h~~~~~~~c~~~ 278 (444)
T KOG1815|consen 248 KSASCKHEFCWVCLASLSDHGSSTGYSCNRY 278 (444)
T ss_pred ccCCcCCeeceeeecccccccccceeeeeee
Confidence 55 9999999998777 64 3456433
No 40
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=92.40 E-value=0.024 Score=37.18 Aligned_cols=30 Identities=23% Similarity=0.554 Sum_probs=15.1
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVK 93 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~ 93 (216)
.-|++|.+-.... +.+..|.|.||..|++.
T Consensus 8 LrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~ 37 (65)
T PF14835_consen 8 LRCSICFDILKEP--VCLGGCEHIFCSSCIRD 37 (65)
T ss_dssp TS-SSS-S--SS---B---SSS--B-TTTGGG
T ss_pred cCCcHHHHHhcCC--ceeccCccHHHHHHhHH
Confidence 4699999876433 34568999999999966
No 41
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=92.35 E-value=0.1 Score=35.00 Aligned_cols=41 Identities=15% Similarity=0.260 Sum_probs=19.3
Q ss_pred CCCCcccccCCC-CCCcee----eCCCCCccchHHHHHHHHHHhhc
Q 041841 61 KRPFSICMEPKS-TNELFS----IEFCSYSYCTDCIVKYVDSKLRE 101 (216)
Q Consensus 61 ~~~C~IC~~~~~-~~~~~~----~~~C~H~fC~~C~~~y~~~~i~~ 101 (216)
..+|.||+.... ..+... ...|+..|...||.+||...-..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~ 47 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKS 47 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSS
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccC
Confidence 358999999865 322211 24788999999999999876554
No 42
>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=92.26 E-value=0.075 Score=28.54 Aligned_cols=23 Identities=30% Similarity=0.647 Sum_probs=17.2
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
.|| +|+..+... ...||.||+.|
T Consensus 2 ~CP--~C~~~V~~~------~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVPES------AKFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchhh------cCcCCCCCCCC
Confidence 577 899888442 35799999876
No 43
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=91.92 E-value=0.11 Score=30.04 Aligned_cols=30 Identities=23% Similarity=0.522 Sum_probs=22.6
Q ss_pred cccCcCCCCceeecCCC---CCCCceeCCCCchhc
Q 041841 134 FYCPFKDCSALLINDGL---KNMKESKRPYCKRMF 165 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~f 165 (216)
+.|| .|+..+..++. .....++|+.|+..|
T Consensus 3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4688 79998877643 345679999999875
No 44
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=91.83 E-value=0.14 Score=32.85 Aligned_cols=43 Identities=21% Similarity=0.508 Sum_probs=26.6
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCccccccC
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCPI 110 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp~ 110 (216)
+..|+|-...+. +-+....|+|.|-++-+.+|| .+...++||+
T Consensus 11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCC
Confidence 568999998754 334557899999999999999 2223578873
No 45
>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=91.67 E-value=0.072 Score=40.21 Aligned_cols=41 Identities=17% Similarity=0.364 Sum_probs=29.6
Q ss_pred CCCCcccccCCCCCCceeeCCCC------CccchHHHHHHHHHHhhc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCS------YSYCTDCIVKYVDSKLRE 101 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~------H~fC~~C~~~y~~~~i~~ 101 (216)
..+|.||++.+...+.+....|+ |.||.+|+++|-...-++
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rD 72 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRD 72 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCC
Confidence 56999999998763444445566 789999999995443333
No 46
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=91.52 E-value=0.11 Score=29.97 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=18.8
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
++|| .|++++.......... .|..|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence 5798 8999997765433333 78888874
No 47
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.47 E-value=0.21 Score=42.06 Aligned_cols=45 Identities=29% Similarity=0.555 Sum_probs=31.4
Q ss_pred CCCCCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 58 GKRKRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 58 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
.....+|++|.+.-... +.+..|+|.||--|++.-+.... .+.||
T Consensus 236 ~t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~a-----sf~Cp 280 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDA-----SFTCP 280 (298)
T ss_pred ccCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchh-----hcccC
Confidence 34478999999865433 34567999999999987555322 25676
No 48
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.37 E-value=0.18 Score=31.26 Aligned_cols=28 Identities=25% Similarity=0.511 Sum_probs=19.5
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
.+|| .|+.++............|+.||+
T Consensus 1 ~FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCP--KCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCC--CCCCccccccCCCCCEEECCcCCC
Confidence 3788 899988665433224678888885
No 49
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=91.33 E-value=0.061 Score=50.94 Aligned_cols=36 Identities=17% Similarity=0.441 Sum_probs=27.3
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHh
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKL 99 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i 99 (216)
-..|++|-+-. -+ ..+..|+|.||.+|++..+.++-
T Consensus 643 ~LkCs~Cn~R~-Kd--~vI~kC~H~FC~~Cvq~r~etRq 678 (698)
T KOG0978|consen 643 LLKCSVCNTRW-KD--AVITKCGHVFCEECVQTRYETRQ 678 (698)
T ss_pred ceeCCCccCch-hh--HHHHhcchHHHHHHHHHHHHHhc
Confidence 46899999432 22 33568999999999999888754
No 50
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=90.68 E-value=0.22 Score=43.77 Aligned_cols=38 Identities=16% Similarity=0.352 Sum_probs=28.9
Q ss_pred CCCCCcccccCC-CCC---------CceeeCCCCCccchHHHHHHHHH
Q 041841 60 RKRPFSICMEPK-STN---------ELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 60 ~~~~C~IC~~~~-~~~---------~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
+...|.||+|+. ... ....-++|||.+...|++.|++-
T Consensus 286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER 333 (491)
T COG5243 286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER 333 (491)
T ss_pred CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh
Confidence 357999999993 222 11235899999999999999984
No 51
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.32 E-value=0.23 Score=46.29 Aligned_cols=37 Identities=14% Similarity=0.299 Sum_probs=29.9
Q ss_pred CCCCcccccCCCCCCc--eeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNEL--FSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~--~~~~~C~H~fC~~C~~~y~~~ 97 (216)
...|.||.|+.....- ...+.|+|.|+..|+++|++.
T Consensus 291 ~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er 329 (543)
T KOG0802|consen 291 DELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER 329 (543)
T ss_pred CCeeeeechhhccccccccceeecccchHHHHHHHHHHH
Confidence 5789999998754211 345899999999999999996
No 52
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=87.53 E-value=0.34 Score=28.08 Aligned_cols=30 Identities=17% Similarity=0.392 Sum_probs=20.9
Q ss_pred cccCcCCCCceeecCCC---CCCCceeCCCCchhc
Q 041841 134 FYCPFKDCSALLINDGL---KNMKESKRPYCKRMF 165 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~f 165 (216)
+-|| .|+..+..+.. .....+.|++||..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 3588 79998776632 123468999999765
No 53
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=86.95 E-value=0.4 Score=42.90 Aligned_cols=35 Identities=17% Similarity=0.487 Sum_probs=27.2
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
+..|++|.......- .+ ..|+|.||..|+..+++.
T Consensus 21 ~l~C~~C~~vl~~p~-~~-~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 21 NLLCPICMSVLRDPV-QT-TTCGHRFCAGCLLESLSN 55 (391)
T ss_pred cccCccccccccCCC-CC-CCCCCcccccccchhhcc
Confidence 578999998765321 11 489999999999988886
No 54
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.59 E-value=0.44 Score=41.62 Aligned_cols=34 Identities=26% Similarity=0.530 Sum_probs=27.0
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
...|+||+.. +.+.++ .+|+|+-|.+|+.+|+.+
T Consensus 422 d~lCpICyA~-pi~Avf--~PC~H~SC~~CI~qHlmN 455 (489)
T KOG4692|consen 422 DNLCPICYAG-PINAVF--APCSHRSCYGCITQHLMN 455 (489)
T ss_pred cccCcceecc-cchhhc--cCCCCchHHHHHHHHHhc
Confidence 4689999964 444444 589999999999999875
No 55
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.61 E-value=0.43 Score=40.79 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=26.4
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..+|.||+.+.-.. ..+.|+|.||.-|++.-+..
T Consensus 7 ~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~n 40 (324)
T KOG0824|consen 7 KKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKN 40 (324)
T ss_pred CCcceeeeccCCcC---ccccccchhhhhhhcchhhc
Confidence 46899999976433 35799999999999865553
No 56
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.43 E-value=0.9 Score=27.59 Aligned_cols=30 Identities=20% Similarity=0.448 Sum_probs=21.6
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhccc
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMFCA 167 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 167 (216)
..|| +|+..+..+... ..+.||.||..+=.
T Consensus 4 y~C~--~CG~~~~~~~~~--~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCA--RCGREVELDEYG--TGVRCPYCGYRILF 33 (46)
T ss_pred EECC--CCCCEEEECCCC--CceECCCCCCeEEE
Confidence 3587 899988776432 26899999976543
No 57
>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=85.42 E-value=1 Score=27.90 Aligned_cols=36 Identities=11% Similarity=0.394 Sum_probs=26.0
Q ss_pred CCcccccCCCCCCceeeCCCC-----CccchHHHHHHHHHHh
Q 041841 63 PFSICMEPKSTNELFSIEFCS-----YSYCTDCIVKYVDSKL 99 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~-----H~fC~~C~~~y~~~~i 99 (216)
.|-||++.....+.+ ..+|. |.+..+|+.+++..+-
T Consensus 1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~ 41 (49)
T smart00744 1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESG 41 (49)
T ss_pred CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcC
Confidence 388999843333333 35775 7899999999998754
No 58
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=84.99 E-value=1.2 Score=29.84 Aligned_cols=34 Identities=15% Similarity=0.067 Sum_probs=25.3
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
...|+|+.+-... ...+++||.|++.++.+|+..
T Consensus 4 ~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~ 37 (73)
T PF04564_consen 4 EFLCPITGELMRD---PVILPSGHTYERSAIERWLEQ 37 (73)
T ss_dssp GGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCT
T ss_pred ccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHc
Confidence 3579999986532 234689999999999999986
No 59
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.69 E-value=0.91 Score=33.28 Aligned_cols=71 Identities=20% Similarity=0.450 Sum_probs=45.8
Q ss_pred cccccc------CCCHHHHHHHHHHHHH-hhhc-----CCCCcccCcCCCCceeecCC------CCCCCceeCCCCchhc
Q 041841 104 TSIRCP------IVPKEVSDRWGNALCE-GVIN-----GAEKFYCPFKDCSALLINDG------LKNMKESKRPYCKRMF 165 (216)
Q Consensus 104 ~~i~Cp------~l~~~~~~~y~~~~~~-~~v~-----~~~~~~Cp~~~C~~~~~~~~------~~~~~~~~C~~C~~~f 165 (216)
.|+.|| ++++.+-..|..+.-- .+.+ ......|- +|+..+.... ........|+.|+..|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCccc--CcCCCCCCcccccccccccccceeCCCCCCcc
Confidence 588999 6688888888875322 1211 11134576 7887664321 1123457899999999
Q ss_pred cccCCCCCCCC
Q 041841 166 CAQCKVPWHAG 176 (216)
Q Consensus 166 C~~C~~~~H~~ 176 (216)
|..|..=+|+-
T Consensus 92 C~dCD~fiHe~ 102 (112)
T TIGR00622 92 CVDCDVFVHES 102 (112)
T ss_pred ccccchhhhhh
Confidence 99998877764
No 60
>PHA03096 p28-like protein; Provisional
Probab=84.28 E-value=0.64 Score=39.76 Aligned_cols=47 Identities=15% Similarity=0.251 Sum_probs=34.1
Q ss_pred CCCcccccCCCC----CCce-eeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 62 RPFSICMEPKST----NELF-SIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 62 ~~C~IC~~~~~~----~~~~-~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
.+|.||++.... +..+ .+..|.|.||..|.+.+...+... ...-.||
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~-e~~~~c~ 230 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYK-ETEPENR 230 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhc-ccCcccc
Confidence 689999997643 2222 357999999999999999987632 2334566
No 61
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.57 E-value=1.1 Score=39.88 Aligned_cols=44 Identities=25% Similarity=0.573 Sum_probs=33.5
Q ss_pred CCCCcccccCCC--CCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKS--TNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~--~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..+|+||++++. .+.-+..+.|+|.|=.+|++.++- ++ ....||
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-k~----~~~~cp 49 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-KK----TKMQCP 49 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-hh----hhhhCc
Confidence 468999999874 333344589999999999999993 22 357888
No 62
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=82.98 E-value=0.54 Score=38.88 Aligned_cols=30 Identities=20% Similarity=0.556 Sum_probs=23.4
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVK 93 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~ 93 (216)
.|..|+---+ ...+.+++|.|.||..|.+.
T Consensus 5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~ 34 (233)
T KOG4739|consen 5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKA 34 (233)
T ss_pred EeccccccCC-CCceeeeechhhhhhhhccc
Confidence 5888887666 44455789999999999864
No 63
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=82.55 E-value=0.33 Score=41.93 Aligned_cols=35 Identities=26% Similarity=0.570 Sum_probs=27.2
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..+|.+|---+-.. .+...|-|.||+.|+-.|++.
T Consensus 15 ~itC~LC~GYliDA--TTI~eCLHTFCkSCivk~l~~ 49 (331)
T KOG2660|consen 15 HITCRLCGGYLIDA--TTITECLHTFCKSCIVKYLEE 49 (331)
T ss_pred ceehhhccceeecc--hhHHHHHHHHHHHHHHHHHHH
Confidence 35899998765322 234689999999999999997
No 64
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=82.31 E-value=0.6 Score=37.59 Aligned_cols=42 Identities=19% Similarity=0.424 Sum_probs=28.5
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
...|.||-.++... ....|||.||..|... ..+.|-.-+.|-
T Consensus 196 PF~C~iCKkdy~sp---vvt~CGH~FC~~Cai~----~y~kg~~C~~Cg 237 (259)
T COG5152 196 PFLCGICKKDYESP---VVTECGHSFCSLCAIR----KYQKGDECGVCG 237 (259)
T ss_pred ceeehhchhhccch---hhhhcchhHHHHHHHH----HhccCCcceecc
Confidence 46899999988542 2468999999999853 334453334453
No 65
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.06 E-value=0.75 Score=40.67 Aligned_cols=41 Identities=15% Similarity=0.477 Sum_probs=31.2
Q ss_pred CCCCcccccCCCCCCce-eeCCCCCccchHHHHHHHHHHhhc
Q 041841 61 KRPFSICMEPKSTNELF-SIEFCSYSYCTDCIVKYVDSKLRE 101 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~-~~~~C~H~fC~~C~~~y~~~~i~~ 101 (216)
..+|.||-+-++...-+ ..-.|||.|...|+.+|++..-..
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~ 45 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN 45 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc
Confidence 46899997777655433 344599999999999999976553
No 66
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.00 E-value=0.21 Score=43.49 Aligned_cols=33 Identities=24% Similarity=0.499 Sum_probs=25.1
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYV 95 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~ 95 (216)
+..|+||++-+...- +...|.|+||.+|+-.-+
T Consensus 43 ~v~c~icl~llk~tm--ttkeClhrfc~~ci~~a~ 75 (381)
T KOG0311|consen 43 QVICPICLSLLKKTM--TTKECLHRFCFDCIWKAL 75 (381)
T ss_pred hhccHHHHHHHHhhc--ccHHHHHHHHHHHHHHHH
Confidence 678999999765432 346899999999986433
No 67
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.79 E-value=0.78 Score=41.79 Aligned_cols=38 Identities=21% Similarity=0.662 Sum_probs=29.1
Q ss_pred CCCCCCcccccCCCCCC-----c---------eeeCCCCCccchHHHHHHHH
Q 041841 59 KRKRPFSICMEPKSTNE-----L---------FSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 59 ~~~~~C~IC~~~~~~~~-----~---------~~~~~C~H~fC~~C~~~y~~ 96 (216)
++...|.||+.+++... + +-+.+|.|.|.++|+.++..
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd 620 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMD 620 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHh
Confidence 34679999999876421 1 22469999999999999988
No 68
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=81.40 E-value=1.2 Score=45.01 Aligned_cols=30 Identities=23% Similarity=0.683 Sum_probs=20.1
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhc-----cccCCCC
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMF-----CAQCKVP 172 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f-----C~~C~~~ 172 (216)
.+.|| .|+..... ..|+.||... |..|+..
T Consensus 667 ~rkCP--kCG~~t~~--------~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 667 RRRCP--SCGTETYE--------NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEECC--CCCCcccc--------ccCcccCCcCCCceeCccCCCc
Confidence 46898 78886421 2688888664 7777664
No 69
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=81.38 E-value=0.96 Score=38.72 Aligned_cols=40 Identities=18% Similarity=0.428 Sum_probs=32.6
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhh
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLR 100 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~ 100 (216)
...|.||+=-+..++-|+...|-|.|..-|+.+||.....
T Consensus 115 ~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~ 154 (368)
T KOG4445|consen 115 NGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLT 154 (368)
T ss_pred CCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHH
Confidence 4679888877766665667899999999999999987653
No 70
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=81.12 E-value=0.57 Score=40.46 Aligned_cols=78 Identities=21% Similarity=0.503 Sum_probs=50.1
Q ss_pred ccchHHHHHHHHHHhhcCCcccccc------CCCHHHHHHHHHHHHH-hhhcC-----CCCcccCcCCCCceeecCCCCC
Q 041841 85 SYCTDCIVKYVDSKLRESITSIRCP------IVPKEVSDRWGNALCE-GVING-----AEKFYCPFKDCSALLINDGLKN 152 (216)
Q Consensus 85 ~fC~~C~~~y~~~~i~~~~~~i~Cp------~l~~~~~~~y~~~~~~-~~v~~-----~~~~~Cp~~~C~~~~~~~~~~~ 152 (216)
.||-.|-..+.+ .|+.|| ++++.+-..|..+.-- .+.+. ++...|- .|+.-. ..
T Consensus 277 y~CP~CkakvCs-------LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~~~~-----~~ 342 (378)
T KOG2807|consen 277 YFCPQCKAKVCS-------LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQGEL-----LS 342 (378)
T ss_pred eeCCcccCeeec-------CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCccee--eecccc-----CC
Confidence 466666544443 589999 5688888889876432 22221 2334565 562222 22
Q ss_pred CCceeCCCCchhccccCCCCCCCC
Q 041841 153 MKESKRPYCKRMFCAQCKVPWHAG 176 (216)
Q Consensus 153 ~~~~~C~~C~~~fC~~C~~~~H~~ 176 (216)
....+|..|+..||..|..-.|+-
T Consensus 343 ~~~y~C~~Ck~~FCldCDv~iHes 366 (378)
T KOG2807|consen 343 SGRYRCESCKNVFCLDCDVFIHES 366 (378)
T ss_pred CCcEEchhccceeeccchHHHHhh
Confidence 445899999999999998777754
No 71
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.08 E-value=0.7 Score=38.02 Aligned_cols=19 Identities=26% Similarity=0.740 Sum_probs=14.3
Q ss_pred CCceeCCCCchhccccCCCCC
Q 041841 153 MKESKRPYCKRMFCAQCKVPW 173 (216)
Q Consensus 153 ~~~~~C~~C~~~fC~~C~~~~ 173 (216)
.+.+++ ||+.||+-|--.|
T Consensus 59 dPVvTl--CGHLFCWpClyqW 77 (230)
T KOG0823|consen 59 DPVVTL--CGHLFCWPCLYQW 77 (230)
T ss_pred CCEEee--cccceehHHHHHH
Confidence 455676 9999999886544
No 72
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=80.63 E-value=1.6 Score=26.99 Aligned_cols=33 Identities=18% Similarity=0.440 Sum_probs=16.2
Q ss_pred CcccccCCCCCC-ceeeCCCCCccchHHHHHHHH
Q 041841 64 FSICMEPKSTNE-LFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 64 C~IC~~~~~~~~-~~~~~~C~H~fC~~C~~~y~~ 96 (216)
|++|.++.+..+ .+.--.|++..|+.||..-++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE 34 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh
Confidence 688998875443 222257899999999976554
No 73
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=80.62 E-value=1.3 Score=31.52 Aligned_cols=28 Identities=21% Similarity=0.583 Sum_probs=18.1
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
.+|| .|++++++........+.|..|.+
T Consensus 2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY 29 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGESCNRFSCRTCPY 29 (105)
T ss_pred cccC--CCCCEEEEecCCeEeeEEcCCCCc
Confidence 5799 799999887654334445554443
No 74
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=79.77 E-value=0.79 Score=24.36 Aligned_cols=23 Identities=30% Similarity=0.746 Sum_probs=13.5
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
+.|| .|+..+..+ ...|+.||..
T Consensus 3 ~~Cp--~Cg~~~~~~------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDPD------AKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCcc------cccChhhCCC
Confidence 4687 788854221 2457777653
No 75
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=79.67 E-value=1 Score=25.70 Aligned_cols=29 Identities=21% Similarity=0.457 Sum_probs=15.3
Q ss_pred cccCcCCCCceeecC--CCCCCCceeCCCCchh
Q 041841 134 FYCPFKDCSALLIND--GLKNMKESKRPYCKRM 164 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~--~~~~~~~~~C~~C~~~ 164 (216)
+||| .|+..+... .++......|+.||..
T Consensus 1 kfC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCP--QCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Cccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence 4788 788876553 2345567899999864
No 76
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=79.37 E-value=2.3 Score=29.62 Aligned_cols=19 Identities=26% Similarity=0.733 Sum_probs=17.3
Q ss_pred CCCCCccchHHHHHHHHHH
Q 041841 80 EFCSYSYCTDCIVKYVDSK 98 (216)
Q Consensus 80 ~~C~H~fC~~C~~~y~~~~ 98 (216)
-.|+|.|...|+.+++.+.
T Consensus 50 g~C~H~FH~hCI~kWl~~~ 68 (85)
T PF12861_consen 50 GKCSHNFHMHCILKWLSTQ 68 (85)
T ss_pred ccCccHHHHHHHHHHHccc
Confidence 4799999999999999975
No 77
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=78.64 E-value=1.8 Score=31.85 Aligned_cols=30 Identities=20% Similarity=0.340 Sum_probs=22.1
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
.++|| .|++++............|++||+.
T Consensus 2 m~FCp--~Cgsll~p~~~~~~~~l~C~kCgye 31 (113)
T COG1594 2 MRFCP--KCGSLLYPKKDDEGGKLVCRKCGYE 31 (113)
T ss_pred ccccC--CccCeeEEeEcCCCcEEECCCCCcc
Confidence 46899 8999997754333457888888875
No 78
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=77.53 E-value=2.9 Score=26.52 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=22.9
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
+-|| .|+.-+........-.+.|+.||..+
T Consensus 3 ~~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4688 89998877654446678999999765
No 79
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.07 E-value=1.7 Score=37.01 Aligned_cols=42 Identities=26% Similarity=0.596 Sum_probs=32.0
Q ss_pred CCCcccccCCCCC---CceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 62 RPFSICMEPKSTN---ELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 62 ~~C~IC~~~~~~~---~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..|.||-++++.. .....+.|||.+|..|....+.. ..+.||
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~------~~i~cp 48 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN------SRILCP 48 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcC------ceeecc
Confidence 4799999998643 34567899999999999877764 235667
No 80
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=75.67 E-value=2.2 Score=41.41 Aligned_cols=49 Identities=27% Similarity=0.504 Sum_probs=39.3
Q ss_pred CCCCcccccCCCCC-CceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTN-ELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~-~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..+|.||++.+... .+++-..|-|.|...|++.|....-++|...-+||
T Consensus 191 ~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP 240 (950)
T KOG1952|consen 191 KYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP 240 (950)
T ss_pred ceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC
Confidence 68999999998654 45666788899999999999999445554556888
No 81
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.03 E-value=1.4 Score=22.79 Aligned_cols=22 Identities=36% Similarity=0.851 Sum_probs=13.2
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
+|| .|+.-+..+ ...|+.||+.
T Consensus 1 ~Cp--~CG~~~~~~------~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDD------AKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCc------CcchhhhCCc
Confidence 477 788877332 2347777754
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=73.82 E-value=4.5 Score=26.12 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=20.6
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhccccC
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQC 169 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C 169 (216)
..|. .|+..+...+ ....+.||.||...=.+|
T Consensus 10 ~~Ct--SCg~~i~p~e--~~v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 10 PVCT--SCGREIAPGE--TAVKFPCPNCGEVEIYRC 41 (61)
T ss_pred ceec--cCCCEeccCC--ceeEeeCCCCCceeeehh
Confidence 3565 6888774432 355688999996655544
No 83
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=73.25 E-value=1.8 Score=25.89 Aligned_cols=38 Identities=26% Similarity=0.655 Sum_probs=19.8
Q ss_pred cCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCCCCCCChHhH
Q 041841 136 CPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPWHAGMRCEKF 182 (216)
Q Consensus 136 Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C~~~ 182 (216)
|..++|..... ..+.|+.|+..||...+.+ +.+.|...
T Consensus 1 C~~~~C~~~~~-------~~~~C~~C~~~FC~~Hr~~--e~H~C~~~ 38 (43)
T PF01428_consen 1 CSFPGCKKKDF-------LPFKCKHCGKSFCLKHRLP--EDHNCSKL 38 (43)
T ss_dssp -SSTTT--BCT-------SHEE-TTTS-EE-TTTHST--TTCT-SST
T ss_pred CccCcCcCccC-------CCeECCCCCcccCccccCc--cccCCcch
Confidence 44456766543 2478999999999987653 23466553
No 84
>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=73.24 E-value=3.6 Score=22.84 Aligned_cols=28 Identities=18% Similarity=0.258 Sum_probs=16.2
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
-+||| .|+........ .....|+.|+..
T Consensus 3 ~rfC~--~CG~~t~~~~~--g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCG--RCGAPTKPAPG--GWARRCPSCGHE 30 (32)
T ss_dssp TSB-T--TT--BEEE-SS--SS-EEESSSS-E
T ss_pred CcccC--cCCccccCCCC--cCEeECCCCcCE
Confidence 36898 79988877643 566889999864
No 85
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.17 E-value=3.2 Score=41.27 Aligned_cols=33 Identities=21% Similarity=0.622 Sum_probs=24.0
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCch-----hccccCCCCCC
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKR-----MFCAQCKVPWH 174 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~-----~fC~~C~~~~H 174 (216)
..+.|| .|+... ....||.||. .||..|+....
T Consensus 625 g~RfCp--sCG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 625 GRRKCP--SCGKET--------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cCccCC--CCCCcC--------CcccCCCCCCCCCcceeCccccCcCC
Confidence 367999 798874 2367999985 48888876544
No 86
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.42 E-value=2.8 Score=36.69 Aligned_cols=33 Identities=15% Similarity=0.380 Sum_probs=25.5
Q ss_pred CCCCCcccccCCCCCCceeeCCCCCc-cchHHHHHHH
Q 041841 60 RKRPFSICMEPKSTNELFSIEFCSYS-YCTDCIVKYV 95 (216)
Q Consensus 60 ~~~~C~IC~~~~~~~~~~~~~~C~H~-fC~~C~~~y~ 95 (216)
+..+|.||+.+... ..+++|.|. .|.+|-+..-
T Consensus 289 ~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr 322 (349)
T KOG4265|consen 289 SGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLR 322 (349)
T ss_pred CCCeeEEEecCCcc---eEEecchhhehhHhHHHHHH
Confidence 36899999987532 446899997 9999987644
No 87
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=72.31 E-value=3.1 Score=25.91 Aligned_cols=27 Identities=15% Similarity=0.392 Sum_probs=19.4
Q ss_pred CcccCcCCCCc-eeecCCCCCCCceeCCCCchhc
Q 041841 133 KFYCPFKDCSA-LLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 133 ~~~Cp~~~C~~-~~~~~~~~~~~~~~C~~C~~~f 165 (216)
..+|| .|+. ++.... ....|..||+.+
T Consensus 20 ~~fCP--~Cg~~~m~~~~----~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCP--RCGSGFMAEHL----DRWHCGKCGYTE 47 (50)
T ss_pred cCcCc--CCCcchheccC----CcEECCCcCCEE
Confidence 46999 6888 664432 468899999764
No 88
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=71.35 E-value=2 Score=38.32 Aligned_cols=32 Identities=31% Similarity=0.614 Sum_probs=25.6
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
+-|.||.+... -+.+.+|||..|..|+..|-.
T Consensus 370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~ 401 (563)
T KOG1785|consen 370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQD 401 (563)
T ss_pred HHHHHhhccCC---CcccccccchHHHHHHHhhcc
Confidence 46999998643 355789999999999988754
No 89
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.27 E-value=3 Score=40.73 Aligned_cols=39 Identities=21% Similarity=0.414 Sum_probs=31.8
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhh
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLR 100 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~ 100 (216)
+..|.+|........++. .+|||.|.++|+.+++.....
T Consensus 817 ~d~C~~C~~~ll~~pF~v-f~CgH~FH~~Cl~~~v~~~~~ 855 (911)
T KOG2034|consen 817 QDSCDHCGRPLLIKPFYV-FPCGHCFHRDCLIRHVLSLLS 855 (911)
T ss_pred ccchHHhcchhhcCccee-eeccchHHHHHHHHHHHcccc
Confidence 678999999887666554 689999999999998876443
No 90
>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=70.14 E-value=3 Score=30.40 Aligned_cols=29 Identities=31% Similarity=0.441 Sum_probs=18.7
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhcc
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFC 166 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC 166 (216)
.+-|| .|+.-| ++-. ..-++||+||..|=
T Consensus 9 KR~Cp--~CG~kF-YDLn--k~PivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCP--SCGAKF-YDLN--KDPIVCPKCGTEFP 37 (108)
T ss_pred cccCC--CCcchh-ccCC--CCCccCCCCCCccC
Confidence 56788 788765 3322 24477998887653
No 91
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=70.10 E-value=2.2 Score=40.90 Aligned_cols=32 Identities=25% Similarity=0.682 Sum_probs=25.5
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
.+|.||.+ ... .....|+|.||.+||..++..
T Consensus 455 ~~c~ic~~---~~~-~~it~c~h~~c~~c~~~~i~~ 486 (674)
T KOG1001|consen 455 HWCHICCD---LDS-FFITRCGHDFCVECLKKSIQQ 486 (674)
T ss_pred cccccccc---ccc-ceeecccchHHHHHHHhcccc
Confidence 79999999 222 334689999999999988774
No 92
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=69.86 E-value=4 Score=34.08 Aligned_cols=36 Identities=6% Similarity=0.125 Sum_probs=29.3
Q ss_pred CCCCcccccCCCCC-CceeeCCCCCccchHHHHHHHH
Q 041841 61 KRPFSICMEPKSTN-ELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 61 ~~~C~IC~~~~~~~-~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
...|+||-++.... ....+.+|||.||.+|...+|.
T Consensus 221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir 257 (303)
T KOG3039|consen 221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR 257 (303)
T ss_pred ceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc
Confidence 57899999987532 3445789999999999998877
No 93
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=69.48 E-value=2.1 Score=30.30 Aligned_cols=31 Identities=23% Similarity=0.415 Sum_probs=25.0
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIV 92 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~ 92 (216)
...|.+|...+..+. +...+|||.|...|.+
T Consensus 78 ~~~C~vC~k~l~~~~-f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSV-FVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCce-EEEeCCCeEEeccccc
Confidence 457999999987654 5557999999999975
No 94
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=69.09 E-value=2.8 Score=25.79 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=17.9
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
++.||++.|+..+..... .....|.+||.
T Consensus 18 rk~CP~~~CG~GvFMA~H--~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEH--KDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE---SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeec--CCCccCCCccc
Confidence 578999999984433322 34567777775
No 95
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.89 E-value=2 Score=33.56 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=24.1
Q ss_pred CCCCCcccccCCCCCCceeeCCCCCccch
Q 041841 60 RKRPFSICMEPKSTNELFSIEFCSYSYCT 88 (216)
Q Consensus 60 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~ 88 (216)
...+|.||+++....+.+.-++|...|.+
T Consensus 176 dkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 176 DKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cCCcEEEEhhhccCCCceeccceEEEeec
Confidence 36799999999988888888899877754
No 96
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.65 E-value=2.9 Score=37.54 Aligned_cols=31 Identities=16% Similarity=0.527 Sum_probs=23.9
Q ss_pred CCCCCcccccCCCCCCceeeCCCCCccchHHHHH
Q 041841 60 RKRPFSICMEPKSTNELFSIEFCSYSYCTDCIVK 93 (216)
Q Consensus 60 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~ 93 (216)
++.+|.||+...... . .++|||.||..|+.+
T Consensus 83 sef~c~vc~~~l~~p--v-~tpcghs~c~~Cl~r 113 (398)
T KOG4159|consen 83 SEFECCVCSRALYPP--V-VTPCGHSFCLECLDR 113 (398)
T ss_pred chhhhhhhHhhcCCC--c-cccccccccHHHHHH
Confidence 368999998876432 2 359999999999766
No 97
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=67.46 E-value=0.76 Score=28.60 Aligned_cols=38 Identities=21% Similarity=0.478 Sum_probs=30.4
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHH-HHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVK-YVDSK 98 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~-y~~~~ 98 (216)
+.+|..|-+..+..++-...-||-..|..||+. |..-+
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~Ck 45 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCK 45 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHH
Confidence 678999999998877655567999999999986 44433
No 98
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=67.38 E-value=0.7 Score=37.15 Aligned_cols=32 Identities=25% Similarity=0.635 Sum_probs=20.2
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCC
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPW 173 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 173 (216)
....|| =|...+. .+ +. ..||+.||..|-..|
T Consensus 17 ~~~~Cp--ICld~~~------dP-Vv-T~CGH~FC~~CI~~w 48 (193)
T PLN03208 17 GDFDCN--ICLDQVR------DP-VV-TLCGHLFCWPCIHKW 48 (193)
T ss_pred CccCCc--cCCCcCC------Cc-EE-cCCCchhHHHHHHHH
Confidence 345677 5655431 11 23 359999999997766
No 99
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=66.87 E-value=6.5 Score=40.97 Aligned_cols=49 Identities=18% Similarity=0.315 Sum_probs=36.2
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcC-C--cccccc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRES-I--TSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~-~--~~i~Cp 109 (216)
..-|.|||.+...-.-...+.|+|.|...|.+..++.+-..- + ..|.||
T Consensus 3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP 3537 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP 3537 (3738)
T ss_pred CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc
Confidence 457999998864332223479999999999999999876552 2 248999
No 100
>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=66.38 E-value=5.1 Score=26.41 Aligned_cols=17 Identities=24% Similarity=0.800 Sum_probs=13.3
Q ss_pred ccchHHHHHHHHHHhhc
Q 041841 85 SYCTDCIVKYVDSKLRE 101 (216)
Q Consensus 85 ~fC~~C~~~y~~~~i~~ 101 (216)
-||++||..++...-.+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 49999999999998876
No 101
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=66.03 E-value=2.5 Score=40.46 Aligned_cols=13 Identities=31% Similarity=1.002 Sum_probs=10.2
Q ss_pred CCCchhccccCCC
Q 041841 159 PYCKRMFCAQCKV 171 (216)
Q Consensus 159 ~~C~~~fC~~C~~ 171 (216)
+.||+.||..|-.
T Consensus 659 ~kC~H~FC~~Cvq 671 (698)
T KOG0978|consen 659 TKCGHVFCEECVQ 671 (698)
T ss_pred HhcchHHHHHHHH
Confidence 3699999998843
No 102
>PF14369 zf-RING_3: zinc-finger
Probab=65.73 E-value=7.4 Score=22.26 Aligned_cols=30 Identities=17% Similarity=0.507 Sum_probs=20.0
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
..||- .|...+...... ...+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~-~~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSP-DSDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCC-CCCcCCcCCCCcE
Confidence 45888 799988764321 2334699998655
No 103
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=65.13 E-value=7.3 Score=24.69 Aligned_cols=33 Identities=18% Similarity=0.370 Sum_probs=27.3
Q ss_pred CCCCcccccCCC-CCCceeeCCCCCccchHHHHH
Q 041841 61 KRPFSICMEPKS-TNELFSIEFCSYSYCTDCIVK 93 (216)
Q Consensus 61 ~~~C~IC~~~~~-~~~~~~~~~C~H~fC~~C~~~ 93 (216)
...|++|-+.+. ..+.+.-..|+-.+.++||..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 457999999985 566677789999999999964
No 104
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.00 E-value=2.5 Score=26.85 Aligned_cols=33 Identities=18% Similarity=0.476 Sum_probs=23.3
Q ss_pred CCCCcccccCCCCCCceeeCCCCCc-cchHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYS-YCTDCIVKYVD 96 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~-fC~~C~~~y~~ 96 (216)
..+|.||++.- .+.. +-.|||. .|.+|-.+..+
T Consensus 7 ~dECTICye~p-vdsV--lYtCGHMCmCy~Cg~rl~~ 40 (62)
T KOG4172|consen 7 SDECTICYEHP-VDSV--LYTCGHMCMCYACGLRLKK 40 (62)
T ss_pred ccceeeeccCc-chHH--HHHcchHHhHHHHHHHHHH
Confidence 36899999863 2322 3469997 89999876555
No 105
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=64.99 E-value=4.5 Score=34.25 Aligned_cols=44 Identities=14% Similarity=0.344 Sum_probs=32.6
Q ss_pred CCCCCcccccCCCCC--------CceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 60 RKRPFSICMEPKSTN--------ELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 60 ~~~~C~IC~~~~~~~--------~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
++..|.||...+..+ +.++ ++|+|.|.-.|++.+... |. .-.||
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~-LsCnHvFHEfCIrGWciv----GK-kqtCP 274 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYK-LSCNHVFHEFCIRGWCIV----GK-KQTCP 274 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhhee-eecccchHHHhhhhheee----cC-CCCCc
Confidence 367899999877543 3444 799999999999998765 22 23688
No 106
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=64.81 E-value=4.2 Score=35.08 Aligned_cols=28 Identities=21% Similarity=0.446 Sum_probs=21.9
Q ss_pred CCCCcccccCCCCCCceeeCCC--CCccchHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFC--SYSYCTDCIV 92 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C--~H~fC~~C~~ 92 (216)
-.+||||++.+...- ..| ||..|.+|-.
T Consensus 48 lleCPvC~~~l~~Pi----~QC~nGHlaCssC~~ 77 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPI----FQCDNGHLACSSCRT 77 (299)
T ss_pred hccCchhhccCcccc----eecCCCcEehhhhhh
Confidence 369999999886543 345 5999999986
No 107
>PRK00420 hypothetical protein; Validated
Probab=63.43 E-value=17 Score=26.67 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 113 KEVSDRWGNALCEGVINGAEKFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 113 ~~~~~~y~~~~~~~~v~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
.+...+..++++..+... -..|| .|+..+.... ...+.||.||..
T Consensus 5 ~~~~k~~a~~Ll~Ga~ml--~~~CP--~Cg~pLf~lk---~g~~~Cp~Cg~~ 49 (112)
T PRK00420 5 EDIVKKAAELLLKGAKML--SKHCP--VCGLPLFELK---DGEVVCPVHGKV 49 (112)
T ss_pred HHHHHHHHHHHHhHHHHc--cCCCC--CCCCcceecC---CCceECCCCCCe
Confidence 455566666666644432 26899 6998876521 234677777763
No 108
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=62.82 E-value=4.3 Score=24.48 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=9.7
Q ss_pred CceecCCCCcc
Q 041841 205 KWKRCPHCNYS 215 (216)
Q Consensus 205 ~~k~CP~C~~~ 215 (216)
++|+||+|++.
T Consensus 10 GirkCp~CGt~ 20 (44)
T PF14952_consen 10 GIRKCPKCGTY 20 (44)
T ss_pred ccccCCcCcCc
Confidence 88999999874
No 109
>PHA00626 hypothetical protein
Probab=62.75 E-value=7.8 Score=24.73 Aligned_cols=30 Identities=13% Similarity=0.189 Sum_probs=17.2
Q ss_pred ccCcCCCCce-eecCCC--CCCCceeCCCCchhcc
Q 041841 135 YCPFKDCSAL-LINDGL--KNMKESKRPYCKRMFC 166 (216)
Q Consensus 135 ~Cp~~~C~~~-~~~~~~--~~~~~~~C~~C~~~fC 166 (216)
.|| +|+.. +..-+. .......|+.||+.|=
T Consensus 2 ~CP--~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCP--KCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCC--CCCCceeeeeceecccCcceEcCCCCCeec
Confidence 477 77773 222111 1135578999998763
No 110
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=62.21 E-value=4.9 Score=36.37 Aligned_cols=34 Identities=18% Similarity=0.499 Sum_probs=25.9
Q ss_pred CCCCcccccCCCCC-CceeeCCCCCccchHHHHHH
Q 041841 61 KRPFSICMEPKSTN-ELFSIEFCSYSYCTDCIVKY 94 (216)
Q Consensus 61 ~~~C~IC~~~~~~~-~~~~~~~C~H~fC~~C~~~y 94 (216)
..+|+||++-.+.+ .++....|+|.|--.|+..|
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w 209 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW 209 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhc
Confidence 47999999977543 23334679999999999765
No 111
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=61.48 E-value=13 Score=24.02 Aligned_cols=30 Identities=13% Similarity=0.319 Sum_probs=18.7
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchhcccc
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQ 168 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~ 168 (216)
.|. .|+..+...+ ....+.||.||...=.+
T Consensus 9 ~Ct--SCg~~i~~~~--~~~~F~CPnCG~~~I~R 38 (59)
T PRK14890 9 KCT--SCGIEIAPRE--KAVKFLCPNCGEVIIYR 38 (59)
T ss_pred ccc--CCCCcccCCC--ccCEeeCCCCCCeeEee
Confidence 465 6777774332 24678899898764333
No 112
>PF12773 DZR: Double zinc ribbon
Probab=61.35 E-value=5.9 Score=24.14 Aligned_cols=27 Identities=22% Similarity=0.593 Sum_probs=16.6
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+..+|| .|+..+.. .....+.|+.||+
T Consensus 11 ~~~fC~--~CG~~l~~---~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCP--HCGTPLPP---PDQSKKICPNCGA 37 (50)
T ss_pred cccCCh--hhcCChhh---ccCCCCCCcCCcC
Confidence 356788 78887751 1233466777765
No 113
>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=60.56 E-value=2.6 Score=26.42 Aligned_cols=37 Identities=24% Similarity=0.527 Sum_probs=18.5
Q ss_pred CCCceeecCCC--CCCCceeCCCCchhccccCCCCCCCC
Q 041841 140 DCSALLINDGL--KNMKESKRPYCKRMFCAQCKVPWHAG 176 (216)
Q Consensus 140 ~C~~~~~~~~~--~~~~~~~C~~C~~~fC~~C~~~~H~~ 176 (216)
+|...+..... .......|+.|+..||..|-.=.|+-
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 45555533211 11356899999999999998777764
No 114
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=59.68 E-value=4.8 Score=19.42 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=13.3
Q ss_pred ccccCCCCCCCCCChH
Q 041841 165 FCAQCKVPWHAGMRCE 180 (216)
Q Consensus 165 fC~~C~~~~H~~~~C~ 180 (216)
.|+.|++.-|.-..|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5899999999877774
No 115
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=59.58 E-value=11 Score=31.71 Aligned_cols=67 Identities=15% Similarity=0.408 Sum_probs=41.7
Q ss_pred CCCcccccCCCCCCceeeCCCCCc-cchHHHHHHHHHHhhc---CCcccccc---CCCHHHHHHHHHHHHHhhhcCCCCc
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYS-YCTDCIVKYVDSKLRE---SITSIRCP---IVPKEVSDRWGNALCEGVINGAEKF 134 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~-fC~~C~~~y~~~~i~~---~~~~i~Cp---~l~~~~~~~y~~~~~~~~v~~~~~~ 134 (216)
.+|.+|...++.+.-. =+|. -|..|-+ .+-|+. |+.-++|| ||--. .++.++
T Consensus 66 v~CrVCq~~I~i~gk~----~QhVVkC~~CnE---ATPIr~aPpGKKYVRCPCNCLLICk--------------~sS~rI 124 (256)
T PF09788_consen 66 VTCRVCQSLIDIEGKM----HQHVVKCSVCNE---ATPIRNAPPGKKYVRCPCNCLLICK--------------SSSQRI 124 (256)
T ss_pred EEeecCCceecccCcc----ceeeEECCCCCc---cccccCCCCCCeeEecCCceEEEee--------------cccccc
Confidence 5899999877654311 1232 3445544 255555 45568898 33211 235678
Q ss_pred ccCcCCCCceeecCC
Q 041841 135 YCPFKDCSALLINDG 149 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~ 149 (216)
-||.++|.++|....
T Consensus 125 aCPRp~CkRiI~L~~ 139 (256)
T PF09788_consen 125 ACPRPNCKRIINLGP 139 (256)
T ss_pred cCCCCCCcceEEeCC
Confidence 999999999997654
No 116
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=57.55 E-value=5.2 Score=35.64 Aligned_cols=44 Identities=20% Similarity=0.434 Sum_probs=32.9
Q ss_pred CCCCcccccCCCC-CCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKST-NELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~-~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
+..|..|.+.+.. ++....++|.|.|...|+..|++. ++ +-.||
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~--~rsCP 409 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NG--TRSCP 409 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CC--CCCCc
Confidence 5689999998753 334455899999999999999942 22 44666
No 117
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=57.37 E-value=4.7 Score=21.13 Aligned_cols=11 Identities=36% Similarity=0.637 Sum_probs=8.4
Q ss_pred ceeCCCCchhc
Q 041841 155 ESKRPYCKRMF 165 (216)
Q Consensus 155 ~~~C~~C~~~f 165 (216)
.+.|+.||+.|
T Consensus 2 l~~C~~CgR~F 12 (25)
T PF13913_consen 2 LVPCPICGRKF 12 (25)
T ss_pred CCcCCCCCCEE
Confidence 35688888877
No 118
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=56.74 E-value=7.7 Score=25.61 Aligned_cols=32 Identities=16% Similarity=0.331 Sum_probs=22.8
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhccc
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCA 167 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 167 (216)
++.|| +|++....-. .....+.|..||...+.
T Consensus 19 ~VkCp--dC~N~q~vFs-hast~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVFS-HASTVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEec-cCceEEEecccccEEEe
Confidence 45799 8998554422 34567999999988764
No 119
>PF04641 Rtf2: Rtf2 RING-finger
Probab=56.07 E-value=12 Score=31.56 Aligned_cols=36 Identities=3% Similarity=0.130 Sum_probs=29.2
Q ss_pred CCCCCCcccccCCCC-CCceeeCCCCCccchHHHHHH
Q 041841 59 KRKRPFSICMEPKST-NELFSIEFCSYSYCTDCIVKY 94 (216)
Q Consensus 59 ~~~~~C~IC~~~~~~-~~~~~~~~C~H~fC~~C~~~y 94 (216)
.+...|||...++.. ..++.+.+|||.|+..++++.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~ 147 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL 147 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh
Confidence 336789999998854 456667899999999999876
No 120
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=55.91 E-value=3.1 Score=40.20 Aligned_cols=20 Identities=15% Similarity=0.272 Sum_probs=11.7
Q ss_pred CCCCccchHHHHHHHHHHhh
Q 041841 81 FCSYSYCTDCIVKYVDSKLR 100 (216)
Q Consensus 81 ~C~H~fC~~C~~~y~~~~i~ 100 (216)
.|+|.+|-.|+..+....+.
T Consensus 120 ~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 120 THVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred hhhhhhhhHHHHHHHHHhhc
Confidence 36666666666665554443
No 121
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=55.01 E-value=9.5 Score=21.96 Aligned_cols=28 Identities=18% Similarity=0.335 Sum_probs=17.8
Q ss_pred cccCcCCCCceeecCCC-CCCCceeCCCCch
Q 041841 134 FYCPFKDCSALLINDGL-KNMKESKRPYCKR 163 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~-~~~~~~~C~~C~~ 163 (216)
..|+ .|+..+..... .....+.||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcC--CCCCEEEEEEecCCCCCCCCCCCCC
Confidence 3577 79986644321 2245678998886
No 122
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=54.95 E-value=8.3 Score=28.23 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=16.2
Q ss_pred CceeCCCCchhc--------cccCCCCCCCC
Q 041841 154 KESKRPYCKRMF--------CAQCKVPWHAG 176 (216)
Q Consensus 154 ~~~~C~~C~~~f--------C~~C~~~~H~~ 176 (216)
..++||+|++.+ |..|+++-+-.
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHCKEPLTLD 98 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcCCCcCccC
Confidence 456777777765 88888876544
No 123
>PLN00209 ribosomal protein S27; Provisional
Probab=54.82 E-value=10 Score=26.33 Aligned_cols=33 Identities=12% Similarity=0.301 Sum_probs=23.2
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhccccC
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQC 169 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C 169 (216)
+.|| +|.+.-..-. .....|.|..||...|--=
T Consensus 37 VkCp--~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PT 69 (86)
T PLN00209 37 VKCQ--GCFNITTVFS-HSQTVVVCGSCQTVLCQPT 69 (86)
T ss_pred EECC--CCCCeeEEEe-cCceEEEccccCCEeeccC
Confidence 5799 8987554322 2356799999999887543
No 124
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=53.57 E-value=11 Score=26.20 Aligned_cols=35 Identities=17% Similarity=0.292 Sum_probs=24.1
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhccccCCC
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKV 171 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 171 (216)
+.|| +|.+.-..-. .....|.|..||...|--=+.
T Consensus 36 VkCp--~C~n~q~VFS-hA~t~V~C~~Cg~~L~~PTGG 70 (85)
T PTZ00083 36 VKCP--GCSQITTVFS-HAQTVVLCGGCSSQLCQPTGG 70 (85)
T ss_pred EECC--CCCCeeEEEe-cCceEEEccccCCEeeccCCC
Confidence 5799 8987554322 235679999999988864333
No 125
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=52.80 E-value=5.7 Score=25.25 Aligned_cols=27 Identities=19% Similarity=0.417 Sum_probs=18.2
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIV 92 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~ 92 (216)
.|..|...... -..++|+|..|..||-
T Consensus 9 ~~~~~~~~~~~---~~~~pCgH~I~~~~f~ 35 (55)
T PF14447_consen 9 PCVFCGFVGTK---GTVLPCGHLICDNCFP 35 (55)
T ss_pred eEEEccccccc---cccccccceeeccccC
Confidence 45555544322 2357999999999985
No 126
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=51.87 E-value=20 Score=19.94 Aligned_cols=26 Identities=19% Similarity=0.483 Sum_probs=20.0
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
.|. +|+..+.+..+ .+.+.|..|+..
T Consensus 3 ~C~--~C~t~L~yP~g--A~~vrCs~C~~v 28 (31)
T TIGR01053 3 VCG--GCRTLLMYPRG--ASSVRCALCQTV 28 (31)
T ss_pred CcC--CCCcEeecCCC--CCeEECCCCCeE
Confidence 566 79999888754 678999988753
No 127
>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=51.38 E-value=11 Score=28.32 Aligned_cols=28 Identities=25% Similarity=0.445 Sum_probs=18.5
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
.+-|| .|+.-+ ++-. ..-++||+||..|
T Consensus 9 Kr~Cp--~cg~kF-YDLn--k~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICP--NTGSKF-YDLN--RRPAVSPYTGEQF 36 (129)
T ss_pred cccCC--CcCccc-cccC--CCCccCCCcCCcc
Confidence 56798 688765 3321 2458899888764
No 128
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=51.17 E-value=14 Score=26.47 Aligned_cols=51 Identities=18% Similarity=0.195 Sum_probs=26.8
Q ss_pred CCCcccCcCCCCceeec-CCCCCCCceeCCCCchhccccCCCCCCCCCChHhHHHhc
Q 041841 131 AEKFYCPFKDCSALLIN-DGLKNMKESKRPYCKRMFCAQCKVPWHAGMRCEKFRKLN 186 (216)
Q Consensus 131 ~~~~~Cp~~~C~~~~~~-~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C~~~~~~~ 186 (216)
+.++.|| .|+..... .-......+.|+.||+.+=.. -.+.-..=+-|.+|.
T Consensus 19 pt~f~CP--~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~---V~~l~epIDVY~~wi 70 (99)
T PRK14892 19 PKIFECP--RCGKVSISVKIKKNIAIITCGNCGLYTEFE---VPSVYDEVDVYNKFI 70 (99)
T ss_pred CcEeECC--CCCCeEeeeecCCCcceEECCCCCCccCEE---CCccccchhhHHHHH
Confidence 5578899 68743221 111134568899898864222 112222335566665
No 129
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=50.89 E-value=8 Score=22.70 Aligned_cols=26 Identities=27% Similarity=0.524 Sum_probs=12.5
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCc
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCK 162 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~ 162 (216)
.|| .|+..+..........-.|+.|+
T Consensus 1 ~CP--~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCP--RCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcC--CCCcccceEEECCEEEEECCCCC
Confidence 367 68776544332223333455444
No 130
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=50.84 E-value=9.9 Score=21.45 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=20.4
Q ss_pred CceeCCCCchhccccCCCCCCCCCC
Q 041841 154 KESKRPYCKRMFCAQCKVPWHAGMR 178 (216)
Q Consensus 154 ~~~~C~~C~~~fC~~C~~~~H~~~~ 178 (216)
..+.|..|+...|..|....|.++.
T Consensus 11 ~~~fC~~~~~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 11 LSLFCETDRALLCVDCDLSVHSGHR 35 (39)
T ss_pred eEEEeCccChhhhhhcChhhcCCCC
Confidence 3578999999999999877687653
No 131
>PF14353 CpXC: CpXC protein
Probab=49.80 E-value=14 Score=27.39 Aligned_cols=13 Identities=23% Similarity=0.439 Sum_probs=8.0
Q ss_pred CCceeCCCCchhc
Q 041841 153 MKESKRPYCKRMF 165 (216)
Q Consensus 153 ~~~~~C~~C~~~f 165 (216)
...++||.||..|
T Consensus 36 l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 36 LFSFTCPSCGHKF 48 (128)
T ss_pred cCEEECCCCCCce
Confidence 3356677777665
No 132
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=49.65 E-value=12 Score=26.66 Aligned_cols=24 Identities=25% Similarity=0.659 Sum_probs=17.6
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
+|| .|++++.... ..+.|+.|++.
T Consensus 2 fC~--~Cg~~l~~~~----~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCP--KCGSLMTPKN----GVYVCPSCGYE 25 (104)
T ss_pred CCc--ccCcccccCC----CeEECcCCCCc
Confidence 688 8999995532 35788888875
No 133
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.64 E-value=5.7 Score=33.99 Aligned_cols=33 Identities=18% Similarity=0.305 Sum_probs=24.6
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
..-|.||-..+... ....|+|.||..|....+.
T Consensus 241 Pf~c~icr~~f~~p---Vvt~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 241 PFKCFICRKYFYRP---VVTKCGHYFCEVCALKPYQ 273 (313)
T ss_pred Cccccccccccccc---hhhcCCceeehhhhccccc
Confidence 35699999987432 2368999999999876554
No 134
>PRK12495 hypothetical protein; Provisional
Probab=49.50 E-value=26 Score=28.81 Aligned_cols=14 Identities=14% Similarity=0.551 Sum_probs=10.9
Q ss_pred CCcccCcCCCCceeec
Q 041841 132 EKFYCPFKDCSALLIN 147 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~ 147 (216)
..++|+ .|+..|..
T Consensus 41 sa~hC~--~CG~PIpa 54 (226)
T PRK12495 41 TNAHCD--ECGDPIFR 54 (226)
T ss_pred chhhcc--cccCcccC
Confidence 357998 89998863
No 135
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=48.93 E-value=3.6 Score=24.04 Aligned_cols=24 Identities=25% Similarity=0.502 Sum_probs=20.7
Q ss_pred CceeCCCCchhccccCCCCCCCCC
Q 041841 154 KESKRPYCKRMFCAQCKVPWHAGM 177 (216)
Q Consensus 154 ~~~~C~~C~~~fC~~C~~~~H~~~ 177 (216)
..+.|..|+..+|..|....|.++
T Consensus 14 ~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 14 LSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp EEEEETTTTEEEEHHHHHTSTTTS
T ss_pred eEEEecCCCCccCccCCCCCCCCC
Confidence 457899999999999998878874
No 136
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.51 E-value=15 Score=25.88 Aligned_cols=17 Identities=12% Similarity=0.683 Sum_probs=15.2
Q ss_pred ccchHHHHHHHHHHhhc
Q 041841 85 SYCTDCIVKYVDSKLRE 101 (216)
Q Consensus 85 ~fC~~C~~~y~~~~i~~ 101 (216)
-||++|+..|+..+-..
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999998876
No 137
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=47.70 E-value=32 Score=30.04 Aligned_cols=34 Identities=24% Similarity=0.707 Sum_probs=25.8
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
...|+||....-..- .+.-=|-.||-.|.-+|+.
T Consensus 300 ~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~ 333 (357)
T KOG0826|consen 300 REVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVV 333 (357)
T ss_pred cccChhHHhccCCCc--eEEecceEEeHHHHHHHHH
Confidence 468999998764322 2334588999999999998
No 138
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=47.54 E-value=16 Score=22.17 Aligned_cols=33 Identities=21% Similarity=0.561 Sum_probs=21.8
Q ss_pred CcccccCCCCCCceeeCCCCC-----ccchHHHHHHHHH
Q 041841 64 FSICMEPKSTNELFSIEFCSY-----SYCTDCIVKYVDS 97 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H-----~fC~~C~~~y~~~ 97 (216)
|-||+++...++.+ ..+|.. ....+|+.+++..
T Consensus 1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHh
Confidence 66899887655522 245553 5788999999997
No 139
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=47.45 E-value=13 Score=28.08 Aligned_cols=24 Identities=29% Similarity=0.574 Sum_probs=17.6
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
..|| .|+..++... -.+.||.|++
T Consensus 29 ~hCp--~Cg~PLF~Kd----G~v~CPvC~~ 52 (131)
T COG1645 29 KHCP--KCGTPLFRKD----GEVFCPVCGY 52 (131)
T ss_pred hhCc--ccCCcceeeC----CeEECCCCCc
Confidence 5799 7998876643 2578888885
No 140
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=47.38 E-value=17 Score=20.37 Aligned_cols=23 Identities=17% Similarity=0.286 Sum_probs=14.6
Q ss_pred CCCceeecCCCCCCCceeCCCCchhc
Q 041841 140 DCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 140 ~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
+|+..+.... ...+.|+.||..+
T Consensus 5 ~Cg~~~~~~~---~~~irC~~CG~RI 27 (32)
T PF03604_consen 5 ECGAEVELKP---GDPIRCPECGHRI 27 (32)
T ss_dssp SSSSSE-BST---SSTSSBSSSS-SE
T ss_pred cCCCeeEcCC---CCcEECCcCCCeE
Confidence 7888776443 3457899998753
No 141
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=46.96 E-value=9.5 Score=33.20 Aligned_cols=37 Identities=24% Similarity=0.530 Sum_probs=28.7
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHh
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKL 99 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i 99 (216)
..|-.|.++......++...|.+.||.+|=. |+...+
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv-~iHesL 367 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNVFCLDCDV-FIHESL 367 (378)
T ss_pred cceeeeccccCCCCcEEchhccceeeccchH-HHHhhh
Confidence 4599998887777778888999999999964 444444
No 142
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.46 E-value=8.7 Score=32.94 Aligned_cols=29 Identities=28% Similarity=0.572 Sum_probs=20.7
Q ss_pred CCCcccccCCCCCCceeeCCCCCc-cchHHHHH
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYS-YCTDCIVK 93 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~-fC~~C~~~ 93 (216)
.-|.||||.- -+.+ ++.|||. .|..|=+.
T Consensus 301 ~LC~ICmDaP--~DCv-fLeCGHmVtCt~CGkr 330 (350)
T KOG4275|consen 301 RLCAICMDAP--RDCV-FLECGHMVTCTKCGKR 330 (350)
T ss_pred HHHHHHhcCC--cceE-EeecCcEEeehhhccc
Confidence 4699999853 3333 5799995 78888543
No 143
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=46.16 E-value=26 Score=26.63 Aligned_cols=73 Identities=16% Similarity=0.271 Sum_probs=35.5
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhc--ccc-CCC--CCCCC--CChHhHHHhcccCCChhHHHHHHHHhcC-
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMF--CAQ-CKV--PWHAG--MRCEKFRKLNKNEKNSEDMELIKLAEEK- 204 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f--C~~-C~~--~~H~~--~~C~~~~~~~~~e~~~~d~~~~~~~~~~- 204 (216)
++-|| .|+.++.+. . .-.||.|...- =|. .+. .-|.+ .+=.++..-. +-....+..|+++.
T Consensus 3 l~nC~--~CgklF~~~-~----~~iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~t----gVs~~~I~~~IreGR 71 (137)
T TIGR03826 3 LANCP--KCGRLFVKT-G----RDVCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEET----GVSEKLILKFIREGR 71 (137)
T ss_pred Ccccc--ccchhhhhc-C----CccCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH----CcCHHHHHHHHHcCC
Confidence 45687 788887552 1 12366555310 000 000 01444 4444443322 12233455666542
Q ss_pred --------CceecCCCCccC
Q 041841 205 --------KWKRCPHCNYSV 216 (216)
Q Consensus 205 --------~~k~CP~C~~~I 216 (216)
..-+|.+|+.+|
T Consensus 72 L~~~~~~nl~~~CE~CG~~I 91 (137)
T TIGR03826 72 LQLKHFPNLGYPCERCGTSI 91 (137)
T ss_pred eeccCCCCCcCcccccCCcC
Confidence 236899999887
No 144
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=45.89 E-value=22 Score=22.08 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=22.2
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVKY 94 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y 94 (216)
.|+||..+......+. +.=| ..|.+|++..
T Consensus 1 ~C~iCg~kigl~~~~k-~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK-IKDG-YICKDCLKKL 30 (51)
T ss_pred CCCcccccccccccee-ccCc-cchHHHHHHh
Confidence 4899999887644444 3556 7999999875
No 145
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=45.08 E-value=38 Score=29.76 Aligned_cols=32 Identities=25% Similarity=0.556 Sum_probs=24.1
Q ss_pred CCCcccccCCCCCC-ceeeCCCCCccchHHHHH
Q 041841 62 RPFSICMEPKSTNE-LFSIEFCSYSYCTDCIVK 93 (216)
Q Consensus 62 ~~C~IC~~~~~~~~-~~~~~~C~H~fC~~C~~~ 93 (216)
.-|+.|+++.+..+ .|.-..||-+.|+-||..
T Consensus 15 d~cplcie~mditdknf~pc~cgy~ic~fc~~~ 47 (480)
T COG5175 15 DYCPLCIEPMDITDKNFFPCPCGYQICQFCYNN 47 (480)
T ss_pred ccCcccccccccccCCcccCCcccHHHHHHHHH
Confidence 35999999987654 232368999999999964
No 146
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.02 E-value=28 Score=26.29 Aligned_cols=36 Identities=28% Similarity=0.404 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHHHHhhh-cC--------CCCcccCcCCCCceeecC
Q 041841 111 VPKEVSDRWGNALCEGVI-NG--------AEKFYCPFKDCSALLIND 148 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~v-~~--------~~~~~Cp~~~C~~~~~~~ 148 (216)
+.++.++.....+.+..+ .. +...+|+ +|+..+...
T Consensus 39 V~pe~L~fafe~l~~gt~~ega~L~i~~~p~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 39 VDKEIVEFALNELLKGTILEGAEIIFEEEEAVLKCR--NCGNEWSLK 83 (135)
T ss_pred hhHHHHHHHHHHHHcCCcccCCEEEEEecceEEECC--CCCCEEecc
Confidence 355555554444444322 11 2356898 899877664
No 147
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=44.77 E-value=51 Score=24.09 Aligned_cols=36 Identities=19% Similarity=0.289 Sum_probs=24.6
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCC
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVP 172 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 172 (216)
+...|. -|+..+..- ......|..|+..+|..|+..
T Consensus 53 ~~~~C~--~C~~~fg~l---~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCA--RCGKPFGFL---FNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-T--TTS-BCSCT---STTCEEETTTTEEEETTSEEE
T ss_pred CCcchh--hhCCccccc---CCCCCcCCcCCccccCccCCc
Confidence 345777 677655332 234589999999999999985
No 148
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=44.71 E-value=15 Score=30.63 Aligned_cols=53 Identities=21% Similarity=0.292 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHh-hhc-CC-CCcccCcCCCCceeecCCC----CCCCceeCCCCchh
Q 041841 110 IVPKEVSDRWGNALCEG-VIN-GA-EKFYCPFKDCSALLINDGL----KNMKESKRPYCKRM 164 (216)
Q Consensus 110 ~l~~~~~~~y~~~~~~~-~v~-~~-~~~~Cp~~~C~~~~~~~~~----~~~~~~~C~~C~~~ 164 (216)
-++++++..|.+..... -+- .+ ...-|- +|...+..... .....+.||+||+.
T Consensus 171 ~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 171 KLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred hcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 46899999999877664 221 11 234676 78877754321 13456899999863
No 149
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=44.49 E-value=16 Score=20.99 Aligned_cols=28 Identities=18% Similarity=0.265 Sum_probs=16.7
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+.|| .|+.++............|..||.
T Consensus 2 r~C~--~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICP--KCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEET--TTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcC--CCCCccccccCCCCCCCccCCCCC
Confidence 3466 688887665433344467777764
No 150
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.19 E-value=13 Score=31.76 Aligned_cols=44 Identities=16% Similarity=0.463 Sum_probs=31.1
Q ss_pred CCCCcccccCCCCCCceeeCCCC----CccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCS----YSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~----H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..-|.+|-+-.....++ .|- |.||..|-++.|+.+=..| .+-||
T Consensus 268 pLcCTLC~ERLEDTHFV---QCPSVp~HKFCFPCSResIK~Qg~sg--evYCP 315 (352)
T KOG3579|consen 268 PLCCTLCHERLEDTHFV---QCPSVPSHKFCFPCSRESIKQQGASG--EVYCP 315 (352)
T ss_pred ceeehhhhhhhccCcee---ecCCCcccceecccCHHHHHhhcCCC--ceeCC
Confidence 35689999876554433 454 9999999999888765555 45555
No 151
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=43.79 E-value=18 Score=35.07 Aligned_cols=58 Identities=19% Similarity=0.404 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHHh-----hhcCCC------------CcccCcCCCCceeecCCCCCCCceeCCCCchh-----cccc
Q 041841 111 VPKEVSDRWGNALCEG-----VINGAE------------KFYCPFKDCSALLINDGLKNMKESKRPYCKRM-----FCAQ 168 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~-----~v~~~~------------~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~-----fC~~ 168 (216)
+++.+++...+.+... +++... ..-|| +|+..+..+.. .....|..||+. .|..
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp--~Cd~~lt~H~~--~~~L~CH~Cg~~~~~p~~Cp~ 480 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECP--NCDSPLTLHKA--TGQLRCHYCGYQEPIPQSCPE 480 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCC--CCCcceEEecC--CCeeEeCCCCCCCCCCCCCCC
Confidence 5677777776655442 112111 22455 67777666543 467899999987 7999
Q ss_pred CCCC
Q 041841 169 CKVP 172 (216)
Q Consensus 169 C~~~ 172 (216)
|+..
T Consensus 481 Cgs~ 484 (730)
T COG1198 481 CGSE 484 (730)
T ss_pred CCCC
Confidence 9887
No 152
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.63 E-value=7.5 Score=35.72 Aligned_cols=33 Identities=27% Similarity=0.673 Sum_probs=22.5
Q ss_pred CCchhccccCCCCCCCCCChHhHHHhcccCCChhHHHHHHHHhcCCceecCCCCccC
Q 041841 160 YCKRMFCAQCKVPWHAGMRCEKFRKLNKNEKNSEDMELIKLAEEKKWKRCPHCNYSV 216 (216)
Q Consensus 160 ~C~~~fC~~C~~~~H~~~~C~~~~~~~~~e~~~~d~~~~~~~~~~~~k~CP~C~~~I 216 (216)
.||+.||+.|- ++-|.. .+...++.||-|...|
T Consensus 203 ~CGHiFC~~Ci-----------Lqy~~~-------------s~~~~~~~CPiC~s~I 235 (513)
T KOG2164|consen 203 NCGHIFCGPCI-----------LQYWNY-------------SAIKGPCSCPICRSTI 235 (513)
T ss_pred ccCceeeHHHH-----------HHHHhh-------------hcccCCccCCchhhhc
Confidence 49999999873 333331 1234889999998765
No 153
>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=43.17 E-value=14 Score=24.03 Aligned_cols=33 Identities=18% Similarity=0.422 Sum_probs=17.6
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCC
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKV 171 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 171 (216)
...|+ .|+..+.. ..+.-.|..||..||..|..
T Consensus 9 ~~~C~--~C~~~F~~----~~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 9 ASNCM--ICGKKFSL----FRRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp -SB-T--TT--B-BS----SS-EEE-TTT--EEECCCS-
T ss_pred CCcCc--CcCCcCCC----ceeeEccCCCCCEECCchhC
Confidence 45677 58877733 25678999999999999975
No 154
>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=43.02 E-value=8.8 Score=23.88 Aligned_cols=36 Identities=14% Similarity=0.341 Sum_probs=25.1
Q ss_pred CCCcccccCCCCCC-ceeeCCCCCccchHHHHHHHHH
Q 041841 62 RPFSICMEPKSTNE-LFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 62 ~~C~IC~~~~~~~~-~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..|.+|-..+.... -..-..||+.||.+|+......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 46888887665421 1234689999999999877554
No 155
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=42.32 E-value=8.9 Score=23.95 Aligned_cols=30 Identities=33% Similarity=0.522 Sum_probs=17.6
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
+.|+ .|+..+...+....-.+.||.|+...
T Consensus 5 iRC~--~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 5 IRCG--HCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred eecc--chhHHHhhhcCccEEEEECCCCCccc
Confidence 3566 67776655332223457788777653
No 156
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=41.94 E-value=16 Score=35.00 Aligned_cols=31 Identities=23% Similarity=0.643 Sum_probs=21.0
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh------ccccCCCCC
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM------FCAQCKVPW 173 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~------fC~~C~~~~ 173 (216)
.++|| .|+..+.. ..|+.||.. ||..|+.+-
T Consensus 15 akFC~--~CG~~l~~--------~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 15 NRFCQ--KCGTSLTH--------KPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred Ccccc--ccCCCCCC--------CcCCCCCCCCCcccccccccCCcc
Confidence 56777 67665521 358888877 888888753
No 157
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.71 E-value=31 Score=20.77 Aligned_cols=23 Identities=9% Similarity=0.069 Sum_probs=15.4
Q ss_pred CCCceeecCCCCCCCceeCCCCchhc
Q 041841 140 DCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 140 ~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
+|+.-+.... ...+.|+.||...
T Consensus 7 ~Cg~~~~~~~---~~~irC~~CG~rI 29 (44)
T smart00659 7 ECGRENEIKS---KDVVRCRECGYRI 29 (44)
T ss_pred CCCCEeecCC---CCceECCCCCceE
Confidence 6887665542 3558898888653
No 158
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.43 E-value=40 Score=31.21 Aligned_cols=33 Identities=27% Similarity=0.632 Sum_probs=24.1
Q ss_pred cCcCCCCceeecCCCCCCCceeCCCCchh-----ccccCCCC
Q 041841 136 CPFKDCSALLINDGLKNMKESKRPYCKRM-----FCAQCKVP 172 (216)
Q Consensus 136 Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~-----fC~~C~~~ 172 (216)
|| .|+..+.++.. .....|+.||+. .|..|+..
T Consensus 225 C~--~C~~~l~~h~~--~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 225 CP--NCDVSLTYHKK--EGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CC--CCCCceEEecC--CCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 66 67776666532 457899999987 59999874
No 159
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.18 E-value=32 Score=21.51 Aligned_cols=19 Identities=16% Similarity=0.464 Sum_probs=13.3
Q ss_pred HHHHhcCCceecCCCCccC
Q 041841 198 IKLAEEKKWKRCPHCNYSV 216 (216)
Q Consensus 198 ~~~~~~~~~k~CP~C~~~I 216 (216)
.++.+....-.||.|++.+
T Consensus 38 ~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 38 NEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred HHHHcCCCeEECcCCCccC
Confidence 3444445789999999864
No 160
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=40.17 E-value=21 Score=20.84 Aligned_cols=18 Identities=28% Similarity=0.728 Sum_probs=14.8
Q ss_pred ceeCCCCchhccccCCCC
Q 041841 155 ESKRPYCKRMFCAQCKVP 172 (216)
Q Consensus 155 ~~~C~~C~~~fC~~C~~~ 172 (216)
.+.|..|+..||..-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 478999999999986653
No 161
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=39.29 E-value=35 Score=30.12 Aligned_cols=30 Identities=20% Similarity=0.423 Sum_probs=23.6
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVK 93 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~ 93 (216)
...|.||.....- ..+++|+|..|.-|--+
T Consensus 61 n~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~R 90 (493)
T COG5236 61 NMNCQICAGSTTY---SARYPCGHQICHACAVR 90 (493)
T ss_pred cceeEEecCCceE---EEeccCCchHHHHHHHH
Confidence 5689999986542 34689999999999755
No 162
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=39.20 E-value=28 Score=18.19 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=12.8
Q ss_pred CCCceeecCCCCCCCceeCCCCch
Q 041841 140 DCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 140 ~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
.|+..+... .....+.||+||.
T Consensus 3 sC~~~i~~r--~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 3 SCGRPIAPR--EQAVPFPCPNCGF 24 (24)
T ss_pred cCCCcccCc--ccCceEeCCCCCC
Confidence 455555332 2245678998873
No 163
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=39.19 E-value=15 Score=23.74 Aligned_cols=37 Identities=22% Similarity=0.386 Sum_probs=25.5
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCCC
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVPW 173 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 173 (216)
-|| -|..-......+....-.|..|+...|..|+...
T Consensus 4 ~CP--lCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 4 LCP--LCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred cCC--cccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 466 5665543333344566789999999999999743
No 164
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=38.61 E-value=26 Score=31.42 Aligned_cols=33 Identities=21% Similarity=0.514 Sum_probs=25.9
Q ss_pred CCCcccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 131 AEKFYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 131 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
....-|| +|+..+.....+....+.||.||+..
T Consensus 16 ~~~~~C~--eCd~~~~~P~l~~~q~A~CPRC~~~l 48 (418)
T COG2995 16 GHLILCP--ECDMLVSLPRLDSGQSAYCPRCGHTL 48 (418)
T ss_pred cceecCC--CCCceeccccCCCCCcccCCCCCCcc
Confidence 3467899 89988877766667789999999764
No 165
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=38.45 E-value=10 Score=32.88 Aligned_cols=70 Identities=20% Similarity=0.445 Sum_probs=43.4
Q ss_pred cccccc------CCCHHHHHHHHHHHH-HhhhcCCC-----CcccCcCCCCceeecCCC------CCCCceeCCCCchhc
Q 041841 104 TSIRCP------IVPKEVSDRWGNALC-EGVINGAE-----KFYCPFKDCSALLINDGL------KNMKESKRPYCKRMF 165 (216)
Q Consensus 104 ~~i~Cp------~l~~~~~~~y~~~~~-~~~v~~~~-----~~~Cp~~~C~~~~~~~~~------~~~~~~~C~~C~~~f 165 (216)
.||.|| +++..+...|..+.- +.+++.+. ...|- .|+..+..... .....-.|+.|+..|
T Consensus 321 LPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf--~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~F 398 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCF--VCQGPFPKPPVSPFDESTSSGRYQCELCKSTF 398 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccce--eccCCCCCCCCCcccccccccceechhhhhhh
Confidence 589999 567777777877643 23333221 23454 46665544321 123347899999999
Q ss_pred cccCCCCCCC
Q 041841 166 CAQCKVPWHA 175 (216)
Q Consensus 166 C~~C~~~~H~ 175 (216)
|..|.+-.|+
T Consensus 399 C~dCdvfiHe 408 (421)
T COG5151 399 CSDCDVFIHE 408 (421)
T ss_pred hhhhHHHHHH
Confidence 9998876664
No 166
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.28 E-value=8.5 Score=36.50 Aligned_cols=35 Identities=17% Similarity=0.328 Sum_probs=25.2
Q ss_pred CCCcccccCCCCCCc-eeeCCCCCccchHHHHHHHH
Q 041841 62 RPFSICMEPKSTNEL-FSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~-~~~~~C~H~fC~~C~~~y~~ 96 (216)
.-|+||+..+-.+.+ ...+.|||+.|+.|++....
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN 47 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh
Confidence 368999877654332 23479999999999976443
No 167
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=38.06 E-value=81 Score=18.69 Aligned_cols=24 Identities=29% Similarity=0.501 Sum_probs=15.9
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCc
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCK 162 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~ 162 (216)
..|| .|+..+..+. ...+.|+.|+
T Consensus 18 ~~Cp--~C~~PL~~~k---~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCP--DCGTPLMRDK---DGKIYCVSCG 41 (41)
T ss_pred CccC--CCCCeeEEec---CCCEECCCCC
Confidence 4799 7988876632 2346777664
No 168
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=37.92 E-value=12 Score=31.20 Aligned_cols=43 Identities=19% Similarity=0.547 Sum_probs=30.8
Q ss_pred CCCCcccccCCCCC-Cc--eeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTN-EL--FSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~-~~--~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..-||||-.+.-.+ ++ +....|-|+.|-+|+-+.++. .|..||
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~------GpAqCP 55 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR------GPAQCP 55 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC------CCCCCC
Confidence 34799999886443 32 223459999999999887763 367888
No 169
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=37.07 E-value=24 Score=25.66 Aligned_cols=25 Identities=20% Similarity=0.386 Sum_probs=16.3
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
-|| .|+.-+-+.. .....||.|++.
T Consensus 4 ~CP--~C~seytY~d---g~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCP--KCNSEYTYHD---GTQLICPSCLYE 28 (109)
T ss_pred cCC--cCCCcceEec---CCeeECcccccc
Confidence 477 6777665643 345788877764
No 170
>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=36.60 E-value=16 Score=21.82 Aligned_cols=35 Identities=23% Similarity=0.406 Sum_probs=16.9
Q ss_pred CcccccCCCCCCceeeCCCCCccchHHHHHHHHHH
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSK 98 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~ 98 (216)
|.+|-+-......=....|+=.+...|++.|+...
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~ 35 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHR 35 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcC
Confidence 45666654433322224688889999999998853
No 171
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=36.33 E-value=15 Score=31.82 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=20.5
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHHH
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVKY 94 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y 94 (216)
-|.-|--.+..- -++..|.|.||.+|-+..
T Consensus 92 fCd~Cd~PI~IY--GRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 92 FCDRCDFPIAIY--GRMIPCKHVFCLECARSD 121 (389)
T ss_pred eecccCCcceee--ecccccchhhhhhhhhcC
Confidence 467676554321 236799999999998753
No 172
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=36.10 E-value=32 Score=22.21 Aligned_cols=32 Identities=19% Similarity=0.389 Sum_probs=21.6
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhccc
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCA 167 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 167 (216)
.+.|| +|++....-. .....+.|..||...+.
T Consensus 11 ~VkCp--~C~n~q~vFs-ha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 11 KVKCP--DCGNEQVVFS-HASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEECC--CCCCeEEEEe-cCCcEEECcccCCCccc
Confidence 35798 8988554322 23567899999987653
No 173
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=36.09 E-value=28 Score=30.04 Aligned_cols=40 Identities=20% Similarity=0.594 Sum_probs=26.4
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
.-|+.|-.-.. +. .....|+|.||.+|+..-|. + ..+.||
T Consensus 275 LkCplc~~Llr-np-~kT~cC~~~fc~eci~~al~----d--sDf~Cp 314 (427)
T COG5222 275 LKCPLCHCLLR-NP-MKTPCCGHTFCDECIGTALL----D--SDFKCP 314 (427)
T ss_pred ccCcchhhhhh-Cc-ccCccccchHHHHHHhhhhh----h--ccccCC
Confidence 56888875432 22 22368999999999975443 3 346788
No 174
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=35.87 E-value=21 Score=25.81 Aligned_cols=19 Identities=16% Similarity=0.709 Sum_probs=16.9
Q ss_pred CCCCCccchHHHHHHHHHH
Q 041841 80 EFCSYSYCTDCIVKYVDSK 98 (216)
Q Consensus 80 ~~C~H~fC~~C~~~y~~~~ 98 (216)
-.|+|.|..-|+.++|+++
T Consensus 79 G~CNHaFH~hCisrWlktr 97 (114)
T KOG2930|consen 79 GVCNHAFHFHCISRWLKTR 97 (114)
T ss_pred eecchHHHHHHHHHHHhhc
Confidence 4799999999999999963
No 175
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=35.80 E-value=21 Score=21.05 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=13.4
Q ss_pred ccCcCCCCcee-ecCCCCCCCceeCCCCchh
Q 041841 135 YCPFKDCSALL-INDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 135 ~Cp~~~C~~~~-~~~~~~~~~~~~C~~C~~~ 164 (216)
.|| .|+.-. ..+ .....+.|+.||..
T Consensus 2 ~Cp--~Cg~~~~~~D--~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCP--NCGSKEIVFD--PERGELVCPNCGLV 28 (43)
T ss_dssp SBT--TTSSSEEEEE--TTTTEEEETTT-BB
T ss_pred CCc--CCcCCceEEc--CCCCeEECCCCCCE
Confidence 477 576643 222 22345678777753
No 176
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.66 E-value=24 Score=25.79 Aligned_cols=48 Identities=17% Similarity=0.410 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHHhhh-cC--------CCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 111 VPKEVSDRWGNALCEGVI-NG--------AEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~v-~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+.++.++-.-..+.+..+ +. +...||+ +|+..+..... ....||.||.
T Consensus 39 V~p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~--~Cg~~~~~~~~---~~~~CP~Cgs 95 (114)
T PRK03681 39 VETSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCE--TCQQYVTLLTQ---RVRRCPQCHG 95 (114)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCeeecCCc---cCCcCcCcCC
Confidence 456666654444444322 11 2356898 89987755321 2356888874
No 177
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=35.59 E-value=33 Score=21.88 Aligned_cols=26 Identities=19% Similarity=0.480 Sum_probs=17.4
Q ss_pred cCCCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 129 NGAEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 129 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
..+++..|| .|+.+... ...|+.||+
T Consensus 23 ~~~~l~~C~--~CG~~~~~-------H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECP--NCGEPKLP-------HRVCPSCGY 48 (57)
T ss_pred cCCcceECC--CCCCccCC-------eEECCCCCc
Confidence 345577788 78877633 466887875
No 178
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=35.54 E-value=25 Score=22.85 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=19.3
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
...|| .|+..... ....+...|+.||..
T Consensus 28 Sq~C~--~CG~~~~~--~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCP--RCGHRNKK--RRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCcc--Cccccccc--ccccceEEcCCCCCE
Confidence 45788 78888755 233567888887763
No 179
>smart00336 BBOX B-Box-type zinc finger.
Probab=35.51 E-value=28 Score=19.82 Aligned_cols=23 Identities=26% Similarity=0.499 Sum_probs=19.0
Q ss_pred ceeCCCCchhccccCCCCCCCCC
Q 041841 155 ESKRPYCKRMFCAQCKVPWHAGM 177 (216)
Q Consensus 155 ~~~C~~C~~~fC~~C~~~~H~~~ 177 (216)
.+.|..|....|..|....|.++
T Consensus 15 ~~~C~~c~~~iC~~C~~~~H~~H 37 (42)
T smart00336 15 EFFCEECGALLCRTCDEAEHRGH 37 (42)
T ss_pred EEECCCCCcccccccChhhcCCC
Confidence 57799999999999987777654
No 180
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=34.43 E-value=20 Score=19.79 Aligned_cols=26 Identities=19% Similarity=0.418 Sum_probs=11.7
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
.|| .|+.-.-+. +...+.|+.|+..+
T Consensus 4 ~Cp--~C~se~~y~---D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCP--LCGSEYTYE---DGELLVCPECGHEW 29 (30)
T ss_dssp --T--TT-----EE----SSSEEETTTTEEE
T ss_pred CCC--CCCCcceec---cCCEEeCCcccccC
Confidence 366 566555443 24568898888653
No 182
>PRK10220 hypothetical protein; Provisional
Probab=34.19 E-value=33 Score=24.98 Aligned_cols=25 Identities=20% Similarity=0.428 Sum_probs=16.2
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
-|| .|+.-+-+.. .....||.|++.
T Consensus 5 ~CP--~C~seytY~d---~~~~vCpeC~hE 29 (111)
T PRK10220 5 HCP--KCNSEYTYED---NGMYICPECAHE 29 (111)
T ss_pred cCC--CCCCcceEcC---CCeEECCcccCc
Confidence 477 6777665643 345788877764
No 183
>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=34.16 E-value=27 Score=25.57 Aligned_cols=47 Identities=21% Similarity=0.297 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHHHhhh-cC--------CCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 111 VPKEVSDRWGNALCEGVI-NG--------AEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~v-~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+.++.++-.-..+.+..+ +. +...+|+ +|+..+.... ....||.||.
T Consensus 39 V~p~~L~faf~~~~~~t~~ega~L~I~~~p~~~~C~--~Cg~~~~~~~----~~~~CP~Cgs 94 (115)
T TIGR00100 39 VNPSQLQFAFEVVREGTVAEGAKLNIEDEPVECECE--DCSEEVSPEI----DLYRCPKCHG 94 (115)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC----cCccCcCCcC
Confidence 466666554444443222 11 2356888 7988775542 2356888874
No 184
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.89 E-value=17 Score=25.54 Aligned_cols=21 Identities=33% Similarity=0.630 Sum_probs=10.5
Q ss_pred CCCceeecCCCCCCCceeCCCCc
Q 041841 140 DCSALLINDGLKNMKESKRPYCK 162 (216)
Q Consensus 140 ~C~~~~~~~~~~~~~~~~C~~C~ 162 (216)
+||+.+..+.. .....||.|.
T Consensus 63 kCGfef~~~~i--k~pSRCP~CK 83 (97)
T COG3357 63 KCGFEFRDDKI--KKPSRCPKCK 83 (97)
T ss_pred ccCcccccccc--CCcccCCcch
Confidence 67777644321 2234566554
No 185
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=33.68 E-value=14 Score=22.63 Aligned_cols=17 Identities=29% Similarity=0.680 Sum_probs=14.0
Q ss_pred hccccCCCCCCCCCChH
Q 041841 164 MFCAQCKVPWHAGMRCE 180 (216)
Q Consensus 164 ~fC~~C~~~~H~~~~C~ 180 (216)
.||+.|+...|....|.
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 68999999889877774
No 186
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=32.90 E-value=33 Score=30.85 Aligned_cols=30 Identities=17% Similarity=0.490 Sum_probs=21.5
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
..-|| .|+..+..........+.|+.||..
T Consensus 13 ~~~C~--~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 13 HILCS--QCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred eeeCC--CCCCcccccCCCCCCeeECCCCCCC
Confidence 45688 8999887765555566778888764
No 187
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.90 E-value=46 Score=29.77 Aligned_cols=65 Identities=17% Similarity=0.191 Sum_probs=38.1
Q ss_pred CCCCceecccCCCCCcCCCCCCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCccccccC
Q 041841 41 DDDDLHVLNFLPNDTHFGKRKRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCPI 110 (216)
Q Consensus 41 ~~~~l~~~~~~p~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp~ 110 (216)
+-|.|.+.-..+..- .-.+-..|||=-+.-..++-.-.+.|||..+++=+.+... +|...++||.
T Consensus 315 ~~deLPveIeL~~~~-~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCPY 379 (394)
T KOG2817|consen 315 TKDELPVEIELGKEY-HFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCPY 379 (394)
T ss_pred ccccCccceeccccc-cccceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCCC
Confidence 334555444444322 1122568988665554444444579999999988765443 3544678883
No 188
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=31.57 E-value=41 Score=21.39 Aligned_cols=32 Identities=16% Similarity=0.307 Sum_probs=18.6
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchhcccc
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQ 168 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~ 168 (216)
+.|| +|.+.-..=. .....+.|..|+...|.-
T Consensus 8 VkCp--~C~~~q~vFS-ha~t~V~C~~Cg~~L~~P 39 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFS-HAQTVVKCVVCGTVLAQP 39 (55)
T ss_dssp EE-T--TT-SEEEEET-T-SS-EE-SSSTSEEEEE
T ss_pred EECC--CCCCeeEEEe-cCCeEEEcccCCCEecCC
Confidence 5788 8987554422 345679999999988754
No 189
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=31.40 E-value=58 Score=20.84 Aligned_cols=24 Identities=25% Similarity=0.546 Sum_probs=14.7
Q ss_pred CcccccCCCCCCceeeCCCCCccchH
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTD 89 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~ 89 (216)
|..|... ..+++.-+.|++.+|..
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETT
T ss_pred CCCCCCc--CCceEEeCCCCcccccC
Confidence 4556644 34556668899999983
No 191
>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=30.98 E-value=37 Score=19.99 Aligned_cols=27 Identities=15% Similarity=0.320 Sum_probs=16.2
Q ss_pred ccCcCCCCceeecC-CCCCCCceeCCCCch
Q 041841 135 YCPFKDCSALLIND-GLKNMKESKRPYCKR 163 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~-~~~~~~~~~C~~C~~ 163 (216)
.|+ +|+..+... .......+.||.||.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCE--ECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeC--CCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 466 788655333 122245678888886
No 192
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.95 E-value=41 Score=26.11 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=9.4
Q ss_pred ceeCCCCchhccc
Q 041841 155 ESKRPYCKRMFCA 167 (216)
Q Consensus 155 ~~~C~~C~~~fC~ 167 (216)
.-.|+.||..|=.
T Consensus 28 ~~~c~~c~~~f~~ 40 (154)
T PRK00464 28 RRECLACGKRFTT 40 (154)
T ss_pred eeeccccCCcceE
Confidence 3678888887743
No 193
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.87 E-value=32 Score=25.06 Aligned_cols=47 Identities=21% Similarity=0.484 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHHHhhh-cC--------CCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 111 VPKEVSDRWGNALCEGVI-NG--------AEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~v-~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+.++.++-+-..+.+..+ +. +...+|+ +|+..+.... ....||.||.
T Consensus 39 v~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~--~Cg~~~~~~~----~~~~CP~Cgs 94 (113)
T PRK12380 39 VEESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCW--DCSQVVEIHQ----HDAQCPHCHG 94 (113)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCC----cCccCcCCCC
Confidence 456666554444444322 11 2356888 7887775532 2345888874
No 194
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=30.75 E-value=25 Score=31.94 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=25.5
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~ 97 (216)
..-|+||..-+.. ..++.|+|..|+-|.+..+..
T Consensus 4 elkc~vc~~f~~e---piil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 4 ELKCPVCGSFYRE---PIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred cccCceehhhccC---ceEeecccHHHHHHHHhhccc
Confidence 4569999976643 235799999999999865543
No 195
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.29 E-value=69 Score=24.04 Aligned_cols=31 Identities=29% Similarity=0.453 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHHHHhhhcCCCCcccCcCCCCceeecC
Q 041841 111 VPKEVSDRWGNALCEGVINGAEKFYCPFKDCSALLIND 148 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~v~~~~~~~Cp~~~C~~~~~~~ 148 (216)
.++++.+.|-..--+..+ ..|| .|+..+..+
T Consensus 22 q~pel~eafcskcgeati-----~qcp--~csasirgd 52 (160)
T COG4306 22 QSPELMEAFCSKCGEATI-----TQCP--ICSASIRGD 52 (160)
T ss_pred CCHHHHHHHHhhhchHHH-----hcCC--ccCCccccc
Confidence 367888888766555444 4687 788777554
No 196
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=30.27 E-value=24 Score=19.94 Aligned_cols=12 Identities=33% Similarity=1.010 Sum_probs=8.1
Q ss_pred CceecCCCCccC
Q 041841 205 KWKRCPHCNYSV 216 (216)
Q Consensus 205 ~~k~CP~C~~~I 216 (216)
.+-.||+|+..|
T Consensus 3 ~~~~C~nC~R~v 14 (33)
T PF08209_consen 3 PYVECPNCGRPV 14 (33)
T ss_dssp -EEE-TTTSSEE
T ss_pred CeEECCCCcCCc
Confidence 457899999875
No 197
>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=30.00 E-value=28 Score=18.08 Aligned_cols=12 Identities=50% Similarity=0.996 Sum_probs=8.3
Q ss_pred CceeCCCCchhc
Q 041841 154 KESKRPYCKRMF 165 (216)
Q Consensus 154 ~~~~C~~C~~~f 165 (216)
+...|+.|++.|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 446788887765
No 198
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=29.98 E-value=52 Score=20.55 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=17.8
Q ss_pred CCcccCcCCCCceeecCC--------CCCCCceeCCCCchhc
Q 041841 132 EKFYCPFKDCSALLINDG--------LKNMKESKRPYCKRMF 165 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~--------~~~~~~~~C~~C~~~f 165 (216)
+.+.||+|+|-.-- ... ........|..|++.+
T Consensus 5 gvl~C~Np~CITn~-~E~v~~~F~v~~~~~~~~rC~YCe~~~ 45 (52)
T PF02748_consen 5 GVLKCPNPNCITNS-NEPVESRFYVIDKEPIKLRCHYCERII 45 (52)
T ss_dssp SSSE-SSTTBTTT--TSSS--EEEEEETTTCEEEETTT--EE
T ss_pred eEEEcCCCCcccCC-CCCCCceEEEEeCCCCEEEeeCCCCEe
Confidence 35789999996541 111 1234567898888653
No 199
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=29.82 E-value=45 Score=30.21 Aligned_cols=30 Identities=23% Similarity=0.586 Sum_probs=21.1
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
..-|| .|+..+..........+.|+.||..
T Consensus 10 ~~~C~--~Cd~l~~~~~l~~g~~a~CpRCg~~ 39 (419)
T PRK15103 10 HILCP--QCDMLVALPRLEHGQKAACPRCGTT 39 (419)
T ss_pred cccCC--CCCceeecCCCCCCCeeECCCCCCC
Confidence 45588 8999987765444556778877764
No 200
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=29.76 E-value=20 Score=35.86 Aligned_cols=40 Identities=20% Similarity=0.404 Sum_probs=28.4
Q ss_pred CCCCcccccCCCC-CCc---eeeCCCCCccchHHHHHHHHHHhh
Q 041841 61 KRPFSICMEPKST-NEL---FSIEFCSYSYCTDCIVKYVDSKLR 100 (216)
Q Consensus 61 ~~~C~IC~~~~~~-~~~---~~~~~C~H~fC~~C~~~y~~~~i~ 100 (216)
-.+|+|||.-... ... -+...|.|.|...|+-+|+.+.-+
T Consensus 1469 ~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~ 1512 (1525)
T COG5219 1469 HEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSAR 1512 (1525)
T ss_pred cchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCC
Confidence 4799999975441 111 123568999999999999997543
No 201
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=29.40 E-value=30 Score=20.79 Aligned_cols=33 Identities=12% Similarity=0.429 Sum_probs=24.3
Q ss_pred CcccccCCCCCCceeeCCCCCccchHHHHHHHH
Q 041841 64 FSICMEPKSTNELFSIEFCSYSYCTDCIVKYVD 96 (216)
Q Consensus 64 C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~ 96 (216)
|.||.......+++.-..|+-.|...|+.....
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 778888666677777678888888888765444
No 202
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=29.36 E-value=16 Score=28.47 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=28.7
Q ss_pred CchhccccCCCCCCCC-CChHhHHHhcccCCChhHHHHHHHHhcCCceecCCCCc
Q 041841 161 CKRMFCAQCKVPWHAG-MRCEKFRKLNKNEKNSEDMELIKLAEEKKWKRCPHCNY 214 (216)
Q Consensus 161 C~~~fC~~C~~~~H~~-~~C~~~~~~~~~e~~~~d~~~~~~~~~~~~k~CP~C~~ 214 (216)
.-.-||..|...-|+- ..|.++..-. -..+.+|..+...+.|++|++
T Consensus 112 ~~~wyc~~c~~~~~e~~f~~~d~~~~~-------~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 112 GFQWFCPQCGHKLHRAEVQLENIVTDL-------PPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred ceEEECCCCCCeEEEEEEEecChhhhh-------HHHHHHHhCChhhccCCccCC
Confidence 3455666676666643 3555543311 134566777778899999984
No 203
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=29.28 E-value=46 Score=22.74 Aligned_cols=38 Identities=21% Similarity=0.512 Sum_probs=16.7
Q ss_pred CCCCcccccCCCCC---Cce-eeCCCCCccchHHHHHHHHHHhhcC
Q 041841 61 KRPFSICMEPKSTN---ELF-SIEFCSYSYCTDCIVKYVDSKLRES 102 (216)
Q Consensus 61 ~~~C~IC~~~~~~~---~~~-~~~~C~H~fC~~C~~~y~~~~i~~~ 102 (216)
...|.||.+++... +.| ....|+--.|+.|+. ..+++|
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE----YErkeg 50 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE----YERKEG 50 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS-----HHHHH----HHHHTS
T ss_pred CcccccccCccccCCCCCEEEEEcccCCccchhHHH----HHhhcC
Confidence 57899999987542 333 235677789999985 556666
No 204
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=28.76 E-value=73 Score=16.81 Aligned_cols=22 Identities=18% Similarity=0.382 Sum_probs=16.6
Q ss_pred CCCceeecCCCCCCCceeCCCCch
Q 041841 140 DCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 140 ~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+|...+.+..+ ...+.|..|+.
T Consensus 3 ~Cr~~L~yp~G--A~sVrCa~C~~ 24 (25)
T PF06943_consen 3 GCRTLLMYPRG--APSVRCACCHT 24 (25)
T ss_pred CCCceEEcCCC--CCCeECCccCc
Confidence 68888877654 56799998875
No 205
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=28.75 E-value=30 Score=23.78 Aligned_cols=18 Identities=22% Similarity=0.814 Sum_probs=16.5
Q ss_pred CCCCCccchHHHHHHHHH
Q 041841 80 EFCSYSYCTDCIVKYVDS 97 (216)
Q Consensus 80 ~~C~H~fC~~C~~~y~~~ 97 (216)
--|.|.|...|+.++|.+
T Consensus 52 G~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred EecchHHHHHHHHHHHhh
Confidence 369999999999999998
No 206
>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=28.63 E-value=21 Score=17.55 Aligned_cols=9 Identities=44% Similarity=0.984 Sum_probs=5.3
Q ss_pred eCCCCchhc
Q 041841 157 KRPYCKRMF 165 (216)
Q Consensus 157 ~C~~C~~~f 165 (216)
.|+.|++.|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 466666654
No 207
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=28.23 E-value=50 Score=27.15 Aligned_cols=20 Identities=20% Similarity=0.602 Sum_probs=16.0
Q ss_pred CCCCcccCcCCCCceeecCC
Q 041841 130 GAEKFYCPFKDCSALLINDG 149 (216)
Q Consensus 130 ~~~~~~Cp~~~C~~~~~~~~ 149 (216)
+++++-||.++|..+|-.+.
T Consensus 135 sSqRIACPRpnCkRiInL~p 154 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLDP 154 (275)
T ss_pred ccceeccCCCCcceeeecCC
Confidence 35678899999999987653
No 208
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=28.17 E-value=69 Score=21.02 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=20.0
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
.++-||+-+|..+...... .--.+.|..|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~-g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAIS-GYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecC-ceEEEEcCCCCcC
Confidence 4678997666666555432 2234778777775
No 209
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=27.85 E-value=30 Score=29.45 Aligned_cols=16 Identities=19% Similarity=0.513 Sum_probs=10.1
Q ss_pred eeCCCCch---hccccCCC
Q 041841 156 SKRPYCKR---MFCAQCKV 171 (216)
Q Consensus 156 ~~C~~C~~---~fC~~C~~ 171 (216)
..|..||- .-|+.|..
T Consensus 230 ~~C~~CGg~rFlpC~~C~G 248 (281)
T KOG2824|consen 230 GVCESCGGARFLPCSNCHG 248 (281)
T ss_pred CcCCCcCCcceEecCCCCC
Confidence 56777764 34777754
No 210
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=27.75 E-value=10 Score=32.34 Aligned_cols=18 Identities=28% Similarity=0.933 Sum_probs=14.0
Q ss_pred eeCCCCchhccccCCCCC
Q 041841 156 SKRPYCKRMFCAQCKVPW 173 (216)
Q Consensus 156 ~~C~~C~~~fC~~C~~~~ 173 (216)
-.|.-||+.||+.|-..|
T Consensus 252 pSaTpCGHiFCWsCI~~w 269 (293)
T KOG0317|consen 252 PSATPCGHIFCWSCILEW 269 (293)
T ss_pred CCcCcCcchHHHHHHHHH
Confidence 456679999999986555
No 211
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.61 E-value=57 Score=18.30 Aligned_cols=29 Identities=17% Similarity=0.267 Sum_probs=16.5
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
...|+ .|++...... ......|+.||..|
T Consensus 3 ~~~C~--~C~~~~i~~~--~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCS--KCGGNGIVNK--EDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcC--CCCCCeEEEe--cCCeEEcccCCcEe
Confidence 34576 5777554421 12356788887654
No 212
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=27.57 E-value=18 Score=28.73 Aligned_cols=48 Identities=10% Similarity=0.283 Sum_probs=29.6
Q ss_pred CchhccccCCCCCCCC-CChHhHHHhcccCCChhHHHHHHHHhcCCceecCCCCcc
Q 041841 161 CKRMFCAQCKVPWHAG-MRCEKFRKLNKNEKNSEDMELIKLAEEKKWKRCPHCNYS 215 (216)
Q Consensus 161 C~~~fC~~C~~~~H~~-~~C~~~~~~~~~e~~~~d~~~~~~~~~~~~k~CP~C~~~ 215 (216)
.-.-||..|+..-|+- ..|.++..-. -..+.+|..+...+.|++|++.
T Consensus 118 ~~~wyc~~c~~~~~e~~f~~~d~~~~~-------~~~~~~f~~~~e~rtC~~CG~v 166 (177)
T PRK13264 118 GFQWYCDECNHKVHEVEVQLTDIETDL-------PPVFAAFYASEELRTCDNCGTV 166 (177)
T ss_pred ceEEECCCCCCeEEEEEEEecChhhhh-------HHHHHHHhcCHhhccCCcCCcc
Confidence 4455666776666643 3565543311 1345667777788999999863
No 213
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.50 E-value=1.1e+02 Score=25.38 Aligned_cols=47 Identities=13% Similarity=0.342 Sum_probs=34.6
Q ss_pred CCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcC-Ccccccc
Q 041841 62 RPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRES-ITSIRCP 109 (216)
Q Consensus 62 ~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~-~~~i~Cp 109 (216)
..|..|-.+....+... +.|-|.|.-+|+......--.+- -..-.||
T Consensus 51 pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP 98 (299)
T KOG3970|consen 51 PNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCP 98 (299)
T ss_pred CCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCC
Confidence 46999998887777776 68999999999998776544331 1224677
No 214
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.38 E-value=42 Score=20.88 Aligned_cols=28 Identities=14% Similarity=0.307 Sum_probs=16.0
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchh
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRM 164 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 164 (216)
.+.|| .|+..+..... .....|..||++
T Consensus 19 ~~~CP--rCG~gvfmA~H--~dR~~CGkCgyT 46 (51)
T COG1998 19 NRFCP--RCGPGVFMADH--KDRWACGKCGYT 46 (51)
T ss_pred cccCC--CCCCcchhhhc--CceeEeccccce
Confidence 45899 58853323222 235678778764
No 215
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.20 E-value=43 Score=20.76 Aligned_cols=24 Identities=21% Similarity=0.505 Sum_probs=15.3
Q ss_pred CCCceeecCCCCCCCceeCCCCchhc
Q 041841 140 DCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 140 ~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
.|+..+... .....+.||.||...
T Consensus 11 ~Cg~~~~~~--~~~~~irCp~Cg~rI 34 (49)
T COG1996 11 RCGREVELD--QETRGIRCPYCGSRI 34 (49)
T ss_pred hcCCeeehh--hccCceeCCCCCcEE
Confidence 677777432 234568888888754
No 216
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.18 E-value=34 Score=22.24 Aligned_cols=31 Identities=19% Similarity=0.502 Sum_probs=19.0
Q ss_pred CcccCcCCCC----ceeecCCCCCCCceeCCCCchhc
Q 041841 133 KFYCPFKDCS----ALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 133 ~~~Cp~~~C~----~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
.+.|++++=. .++... .....+.||.|++.|
T Consensus 24 ~l~C~g~~~p~~HPrV~L~m--g~~gev~CPYC~t~y 58 (62)
T COG4391 24 PLMCPGPEPPNDHPRVFLDM--GDEGEVVCPYCSTRY 58 (62)
T ss_pred eEEcCCCCCCCCCCEEEEEc--CCCCcEecCccccEE
Confidence 4678875432 222111 345679999999876
No 217
>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=26.71 E-value=54 Score=19.93 Aligned_cols=27 Identities=15% Similarity=0.279 Sum_probs=15.7
Q ss_pred ccCcCCCCceeecCC-CCCCCceeCCCCch
Q 041841 135 YCPFKDCSALLINDG-LKNMKESKRPYCKR 163 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~-~~~~~~~~C~~C~~ 163 (216)
.|+ +|+..+.... .+....+.||.||.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCT--ACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeC--CCCCEeEEEEecCCCCCCCCCCCCC
Confidence 576 7887543321 12234567888886
No 218
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=26.52 E-value=35 Score=24.39 Aligned_cols=29 Identities=24% Similarity=0.386 Sum_probs=22.8
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHH
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDC 90 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C 90 (216)
.++|.-||-....+++-. ..=|+.+|++|
T Consensus 70 EFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 579999999887777554 44588899988
No 219
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.45 E-value=54 Score=20.72 Aligned_cols=25 Identities=20% Similarity=0.576 Sum_probs=15.6
Q ss_pred CCCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 130 GAEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 130 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
.+++..|| .|+.+... ...|+.||+
T Consensus 23 ~p~l~~C~--~cG~~~~~-------H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCP--NCGEFKLP-------HRVCPSCGY 47 (55)
T ss_pred CCcceECC--CCCCcccC-------eeECCccCe
Confidence 35566777 67776533 356777774
No 220
>PRK02935 hypothetical protein; Provisional
Probab=26.31 E-value=55 Score=23.71 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=6.5
Q ss_pred ccccCCCCCC
Q 041841 165 FCAQCKVPWH 174 (216)
Q Consensus 165 fC~~C~~~~H 174 (216)
.|..|++|-+
T Consensus 88 ~CM~C~~PLT 97 (110)
T PRK02935 88 ACMHCNQPLT 97 (110)
T ss_pred ecCcCCCcCC
Confidence 5677777654
No 221
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.07 E-value=57 Score=24.82 Aligned_cols=31 Identities=16% Similarity=0.292 Sum_probs=18.8
Q ss_pred CCcccCcCCCCceeecCCC----CCCCceeCCCCchh
Q 041841 132 EKFYCPFKDCSALLINDGL----KNMKESKRPYCKRM 164 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~----~~~~~~~C~~C~~~ 164 (216)
....|| .|+.-+..... +....+.||.||..
T Consensus 98 ~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 98 AYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred cEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 356798 68877654321 11233888888764
No 222
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=25.93 E-value=57 Score=21.04 Aligned_cols=28 Identities=25% Similarity=0.589 Sum_probs=19.2
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
-|.+.+|..++..+ ......-.||-|+.
T Consensus 20 ~Ct~e~C~gWmR~n-Fs~~~~p~CPlC~s 47 (59)
T PF14169_consen 20 ECTSEDCNGWMRDN-FSFEEEPVCPLCKS 47 (59)
T ss_pred EeCCCCCCcccccc-cccCCCccCCCcCC
Confidence 49999999999654 33333456777764
No 223
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.67 E-value=66 Score=25.25 Aligned_cols=16 Identities=31% Similarity=0.565 Sum_probs=11.9
Q ss_pred CCCcccCcCCCCceeecC
Q 041841 131 AEKFYCPFKDCSALLIND 148 (216)
Q Consensus 131 ~~~~~Cp~~~C~~~~~~~ 148 (216)
+....|| .|+..+...
T Consensus 95 ~e~~RCp--~CN~~L~~v 110 (165)
T COG1656 95 PEFSRCP--ECNGELEKV 110 (165)
T ss_pred cccccCc--ccCCEeccC
Confidence 3467899 899988654
No 224
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=24.20 E-value=25 Score=33.75 Aligned_cols=42 Identities=24% Similarity=0.407 Sum_probs=31.0
Q ss_pred CCCCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 61 KRPFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 61 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
..+|+||+..+... .++.|.|.||.-||..-+...-. ...||
T Consensus 21 ~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~----~~~~~ 62 (684)
T KOG4362|consen 21 ILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKG----PKQCA 62 (684)
T ss_pred hccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCc----cccch
Confidence 46899999987544 46799999999999876654321 45666
No 225
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.10 E-value=39 Score=24.80 Aligned_cols=48 Identities=17% Similarity=0.254 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHHHhh-h-cC--------CCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 111 VPKEVSDRWGNALCEGV-I-NG--------AEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~-v-~~--------~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
+.++.++-.-..+.+.. + +. +.+.+|. +|+..+..... ....||.||.
T Consensus 39 V~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~--~Cg~~~~~~~~---~~~~CP~Cgs 96 (117)
T PRK00564 39 MDKSLFVSAFETFREESLVCKDAILDIVDEKVELECK--DCSHVFKPNAL---DYGVCEKCHS 96 (117)
T ss_pred cCHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhh--hCCCccccCCc---cCCcCcCCCC
Confidence 56666665444444443 2 21 2345888 78877655321 2235887774
No 226
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=23.95 E-value=34 Score=21.64 Aligned_cols=8 Identities=50% Similarity=1.464 Sum_probs=7.0
Q ss_pred eecCCCCc
Q 041841 207 KRCPHCNY 214 (216)
Q Consensus 207 k~CP~C~~ 214 (216)
+.||+|+.
T Consensus 25 ~KCPrCK~ 32 (60)
T COG4416 25 KKCPRCKE 32 (60)
T ss_pred ecCCccce
Confidence 79999985
No 227
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.74 E-value=63 Score=31.06 Aligned_cols=40 Identities=23% Similarity=0.480 Sum_probs=27.6
Q ss_pred cccCcCCCCceeecCCCCCCCceeCCCCchh----ccccCCCCCCCCC-ChHh
Q 041841 134 FYCPFKDCSALLINDGLKNMKESKRPYCKRM----FCAQCKVPWHAGM-RCEK 181 (216)
Q Consensus 134 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~----fC~~C~~~~H~~~-~C~~ 181 (216)
+.|| .|+...... ...|+.||.. +|.+|+.+...+. -|.+
T Consensus 2 ~~Cp--~Cg~~n~~~------akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~ 46 (645)
T PRK14559 2 LICP--QCQFENPNN------NRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPN 46 (645)
T ss_pred CcCC--CCCCcCCCC------CccccccCCCCCCCcCCCCCCCCCcccccccc
Confidence 4688 798876332 2469999987 5999998866543 3443
No 228
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.30 E-value=65 Score=31.08 Aligned_cols=34 Identities=24% Similarity=0.504 Sum_probs=23.9
Q ss_pred ccCcCCCCceeecCCCCCCCceeCCCCchh-----ccccCCCC
Q 041841 135 YCPFKDCSALLINDGLKNMKESKRPYCKRM-----FCAQCKVP 172 (216)
Q Consensus 135 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~-----fC~~C~~~ 172 (216)
.|| .|+..+.++. ......|+.||+. .|..|+..
T Consensus 392 ~C~--~C~~~l~~h~--~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECP--HCDASLTLHR--FQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCC--CCCCceeEEC--CCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 355 5776665543 2456899999987 59999774
No 229
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.09 E-value=1.4e+02 Score=21.55 Aligned_cols=28 Identities=29% Similarity=0.747 Sum_probs=18.7
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCCC
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKVP 172 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 172 (216)
...|+ +|+..... ..+|+..+|.+|+..
T Consensus 42 ~~~C~--~Cg~~~~~----------~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCE--DCGHEKIV----------YNSCKNRHCPSCQAK 69 (111)
T ss_pred eeecC--CCCceEEe----------cCcccCcCCCCCCCh
Confidence 45677 57766533 335888899988763
No 230
>PLN03086 PRLI-interacting factor K; Provisional
Probab=22.66 E-value=58 Score=30.74 Aligned_cols=32 Identities=19% Similarity=0.476 Sum_probs=23.1
Q ss_pred CCcccCcCCCCceeecCCCCCCCceeCCCCchhc
Q 041841 132 EKFYCPFKDCSALLINDGLKNMKESKRPYCKRMF 165 (216)
Q Consensus 132 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 165 (216)
+.+-||..+|+..+..... .....|+.|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEA--KNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeecccc--ccCccCCCCCCcc
Confidence 3467997789998866543 4557898888765
No 231
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=22.36 E-value=1.3e+02 Score=22.77 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHHhhhc---CCCCcccCcCCCCceeecCCCC-------------CCCceeCCCCchhc
Q 041841 111 VPKEVSDRWGNALCEGVIN---GAEKFYCPFKDCSALLINDGLK-------------NMKESKRPYCKRMF 165 (216)
Q Consensus 111 l~~~~~~~y~~~~~~~~v~---~~~~~~Cp~~~C~~~~~~~~~~-------------~~~~~~C~~C~~~f 165 (216)
.+.+..+...+.+...-+. .+....|+ .|+..+.....+ ....-.|+.||+.|
T Consensus 66 ~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 66 RSDDPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred cCCCHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 3445555666555444332 23367899 788876544221 12346788888765
No 232
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.28 E-value=56 Score=20.90 Aligned_cols=13 Identities=23% Similarity=0.432 Sum_probs=8.6
Q ss_pred CCceeCCCCchhc
Q 041841 153 MKESKRPYCKRMF 165 (216)
Q Consensus 153 ~~~~~C~~C~~~f 165 (216)
...+.||.|+..|
T Consensus 15 E~~lrCPRC~~~F 27 (65)
T COG4049 15 EEFLRCPRCGMVF 27 (65)
T ss_pred ceeeeCCchhHHH
Confidence 3456777777765
No 233
>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=22.02 E-value=93 Score=19.07 Aligned_cols=42 Identities=17% Similarity=0.373 Sum_probs=21.2
Q ss_pred CCcccccCCCCCCceeeCCCCCccchHHHHHHHHHHhhcCCcccccc
Q 041841 63 PFSICMEPKSTNELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCP 109 (216)
Q Consensus 63 ~C~IC~~~~~~~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp 109 (216)
.|+|-+..+.. -.++..|.|.-|.| +..||....+.+. -+||
T Consensus 4 ~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~--W~CP 45 (50)
T PF02891_consen 4 RCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPK--WKCP 45 (50)
T ss_dssp B-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS-----B-T
T ss_pred eCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCC--eECc
Confidence 46666655432 24578999998865 6778887776543 4666
No 234
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.92 E-value=32 Score=26.13 Aligned_cols=19 Identities=32% Similarity=0.753 Sum_probs=16.1
Q ss_pred ceeCCCCchhccccCCCCC
Q 041841 155 ESKRPYCKRMFCAQCKVPW 173 (216)
Q Consensus 155 ~~~C~~C~~~fC~~C~~~~ 173 (216)
--.|..|...||.+|+...
T Consensus 81 GH~C~YCq~r~CARCGGrv 99 (169)
T KOG3799|consen 81 GHNCSYCQTRFCARCGGRV 99 (169)
T ss_pred CcccchhhhhHHHhcCCee
Confidence 3569999999999999854
No 235
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.48 E-value=1.2e+02 Score=18.96 Aligned_cols=10 Identities=50% Similarity=1.138 Sum_probs=6.1
Q ss_pred CCcccCcCCCCc
Q 041841 132 EKFYCPFKDCSA 143 (216)
Q Consensus 132 ~~~~Cp~~~C~~ 143 (216)
.++-||. |+.
T Consensus 2 ~LkPCPF--CG~ 11 (61)
T PF14354_consen 2 ELKPCPF--CGS 11 (61)
T ss_pred CCcCCCC--CCC
Confidence 3567985 553
No 236
>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=21.42 E-value=43 Score=16.02 Aligned_cols=9 Identities=33% Similarity=0.921 Sum_probs=3.7
Q ss_pred eCCCCchhc
Q 041841 157 KRPYCKRMF 165 (216)
Q Consensus 157 ~C~~C~~~f 165 (216)
.|+.|+..|
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 456666544
No 237
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=21.38 E-value=52 Score=28.06 Aligned_cols=46 Identities=22% Similarity=0.306 Sum_probs=33.3
Q ss_pred CCCCcccccCCCC-CCceeeCCCCCccchHHHHHHHHHHhhcCCccccccCCCH
Q 041841 61 KRPFSICMEPKST-NELFSIEFCSYSYCTDCIVKYVDSKLRESITSIRCPIVPK 113 (216)
Q Consensus 61 ~~~C~IC~~~~~~-~~~~~~~~C~H~fC~~C~~~y~~~~i~~~~~~i~Cp~l~~ 113 (216)
...|+||.+.... ......+.|+|..-..|++.++.. | ..||+-..
T Consensus 158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~----~---y~CP~C~~ 204 (276)
T KOG1940|consen 158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE----G---YTCPICSK 204 (276)
T ss_pred cCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc----C---CCCCcccc
Confidence 4569999998743 333446899999999999887663 3 68885433
No 238
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=21.17 E-value=77 Score=19.96 Aligned_cols=24 Identities=21% Similarity=0.534 Sum_probs=15.2
Q ss_pred CCCcccCcCCCCceeecCCCCCCCceeCCCCch
Q 041841 131 AEKFYCPFKDCSALLINDGLKNMKESKRPYCKR 163 (216)
Q Consensus 131 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 163 (216)
.++..|| .|+.+... ...|+.||+
T Consensus 24 ~~l~~c~--~cg~~~~~-------H~vc~~cG~ 47 (56)
T PF01783_consen 24 PNLVKCP--NCGEPKLP-------HRVCPSCGY 47 (56)
T ss_dssp TSEEESS--SSSSEEST-------TSBCTTTBB
T ss_pred cceeeec--cCCCEecc-------cEeeCCCCe
Confidence 4567788 67776533 356777764
No 239
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.02 E-value=67 Score=20.96 Aligned_cols=30 Identities=20% Similarity=0.487 Sum_probs=22.1
Q ss_pred CcccCcCCCCceeecCCCCCCCceeCCCCchhccccCCC
Q 041841 133 KFYCPFKDCSALLINDGLKNMKESKRPYCKRMFCAQCKV 171 (216)
Q Consensus 133 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 171 (216)
...|..++|+.. ..+.|..|.+.+|+..-.
T Consensus 27 ~~~C~~~gC~~~---------s~I~C~~Ckk~~Cf~Hfi 56 (63)
T PF04236_consen 27 AGDCDITGCNNT---------SFIRCAYCKKSLCFNHFI 56 (63)
T ss_pred cCcCCCCCCCCc---------CEEEccccCCccccccee
Confidence 456777777553 347799999999998755
Done!