Query 042112
Match_columns 132
No_of_seqs 172 out of 1282
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 02:59:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4628 Predicted E3 ubiquitin 99.8 8.8E-19 1.9E-23 134.1 7.5 72 34-106 213-284 (348)
2 PF13639 zf-RING_2: Ring finge 99.6 1.6E-16 3.4E-21 88.4 2.2 44 52-96 1-44 (44)
3 COG5540 RING-finger-containing 99.5 2.5E-14 5.3E-19 107.2 4.0 52 50-101 322-373 (374)
4 PF12678 zf-rbx1: RING-H2 zinc 99.4 3E-13 6.5E-18 83.0 4.1 45 51-96 19-73 (73)
5 COG5243 HRD1 HRD ubiquitin lig 99.4 1.3E-12 2.8E-17 100.4 5.7 51 49-100 285-345 (491)
6 KOG0317 Predicted E3 ubiquitin 99.3 1.8E-12 4E-17 96.5 6.1 52 49-104 237-288 (293)
7 PHA02929 N1R/p28-like protein; 99.3 1E-12 2.2E-17 96.8 4.1 51 49-100 172-227 (238)
8 PLN03208 E3 ubiquitin-protein 99.3 3.6E-12 7.8E-17 90.7 4.2 56 49-107 16-86 (193)
9 PF12861 zf-Apc11: Anaphase-pr 99.3 3.6E-12 7.8E-17 79.5 3.4 52 50-101 20-83 (85)
10 PF13920 zf-C3HC4_3: Zinc fing 99.2 1.1E-11 2.3E-16 70.6 3.4 47 50-100 1-48 (50)
11 cd00162 RING RING-finger (Real 99.2 1.7E-11 3.6E-16 67.2 3.9 45 53-99 1-45 (45)
12 KOG0823 Predicted E3 ubiquitin 99.2 2.1E-11 4.6E-16 88.5 3.2 53 49-104 45-99 (230)
13 KOG1734 Predicted RING-contain 99.2 2.2E-11 4.8E-16 90.1 3.1 64 49-112 222-293 (328)
14 PF13923 zf-C3HC4_2: Zinc fing 99.1 4.8E-11 1E-15 64.5 3.1 39 54-95 1-39 (39)
15 PHA02926 zinc finger-like prot 99.1 4.7E-11 1E-15 86.3 3.5 52 49-100 168-230 (242)
16 PF15227 zf-C3HC4_4: zinc fing 99.1 9.3E-11 2E-15 64.4 3.6 39 54-95 1-42 (42)
17 KOG0320 Predicted E3 ubiquitin 99.1 6.3E-11 1.4E-15 82.9 3.4 54 49-104 129-182 (187)
18 PF14634 zf-RING_5: zinc-RING 99.1 1.3E-10 2.9E-15 64.4 3.5 44 53-97 1-44 (44)
19 PF00097 zf-C3HC4: Zinc finger 99.0 3.3E-10 7.2E-15 61.6 3.1 40 54-95 1-41 (41)
20 smart00184 RING Ring finger. E 99.0 4.6E-10 9.9E-15 59.3 3.5 39 54-95 1-39 (39)
21 KOG0828 Predicted E3 ubiquitin 99.0 8.2E-10 1.8E-14 87.7 6.2 53 49-101 569-635 (636)
22 KOG0802 E3 ubiquitin ligase [P 99.0 2.3E-10 5E-15 93.6 2.7 51 49-100 289-341 (543)
23 COG5194 APC11 Component of SCF 98.9 1.1E-09 2.4E-14 67.0 3.1 51 52-103 21-84 (88)
24 smart00504 Ubox Modified RING 98.9 1.9E-09 4.2E-14 63.7 4.1 51 52-106 2-52 (63)
25 KOG1493 Anaphase-promoting com 98.9 2.5E-10 5.5E-15 69.2 0.2 51 50-100 19-81 (84)
26 TIGR00599 rad18 DNA repair pro 98.8 5.1E-09 1.1E-13 82.4 3.9 50 49-102 24-73 (397)
27 COG5574 PEX10 RING-finger-cont 98.7 7.6E-09 1.6E-13 76.5 2.6 53 49-104 213-266 (271)
28 PF13445 zf-RING_UBOX: RING-ty 98.7 1.4E-08 3E-13 55.9 2.7 39 54-93 1-43 (43)
29 TIGR00570 cdk7 CDK-activating 98.6 3E-08 6.5E-13 75.5 4.4 56 50-105 2-59 (309)
30 KOG2930 SCF ubiquitin ligase, 98.6 3.2E-08 6.9E-13 63.5 2.5 52 50-102 45-110 (114)
31 KOG2164 Predicted E3 ubiquitin 98.6 3E-08 6.5E-13 79.2 2.4 55 51-108 186-244 (513)
32 smart00744 RINGv The RING-vari 98.6 9.1E-08 2E-12 54.1 3.7 43 53-96 1-49 (49)
33 PF04564 U-box: U-box domain; 98.5 7.9E-08 1.7E-12 58.8 2.7 54 50-106 3-56 (73)
34 KOG0804 Cytoplasmic Zn-finger 98.4 1.1E-07 2.4E-12 75.0 1.8 49 49-100 173-222 (493)
35 PF11793 FANCL_C: FANCL C-term 98.4 4.5E-08 9.8E-13 59.4 -0.6 50 51-100 2-66 (70)
36 KOG0287 Postreplication repair 98.4 1.4E-07 3E-12 72.3 1.5 51 50-104 22-72 (442)
37 COG5432 RAD18 RING-finger-cont 98.3 2.6E-07 5.6E-12 69.6 2.1 51 50-104 24-74 (391)
38 COG5219 Uncharacterized conser 98.3 1.7E-07 3.7E-12 79.6 1.0 52 49-100 1467-1523(1525)
39 KOG2177 Predicted E3 ubiquitin 98.3 3.6E-07 7.8E-12 67.7 1.8 44 49-96 11-54 (386)
40 KOG0824 Predicted E3 ubiquitin 98.2 4.6E-07 1E-11 68.3 1.9 50 50-102 6-55 (324)
41 KOG4265 Predicted E3 ubiquitin 98.2 1.5E-06 3.4E-11 66.9 3.9 49 49-101 288-337 (349)
42 KOG0311 Predicted E3 ubiquitin 98.2 2.5E-07 5.4E-12 71.1 -0.5 56 49-107 41-97 (381)
43 KOG0978 E3 ubiquitin ligase in 98.1 6.4E-07 1.4E-11 74.5 1.0 52 51-105 643-694 (698)
44 KOG0297 TNF receptor-associate 98.1 1.6E-06 3.4E-11 68.6 2.1 80 47-130 17-99 (391)
45 KOG0827 Predicted E3 ubiquitin 98.1 1.9E-06 4.1E-11 67.1 2.1 51 51-102 4-58 (465)
46 KOG1039 Predicted E3 ubiquitin 98.0 2.3E-06 4.9E-11 66.4 2.0 52 49-100 159-221 (344)
47 PF14835 zf-RING_6: zf-RING of 98.0 1.3E-06 2.9E-11 51.6 -0.2 50 51-105 7-56 (65)
48 KOG4172 Predicted E3 ubiquitin 97.9 1.9E-06 4.1E-11 49.2 -0.3 46 51-99 7-53 (62)
49 KOG1645 RING-finger-containing 97.8 1.6E-05 3.5E-10 62.4 3.4 49 50-98 3-54 (463)
50 KOG1002 Nucleotide excision re 97.8 5.4E-06 1.2E-10 67.0 0.4 79 49-130 534-617 (791)
51 KOG0825 PHD Zn-finger protein 97.8 5.8E-06 1.3E-10 69.4 0.5 57 51-108 123-179 (1134)
52 KOG3970 Predicted E3 ubiquitin 97.6 5.9E-05 1.3E-09 55.1 3.4 56 46-102 45-107 (299)
53 KOG1785 Tyrosine kinase negati 97.6 3E-05 6.4E-10 60.9 1.3 48 50-100 368-416 (563)
54 PF14570 zf-RING_4: RING/Ubox 97.5 7.3E-05 1.6E-09 41.9 2.1 45 54-99 1-47 (48)
55 KOG1941 Acetylcholine receptor 97.5 3.5E-05 7.6E-10 60.3 1.0 48 50-97 364-413 (518)
56 KOG1428 Inhibitor of type V ad 97.4 0.00014 3.1E-09 64.9 3.4 67 35-101 3470-3545(3738)
57 KOG4159 Predicted E3 ubiquitin 97.4 0.00011 2.3E-09 58.3 2.3 49 49-101 82-130 (398)
58 PF12906 RINGv: RING-variant d 97.3 0.00012 2.6E-09 40.9 1.7 41 54-95 1-47 (47)
59 PF11789 zf-Nse: Zinc-finger o 97.3 0.00016 3.6E-09 42.0 2.2 44 49-94 9-53 (57)
60 KOG2879 Predicted E3 ubiquitin 97.3 0.0011 2.3E-08 49.9 6.4 50 49-100 237-287 (298)
61 PHA02825 LAP/PHD finger-like p 97.2 0.00036 7.8E-09 48.4 3.2 50 49-102 6-61 (162)
62 PF05883 Baculo_RING: Baculovi 97.1 0.00023 5E-09 48.1 1.4 36 51-86 26-67 (134)
63 PHA02862 5L protein; Provision 97.0 0.00059 1.3E-08 46.7 2.6 48 51-102 2-55 (156)
64 KOG4185 Predicted E3 ubiquitin 97.0 0.00051 1.1E-08 52.2 2.5 48 52-99 4-54 (296)
65 PF10367 Vps39_2: Vacuolar sor 96.8 0.00046 9.9E-09 44.5 1.0 33 49-82 76-108 (109)
66 KOG0801 Predicted E3 ubiquitin 96.8 0.0004 8.7E-09 48.4 0.7 41 37-78 164-204 (205)
67 COG5175 MOT2 Transcriptional r 96.8 0.00099 2.2E-08 51.6 2.6 54 49-102 12-66 (480)
68 PF08746 zf-RING-like: RING-li 96.7 0.00075 1.6E-08 36.9 1.3 42 54-95 1-43 (43)
69 KOG1952 Transcription factor N 96.7 0.0009 1.9E-08 57.0 2.2 49 49-97 189-244 (950)
70 KOG3039 Uncharacterized conser 96.7 0.0019 4.1E-08 48.0 3.6 53 50-103 220-273 (303)
71 COG5152 Uncharacterized conser 96.7 0.00061 1.3E-08 49.1 0.8 45 51-99 196-240 (259)
72 COG5236 Uncharacterized conser 96.7 0.0015 3.2E-08 50.8 2.9 57 41-100 51-108 (493)
73 KOG1571 Predicted E3 ubiquitin 96.7 0.001 2.2E-08 51.7 1.9 45 49-100 303-347 (355)
74 PF14447 Prok-RING_4: Prokaryo 96.6 0.0012 2.5E-08 37.9 1.6 46 52-103 8-53 (55)
75 KOG4445 Uncharacterized conser 96.5 0.0019 4.2E-08 49.2 2.3 53 49-101 113-187 (368)
76 PF04641 Rtf2: Rtf2 RING-finge 96.4 0.0049 1.1E-07 46.3 4.4 54 49-104 111-165 (260)
77 KOG3800 Predicted E3 ubiquitin 96.4 0.0031 6.6E-08 47.8 3.0 52 53-104 2-55 (300)
78 COG5222 Uncharacterized conser 96.4 0.0017 3.7E-08 49.5 1.6 54 51-107 274-329 (427)
79 KOG2817 Predicted E3 ubiquitin 96.3 0.0034 7.5E-08 49.3 3.1 50 50-99 333-384 (394)
80 KOG4739 Uncharacterized protei 96.3 0.0024 5.1E-08 47.2 1.8 51 53-107 5-55 (233)
81 KOG0826 Predicted E3 ubiquitin 96.2 0.019 4.1E-07 44.3 6.2 47 49-98 298-344 (357)
82 KOG2660 Locus-specific chromos 96.2 0.0016 3.5E-08 50.0 0.4 51 50-103 14-64 (331)
83 KOG4692 Predicted E3 ubiquitin 96.1 0.0034 7.3E-08 49.0 2.1 48 49-100 420-467 (489)
84 KOG1813 Predicted E3 ubiquitin 96.1 0.0032 6.9E-08 47.8 1.8 47 50-100 240-286 (313)
85 KOG1814 Predicted E3 ubiquitin 96.1 0.0054 1.2E-07 48.5 3.1 36 50-85 183-218 (445)
86 KOG3268 Predicted E3 ubiquitin 96.0 0.0068 1.5E-07 43.0 2.8 34 70-103 188-231 (234)
87 COG5220 TFB3 Cdk activating ki 96.0 0.0035 7.7E-08 46.4 1.4 50 50-99 9-63 (314)
88 PHA03096 p28-like protein; Pro 95.9 0.0042 9.1E-08 47.3 1.8 46 52-97 179-231 (284)
89 PF10272 Tmpp129: Putative tra 95.8 0.011 2.4E-07 46.4 3.7 30 72-101 311-352 (358)
90 KOG4275 Predicted E3 ubiquitin 95.4 0.0034 7.4E-08 47.7 -0.5 41 51-99 300-341 (350)
91 KOG1940 Zn-finger protein [Gen 95.3 0.011 2.3E-07 44.8 1.9 47 50-97 157-204 (276)
92 KOG2114 Vacuolar assembly/sort 95.0 0.014 3E-07 50.0 1.9 43 51-99 840-882 (933)
93 PF03854 zf-P11: P-11 zinc fin 94.9 0.0081 1.7E-07 33.4 0.2 43 53-101 4-47 (50)
94 PF07800 DUF1644: Protein of u 94.8 0.041 8.8E-07 38.3 3.4 36 50-85 1-46 (162)
95 KOG3002 Zn finger protein [Gen 94.6 0.0097 2.1E-07 45.7 0.1 43 50-100 47-91 (299)
96 COG5183 SSM4 Protein involved 94.2 0.045 9.7E-07 47.0 3.1 69 47-116 8-82 (1175)
97 KOG2034 Vacuolar sorting prote 94.1 0.026 5.7E-07 48.6 1.6 35 49-84 815-849 (911)
98 KOG1001 Helicase-like transcri 94.1 0.012 2.5E-07 49.9 -0.5 49 52-104 455-504 (674)
99 KOG0827 Predicted E3 ubiquitin 93.8 0.0028 6.1E-08 49.8 -4.3 51 51-102 196-247 (465)
100 KOG3053 Uncharacterized conser 93.1 0.049 1.1E-06 40.8 1.3 52 49-100 18-82 (293)
101 COG5109 Uncharacterized conser 92.8 0.35 7.6E-06 37.4 5.6 48 49-96 334-383 (396)
102 KOG1609 Protein involved in mR 92.4 0.085 1.8E-06 40.1 2.0 50 51-100 78-134 (323)
103 KOG3899 Uncharacterized conser 92.4 0.071 1.5E-06 40.8 1.5 30 72-101 325-366 (381)
104 KOG1812 Predicted E3 ubiquitin 92.3 0.065 1.4E-06 42.6 1.2 37 50-86 145-182 (384)
105 KOG2932 E3 ubiquitin ligase in 91.7 0.091 2E-06 40.5 1.4 43 53-100 92-134 (389)
106 PF05290 Baculo_IE-1: Baculovi 91.1 0.24 5.2E-06 33.6 2.8 54 50-103 79-135 (140)
107 KOG0309 Conserved WD40 repeat- 90.5 0.2 4.2E-06 43.0 2.3 39 54-94 1031-1069(1081)
108 KOG4367 Predicted Zn-finger pr 90.3 0.17 3.7E-06 40.8 1.7 35 49-86 2-36 (699)
109 PF14446 Prok-RING_1: Prokaryo 89.9 0.51 1.1E-05 27.0 3.0 44 50-98 4-50 (54)
110 KOG3113 Uncharacterized conser 89.5 0.42 9E-06 35.9 3.1 53 50-105 110-163 (293)
111 PF14569 zf-UDP: Zinc-binding 86.0 0.81 1.7E-05 28.1 2.4 51 50-100 8-62 (80)
112 KOG4362 Transcriptional regula 85.6 0.19 4.1E-06 42.5 -0.7 49 51-102 21-71 (684)
113 KOG0298 DEAD box-containing he 85.4 0.24 5.1E-06 44.6 -0.2 47 50-99 1152-1198(1394)
114 smart00132 LIM Zinc-binding do 84.6 1.3 2.7E-05 22.4 2.5 38 53-100 1-38 (39)
115 smart00249 PHD PHD zinc finger 83.5 0.39 8.4E-06 25.4 0.2 31 53-83 1-31 (47)
116 KOG3161 Predicted E3 ubiquitin 82.0 0.57 1.2E-05 39.6 0.7 43 51-97 11-54 (861)
117 KOG0802 E3 ubiquitin ligase [P 81.7 1.2 2.5E-05 37.0 2.4 52 49-108 477-528 (543)
118 PF13901 DUF4206: Domain of un 81.3 0.92 2E-05 32.9 1.5 40 51-96 152-196 (202)
119 KOG0269 WD40 repeat-containing 81.2 1.8 3.9E-05 37.2 3.3 42 51-94 779-820 (839)
120 KOG1100 Predicted E3 ubiquitin 81.1 0.79 1.7E-05 33.4 1.1 39 54-100 161-200 (207)
121 KOG1829 Uncharacterized conser 80.3 0.58 1.3E-05 39.1 0.2 24 68-95 533-556 (580)
122 KOG4718 Non-SMC (structural ma 80.2 0.97 2.1E-05 33.1 1.3 45 50-97 180-224 (235)
123 PF02891 zf-MIZ: MIZ/SP-RING z 80.2 1.9 4.1E-05 24.1 2.3 44 52-98 3-50 (50)
124 PF12273 RCR: Chitin synthesis 76.7 1.8 3.9E-05 29.0 1.7 15 6-20 4-18 (130)
125 PLN02195 cellulose synthase A 76.3 4.1 8.9E-05 36.2 4.1 54 50-103 5-62 (977)
126 KOG1815 Predicted E3 ubiquitin 76.2 4.2 9.2E-05 32.9 4.0 38 49-88 68-105 (444)
127 KOG2068 MOT2 transcription fac 76.2 3.3 7.2E-05 32.2 3.2 49 51-100 249-298 (327)
128 PLN02189 cellulose synthase 74.4 3.4 7.5E-05 36.9 3.2 51 50-100 33-87 (1040)
129 KOG1812 Predicted E3 ubiquitin 74.2 1.8 3.9E-05 34.5 1.4 45 50-95 305-351 (384)
130 KOG3842 Adaptor protein Pellin 72.9 4.4 9.5E-05 31.6 3.1 53 50-102 340-416 (429)
131 PF00412 LIM: LIM domain; Int 71.8 3.3 7.1E-05 23.1 1.8 40 54-103 1-40 (58)
132 PF07191 zinc-ribbons_6: zinc- 71.8 0.2 4.4E-06 30.2 -3.4 40 52-100 2-41 (70)
133 KOG3005 GIY-YIG type nuclease 70.4 3.1 6.7E-05 31.5 1.8 50 51-100 182-243 (276)
134 PLN02436 cellulose synthase A 70.3 5.6 0.00012 35.7 3.6 51 50-100 35-89 (1094)
135 KOG4185 Predicted E3 ubiquitin 69.7 0.61 1.3E-05 35.4 -2.1 49 50-98 206-265 (296)
136 PF00628 PHD: PHD-finger; Int 68.4 2.3 5E-05 23.3 0.6 44 53-96 1-49 (51)
137 KOG0825 PHD Zn-finger protein 67.4 3.5 7.6E-05 35.9 1.7 51 50-100 95-154 (1134)
138 KOG2066 Vacuolar assembly/sort 66.7 2.5 5.5E-05 36.5 0.8 37 50-86 783-823 (846)
139 PLN02638 cellulose synthase A 66.6 7 0.00015 35.2 3.4 51 50-100 16-70 (1079)
140 PLN02915 cellulose synthase A 64.9 9.3 0.0002 34.3 3.8 51 50-100 14-68 (1044)
141 KOG2807 RNA polymerase II tran 64.8 8.6 0.00019 30.1 3.3 62 35-97 313-375 (378)
142 PF06844 DUF1244: Protein of u 64.6 4.7 0.0001 24.0 1.4 12 75-86 11-22 (68)
143 PF10571 UPF0547: Uncharacteri 64.2 4 8.6E-05 19.6 0.9 11 91-101 2-12 (26)
144 PF07649 C1_3: C1-like domain; 63.9 5.2 0.00011 19.6 1.3 29 53-81 2-30 (30)
145 PLN02400 cellulose synthase 62.2 7.5 0.00016 35.0 2.8 51 50-100 35-89 (1085)
146 PF06906 DUF1272: Protein of u 61.8 19 0.00041 20.7 3.5 47 51-100 5-52 (57)
147 PF01363 FYVE: FYVE zinc finge 60.7 3.8 8.3E-05 24.0 0.6 36 49-84 7-43 (69)
148 PF13717 zinc_ribbon_4: zinc-r 59.9 4.9 0.00011 20.8 0.9 13 53-65 4-16 (36)
149 PF04710 Pellino: Pellino; In 59.7 3 6.5E-05 33.3 0.0 51 51-101 328-402 (416)
150 PF07975 C1_4: TFIIH C1-like d 59.5 7.5 0.00016 21.9 1.6 42 54-96 2-50 (51)
151 PF04423 Rad50_zn_hook: Rad50 58.9 2.6 5.6E-05 23.7 -0.4 11 91-101 22-32 (54)
152 KOG2231 Predicted E3 ubiquitin 56.0 12 0.00026 32.0 2.9 50 53-105 2-57 (669)
153 KOG3039 Uncharacterized conser 53.6 7.6 0.00016 29.3 1.3 34 49-85 41-74 (303)
154 TIGR00622 ssl1 transcription f 53.6 17 0.00038 23.9 2.8 46 51-97 55-111 (112)
155 cd00065 FYVE FYVE domain; Zinc 53.5 10 0.00023 21.0 1.6 34 52-85 3-37 (57)
156 smart00064 FYVE Protein presen 52.3 12 0.00026 21.7 1.8 35 51-85 10-45 (68)
157 PF02318 FYVE_2: FYVE-type zin 52.1 6 0.00013 26.0 0.5 34 50-83 53-88 (118)
158 KOG1729 FYVE finger containing 50.8 3.1 6.8E-05 31.9 -1.1 43 52-94 215-257 (288)
159 PF01102 Glycophorin_A: Glycop 50.5 19 0.00041 24.1 2.7 21 5-25 68-88 (122)
160 PF09889 DUF2116: Uncharacteri 50.0 12 0.00026 21.7 1.5 16 88-103 2-17 (59)
161 PF13832 zf-HC5HC2H_2: PHD-zin 49.9 11 0.00024 24.1 1.5 32 50-83 54-87 (110)
162 COG4847 Uncharacterized protei 49.0 18 0.00039 23.1 2.3 35 51-86 6-40 (103)
163 PF06750 DiS_P_DiS: Bacterial 48.8 25 0.00054 22.1 3.0 39 50-101 32-70 (92)
164 PF12773 DZR: Double zinc ribb 48.7 16 0.00035 19.8 1.9 11 90-100 30-40 (50)
165 PF12273 RCR: Chitin synthesis 48.0 27 0.00058 23.2 3.2 21 2-22 3-23 (130)
166 KOG3579 Predicted E3 ubiquitin 46.9 13 0.00029 28.6 1.7 50 50-102 267-330 (352)
167 cd00350 rubredoxin_like Rubred 46.4 20 0.00042 18.0 1.8 9 89-97 17-25 (33)
168 PF13771 zf-HC5HC2H: PHD-like 45.6 12 0.00026 22.9 1.1 34 50-83 35-68 (90)
169 PF13719 zinc_ribbon_5: zinc-r 45.1 12 0.00025 19.4 0.8 13 53-65 4-16 (37)
170 COG4357 Zinc finger domain con 43.6 23 0.0005 22.7 2.1 30 71-102 64-93 (105)
171 KOG3799 Rab3 effector RIM1 and 40.5 12 0.00025 25.7 0.4 50 49-98 63-116 (169)
172 PF10497 zf-4CXXC_R1: Zinc-fin 40.4 47 0.001 21.4 3.3 46 51-97 7-69 (105)
173 KOG2041 WD40 repeat protein [G 40.2 44 0.00095 29.4 3.9 25 71-100 1161-1185(1189)
174 KOG4218 Nuclear hormone recept 40.0 29 0.00062 27.6 2.6 24 49-73 13-36 (475)
175 smart00734 ZnF_Rad18 Rad18-lik 39.8 16 0.00034 17.4 0.8 10 91-100 3-12 (26)
176 PF05715 zf-piccolo: Piccolo Z 38.9 25 0.00055 20.5 1.6 10 90-99 3-12 (61)
177 PF07423 DUF1510: Protein of u 38.5 36 0.00077 25.1 2.8 23 4-26 15-37 (217)
178 PF04216 FdhE: Protein involve 38.0 3 6.5E-05 31.7 -3.0 43 50-98 171-220 (290)
179 PF09943 DUF2175: Uncharacteri 37.3 36 0.00078 22.0 2.3 34 52-86 3-36 (101)
180 TIGR00627 tfb4 transcription f 35.7 29 0.00063 26.5 2.0 9 90-98 270-278 (279)
181 PRK01343 zinc-binding protein; 35.5 24 0.00052 20.4 1.2 12 89-100 9-20 (57)
182 KOG0824 Predicted E3 ubiquitin 35.3 19 0.00042 27.9 1.0 51 49-102 103-153 (324)
183 PF00130 C1_1: Phorbol esters/ 35.3 27 0.00059 19.0 1.4 34 50-83 10-45 (53)
184 KOG2071 mRNA cleavage and poly 34.8 24 0.00051 29.8 1.5 37 49-85 511-557 (579)
185 COG3492 Uncharacterized protei 34.7 23 0.0005 22.5 1.1 12 75-86 42-53 (104)
186 smart00746 TRASH metallochaper 34.0 33 0.00071 15.9 1.5 9 92-100 1-9 (39)
187 PRK00418 DNA gyrase inhibitor; 33.6 23 0.0005 20.8 0.9 11 90-100 7-17 (62)
188 PF13453 zf-TFIIB: Transcripti 31.8 23 0.0005 18.5 0.7 13 91-103 1-13 (41)
189 COG4068 Uncharacterized protei 31.3 34 0.00074 19.9 1.4 16 89-104 8-23 (64)
190 PF09986 DUF2225: Uncharacteri 31.2 19 0.00041 26.3 0.4 20 89-108 5-24 (214)
191 PRK11088 rrmA 23S rRNA methylt 31.0 35 0.00075 25.4 1.8 25 52-76 3-27 (272)
192 PF07423 DUF1510: Protein of u 30.9 40 0.00086 24.8 2.0 26 1-26 15-40 (217)
193 PRK03564 formate dehydrogenase 30.8 15 0.00032 28.6 -0.3 42 50-97 186-234 (309)
194 TIGR02652 conserved hypothetic 30.1 19 0.0004 24.8 0.2 14 89-102 9-22 (163)
195 PF09654 DUF2396: Protein of u 30.0 19 0.00041 24.7 0.2 14 89-102 6-19 (161)
196 COG1545 Predicted nucleic-acid 29.9 30 0.00065 23.5 1.2 21 70-99 33-53 (140)
197 PF14169 YdjO: Cold-inducible 29.5 38 0.00082 19.7 1.4 16 49-64 37-52 (59)
198 PF14311 DUF4379: Domain of un 29.4 40 0.00087 18.7 1.5 7 89-95 49-55 (55)
199 PF06937 EURL: EURL protein; 28.6 51 0.0011 25.2 2.2 44 52-95 31-76 (285)
200 PF13956 Ibs_toxin: Toxin Ibs, 28.6 28 0.00061 15.3 0.6 8 2-9 2-9 (19)
201 PF06024 DUF912: Nucleopolyhed 28.4 47 0.001 21.2 1.8 10 6-15 63-72 (101)
202 COG3763 Uncharacterized protei 28.3 1.2E+02 0.0027 18.2 3.5 25 2-26 2-26 (71)
203 PF15353 HECA: Headcase protei 27.9 42 0.00091 21.9 1.5 15 71-85 39-53 (107)
204 PF05568 ASFV_J13L: African sw 27.7 1E+02 0.0022 21.5 3.4 6 10-15 38-43 (189)
205 PF09125 COX2-transmemb: Cytoc 27.5 1E+02 0.0022 16.1 3.2 14 3-16 15-28 (38)
206 PF15122 TMEM206: TMEM206 prot 27.5 70 0.0015 24.2 2.8 12 67-78 70-81 (298)
207 PF10083 DUF2321: Uncharacteri 27.0 42 0.0009 23.5 1.5 26 73-102 27-52 (158)
208 PF03119 DNA_ligase_ZBD: NAD-d 26.7 19 0.0004 17.5 -0.2 10 91-100 1-10 (28)
209 PF10717 ODV-E18: Occlusion-de 26.6 1.1E+02 0.0025 19.0 3.2 8 19-26 38-45 (85)
210 COG2835 Uncharacterized conser 26.2 33 0.00072 20.0 0.7 11 90-100 9-19 (60)
211 PRK11827 hypothetical protein; 25.9 36 0.00078 19.8 0.9 12 90-101 9-20 (60)
212 PF05545 FixQ: Cbb3-type cytoc 25.8 1.2E+02 0.0025 16.4 2.9 7 9-15 14-20 (49)
213 PF01485 IBR: IBR domain; Int 25.3 3.5 7.7E-05 23.3 -3.6 33 52-84 19-58 (64)
214 KOG2979 Protein involved in DN 25.0 37 0.0008 25.7 1.0 45 51-97 176-221 (262)
215 COG2991 Uncharacterized protei 24.8 1.3E+02 0.0028 18.3 3.1 28 2-29 2-29 (77)
216 smart00647 IBR In Between Ring 24.3 11 0.00025 21.2 -1.5 15 71-85 45-59 (64)
217 KOG1245 Chromatin remodeling c 24.3 27 0.00058 32.7 0.1 53 47-99 1104-1159(1404)
218 COG4338 Uncharacterized protei 23.8 28 0.00061 19.4 0.1 11 90-100 13-23 (54)
219 KOG1512 PHD Zn-finger protein 23.6 32 0.0007 26.6 0.4 33 50-82 313-345 (381)
220 cd00029 C1 Protein kinase C co 23.4 46 0.001 17.5 1.0 33 51-83 11-45 (50)
221 KOG1701 Focal adhesion adaptor 23.4 13 0.00028 30.1 -1.7 17 90-106 395-411 (468)
222 smart00109 C1 Protein kinase C 23.4 62 0.0013 16.8 1.5 33 51-83 11-44 (49)
223 COG5216 Uncharacterized conser 23.2 23 0.00049 20.7 -0.3 26 71-96 26-51 (67)
224 KOG4443 Putative transcription 23.2 53 0.0011 28.2 1.6 49 51-99 18-72 (694)
225 PRK01844 hypothetical protein; 23.0 1.8E+02 0.0038 17.6 3.5 18 3-20 3-20 (72)
226 COG3813 Uncharacterized protei 23.0 1.3E+02 0.0029 18.3 2.9 44 53-100 7-52 (84)
227 PRK11875 psbT photosystem II r 22.8 1.2E+02 0.0026 15.2 2.6 14 3-16 5-18 (31)
228 PF12292 DUF3624: Protein of u 22.6 20 0.00043 22.0 -0.7 21 77-97 3-23 (77)
229 PF03107 C1_2: C1 domain; Int 22.4 47 0.001 16.1 0.8 28 53-80 2-29 (30)
230 TIGR01562 FdhE formate dehydro 22.2 47 0.001 25.8 1.1 41 51-97 184-232 (305)
231 KOG0956 PHD finger protein AF1 21.9 49 0.0011 28.8 1.2 51 50-100 116-182 (900)
232 PF11682 DUF3279: Protein of u 21.8 70 0.0015 21.6 1.7 22 70-101 101-122 (128)
233 CHL00031 psbT photosystem II p 21.6 1.2E+02 0.0025 15.5 2.1 13 3-15 5-17 (33)
234 PF09538 FYDLN_acid: Protein o 21.1 55 0.0012 21.3 1.1 14 89-102 26-39 (108)
235 PF13240 zinc_ribbon_2: zinc-r 21.0 71 0.0015 14.6 1.2 10 92-101 2-11 (23)
236 cd04718 BAH_plant_2 BAH, or Br 21.0 37 0.00079 23.5 0.3 28 76-103 2-32 (148)
237 PLN02248 cellulose synthase-li 20.9 1.1E+02 0.0024 28.1 3.2 29 71-100 149-177 (1135)
238 KOG3726 Uncharacterized conser 20.9 58 0.0013 28.1 1.5 41 51-95 654-695 (717)
No 1
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=8.8e-19 Score=134.12 Aligned_cols=72 Identities=29% Similarity=0.659 Sum_probs=56.8
Q ss_pred ccccceecccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112 34 QLVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT 106 (132)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~ 106 (132)
.+++...|......... ..|+||+|+|++|++++.|||+|.||..||++|+.+....||+|+.++.......
T Consensus 213 ~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~~~ 284 (348)
T KOG4628|consen 213 KKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSGSE 284 (348)
T ss_pred hhCCcEEeccccccCCC-ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCCCC
Confidence 35566666655554333 6999999999999999999999999999999999765456999999886554433
No 2
>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=99.62 E-value=1.6e-16 Score=88.37 Aligned_cols=44 Identities=41% Similarity=1.132 Sum_probs=38.8
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCH 96 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr 96 (132)
++|+||++++..++.+..++|+|.||.+|+.+|++. +.+||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR-NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence 479999999998888888999999999999999986 47999997
No 3
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.48 E-value=2.5e-14 Score=107.15 Aligned_cols=52 Identities=40% Similarity=1.007 Sum_probs=47.1
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
.+-+|+|||+++..+++.+.+||+|.||..|+++|+......||+||+++++
T Consensus 322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 4679999999999999999999999999999999996445689999999986
No 4
>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=99.40 E-value=3e-13 Score=82.95 Aligned_cols=45 Identities=31% Similarity=0.827 Sum_probs=34.4
Q ss_pred ccccccccccccCC----------CceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEG----------EEIRELSCHHLFHAVCLDTWISNNYAICPVCH 96 (132)
Q Consensus 51 ~~~C~IC~~~~~~~----------~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr 96 (132)
++.|+||++++.+. -.+...+|||.||..||.+|++. +.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence 45699999999332 12343499999999999999975 46999997
No 5
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=99.35 E-value=1.3e-12 Score=100.40 Aligned_cols=51 Identities=24% Similarity=0.817 Sum_probs=42.5
Q ss_pred Ccccccccccccc-cCC---------CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHI-EEG---------EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~-~~~---------~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.++..|.||++++ ..+ ..++.|||||.+|.+|++.|+. ++++||.||.++.
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-RqQTCPICr~p~i 345 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVI 345 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-hccCCCcccCccc
Confidence 5688999999994 333 2467899999999999999997 4689999999953
No 6
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.34 E-value=1.8e-12 Score=96.52 Aligned_cols=52 Identities=29% Similarity=0.766 Sum_probs=44.4
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
+....|.+|++..++ +..+||||+||..||..|...+ ..||+||.++.+.+.
T Consensus 237 ~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek-~eCPlCR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEK-AECPLCREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccc-cCCCcccccCCCcce
Confidence 456899999998777 6668999999999999999764 679999999877654
No 7
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.33 E-value=1e-12 Score=96.83 Aligned_cols=51 Identities=29% Similarity=0.753 Sum_probs=41.0
Q ss_pred CcccccccccccccCCCc-----eEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEE-----IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~-----~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
..+.+|+||++.+.+++. ...++|+|.||..||.+|++. +.+||+||.++.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEee
Confidence 346799999999876431 233489999999999999975 579999999775
No 8
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.28 E-value=3.6e-12 Score=90.75 Aligned_cols=56 Identities=23% Similarity=0.652 Sum_probs=43.8
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc---------------CCCCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN---------------NYAICPVCHDSIAPSRWLTG 107 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~---------------~~~~CP~Cr~~~~~~~~~~~ 107 (132)
.++.+|+||++.+++ +..++|||.||..||..|+.. +...||+||.++......+-
T Consensus 16 ~~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPi 86 (193)
T PLN03208 16 GGDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPI 86 (193)
T ss_pred CCccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEe
Confidence 356799999998876 566799999999999999842 12479999999976544433
No 9
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=99.27 E-value=3.6e-12 Score=79.46 Aligned_cols=52 Identities=25% Similarity=0.677 Sum_probs=39.3
Q ss_pred cccccccccccccC--------CCc-eEEe-CCCCcccHHhHHHHHhc--CCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEE--------GEE-IREL-SCHHLFHAVCLDTWISN--NYAICPVCHDSIAP 101 (132)
Q Consensus 50 ~~~~C~IC~~~~~~--------~~~-~~~l-~C~H~fh~~Ci~~wl~~--~~~~CP~Cr~~~~~ 101 (132)
+++.|.||...|.. ++. +..+ .|+|.||..||.+|+.. .+..||+||+++..
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF 83 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence 36789999988852 222 2333 89999999999999953 34689999998754
No 10
>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=99.22 E-value=1.1e-11 Score=70.60 Aligned_cols=47 Identities=30% Similarity=0.796 Sum_probs=38.3
Q ss_pred cccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
++..|.||++...+ +..+||||. ||..|+..|++. ...||+||+++.
T Consensus 1 ~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~-~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 1 EDEECPICFENPRD---VVLLPCGHLCFCEECAERLLKR-KKKCPICRQPIE 48 (50)
T ss_dssp -HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHT-TSBBTTTTBB-S
T ss_pred CcCCCccCCccCCc---eEEeCCCChHHHHHHhHHhccc-CCCCCcCChhhc
Confidence 35689999998665 777899999 999999999984 589999999874
No 11
>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=99.21 E-value=1.7e-11 Score=67.17 Aligned_cols=45 Identities=36% Similarity=1.004 Sum_probs=36.1
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
+|+||++.+.. .....+|+|.||..|+..|++.++..||+||..+
T Consensus 1 ~C~iC~~~~~~--~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhC--ceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 59999999832 3444479999999999999976457899999764
No 12
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.16 E-value=2.1e-11 Score=88.46 Aligned_cols=53 Identities=26% Similarity=0.640 Sum_probs=42.5
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC--CCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN--YAICPVCHDSIAPSRW 104 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~~~ 104 (132)
....+|.||++.-++ +.++.|||.||..||.+|++.. ...||+|+..+..++.
T Consensus 45 ~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v 99 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV 99 (230)
T ss_pred CCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence 456799999998666 6777899999999999999432 3468999998875543
No 13
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.15 E-value=2.2e-11 Score=90.11 Aligned_cols=64 Identities=28% Similarity=0.660 Sum_probs=52.0
Q ss_pred CcccccccccccccCCC-------ceEEeCCCCcccHHhHHHHH-hcCCCCCCCCCCCCCCCCCCCCCCCcE
Q 042112 49 AEAVECAVCLSHIEEGE-------EIRELSCHHLFHAVCLDTWI-SNNYAICPVCHDSIAPSRWLTGHGEEV 112 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~-------~~~~l~C~H~fh~~Ci~~wl-~~~~~~CP~Cr~~~~~~~~~~~~~~~~ 112 (132)
.++..|+||-..+.... +.-.|.|+|+||..||+.|. .++..+||.|+..++.+++-.++.+..
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsnpWekp 293 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSNPWEKP 293 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccCccccc
Confidence 46789999999885544 56678999999999999998 445679999999999888877765543
No 14
>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=99.13 E-value=4.8e-11 Score=64.47 Aligned_cols=39 Identities=28% Similarity=0.924 Sum_probs=32.1
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~C 95 (132)
|+||++.+.+ .+..++|||.||..|+.+|++. +..||+|
T Consensus 1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~-~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEK-NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred CCCCCCcccC--cCEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence 8999998877 2356799999999999999986 5899998
No 15
>PHA02926 zinc finger-like protein; Provisional
Probab=99.12 E-value=4.7e-11 Score=86.35 Aligned_cols=52 Identities=25% Similarity=0.745 Sum_probs=38.9
Q ss_pred CcccccccccccccCC----C-ceEEe-CCCCcccHHhHHHHHhcC-----CCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEG----E-EIREL-SCHHLFHAVCLDTWISNN-----YAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~----~-~~~~l-~C~H~fh~~Ci~~wl~~~-----~~~CP~Cr~~~~ 100 (132)
..+.+|+||++..-+. + ....| +|+|.||..||..|.+.+ ..+||+||..+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 4568999999986432 1 12344 999999999999999643 245999999764
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.11 E-value=9.3e-11 Score=64.37 Aligned_cols=39 Identities=31% Similarity=0.772 Sum_probs=29.8
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHhcCC---CCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY---AICPVC 95 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~---~~CP~C 95 (132)
|+||++.+.+ +..|+|||.|+..||..|.+..+ ..||.|
T Consensus 1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999999998 78799999999999999995433 369987
No 17
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.10 E-value=6.3e-11 Score=82.89 Aligned_cols=54 Identities=24% Similarity=0.669 Sum_probs=43.4
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
++-..|+|||+.+.+... .-+.|||+||..||+..++. ...||+|++.+..+..
T Consensus 129 ~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKN-TNKCPTCRKKITHKQF 182 (187)
T ss_pred ccccCCCceecchhhccc-cccccchhHHHHHHHHHHHh-CCCCCCcccccchhhh
Confidence 456799999999887432 33689999999999999975 4789999998865543
No 18
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=99.08 E-value=1.3e-10 Score=64.37 Aligned_cols=44 Identities=30% Similarity=0.762 Sum_probs=37.4
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
.|++|++++.+......++|||.||..|+.... .....||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-CCCCCCcCCCC
Confidence 499999999666667878999999999999988 34578999985
No 19
>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=99.01 E-value=3.3e-10 Score=61.61 Aligned_cols=40 Identities=35% Similarity=0.966 Sum_probs=33.4
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHh-cCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS-NNYAICPVC 95 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~-~~~~~CP~C 95 (132)
|+||++.+.+. ...++|+|.||..|+.+|++ .+...||+|
T Consensus 1 C~iC~~~~~~~--~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDP--VILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSE--EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCC--CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999988773 23679999999999999997 445679998
No 20
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=99.00 E-value=4.6e-10 Score=59.31 Aligned_cols=39 Identities=31% Similarity=1.011 Sum_probs=32.4
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~C 95 (132)
|+||++... ....++|+|.||..|++.|++..+..||+|
T Consensus 1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 789998833 367789999999999999997445779987
No 21
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.00 E-value=8.2e-10 Score=87.68 Aligned_cols=53 Identities=32% Similarity=0.857 Sum_probs=41.1
Q ss_pred CcccccccccccccCCC--------------ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGE--------------EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~--------------~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
+...+|+|||.++.--. ....+||+|+||..|+.+|....+-.||+||.++++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 34568999999873211 124459999999999999997445689999999975
No 22
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=2.3e-10 Score=93.56 Aligned_cols=51 Identities=29% Similarity=0.858 Sum_probs=43.6
Q ss_pred CcccccccccccccCCCc--eEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEE--IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~--~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
..+..|+||++.+..+.+ ++.++|+|.||..|+..|++. +++||+||..+.
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~ 341 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLY 341 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-hCcCCcchhhhh
Confidence 347899999999988655 677899999999999999985 589999999554
No 23
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.91 E-value=1.1e-09 Score=67.03 Aligned_cols=51 Identities=29% Similarity=0.772 Sum_probs=37.5
Q ss_pred cccccccccc-----------cCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112 52 VECAVCLSHI-----------EEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 52 ~~C~IC~~~~-----------~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~ 103 (132)
+.|+||...+ ..+++.... .|+|.||..||.+|+.. +..||++|+++...+
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~~~~ 84 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWVLAD 84 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeEEec
Confidence 4566666554 344554433 79999999999999976 479999999876544
No 24
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=98.90 E-value=1.9e-09 Score=63.66 Aligned_cols=51 Identities=12% Similarity=0.333 Sum_probs=42.2
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT 106 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~ 106 (132)
..|+||.+.+.+ +..++|||+|++.||.+|++. +..||+|+.++..+....
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCChhhcee
Confidence 469999999887 455799999999999999975 578999999886554433
No 25
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.90 E-value=2.5e-10 Score=69.23 Aligned_cols=51 Identities=25% Similarity=0.749 Sum_probs=37.8
Q ss_pred cccccccccccccC--------CCceE-Ee-CCCCcccHHhHHHHH--hcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEE--------GEEIR-EL-SCHHLFHAVCLDTWI--SNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~--------~~~~~-~l-~C~H~fh~~Ci~~wl--~~~~~~CP~Cr~~~~ 100 (132)
.+++|.||.-+|.. ++... ++ .|.|.||..||.+|+ .+++..||+||+.+.
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 45589999888743 23333 23 799999999999999 334567999999764
No 26
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.79 E-value=5.1e-09 Score=82.37 Aligned_cols=50 Identities=26% Similarity=0.634 Sum_probs=42.2
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
+....|+||++.+.. +..++|+|.||..||..|+.. ...||+||.++...
T Consensus 24 e~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~~ 73 (397)
T TIGR00599 24 DTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQES 73 (397)
T ss_pred ccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccccc
Confidence 456799999999876 456799999999999999975 46899999988654
No 27
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.71 E-value=7.6e-09 Score=76.54 Aligned_cols=53 Identities=30% Similarity=0.743 Sum_probs=42.8
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHH-HHhcCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDT-WISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~-wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
..+..|+||++.... +..++|||+||..||-. |-.++...||+||+...+++.
T Consensus 213 ~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence 457899999998776 66689999999999999 876544459999998766543
No 28
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.69 E-value=1.4e-08 Score=55.90 Aligned_cols=39 Identities=28% Similarity=0.642 Sum_probs=22.3
Q ss_pred cccccccccCCC-ceEEeCCCCcccHHhHHHHHhcC---CCCCC
Q 042112 54 CAVCLSHIEEGE-EIRELSCHHLFHAVCLDTWISNN---YAICP 93 (132)
Q Consensus 54 C~IC~~~~~~~~-~~~~l~C~H~fh~~Ci~~wl~~~---~~~CP 93 (132)
|+||.+ +...+ .+..|+|||.|+.+|+.++++.+ ...||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 75544 46778999999999999999643 34576
No 29
>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=98.65 E-value=3e-08 Score=75.47 Aligned_cols=56 Identities=16% Similarity=0.491 Sum_probs=41.1
Q ss_pred cccccccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL 105 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~ 105 (132)
++..||+|...--.+...+.+ +|||.||..|++..+..+...||.|+.++......
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr 59 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR 59 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence 356899999964333333223 79999999999997755557899999988766543
No 30
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.59 E-value=3.2e-08 Score=63.47 Aligned_cols=52 Identities=29% Similarity=0.724 Sum_probs=38.0
Q ss_pred cccccccccccc-------c-----CCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHI-------E-----EGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 50 ~~~~C~IC~~~~-------~-----~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
.-+.|+||...+ + ..++.... .|+|.||..||.+|++++ ..||+|.++....
T Consensus 45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr-~vCPLdn~eW~~q 110 (114)
T KOG2930|consen 45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTR-NVCPLDNKEWVFQ 110 (114)
T ss_pred eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhc-CcCCCcCcceeEe
Confidence 456899998765 1 11223333 799999999999999865 7899998876543
No 31
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.56 E-value=3e-08 Score=79.18 Aligned_cols=55 Identities=22% Similarity=0.570 Sum_probs=42.4
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC----CCCCCCCCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN----YAICPVCHDSIAPSRWLTGH 108 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~----~~~CP~Cr~~~~~~~~~~~~ 108 (132)
+..||||+++... +..+.|||+||..||-+++... ...||+||..+..++..+-.
T Consensus 186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeee
Confidence 7789999998665 4446799999999999887432 35799999998876554443
No 32
>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=98.56 E-value=9.1e-08 Score=54.13 Aligned_cols=43 Identities=23% Similarity=0.714 Sum_probs=32.0
Q ss_pred ccccccccccCCCceEEeCCC-----CcccHHhHHHHHhcC-CCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISNN-YAICPVCH 96 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr 96 (132)
.|.||++.. .++.....||. |.+|..|+.+|+..+ +.+||+|+
T Consensus 1 ~CrIC~~~~-~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEG-DEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCCCC-CCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 489999833 33445557885 899999999999443 45799995
No 33
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=98.51 E-value=7.9e-08 Score=58.76 Aligned_cols=54 Identities=13% Similarity=0.342 Sum_probs=41.4
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLT 106 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~ 106 (132)
+...|+|+.+-|.+ +..+++||.|.+.+|..|+..++..||+++.++.......
T Consensus 3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~p 56 (73)
T PF04564_consen 3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIP 56 (73)
T ss_dssp GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE
T ss_pred cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceE
Confidence 45689999999998 7778999999999999999765689999999887655443
No 34
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.41 E-value=1.1e-07 Score=74.98 Aligned_cols=49 Identities=33% Similarity=0.774 Sum_probs=39.3
Q ss_pred CcccccccccccccCCCce-EEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEI-RELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.+-++||||+|.+...... ....|.|.||..|+..|. ..+||+||.-..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---~~scpvcR~~q~ 222 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---DSSCPVCRYCQS 222 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc---cCcChhhhhhcC
Confidence 3678999999998775433 334899999999999995 468999997655
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=98.38 E-value=4.5e-08 Score=59.43 Aligned_cols=50 Identities=34% Similarity=0.802 Sum_probs=22.9
Q ss_pred cccccccccccc-CCCceEEe----CCCCcccHHhHHHHHhc--CC--------CCCCCCCCCCC
Q 042112 51 AVECAVCLSHIE-EGEEIREL----SCHHLFHAVCLDTWISN--NY--------AICPVCHDSIA 100 (132)
Q Consensus 51 ~~~C~IC~~~~~-~~~~~~~l----~C~H~fh~~Ci~~wl~~--~~--------~~CP~Cr~~~~ 100 (132)
+.+|.||++... .++.+... .|+..||..|+.+|+.. +. ..||.|++++.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 457999999865 33333322 68999999999999932 11 15999998774
No 36
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.36 E-value=1.4e-07 Score=72.27 Aligned_cols=51 Identities=22% Similarity=0.628 Sum_probs=43.2
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
.-..|.||.+-|.. +..+||+|.||..||...+.. +..||.|+.++.+...
T Consensus 22 ~lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~L 72 (442)
T KOG0287|consen 22 DLLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESDL 72 (442)
T ss_pred HHHHHhHHHHHhcC---ceeccccchHHHHHHHHHhcc-CCCCCceecccchhhh
Confidence 45689999999887 666799999999999999985 5899999988876544
No 37
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.32 E-value=2.6e-07 Score=69.55 Aligned_cols=51 Identities=27% Similarity=0.690 Sum_probs=42.2
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
.-..|.||.+-+.. +..++|||.||..||...+.. +..||+||.+..+...
T Consensus 24 s~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~-qp~CP~Cr~~~~esrl 74 (391)
T COG5432 24 SMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGT-QPFCPVCREDPCESRL 74 (391)
T ss_pred hHHHhhhhhheeec---ceecccccchhHHHHHHHhcC-CCCCccccccHHhhhc
Confidence 45679999998887 566799999999999999974 6899999988765443
No 38
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.31 E-value=1.7e-07 Score=79.62 Aligned_cols=52 Identities=31% Similarity=0.772 Sum_probs=38.4
Q ss_pred CcccccccccccccCCCc----eEEeCCCCcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEE----IRELSCHHLFHAVCLDTWISN-NYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~----~~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~ 100 (132)
.+-++|+||+..+..-+. -+.-.|.|.||..|+.+|++. ++++||+||.+++
T Consensus 1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 456789999987752111 122369999999999999943 4568999998875
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.27 E-value=3.6e-07 Score=67.74 Aligned_cols=44 Identities=34% Similarity=0.713 Sum_probs=38.6
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCH 96 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr 96 (132)
.+...|+||++.+... ..++|+|.||..|+..+.. ....||.||
T Consensus 11 ~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-~~~~Cp~cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-GPLSCPVCR 54 (386)
T ss_pred cccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-CCcCCcccC
Confidence 4567899999999985 6679999999999999887 457899999
No 40
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.25 E-value=4.6e-07 Score=68.35 Aligned_cols=50 Identities=26% Similarity=0.557 Sum_probs=41.5
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
-..+|+||+..... +..|+|+|.||..||+.-.+....+||+||.+++..
T Consensus 6 ~~~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 6 KKKECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST 55 (324)
T ss_pred cCCcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence 45689999987665 455899999999999987766667899999999754
No 41
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.20 E-value=1.5e-06 Score=66.87 Aligned_cols=49 Identities=29% Similarity=0.676 Sum_probs=39.0
Q ss_pred CcccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
+.+.+|.||+.+.++ +.+|||.|. .|..|.+...- .+.+||+||+++..
T Consensus 288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~-q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRY-QTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHH-hhcCCCccccchHh
Confidence 457899999998777 788999986 67788887652 24689999999853
No 42
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=2.5e-07 Score=71.10 Aligned_cols=56 Identities=25% Similarity=0.506 Sum_probs=45.4
Q ss_pred CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG 107 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~ 107 (132)
..+..|+||++.++. .+.. .|.|.||.+||..-++.++..||.||+.+.......+
T Consensus 41 ~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~ 97 (381)
T KOG0311|consen 41 DIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRI 97 (381)
T ss_pred hhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCC
Confidence 356789999999887 3333 7999999999999997777899999999876665443
No 43
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.15 E-value=6.4e-07 Score=74.52 Aligned_cols=52 Identities=21% Similarity=0.547 Sum_probs=42.9
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL 105 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~ 105 (132)
-..|++|-..+.+ .....|+|+||..|+..-+..+++.||.|-..|.+.+..
T Consensus 643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH 694 (698)
T ss_pred ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence 4589999976655 555689999999999999977789999999988766543
No 44
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=98.09 E-value=1.6e-06 Score=68.64 Aligned_cols=80 Identities=28% Similarity=0.473 Sum_probs=59.3
Q ss_pred CCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC---CCcEEEeeeecCCCc
Q 042112 47 SRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH---GEEVLVLKFRCFNSR 123 (132)
Q Consensus 47 ~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 123 (132)
..+++..|++|+..+.++-.. +.|||.||..|+..|+.. +..||.|+..+..++..... ..+++.+...+.+..
T Consensus 17 ~~~~~l~C~~C~~vl~~p~~~--~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~ 93 (391)
T KOG0297|consen 17 PLDENLLCPICMSVLRDPVQT--TTCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFAS 93 (391)
T ss_pred CCcccccCccccccccCCCCC--CCCCCcccccccchhhcc-CcCCcccccccchhhccCchHHHHHHHHhcccccccCC
Confidence 346778999999998874321 589999999999999986 68999999988766655432 344444555666666
Q ss_pred ccccccc
Q 042112 124 TERDTWW 130 (132)
Q Consensus 124 ~~~~~~~ 130 (132)
. ||.|-
T Consensus 94 ~-GC~~~ 99 (391)
T KOG0297|consen 94 R-GCRAD 99 (391)
T ss_pred C-Ccccc
Confidence 6 77774
No 45
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.07 E-value=1.9e-06 Score=67.13 Aligned_cols=51 Identities=27% Similarity=0.805 Sum_probs=36.1
Q ss_pred ccccccccccccCC-CceEEe-CCCCcccHHhHHHHHhcCC--CCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEG-EEIREL-SCHHLFHAVCLDTWISNNY--AICPVCHDSIAPS 102 (132)
Q Consensus 51 ~~~C~IC~~~~~~~-~~~~~l-~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~~~ 102 (132)
...|.|| .++.+. ..+.-. .|||+||..|+.+|+..-. +.||.||-.++..
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r 58 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQER 58 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccce
Confidence 4579999 444443 334334 5999999999999995433 4799999555443
No 46
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.04 E-value=2.3e-06 Score=66.41 Aligned_cols=52 Identities=25% Similarity=0.605 Sum_probs=38.9
Q ss_pred CcccccccccccccCCC-----ceEEeCCCCcccHHhHHHHHhcCC------CCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGE-----EIRELSCHHLFHAVCLDTWISNNY------AICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~-----~~~~l~C~H~fh~~Ci~~wl~~~~------~~CP~Cr~~~~ 100 (132)
..+.+|.||++...+.. --+..+|.|.||..||..|-+.++ +.||.||....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 35789999999876543 112237999999999999984333 68999997653
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.97 E-value=1.3e-06 Score=51.61 Aligned_cols=50 Identities=26% Similarity=0.672 Sum_probs=24.5
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL 105 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~ 105 (132)
--.|++|.+-++++ +....|+|.||..||..-+. ..||+|+.+--.++..
T Consensus 7 lLrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT---TB-SSS--B-S-SS--
T ss_pred hcCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHH
Confidence 34799999988762 33348999999999988553 4599999876555443
No 48
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.91 E-value=1.9e-06 Score=49.22 Aligned_cols=46 Identities=24% Similarity=0.561 Sum_probs=33.2
Q ss_pred ccccccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
+++|.||++...+ .....|||. .|..|-.+-++..+..||.||.++
T Consensus 7 ~dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi 53 (62)
T KOG4172|consen 7 SDECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPI 53 (62)
T ss_pred ccceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence 4789999987544 333479986 456776665554568999999976
No 49
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.83 E-value=1.6e-05 Score=62.35 Aligned_cols=49 Identities=29% Similarity=0.820 Sum_probs=38.0
Q ss_pred cccccccccccccCCCceEE--eCCCCcccHHhHHHHHh-cCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRE--LSCHHLFHAVCLDTWIS-NNYAICPVCHDS 98 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~--l~C~H~fh~~Ci~~wl~-~~~~~CP~Cr~~ 98 (132)
...+|+||++.+.-....+. +.|+|.|..+||..|+. .....||.|...
T Consensus 3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 45689999999876554333 58999999999999993 223579999754
No 50
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.80 E-value=5.4e-06 Score=67.01 Aligned_cols=79 Identities=29% Similarity=0.586 Sum_probs=56.0
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHH----hcCCCCCCCCCCCCCCCCCCCCC-CCcEEEeeeecCCCc
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI----SNNYAICPVCHDSIAPSRWLTGH-GEEVLVLKFRCFNSR 123 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl----~~~~~~CP~Cr~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 123 (132)
.+..+|.+|.++-++ .....|.|.||+.|+..+. ...+-+||+|-..+.-....+.. ......++-+|+=++
T Consensus 534 k~~~~C~lc~d~aed---~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~alek~~l~~Fk~sSIlnR 610 (791)
T KOG1002|consen 534 KGEVECGLCHDPAED---YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPALEKTDLKGFKASSILNR 610 (791)
T ss_pred cCceeecccCChhhh---hHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhhhhcchhhhhhHHHhhh
Confidence 467799999998666 6667899999999998876 33346899998877544332222 133444556777777
Q ss_pred ccccccc
Q 042112 124 TERDTWW 130 (132)
Q Consensus 124 ~~~~~~~ 130 (132)
.+-++|.
T Consensus 611 inm~~~q 617 (791)
T KOG1002|consen 611 INMDDWQ 617 (791)
T ss_pred cchhhhc
Confidence 7788885
No 51
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.79 E-value=5.8e-06 Score=69.35 Aligned_cols=57 Identities=23% Similarity=0.471 Sum_probs=40.9
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH 108 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ 108 (132)
...|++|+..+.+.......+|+|.||..|+..|-+. ..+||+||..+..-......
T Consensus 123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~v~V~eS~ 179 (1134)
T KOG0825|consen 123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGEVKVLEST 179 (1134)
T ss_pred hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh-cccCchhhhhhheeeeeccc
Confidence 3456677666655444344589999999999999975 47999999988644443333
No 52
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.61 E-value=5.9e-05 Score=55.13 Aligned_cols=56 Identities=32% Similarity=0.674 Sum_probs=44.7
Q ss_pred CCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-------CCCCCCCCCCCCCC
Q 042112 46 GSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-------YAICPVCHDSIAPS 102 (132)
Q Consensus 46 ~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-------~~~CP~Cr~~~~~~ 102 (132)
..++....|..|-..+..++.++ |.|-|.||.+|+..|..+- .-.||-|-.++.+.
T Consensus 45 ~DsDY~pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp 107 (299)
T KOG3970|consen 45 QDSDYNPNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP 107 (299)
T ss_pred hhcCCCCCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence 34456778999999999988766 7799999999999997421 13799999888654
No 53
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.56 E-value=3e-05 Score=60.94 Aligned_cols=48 Identities=25% Similarity=0.686 Sum_probs=37.6
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-CCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-YAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~ 100 (132)
.-.-|.||-+.=. .++.-||||..|..|+..|-... ...||.||.++.
T Consensus 368 TFeLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK 416 (563)
T KOG1785|consen 368 TFELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIK 416 (563)
T ss_pred hHHHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence 3457999987533 36767999999999999998322 468999998775
No 54
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.50 E-value=7.3e-05 Score=41.85 Aligned_cols=45 Identities=20% Similarity=0.589 Sum_probs=22.5
Q ss_pred cccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
|++|.+++...+. ... +|++..+..|...-++..+..||-||++.
T Consensus 1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7899999844433 223 67899999998887754457899999875
No 55
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=97.49 E-value=3.5e-05 Score=60.34 Aligned_cols=48 Identities=31% Similarity=0.755 Sum_probs=37.6
Q ss_pred cccccccccccccCC-CceEEeCCCCcccHHhHHHHHhc-CCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEG-EEIRELSCHHLFHAVCLDTWISN-NYAICPVCHD 97 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~ 97 (132)
-+..|..|-+.+... +....|||.|+||..|+...+.+ ...+||.||+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence 356799999987543 34566799999999999999943 3468999984
No 56
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.39 E-value=0.00014 Score=64.92 Aligned_cols=67 Identities=19% Similarity=0.499 Sum_probs=48.3
Q ss_pred cccceecccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC---------CCCCCCCCCCCCC
Q 042112 35 LVNIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN---------YAICPVCHDSIAP 101 (132)
Q Consensus 35 ~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~---------~~~CP~Cr~~~~~ 101 (132)
-+|-+.-.......+.++.|.||..+--.....++|.|+|.||..|...-+..+ -.+||.|+.++..
T Consensus 3470 CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3470 CLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred cccccccChhhhhcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence 345444433333435788999999887666778889999999999997755321 1379999988753
No 57
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.00011 Score=58.28 Aligned_cols=49 Identities=29% Similarity=0.627 Sum_probs=41.4
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
..+.+|.||+..+.+ +..+||||.||..||.+-+.. ...||.||.++..
T Consensus 82 ~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCC---CccccccccccHHHHHHHhcc-CCCCccccccccc
Confidence 467899999988777 566799999999999997763 5789999999875
No 58
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=97.34 E-value=0.00012 Score=40.90 Aligned_cols=41 Identities=34% Similarity=0.839 Sum_probs=26.9
Q ss_pred cccccccccCCCceEEeCCC-----CcccHHhHHHHHh-cCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWIS-NNYAICPVC 95 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~-~~~~~CP~C 95 (132)
|-||++.-.+++ .-..||+ ...|..|+.+|+. .++.+|++|
T Consensus 1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 779998866655 2335665 3789999999994 334679887
No 59
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.33 E-value=0.00016 Score=42.01 Aligned_cols=44 Identities=25% Similarity=0.597 Sum_probs=28.2
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHh-cCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS-NNYAICPV 94 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~-~~~~~CP~ 94 (132)
.....|||.+..++++ ++-..|+|.|-+..|.++++ .+...||+
T Consensus 9 ~~~~~CPiT~~~~~~P--V~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFEDP--VKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-SSE--EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred EeccCCCCcCChhhCC--cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 3467899999998872 44458999999999999993 23457998
No 60
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.0011 Score=49.86 Aligned_cols=50 Identities=22% Similarity=0.430 Sum_probs=37.6
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN-NYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~ 100 (132)
..+.+|++|-+.-..+ ....+|+|+||..|+..-... ....||.|-.+..
T Consensus 237 t~~~~C~~Cg~~PtiP--~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIP--HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCC--eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 4678999999875542 333489999999999886632 1368999988775
No 61
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=97.20 E-value=0.00036 Score=48.45 Aligned_cols=50 Identities=20% Similarity=0.570 Sum_probs=36.3
Q ss_pred CcccccccccccccCCCceEEeCCC--C---cccHHhHHHHHhc-CCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCH--H---LFHAVCLDTWISN-NYAICPVCHDSIAPS 102 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~--H---~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~~ 102 (132)
..+..|-||.++-.+ . ..||. . ..|.+|+..|+.. +...||.|+.++...
T Consensus 6 ~~~~~CRIC~~~~~~--~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYDV--V--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCCC--c--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence 567899999987432 1 13555 3 6699999999943 456799999987544
No 62
>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=97.10 E-value=0.00023 Score=48.14 Aligned_cols=36 Identities=25% Similarity=0.663 Sum_probs=30.2
Q ss_pred ccccccccccccCCCceEEeCCC------CcccHHhHHHHHh
Q 042112 51 AVECAVCLSHIEEGEEIRELSCH------HLFHAVCLDTWIS 86 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~------H~fh~~Ci~~wl~ 86 (132)
.-+|.||++.+.+++.+..++|+ |.||.+|+.+|-.
T Consensus 26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence 56899999999885666667776 9999999999953
No 63
>PHA02862 5L protein; Provisional
Probab=97.00 E-value=0.00059 Score=46.65 Aligned_cols=48 Identities=21% Similarity=0.537 Sum_probs=34.8
Q ss_pred ccccccccccccCCCceEEeCCC-----CcccHHhHHHHHhc-CCCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISN-NYAICPVCHDSIAPS 102 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~~ 102 (132)
++.|-||.++-.++ .-||. ...|.+|+.+|+.. ++..||.|+.++..+
T Consensus 2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 46799999974332 23554 67899999999943 345799999887533
No 64
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00051 Score=52.19 Aligned_cols=48 Identities=25% Similarity=0.653 Sum_probs=40.7
Q ss_pred cccccccccccCCC---ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGE---EIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 52 ~~C~IC~~~~~~~~---~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
..|-||-++|...+ .++.|.|||.++..|+..-+......||.||.+.
T Consensus 4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 57999999998764 3677899999999999998876556799999985
No 65
>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=96.83 E-value=0.00046 Score=44.48 Aligned_cols=33 Identities=24% Similarity=0.656 Sum_probs=26.5
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHH
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLD 82 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 82 (132)
.++..|++|...+.. ......||||+||..|++
T Consensus 76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence 456789999999877 344556999999999975
No 66
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.82 E-value=0.0004 Score=48.42 Aligned_cols=41 Identities=24% Similarity=0.554 Sum_probs=31.8
Q ss_pred cceecccccCCCCcccccccccccccCCCceEEeCCCCcccH
Q 042112 37 NIWEDRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHA 78 (132)
Q Consensus 37 ~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~ 78 (132)
|.+.|++.... ++..+|.||+|++..++.+..|||-.+||+
T Consensus 164 PrlsYNdDVL~-ddkGECvICLEdL~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 164 PRLSYNDDVLK-DDKGECVICLEDLEAGDTIARLPCLCIYHK 204 (205)
T ss_pred cccccccchhc-ccCCcEEEEhhhccCCCceeccceEEEeec
Confidence 33444444333 567789999999999999999999999986
No 67
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.77 E-value=0.00099 Score=51.58 Aligned_cols=54 Identities=17% Similarity=0.385 Sum_probs=39.8
Q ss_pred CcccccccccccccCCCceEE-eCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
++++.|+.|++++...++-.. -+||-..|..|...--+.-+..||-||.....+
T Consensus 12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de 66 (480)
T COG5175 12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE 66 (480)
T ss_pred cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence 445569999999876655332 379998899887766554467899999877654
No 68
>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=96.75 E-value=0.00075 Score=36.94 Aligned_cols=42 Identities=21% Similarity=0.700 Sum_probs=23.3
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCC-CCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYA-ICPVC 95 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~-~CP~C 95 (132)
|.+|.+....|+......|+-.+|..|+..+++.+.. .||.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 6778877776654443368889999999999965433 59987
No 69
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=96.73 E-value=0.0009 Score=56.96 Aligned_cols=49 Identities=29% Similarity=0.758 Sum_probs=36.6
Q ss_pred CcccccccccccccCCCce-EEeCCCCcccHHhHHHHHhcCC------CCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEI-RELSCHHLFHAVCLDTWISNNY------AICPVCHD 97 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~wl~~~~------~~CP~Cr~ 97 (132)
....+|.||.+.+.....+ .--.|-|+||..||..|..... =.||.|+.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 4678999999998765432 2225889999999999984321 15999984
No 70
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.73 E-value=0.0019 Score=48.00 Aligned_cols=53 Identities=15% Similarity=0.288 Sum_probs=45.7
Q ss_pred cccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~ 103 (132)
..+.|++|.+.+.+...+..| ||||+|+..|+.+.... -..||+|-.++...+
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrd 273 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRD 273 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccc
Confidence 567899999999998888878 99999999999999874 478999988876554
No 71
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.69 E-value=0.00061 Score=49.05 Aligned_cols=45 Identities=22% Similarity=0.454 Sum_probs=36.9
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
...|.||.++|+. +..+.|||.||..|...-++. ...|-+|-+..
T Consensus 196 PF~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~k-g~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYES---PVVTECGHSFCSLCAIRKYQK-GDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccc---hhhhhcchhHHHHHHHHHhcc-CCcceecchhh
Confidence 3489999999988 566789999999999887764 47899997654
No 72
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.67 E-value=0.0015 Score=50.78 Aligned_cols=57 Identities=16% Similarity=0.340 Sum_probs=41.0
Q ss_pred cccccCCCCcccccccccccccCCCceEEeCCCCcccHHhHHHHH-hcCCCCCCCCCCCCC
Q 042112 41 DRFELGSRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI-SNNYAICPVCHDSIA 100 (132)
Q Consensus 41 ~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl-~~~~~~CP~Cr~~~~ 100 (132)
.......+++...|.||-+.+.- ...+||+|..|--|..+-- -..+..||.||++..
T Consensus 51 tsSaddtDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e 108 (493)
T COG5236 51 TSSADDTDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTETE 108 (493)
T ss_pred cccccccccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence 33344454677899999987765 5667999999999986543 123468999998754
No 73
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.001 Score=51.69 Aligned_cols=45 Identities=27% Similarity=0.558 Sum_probs=34.4
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
...+.|.||+++..+ ...+||||.-| |...... ..+||+||..+.
T Consensus 303 ~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs~~--l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 303 PQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCSKH--LPQCPVCRQRIR 347 (355)
T ss_pred CCCCceEEecCCccc---eeeecCCcEEE--chHHHhh--CCCCchhHHHHH
Confidence 456789999998766 77789999955 7666544 357999998763
No 74
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=96.64 E-value=0.0012 Score=37.91 Aligned_cols=46 Identities=26% Similarity=0.527 Sum_probs=32.2
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~ 103 (132)
..|..|... +.+-..+||+|..+..|..-+ +-+-||.|-+++...+
T Consensus 8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~---rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGE---RYNGCPFCGTPFEFDD 53 (55)
T ss_pred eeEEEcccc---ccccccccccceeeccccChh---hccCCCCCCCcccCCC
Confidence 345555543 223455799999999998764 3467999999886554
No 75
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=96.47 E-value=0.0019 Score=49.17 Aligned_cols=53 Identities=26% Similarity=0.712 Sum_probs=42.2
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhc-----------------C-----CCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISN-----------------N-----YAICPVCHDSIAP 101 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~-----------------~-----~~~CP~Cr~~~~~ 101 (132)
-....|.||+-.|..++....++|.|.||..|+.++++. + ...||+||..+..
T Consensus 113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 456689999999999888888999999999999776511 0 1269999988753
No 76
>PF04641 Rtf2: Rtf2 RING-finger
Probab=96.45 E-value=0.0049 Score=46.31 Aligned_cols=54 Identities=19% Similarity=0.347 Sum_probs=43.3
Q ss_pred CcccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
.....|||...+|........+ +|||+|...++..-- ....||+|-.++...+.
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~~~Di 165 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFTEEDI 165 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCccccCCE
Confidence 5678999999999665555556 999999999999973 24679999999876554
No 77
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=96.41 E-value=0.0031 Score=47.77 Aligned_cols=52 Identities=21% Similarity=0.504 Sum_probs=37.8
Q ss_pred ccccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRW 104 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~ 104 (132)
.|++|..+.--+..+..+ +|+|..|.+|++.-+..+...||.|-..+-....
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhccc
Confidence 589998754332222222 9999999999999997777899999776644433
No 78
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.38 E-value=0.0017 Score=49.53 Aligned_cols=54 Identities=19% Similarity=0.506 Sum_probs=39.5
Q ss_pred ccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCC-CCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVC-HDSIAPSRWLTG 107 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~C-r~~~~~~~~~~~ 107 (132)
...|+.|..-+.+. ..+ -|+|.||..||...|......||.| |+++.......+
T Consensus 274 ~LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD 329 (427)
T COG5222 274 SLKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPD 329 (427)
T ss_pred cccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCcccccchhhccCcc
Confidence 36899999887773 334 5899999999999886556899999 445544444333
No 79
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.0034 Score=49.34 Aligned_cols=50 Identities=20% Similarity=0.333 Sum_probs=41.6
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC--CCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY--AICPVCHDSI 99 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~ 99 (132)
.--.|||=.+.-.+...+..|.|||+..++-+.+..+++. ..||.|=...
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ 384 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence 4568999999888878888899999999999999887655 5799995433
No 80
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=96.28 E-value=0.0024 Score=47.16 Aligned_cols=51 Identities=24% Similarity=0.552 Sum_probs=35.9
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTG 107 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~ 107 (132)
.|..|..--. ++....+.|.|+||..|...-. ...||.|++++-...+..+
T Consensus 5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~---~~~C~lCkk~ir~i~l~~s 55 (233)
T KOG4739|consen 5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS---PDVCPLCKKSIRIIQLNRS 55 (233)
T ss_pred EeccccccCC-CCceeeeechhhhhhhhcccCC---ccccccccceeeeeecccc
Confidence 4777765444 5566777999999999987632 2489999998755444443
No 81
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=96.16 E-value=0.019 Score=44.34 Aligned_cols=47 Identities=23% Similarity=0.465 Sum_probs=36.1
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDS 98 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~ 98 (132)
.+...|++|+....++. ....-|-+||..|+-.+.. +...||+=-.+
T Consensus 298 ~~~~~CpvClk~r~Npt--vl~vSGyVfCY~Ci~~Yv~-~~~~CPVT~~p 344 (357)
T KOG0826|consen 298 PDREVCPVCLKKRQNPT--VLEVSGYVFCYPCIFSYVV-NYGHCPVTGYP 344 (357)
T ss_pred CccccChhHHhccCCCc--eEEecceEEeHHHHHHHHH-hcCCCCccCCc
Confidence 46779999999877632 2225799999999999998 46899985444
No 82
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.15 E-value=0.0016 Score=50.01 Aligned_cols=51 Identities=20% Similarity=0.555 Sum_probs=40.4
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~ 103 (132)
...+|.+|-.-+.++. ....|-|.||+.||...+.. +..||+|...+....
T Consensus 14 ~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t~ 64 (331)
T KOG2660|consen 14 PHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKTH 64 (331)
T ss_pred cceehhhccceeecch--hHHHHHHHHHHHHHHHHHHH-hccCCccceeccCcc
Confidence 5678999988777643 33479999999999999986 579999988775444
No 83
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.15 E-value=0.0034 Score=48.96 Aligned_cols=48 Identities=19% Similarity=0.405 Sum_probs=38.8
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.++..|+||...--. ....||+|.-|..||.+-+.+ .+.|=.|++.+.
T Consensus 420 sEd~lCpICyA~pi~---Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPIN---AVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccch---hhccCCCCchHHHHHHHHHhc-CCeeeEecceee
Confidence 478899999875333 444699999999999999984 578999988765
No 84
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.0032 Score=47.83 Aligned_cols=47 Identities=21% Similarity=0.376 Sum_probs=38.2
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
-...|-||...|.. +.+..|+|.||..|...=++. ...|++|-+...
T Consensus 240 ~Pf~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 240 LPFKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTH 286 (313)
T ss_pred CCcccccccccccc---chhhcCCceeehhhhcccccc-CCcceecccccc
Confidence 35579999999988 566789999999999887764 478999977653
No 85
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.09 E-value=0.0054 Score=48.54 Aligned_cols=36 Identities=22% Similarity=0.661 Sum_probs=29.5
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHH
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI 85 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl 85 (132)
.-..|.||+++..-......+||+|+||+.|...++
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~ 218 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYF 218 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHH
Confidence 356899999986544556667999999999999998
No 86
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.98 E-value=0.0068 Score=43.04 Aligned_cols=34 Identities=35% Similarity=0.914 Sum_probs=26.6
Q ss_pred eCCCCcccHHhHHHHHhc----CC------CCCCCCCCCCCCCC
Q 042112 70 LSCHHLFHAVCLDTWISN----NY------AICPVCHDSIAPSR 103 (132)
Q Consensus 70 l~C~H~fh~~Ci~~wl~~----~~------~~CP~Cr~~~~~~~ 103 (132)
..||.-||.-|+..|++. ++ ..||.|-.++..+-
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm 231 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM 231 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence 479999999999999832 22 27999999886543
No 87
>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=95.97 E-value=0.0035 Score=46.43 Aligned_cols=50 Identities=32% Similarity=0.594 Sum_probs=38.1
Q ss_pred cccccccccccccCCCceEEe--C-CCCcccHHhHHHHHhcCCCCCC--CCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIREL--S-CHHLFHAVCLDTWISNNYAICP--VCHDSI 99 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l--~-C~H~fh~~Ci~~wl~~~~~~CP--~Cr~~~ 99 (132)
.+..||+|..+--.+-.+..+ | |-|..|.+|+++-+..+...|| -|-+-+
T Consensus 9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 466899999875443334444 5 9999999999999977788999 785433
No 88
>PHA03096 p28-like protein; Provisional
Probab=95.94 E-value=0.0042 Score=47.32 Aligned_cols=46 Identities=22% Similarity=0.516 Sum_probs=31.5
Q ss_pred cccccccccccCCC----ceEEe-CCCCcccHHhHHHHHhcCC--CCCCCCCC
Q 042112 52 VECAVCLSHIEEGE----EIREL-SCHHLFHAVCLDTWISNNY--AICPVCHD 97 (132)
Q Consensus 52 ~~C~IC~~~~~~~~----~~~~l-~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~ 97 (132)
..|.||++...... .-..| .|.|.||..|+..|...+. ..||.||.
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~ 231 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR 231 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence 68999999775432 12334 8999999999999984332 34555443
No 89
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=95.84 E-value=0.011 Score=46.40 Aligned_cols=30 Identities=20% Similarity=0.790 Sum_probs=23.2
Q ss_pred CCCcccHHhHHHHHhcCC------------CCCCCCCCCCCC
Q 042112 72 CHHLFHAVCLDTWISNNY------------AICPVCHDSIAP 101 (132)
Q Consensus 72 C~H~fh~~Ci~~wl~~~~------------~~CP~Cr~~~~~ 101 (132)
|....|.+|+.+|+..++ ..||+||+.+..
T Consensus 311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi 352 (358)
T PF10272_consen 311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI 352 (358)
T ss_pred ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence 557789999999994433 269999998764
No 90
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.37 E-value=0.0034 Score=47.67 Aligned_cols=41 Identities=27% Similarity=0.662 Sum_probs=30.5
Q ss_pred ccccccccccccCCCceEEeCCCCcc-cHHhHHHHHhcCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLF-HAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~f-h~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
+.-|+||++...+ ...|+|||.. |..|-+. -..||+||+.+
T Consensus 300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkr-----m~eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKR-----MNECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcc---eEEeecCcEEeehhhccc-----cccCchHHHHH
Confidence 6789999998766 7889999963 3455333 24799999755
No 91
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=95.30 E-value=0.011 Score=44.82 Aligned_cols=47 Identities=26% Similarity=0.671 Sum_probs=37.9
Q ss_pred cccccccccccccCCCc-eEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE-IRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~-~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
....||||.+.+..... +..++|||.-|..|+......+ .+||+|.+
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 34459999997766543 5667999999999999988755 89999987
No 92
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.99 E-value=0.014 Score=50.02 Aligned_cols=43 Identities=23% Similarity=0.685 Sum_probs=32.9
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
...|..|-..+..+ ..-..|+|.||.+|+.. +...||.|+.+.
T Consensus 840 ~skCs~C~~~LdlP--~VhF~CgHsyHqhC~e~----~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 840 VSKCSACEGTLDLP--FVHFLCGHSYHQHCLED----KEDKCPKCLPEL 882 (933)
T ss_pred eeeecccCCccccc--eeeeecccHHHHHhhcc----CcccCCccchhh
Confidence 46899998887763 23347999999999982 457899998743
No 93
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=94.91 E-value=0.0081 Score=33.39 Aligned_cols=43 Identities=23% Similarity=0.627 Sum_probs=24.0
Q ss_pred ccccccccccCCCceEEeCCC-CcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCH-HLFHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
.|.-|+-.... .+.|+ |..|..|+...+.. ...||+|..+++.
T Consensus 4 nCKsCWf~~k~-----Li~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPt 47 (50)
T PF03854_consen 4 NCKSCWFANKG-----LIKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPT 47 (50)
T ss_dssp ---SS-S--SS-----EEE-SS-EEEHHHHHHT-SS-SSEETTTTEE---
T ss_pred cChhhhhcCCC-----eeeecchhHHHHHHHHHhcc-ccCCCcccCcCcc
Confidence 47777754322 23586 99999999999874 4789999998874
No 94
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=94.75 E-value=0.041 Score=38.33 Aligned_cols=36 Identities=31% Similarity=0.697 Sum_probs=22.6
Q ss_pred cccccccccccccCCC---------ceEEeCCC-CcccHHhHHHHH
Q 042112 50 EAVECAVCLSHIEEGE---------EIRELSCH-HLFHAVCLDTWI 85 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~---------~~~~l~C~-H~fh~~Ci~~wl 85 (132)
++..|+|||+--.++- ..+-.-|+ -.-|..|++++.
T Consensus 1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 4578999999765521 11212244 345789999875
No 95
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=94.59 E-value=0.0097 Score=45.66 Aligned_cols=43 Identities=26% Similarity=0.673 Sum_probs=33.5
Q ss_pred cccccccccccccCCCceEEeCC--CCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSC--HHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C--~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
+-.+||||.+.+..+ + ..| ||..|..|-.+ ....||.||.++.
T Consensus 47 ~lleCPvC~~~l~~P---i-~QC~nGHlaCssC~~~----~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPP---I-FQCDNGHLACSSCRTK----VSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCccc---c-eecCCCcEehhhhhhh----hcccCCccccccc
Confidence 456899999998862 2 456 59999988764 3468999999987
No 96
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=94.19 E-value=0.045 Score=47.03 Aligned_cols=69 Identities=14% Similarity=0.412 Sum_probs=48.6
Q ss_pred CCCcccccccccccccCCCceEEeCCC-----CcccHHhHHHHHhc-CCCCCCCCCCCCCCCCCCCCCCCcEEEee
Q 042112 47 SRAEAVECAVCLSHIEEGEEIRELSCH-----HLFHAVCLDTWISN-NYAICPVCHDSIAPSRWLTGHGEEVLVLK 116 (132)
Q Consensus 47 ~~~~~~~C~IC~~~~~~~~~~~~l~C~-----H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~~~~~~~~~~~~~~~~~ 116 (132)
..+++..|.||..+-.++++.- -||. ...|.+|+.+|+.- +...|-.|..++..++.-...-.++..+.
T Consensus 8 mN~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP~~IPfs 82 (1175)
T COG5183 8 MNEDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQIIPFS 82 (1175)
T ss_pred CCccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCCccccee
Confidence 3356789999998766655422 3665 57899999999942 33579999999887776666555555443
No 97
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.12 E-value=0.026 Score=48.55 Aligned_cols=35 Identities=23% Similarity=0.399 Sum_probs=27.6
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHH
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTW 84 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w 84 (132)
++++.|.+|..++... .-...||||.||.+|+.+-
T Consensus 815 ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~ 849 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRH 849 (911)
T ss_pred cCccchHHhcchhhcC-cceeeeccchHHHHHHHHH
Confidence 5678999999887653 3444599999999999664
No 98
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=94.09 E-value=0.012 Score=49.87 Aligned_cols=49 Identities=24% Similarity=0.545 Sum_probs=37.6
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC-CCCCCCCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY-AICPVCHDSIAPSRW 104 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~-~~CP~Cr~~~~~~~~ 104 (132)
..|.+|++ .+.+...+|+|.||..|+..-++..+ ..||.||..+.....
T Consensus 455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL 504 (674)
T ss_pred cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence 78999998 23366679999999999999885433 359999987765443
No 99
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.81 E-value=0.0028 Score=49.83 Aligned_cols=51 Identities=18% Similarity=0.594 Sum_probs=42.2
Q ss_pred ccccccccccccCC-CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEG-EEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 51 ~~~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
...|+||.+.+... ++...+-|||.+|..|+.+|+.. ...||.|+..++..
T Consensus 196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPKN 247 (465)
T ss_pred HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhhh
Confidence 45799999988776 55666789999999999999965 47899999988643
No 100
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.06 E-value=0.049 Score=40.82 Aligned_cols=52 Identities=23% Similarity=0.579 Sum_probs=35.5
Q ss_pred CcccccccccccccCCCce-EEeCCC-----CcccHHhHHHHHhcCCC-------CCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEI-RELSCH-----HLFHAVCLDTWISNNYA-------ICPVCHDSIA 100 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~-~~l~C~-----H~fh~~Ci~~wl~~~~~-------~CP~Cr~~~~ 100 (132)
+.+..|-||+..=+++... =+-||. |=.|..|+..|..+++. .||.|+++..
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence 5677899999864443221 112664 78899999999943322 5999998764
No 101
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.80 E-value=0.35 Score=37.45 Aligned_cols=48 Identities=21% Similarity=0.351 Sum_probs=37.3
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC--CCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY--AICPVCH 96 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~--~~CP~Cr 96 (132)
-.--.||+-.+.-.+...+..|.|||+.-+.-++..-+++. ..||.|-
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 34568999888777766677789999999999998775442 4699994
No 102
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=92.45 E-value=0.085 Score=40.05 Aligned_cols=50 Identities=24% Similarity=0.600 Sum_probs=35.8
Q ss_pred ccccccccccccCCCc-eEEeCCC-----CcccHHhHHHHHhc-CCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEE-IRELSCH-----HLFHAVCLDTWISN-NYAICPVCHDSIA 100 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~-~~~l~C~-----H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~ 100 (132)
+..|-||..+...... ....||. +..|..|+..|+.. +...|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 4689999997654322 2334665 77899999999953 3467999987654
No 103
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.41 E-value=0.071 Score=40.75 Aligned_cols=30 Identities=27% Similarity=0.659 Sum_probs=23.3
Q ss_pred CCCcccHHhHHHHHhcCC------------CCCCCCCCCCCC
Q 042112 72 CHHLFHAVCLDTWISNNY------------AICPVCHDSIAP 101 (132)
Q Consensus 72 C~H~fh~~Ci~~wl~~~~------------~~CP~Cr~~~~~ 101 (132)
|....|.+|+.+|+..++ .+||+||+.+.-
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci 366 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI 366 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence 567889999999984432 379999998764
No 104
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.29 E-value=0.065 Score=42.57 Aligned_cols=37 Identities=27% Similarity=0.593 Sum_probs=27.1
Q ss_pred cccccccccccccCC-CceEEeCCCCcccHHhHHHHHh
Q 042112 50 EAVECAVCLSHIEEG-EEIRELSCHHLFHAVCLDTWIS 86 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~-~~~~~l~C~H~fh~~Ci~~wl~ 86 (132)
...+|.||..+...+ +......|+|.||.+|..+.++
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 467899999444333 3333458999999999998885
No 105
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=91.72 E-value=0.091 Score=40.47 Aligned_cols=43 Identities=30% Similarity=0.617 Sum_probs=28.1
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
-|.-|-..+.. --+..||.|+||.+|...= .-+.||.|-..+.
T Consensus 92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~~---~dK~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAI--YGRMIPCKHVFCLECARSD---SDKICPLCDDRVQ 134 (389)
T ss_pred eecccCCccee--eecccccchhhhhhhhhcC---ccccCcCcccHHH
Confidence 46666554433 1244599999999997641 2357999976553
No 106
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=91.14 E-value=0.24 Score=33.58 Aligned_cols=54 Identities=28% Similarity=0.660 Sum_probs=35.5
Q ss_pred cccccccccccccCCCceEE-eCCCCcccHHhHHH-HH-hcCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDT-WI-SNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~-wl-~~~~~~CP~Cr~~~~~~~ 103 (132)
.-.+|.||.|.-.+..-..- --||-..|.-|-.. |- ..-+..||+|++++..+.
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 45789999987655321110 13898888887765 54 222478999999885443
No 107
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.47 E-value=0.2 Score=43.00 Aligned_cols=39 Identities=26% Similarity=0.696 Sum_probs=26.2
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPV 94 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~ 94 (132)
|+||........ .....|+|+.|.+|...|+..+ ..||.
T Consensus 1031 C~~C~l~V~gss-~~Cg~C~Hv~H~sc~~eWf~~g-d~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVRGSS-NFCGTCGHVGHTSCMMEWFRTG-DVCPS 1069 (1081)
T ss_pred eeeEeeEeeccc-hhhccccccccHHHHHHHHhcC-CcCCC
Confidence 555544433221 2234799999999999999864 68874
No 108
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=90.28 E-value=0.17 Score=40.84 Aligned_cols=35 Identities=29% Similarity=0.538 Sum_probs=30.3
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHh
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS 86 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~ 86 (132)
+++..|+||..-|++ ++.|||+|..|..|...-+.
T Consensus 2 eeelkc~vc~~f~~e---piil~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 2 EEELKCPVCGSFYRE---PIILPCSHNLCQACARNILV 36 (699)
T ss_pred cccccCceehhhccC---ceEeecccHHHHHHHHhhcc
Confidence 467789999998887 78899999999999987664
No 109
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.87 E-value=0.51 Score=27.01 Aligned_cols=44 Identities=25% Similarity=0.625 Sum_probs=30.9
Q ss_pred cccccccccccccCCCceEE-eCCCCcccHHhHHHHHhcCCCCCCC--CCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTWISNNYAICPV--CHDS 98 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~wl~~~~~~CP~--Cr~~ 98 (132)
....|++|-+++.+++...+ -.|+--+|+.|... ...|-. |..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~-----~g~C~~~~c~~~ 50 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK-----AGGCINYSCGTG 50 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh-----CCceEeccCCCC
Confidence 45679999999986555443 38999999999543 245654 5443
No 110
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.51 E-value=0.42 Score=35.90 Aligned_cols=53 Identities=17% Similarity=0.332 Sum_probs=40.0
Q ss_pred cccccccccccccCCCceEEe-CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIREL-SCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWL 105 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~ 105 (132)
....|+|=.-+|.....-..+ +|||+|-..-+.+- +..+|++|...+...+..
T Consensus 110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei---kas~C~~C~a~y~~~dvI 163 (293)
T KOG3113|consen 110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI---KASVCHVCGAAYQEDDVI 163 (293)
T ss_pred ceeecccccceecceEEEEEEeccceeccHHHHHHh---hhccccccCCcccccCeE
Confidence 456899988777765544445 99999999888774 347899999998776643
No 111
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=86.02 E-value=0.81 Score=28.14 Aligned_cols=51 Identities=16% Similarity=0.396 Sum_probs=22.7
Q ss_pred cccccccccccccCCCc--eEE--eCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE--IRE--LSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~--~~~--l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
....|.||-++...... +-. ..|+--.|+.|..-=.+.+++.||.|+++..
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 45689999998744322 222 2677778899988766667789999998875
No 112
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=85.55 E-value=0.19 Score=42.55 Aligned_cols=49 Identities=31% Similarity=0.807 Sum_probs=37.7
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC--CCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN--YAICPVCHDSIAPS 102 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~ 102 (132)
..+|+||.+.+..+ ..+.|.|.|+..|+..-+... ...||+|+..+...
T Consensus 21 ~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~ 71 (684)
T KOG4362|consen 21 ILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR 71 (684)
T ss_pred hccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence 56799999998874 456899999999998766322 35799999776533
No 113
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=85.37 E-value=0.24 Score=44.64 Aligned_cols=47 Identities=21% Similarity=0.574 Sum_probs=36.7
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
+...|.||++.+..-. ....|+|.+|..|...|+.. +..||.|+...
T Consensus 1152 ~~~~c~ic~dil~~~~--~I~~cgh~~c~~c~~~~l~~-~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQG--GIAGCGHEPCCRCDELWLYA-SSRCPICKSIK 1198 (1394)
T ss_pred cccchHHHHHHHHhcC--CeeeechhHhhhHHHHHHHH-hccCcchhhhh
Confidence 4458999999987421 22469999999999999975 57899998543
No 114
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=84.65 E-value=1.3 Score=22.40 Aligned_cols=38 Identities=26% Similarity=0.595 Sum_probs=24.2
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.|..|.+.+..++... ..=+..||..| ..|..|..++.
T Consensus 1 ~C~~C~~~i~~~~~~~-~~~~~~~H~~C---------f~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVL-RALGKVWHPEC---------FKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEE-EeCCccccccC---------CCCcccCCcCc
Confidence 3778888877652322 23467888766 56777776653
No 115
>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 KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.98 E-value=0.57 Score=39.61 Aligned_cols=43 Identities=26% Similarity=0.537 Sum_probs=31.3
Q ss_pred ccccccccccccCCC-ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGE-EIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~-~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
-..|.||+..|-... .++-+.|||..|..|+..-. +.+|| |..
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly---n~scp-~~~ 54 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY---NASCP-TKR 54 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh---hccCC-CCc
Confidence 346999987775433 24557899999999999864 36899 543
No 117
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.69 E-value=1.2 Score=37.01 Aligned_cols=52 Identities=29% Similarity=0.802 Sum_probs=39.0
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSRWLTGH 108 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~ 108 (132)
+....|.+|++.. ..+..+|. |..|+.+|+.. +..||.|+..+......+..
T Consensus 477 ~~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~-~~~~pl~~~~~~~~~~~~~~ 528 (543)
T KOG0802|consen 477 EPNDVCAICYQEM----SARITPCS---HALCLRKWLYV-QEVCPLCHTYMKEDDFLSKN 528 (543)
T ss_pred cccCcchHHHHHH----Hhcccccc---chhHHHhhhhh-ccccCCCchhhhcccccCcc
Confidence 4577899999987 24545677 89999999974 47899999887665554443
No 118
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=81.31 E-value=0.92 Score=32.86 Aligned_cols=40 Identities=28% Similarity=0.755 Sum_probs=26.3
Q ss_pred cccccccccc-----ccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112 51 AVECAVCLSH-----IEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCH 96 (132)
Q Consensus 51 ~~~C~IC~~~-----~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr 96 (132)
+..|.+|-++ |+.+...+--.|+-+||..|..+ ..||-|.
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~------~~CpkC~ 196 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK------KSCPKCA 196 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC------CCCCCcH
Confidence 5678888642 22222234347999999999762 4699994
No 119
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=81.20 E-value=1.8 Score=37.23 Aligned_cols=42 Identities=24% Similarity=0.443 Sum_probs=29.7
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPV 94 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~ 94 (132)
...|.+|...+..-. .-.--|+|.-|.+|+.+|+.. +..||.
T Consensus 779 ~~~CtVC~~vi~G~~-~~c~~C~H~gH~sh~~sw~~~-~s~ca~ 820 (839)
T KOG0269|consen 779 SAKCTVCDLVIRGVD-VWCQVCGHGGHDSHLKSWFFK-ASPCAK 820 (839)
T ss_pred hcCceeecceeeeeE-eecccccccccHHHHHHHHhc-CCCCcc
Confidence 457888877655411 111259999999999999974 567876
No 120
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.11 E-value=0.79 Score=33.42 Aligned_cols=39 Identities=28% Similarity=0.786 Sum_probs=25.8
Q ss_pred cccccccccCCCceEEeCCCCc-ccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHL-FHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
|..|.+.- ..+..+||.|. +|..|-.. -..||+|+.+..
T Consensus 161 Cr~C~~~~---~~VlllPCrHl~lC~~C~~~-----~~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGERE---ATVLLLPCRHLCLCGICDES-----LRICPICRSPKT 200 (207)
T ss_pred ceecCcCC---ceEEeecccceEeccccccc-----CccCCCCcChhh
Confidence 88887652 22566699865 55577443 246999987653
No 121
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=80.29 E-value=0.58 Score=39.08 Aligned_cols=24 Identities=38% Similarity=0.892 Sum_probs=18.9
Q ss_pred EEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112 68 RELSCHHLFHAVCLDTWISNNYAICPVC 95 (132)
Q Consensus 68 ~~l~C~H~fh~~Ci~~wl~~~~~~CP~C 95 (132)
+...|+++||..|... ++..||.|
T Consensus 533 rC~~C~avfH~~C~~r----~s~~CPrC 556 (580)
T KOG1829|consen 533 RCSTCLAVFHKKCLRR----KSPCCPRC 556 (580)
T ss_pred eHHHHHHHHHHHHHhc----cCCCCCch
Confidence 4458999999999765 44559999
No 122
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=80.23 E-value=0.97 Score=33.09 Aligned_cols=45 Identities=33% Similarity=0.792 Sum_probs=34.0
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
.-..|.+|..-.-.+ .+.=.|+-.+|..|+...++. ...||.|-.
T Consensus 180 nlk~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~-~~~cphc~d 224 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQR-RDICPHCGD 224 (235)
T ss_pred HHHHHhHhHHHhhee--eccCcccchhhhHHHHHHhcc-cCcCCchhc
Confidence 345899999865443 333368889999999999985 478999944
No 123
>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=80.23 E-value=1.9 Score=24.07 Aligned_cols=44 Identities=23% Similarity=0.612 Sum_probs=18.9
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHH----hcCCCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI----SNNYAICPVCHDS 98 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl----~~~~~~CP~Cr~~ 98 (132)
..|+|....+.. .++...|.|.-+.+ +..|+ +.+.-.||+|.++
T Consensus 3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence 368888877765 35555899985422 23444 2223469999764
No 124
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=76.74 E-value=1.8 Score=28.98 Aligned_cols=15 Identities=13% Similarity=0.011 Sum_probs=5.4
Q ss_pred HHHHHHHHHHHHHHH
Q 042112 6 IRFLRCLKWACNLLL 20 (132)
Q Consensus 6 i~~~~~l~~~~~~~~ 20 (132)
++++.|+.+++++++
T Consensus 4 l~~iii~~i~l~~~~ 18 (130)
T PF12273_consen 4 LFAIIIVAILLFLFL 18 (130)
T ss_pred eHHHHHHHHHHHHHH
Confidence 333333333333333
No 125
>PLN02195 cellulose synthase A
Probab=76.27 E-value=4.1 Score=36.18 Aligned_cols=54 Identities=19% Similarity=0.355 Sum_probs=37.5
Q ss_pred cccccccccccccCCCc--e--EEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE--I--RELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~--~--~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~ 103 (132)
....|.||-++...... + ..-.|+--.|+.|..-=.+.+++.||.|++...++.
T Consensus 5 ~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk~~~ 62 (977)
T PLN02195 5 GAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYDAEN 62 (977)
T ss_pred CCccceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCcccccc
Confidence 45589999997744322 2 222677779999995544556788999999887433
No 126
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.21 E-value=4.2 Score=32.89 Aligned_cols=38 Identities=26% Similarity=0.687 Sum_probs=30.4
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN 88 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~ 88 (132)
....+|.||.+.+.. ....+.|+|.|+..|....+..+
T Consensus 68 ~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~k 105 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTK 105 (444)
T ss_pred CccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhhe
Confidence 456789999998765 34557999999999999998543
No 127
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=76.15 E-value=3.3 Score=32.24 Aligned_cols=49 Identities=16% Similarity=0.432 Sum_probs=35.0
Q ss_pred ccccccccccccCCCceE-EeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIR-ELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~-~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
...|+||.++....+... -.+|++..|..|...-.. ++..||.||++..
T Consensus 249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~-~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISD-GDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCCcccccccccccccccccchhhhhhcccc-cCCCCCccCCccc
Confidence 368999999874444322 136788888888777665 4689999997764
No 128
>PLN02189 cellulose synthase
Probab=74.38 E-value=3.4 Score=36.88 Aligned_cols=51 Identities=16% Similarity=0.351 Sum_probs=36.1
Q ss_pred cccccccccccccCCC--ceEEe--CCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGE--EIREL--SCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~--~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
....|.||-+++.... .+.+. .|+--.|+.|..-=.+.+++.||.|++...
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 4568999999875322 22222 477778999996544556789999998875
No 129
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.18 E-value=1.8 Score=34.45 Aligned_cols=45 Identities=27% Similarity=0.579 Sum_probs=31.8
Q ss_pred cccccccccccccCCCceEEe--CCCCcccHHhHHHHHhcCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDTWISNNYAICPVC 95 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~wl~~~~~~CP~C 95 (132)
....|+.|.-.++..+....+ .|+|.||..|...|... +..|..|
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~-~~~~~~~ 351 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTH-NGECYEC 351 (384)
T ss_pred hcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhC-CccccCc
Confidence 356899998877665543322 58999999999999874 3455443
No 130
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=72.93 E-value=4.4 Score=31.63 Aligned_cols=53 Identities=23% Similarity=0.426 Sum_probs=35.2
Q ss_pred cccccccccccccC-----C----------Cc-eEEeCCCCcccHHhHHHHHhcC--------CCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEE-----G----------EE-IRELSCHHLFHAVCLDTWISNN--------YAICPVCHDSIAPS 102 (132)
Q Consensus 50 ~~~~C~IC~~~~~~-----~----------~~-~~~l~C~H~fh~~Ci~~wl~~~--------~~~CP~Cr~~~~~~ 102 (132)
.+.+|++|+..-.- + -. ....||||+--+.-..-|.+.. +..||.|-+.+..+
T Consensus 340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~PCGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge 416 (429)
T KOG3842|consen 340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNPCGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGE 416 (429)
T ss_pred ccCcCCeeeeecceeeeeccccceeEecCCCcccccCCcccccchhhhhHhhcCcCCCccccccccCcchhhhhccC
Confidence 46789999874210 0 00 1224999998888889997432 24799998877544
No 131
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=71.83 E-value=3.3 Score=23.08 Aligned_cols=40 Identities=23% Similarity=0.472 Sum_probs=26.8
Q ss_pred cccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCCC
Q 042112 54 CAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPSR 103 (132)
Q Consensus 54 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~ 103 (132)
|+.|.+.+..++... ..-+..||..| ..|-.|+.++....
T Consensus 1 C~~C~~~I~~~~~~~-~~~~~~~H~~C---------f~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTEIVI-KAMGKFWHPEC---------FKCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSSEEE-EETTEEEETTT---------SBETTTTCBTTTSS
T ss_pred CCCCCCCccCcEEEE-EeCCcEEEccc---------cccCCCCCccCCCe
Confidence 667777777544332 24677888766 57888888876554
No 132
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=71.83 E-value=0.2 Score=30.20 Aligned_cols=40 Identities=23% Similarity=0.547 Sum_probs=20.7
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
..||.|..++.... +|..|..|-..... ...||-|..++.
T Consensus 2 ~~CP~C~~~L~~~~-------~~~~C~~C~~~~~~--~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-------GHYHCEACQKDYKK--EAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET-------TEEEETTT--EEEE--EEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC-------CEEECcccccccee--cccCCCcccHHH
Confidence 46999988865422 55666666655433 357999988774
No 133
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=70.41 E-value=3.1 Score=31.54 Aligned_cols=50 Identities=30% Similarity=0.631 Sum_probs=34.7
Q ss_pred ccccccccccccCCCceEEe----CCCCcccHHhHHHHH-hcC-------CCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIREL----SCHHLFHAVCLDTWI-SNN-------YAICPVCHDSIA 100 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l----~C~H~fh~~Ci~~wl-~~~-------~~~CP~Cr~~~~ 100 (132)
..+|.+|.+++.+.+..+.. .|+-.+|..|+..-+ ... ...||.|++.+.
T Consensus 182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~ 243 (276)
T KOG3005|consen 182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS 243 (276)
T ss_pred chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence 36899999999554443322 588899999998844 211 147999987543
No 134
>PLN02436 cellulose synthase A
Probab=70.26 E-value=5.6 Score=35.73 Aligned_cols=51 Identities=20% Similarity=0.353 Sum_probs=35.7
Q ss_pred cccccccccccccCCC--ceEE--eCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGE--EIRE--LSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~--~~~~--l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
....|.||-++..... ++-+ -.|+--.|+.|.+-=.+.+++.||.|++...
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 4558999999873322 2222 2577778999996545556788999999876
No 135
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.67 E-value=0.61 Score=35.38 Aligned_cols=49 Identities=27% Similarity=0.405 Sum_probs=37.6
Q ss_pred cccccccccccccCCC---ceEEeC--------CCCcccHHhHHHHHhcCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGE---EIRELS--------CHHLFHAVCLDTWISNNYAICPVCHDS 98 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~---~~~~l~--------C~H~fh~~Ci~~wl~~~~~~CP~Cr~~ 98 (132)
.+..|.||...+..++ .++.+. |+|..+..|+..-+.+....||.|+..
T Consensus 206 ~~~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~~~~~cp~~~~~ 265 (296)
T KOG4185|consen 206 IEKLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQAGIKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHHhhhcCCcccce
Confidence 3467999999988432 245456 999999999999885444789999874
No 136
>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=68.44 E-value=2.3 Score=23.28 Aligned_cols=44 Identities=27% Similarity=0.606 Sum_probs=26.2
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhHHHHHh-----cCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS-----NNYAICPVCH 96 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~-----~~~~~CP~Cr 96 (132)
.|.||...-..++.+.--.|+..||..|+..-.. ...-.||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 3888988433333333238899999999865331 1123577664
No 137
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.37 E-value=3.5 Score=35.91 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=34.8
Q ss_pred cccccccccccccCCCc-eEEe---CCCCcccHHhHHHHHhcC-----CCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE-IREL---SCHHLFHAVCLDTWISNN-----YAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~-~~~l---~C~H~fh~~Ci~~wl~~~-----~~~CP~Cr~~~~ 100 (132)
+...|.+|..++.+++. .... .|+|.+|..||..|..+- +-.|++|..-|.
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~ 154 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG 154 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence 56678888888776332 1112 599999999999998321 235788876553
No 138
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.71 E-value=2.5 Score=36.51 Aligned_cols=37 Identities=19% Similarity=0.455 Sum_probs=28.0
Q ss_pred cccccccccccccCC----CceEEeCCCCcccHHhHHHHHh
Q 042112 50 EAVECAVCLSHIEEG----EEIRELSCHHLFHAVCLDTWIS 86 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~----~~~~~l~C~H~fh~~Ci~~wl~ 86 (132)
.+..|..|.+..-.. +....+.|+|.||+.|+..-..
T Consensus 783 ~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~ 823 (846)
T KOG2066|consen 783 VEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESL 823 (846)
T ss_pred ehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHH
Confidence 455899999876532 2356679999999999987664
No 139
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=66.60 E-value=7 Score=35.16 Aligned_cols=51 Identities=14% Similarity=0.317 Sum_probs=35.4
Q ss_pred cccccccccccccCCCc--eEE--eCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE--IRE--LSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~--~~~--l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
....|.||-++...... +-+ -.|+-=.|+.|..-=.+.+++.||.|++...
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 35589999998744322 221 2566668999985444556789999998775
No 140
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=64.91 E-value=9.3 Score=34.32 Aligned_cols=51 Identities=22% Similarity=0.388 Sum_probs=36.3
Q ss_pred cccccccccccccCCCc--eE--EeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE--IR--ELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~--~~--~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
....|.||-++...... +- .-.|+--.|+.|.+-=.+.+++.||.|++...
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 56789999998744322 22 12567778999996545556788999998876
No 141
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=64.85 E-value=8.6 Score=30.11 Aligned_cols=62 Identities=18% Similarity=0.222 Sum_probs=38.5
Q ss_pred cccceecccccCC-CCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 35 LVNIWEDRFELGS-RAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 35 ~~~~~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
..|...+.+.... ...+..|-.|.++.......+.-.|.+.||.+|=.---.. =-.||.|..
T Consensus 313 L~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHes-Lh~CpgCeh 375 (378)
T KOG2807|consen 313 LFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHES-LHNCPGCEH 375 (378)
T ss_pred hcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhh-hhcCCCcCC
Confidence 3344444433322 1245569999777666555555589999999996543332 237999964
No 142
>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=64.58 E-value=4.7 Score=24.01 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=8.6
Q ss_pred cccHHhHHHHHh
Q 042112 75 LFHAVCLDTWIS 86 (132)
Q Consensus 75 ~fh~~Ci~~wl~ 86 (132)
-||+.|+.+|..
T Consensus 11 gFCRNCLskWy~ 22 (68)
T PF06844_consen 11 GFCRNCLSKWYR 22 (68)
T ss_dssp S--HHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 499999999984
No 143
>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=64.19 E-value=4 Score=19.65 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=7.9
Q ss_pred CCCCCCCCCCC
Q 042112 91 ICPVCHDSIAP 101 (132)
Q Consensus 91 ~CP~Cr~~~~~ 101 (132)
+||.|++.++.
T Consensus 2 ~CP~C~~~V~~ 12 (26)
T PF10571_consen 2 TCPECGAEVPE 12 (26)
T ss_pred cCCCCcCCchh
Confidence 58888777753
No 144
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=63.88 E-value=5.2 Score=19.57 Aligned_cols=29 Identities=28% Similarity=0.523 Sum_probs=10.2
Q ss_pred ccccccccccCCCceEEeCCCCcccHHhH
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVCL 81 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci 81 (132)
.|.+|.++...+....-..|+-.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 47788877655233344578888888885
No 145
>PLN02400 cellulose synthase
Probab=62.23 E-value=7.5 Score=35.02 Aligned_cols=51 Identities=16% Similarity=0.376 Sum_probs=35.1
Q ss_pred cccccccccccccCCC--ceE--EeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGE--EIR--ELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~--~~~--~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
....|.||-++..... ++- .-.|+--.|+.|..-=-+.+++.||.|++...
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 4568999999874432 122 22566668999985433556688999998875
No 146
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=61.76 E-value=19 Score=20.74 Aligned_cols=47 Identities=21% Similarity=0.492 Sum_probs=31.9
Q ss_pred ccccccccccccCCCc-eEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEE-IRELSCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~-~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
...|--|-.++..+.. ..+-.=...||.+|...-+. ..||.|--.+.
T Consensus 5 rpnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~---~~CPNCgGelv 52 (57)
T PF06906_consen 5 RPNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN---GVCPNCGGELV 52 (57)
T ss_pred CCCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc---CcCcCCCCccc
Confidence 3457788888766552 22212236799999999774 58999977664
No 147
>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=60.69 E-value=3.8 Score=23.96 Aligned_cols=36 Identities=17% Similarity=0.369 Sum_probs=17.4
Q ss_pred CcccccccccccccCCCceEE-eCCCCcccHHhHHHH
Q 042112 49 AEAVECAVCLSHIEEGEEIRE-LSCHHLFHAVCLDTW 84 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~-l~C~H~fh~~Ci~~w 84 (132)
.+...|.+|..+|..-..-.. -.||++|+..|....
T Consensus 7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 346789999999965322111 269999998887543
No 148
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.86 E-value=4.9 Score=20.78 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=9.0
Q ss_pred ccccccccccCCC
Q 042112 53 ECAVCLSHIEEGE 65 (132)
Q Consensus 53 ~C~IC~~~~~~~~ 65 (132)
+|+=|...|..++
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 5777877776654
No 149
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=59.71 E-value=3 Score=33.34 Aligned_cols=51 Identities=20% Similarity=0.393 Sum_probs=0.0
Q ss_pred ccccccccccccC-----C---------Cc--eEEeCCCCcccHHhHHHHHhcC--------CCCCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEE-----G---------EE--IRELSCHHLFHAVCLDTWISNN--------YAICPVCHDSIAP 101 (132)
Q Consensus 51 ~~~C~IC~~~~~~-----~---------~~--~~~l~C~H~fh~~Ci~~wl~~~--------~~~CP~Cr~~~~~ 101 (132)
..+|++|+..-.. + .. ....||||+--.....-|.+.. +..||.|-.++..
T Consensus 328 ~r~CPlCr~~g~~V~L~mG~E~afyvD~~~pthaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g 402 (416)
T PF04710_consen 328 SRTCPLCRQVGPYVPLWMGCEPAFYVDSGPPTHAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDG 402 (416)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred cccCCCccccCCceeEeeccccceeecCCCCceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccC
Confidence 6799999974311 0 01 1224999999889999997321 1479999888863
No 150
>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=59.46 E-value=7.5 Score=21.92 Aligned_cols=42 Identities=29% Similarity=0.562 Sum_probs=19.5
Q ss_pred cccccccccCCCc-----eEE--eCCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112 54 CAVCLSHIEEGEE-----IRE--LSCHHLFHAVCLDTWISNNYAICPVCH 96 (132)
Q Consensus 54 C~IC~~~~~~~~~-----~~~--l~C~H~fh~~Ci~~wl~~~~~~CP~Cr 96 (132)
|.-|..++..... .+. -.|++.|+.+|=.- ....=-+||-|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~f-iHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVF-IHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHT-TTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChh-hhccccCCcCCC
Confidence 5556666655321 121 26899999999543 211123799984
No 151
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=58.91 E-value=2.6 Score=23.73 Aligned_cols=11 Identities=27% Similarity=0.969 Sum_probs=5.6
Q ss_pred CCCCCCCCCCC
Q 042112 91 ICPVCHDSIAP 101 (132)
Q Consensus 91 ~CP~Cr~~~~~ 101 (132)
.||+|.+++..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 79999888754
No 152
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.01 E-value=12 Score=32.04 Aligned_cols=50 Identities=26% Similarity=0.456 Sum_probs=34.5
Q ss_pred ccccccccccCCCceEEeCCCC-cccHHhHHHHH-hcC----CCCCCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSCHH-LFHAVCLDTWI-SNN----YAICPVCHDSIAPSRWL 105 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H-~fh~~Ci~~wl-~~~----~~~CP~Cr~~~~~~~~~ 105 (132)
.|+||-..... ...-.|+| ..+..|..+.. ... ...||+||..+.....+
T Consensus 2 ~c~ic~~s~~~---~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~~~s~~ 57 (669)
T KOG2231|consen 2 SCAICAFSPDF---VGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVETKSNG 57 (669)
T ss_pred CcceeecCccc---cccccccccccchhhhhhhhhhcccccccccCcccccceeeeccc
Confidence 58898766544 44448999 89999998875 222 24579999977644433
No 153
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.65 E-value=7.6 Score=29.29 Aligned_cols=34 Identities=15% Similarity=0.111 Sum_probs=28.5
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHH
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWI 85 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl 85 (132)
.+-+-|..|+.+..+ +...+=||+|++.||-+.+
T Consensus 41 K~FdcCsLtLqPc~d---Pvit~~GylfdrEaILe~i 74 (303)
T KOG3039|consen 41 KPFDCCSLTLQPCRD---PVITPDGYLFDREAILEYI 74 (303)
T ss_pred CCcceeeeecccccC---CccCCCCeeeeHHHHHHHH
Confidence 456789999999888 5667889999999998775
No 154
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.63 E-value=17 Score=23.93 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=31.7
Q ss_pred ccccccccccccCCC-----------ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGE-----------EIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~-----------~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
+..|.-|...|.... ...--.|++.|+.+|=.-+-..- -+||.|.+
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~L-h~CPGC~~ 111 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESL-HCCPGCIH 111 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhc-cCCcCCCC
Confidence 456999999886431 11223799999999977765432 47999963
No 155
>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=53.46 E-value=10 Score=21.04 Aligned_cols=34 Identities=18% Similarity=0.353 Sum_probs=23.1
Q ss_pred cccccccccccCCCce-EEeCCCCcccHHhHHHHH
Q 042112 52 VECAVCLSHIEEGEEI-RELSCHHLFHAVCLDTWI 85 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~-~~l~C~H~fh~~Ci~~wl 85 (132)
..|.+|...|.....- .--.||++|+..|.....
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~ 37 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRI 37 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCee
Confidence 4688998877654321 112699999998876544
No 156
>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 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=52.08 E-value=6 Score=26.01 Aligned_cols=34 Identities=18% Similarity=0.126 Sum_probs=21.7
Q ss_pred cccccccccccccCCC--ceEEeCCCCcccHHhHHH
Q 042112 50 EAVECAVCLSHIEEGE--EIRELSCHHLFHAVCLDT 83 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~--~~~~l~C~H~fh~~Ci~~ 83 (132)
++..|.+|..+|..-. ...-..|+|.+|..|-..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 5679999998764432 334347888888887544
No 158
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=50.82 E-value=3.1 Score=31.89 Aligned_cols=43 Identities=21% Similarity=0.530 Sum_probs=32.1
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCC
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPV 94 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~ 94 (132)
.+|.+|++++..+.......|...+|..|+..|++.....+|.
T Consensus 215 rvC~~CF~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 257 (288)
T KOG1729|consen 215 RVCDICFEELEKGARGDREDSLPVFHGKCYPNWLTTGAASTED 257 (288)
T ss_pred eecHHHHHHHhcccccchhhccccccccccccccccccccccc
Confidence 4899999999875555556666699999999999654434443
No 159
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=50.51 E-value=19 Score=24.08 Aligned_cols=21 Identities=19% Similarity=-0.148 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 042112 5 LIRFLRCLKWACNLLLHFSFF 25 (132)
Q Consensus 5 li~~~~~l~~~~~~~~~~~~~ 25 (132)
.|++..+.+++.++++.+++.
T Consensus 68 ~Ii~gv~aGvIg~Illi~y~i 88 (122)
T PF01102_consen 68 GIIFGVMAGVIGIILLISYCI 88 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred ehhHHHHHHHHHHHHHHHHHH
Confidence 345555566664444433333
No 160
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=49.97 E-value=12 Score=21.74 Aligned_cols=16 Identities=38% Similarity=0.845 Sum_probs=12.2
Q ss_pred CCCCCCCCCCCCCCCC
Q 042112 88 NYAICPVCHDSIAPSR 103 (132)
Q Consensus 88 ~~~~CP~Cr~~~~~~~ 103 (132)
.++.||+|-.++++++
T Consensus 2 ~HkHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDE 17 (59)
T ss_pred CCCcCCcCCCcCCcch
Confidence 3578999998887643
No 161
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=49.87 E-value=11 Score=24.11 Aligned_cols=32 Identities=25% Similarity=0.619 Sum_probs=22.0
Q ss_pred cccccccccccccCCCceEEe--CCCCcccHHhHHH
Q 042112 50 EAVECAVCLSHIEEGEEIREL--SCHHLFHAVCLDT 83 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l--~C~H~fh~~Ci~~ 83 (132)
....|.||... .|..+.-. .|...||..|...
T Consensus 54 ~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHH
Confidence 46789999987 32222222 4888999999865
No 162
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=48.96 E-value=18 Score=23.14 Aligned_cols=35 Identities=26% Similarity=0.356 Sum_probs=28.5
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHh
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS 86 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~ 86 (132)
.-.|.||-..+..++.-...+ .-..|.+|+..-..
T Consensus 6 ewkC~VCg~~iieGqkFTF~~-kGsVH~eCl~~s~~ 40 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTK-KGSVHYECLAESKR 40 (103)
T ss_pred eeeEeeeCCEeeeccEEEEee-CCcchHHHHHHHHh
Confidence 457999999999998877677 66789999987654
No 163
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=48.79 E-value=25 Score=22.12 Aligned_cols=39 Identities=18% Similarity=0.375 Sum_probs=28.6
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
+...|+-|...+.--+... +-.|+-.+ ..|..|+++++.
T Consensus 32 ~rS~C~~C~~~L~~~~lIP------------i~S~l~lr-GrCr~C~~~I~~ 70 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIP------------ILSYLLLR-GRCRYCGAPIPP 70 (92)
T ss_pred CCCcCcCCCCcCcccccch------------HHHHHHhC-CCCcccCCCCCh
Confidence 4567999998887644433 56688643 789999999874
No 164
>PF12773 DZR: Double zinc ribbon
Probab=48.67 E-value=16 Score=19.79 Aligned_cols=11 Identities=36% Similarity=0.848 Sum_probs=7.4
Q ss_pred CCCCCCCCCCC
Q 042112 90 AICPVCHDSIA 100 (132)
Q Consensus 90 ~~CP~Cr~~~~ 100 (132)
..||.|.+.+.
T Consensus 30 ~~C~~Cg~~~~ 40 (50)
T PF12773_consen 30 KICPNCGAENP 40 (50)
T ss_pred CCCcCCcCCCc
Confidence 46888877654
No 165
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=48.04 E-value=27 Score=23.24 Aligned_cols=21 Identities=14% Similarity=0.100 Sum_probs=11.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 042112 2 FGYLIRFLRCLKWACNLLLHF 22 (132)
Q Consensus 2 ~~~li~~~~~l~~~~~~~~~~ 22 (132)
+-|+++++.++.+++.+.++-
T Consensus 3 ~l~~iii~~i~l~~~~~~~~~ 23 (130)
T PF12273_consen 3 VLFAIIIVAILLFLFLFYCHN 23 (130)
T ss_pred eeHHHHHHHHHHHHHHHHHHH
Confidence 345566666666665555553
No 166
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.93 E-value=13 Score=28.56 Aligned_cols=50 Identities=20% Similarity=0.485 Sum_probs=34.2
Q ss_pred cccccccccccccCCCceEEeCC----CCcccHHhHHHHHhcCC----------CCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEEIRELSC----HHLFHAVCLDTWISNNY----------AICPVCHDSIAPS 102 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C----~H~fh~~Ci~~wl~~~~----------~~CP~Cr~~~~~~ 102 (132)
....|.+|.|.+++ .-.+.| .|.||..|-.+-++... ..||+--+.++=.
T Consensus 267 apLcCTLC~ERLED---THFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~vPWA 330 (352)
T KOG3579|consen 267 APLCCTLCHERLED---THFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNVPWA 330 (352)
T ss_pred Cceeehhhhhhhcc---CceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCcccHH
Confidence 45689999999987 333446 59999999998884321 1466665555433
No 167
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=46.36 E-value=20 Score=17.97 Aligned_cols=9 Identities=44% Similarity=1.062 Sum_probs=6.4
Q ss_pred CCCCCCCCC
Q 042112 89 YAICPVCHD 97 (132)
Q Consensus 89 ~~~CP~Cr~ 97 (132)
...||+|..
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 357888865
No 168
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=45.62 E-value=12 Score=22.89 Aligned_cols=34 Identities=18% Similarity=0.456 Sum_probs=22.4
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHHH
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDT 83 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~ 83 (132)
....|.+|.......-....-.|...||..|...
T Consensus 35 ~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 35 RKLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred hCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 3568999987622211222237999999999765
No 169
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=45.12 E-value=12 Score=19.40 Aligned_cols=13 Identities=15% Similarity=0.567 Sum_probs=8.8
Q ss_pred ccccccccccCCC
Q 042112 53 ECAVCLSHIEEGE 65 (132)
Q Consensus 53 ~C~IC~~~~~~~~ 65 (132)
+|+-|...|+.++
T Consensus 4 ~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 4 TCPNCQTRFRVPD 16 (37)
T ss_pred ECCCCCceEEcCH
Confidence 5777777776544
No 170
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=43.63 E-value=23 Score=22.74 Aligned_cols=30 Identities=17% Similarity=0.391 Sum_probs=20.0
Q ss_pred CCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 71 SCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 71 ~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
-||+--|.-=+.++... ..||.|++++.+.
T Consensus 64 iCGvC~~~LT~~EY~~~--~~Cp~C~spFNp~ 93 (105)
T COG4357 64 ICGVCRKLLTRAEYGMC--GSCPYCQSPFNPG 93 (105)
T ss_pred EhhhhhhhhhHHHHhhc--CCCCCcCCCCCcc
Confidence 37766555555665542 4699999998643
No 171
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.47 E-value=12 Score=25.69 Aligned_cols=50 Identities=18% Similarity=0.470 Sum_probs=25.8
Q ss_pred Ccccccccccc-cccCCCceEEeCCCCcccHHhHHHHHhcCCC---CCCCCCCC
Q 042112 49 AEAVECAVCLS-HIEEGEEIRELSCHHLFHAVCLDTWISNNYA---ICPVCHDS 98 (132)
Q Consensus 49 ~~~~~C~IC~~-~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~---~CP~Cr~~ 98 (132)
.++..|.||+. +|.++-.....-|.-.||..|--+--...+. .|-.|+..
T Consensus 63 ~ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 63 GDDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQ 116 (169)
T ss_pred CcCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCceEEeccCCcHH
Confidence 57889999987 4555422222234444444443322111111 48888753
No 172
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=40.36 E-value=47 Score=21.44 Aligned_cols=46 Identities=22% Similarity=0.401 Sum_probs=28.1
Q ss_pred ccccccccccccCCCceEE------eCC---CCcccHHhHHHHHhc--------CCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRE------LSC---HHLFHAVCLDTWISN--------NYAICPVCHD 97 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~------l~C---~H~fh~~Ci~~wl~~--------~~~~CP~Cr~ 97 (132)
+..|.-|..+-.+. ...- ..| .-.||..|+...+.+ .+-.||.||.
T Consensus 7 g~~CHqCrqKt~~~-~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 7 GKTCHQCRQKTLDF-KTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCchhhcCCCCCC-ceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 44677777643321 1111 345 678999999887732 1236999986
No 173
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=40.20 E-value=44 Score=29.40 Aligned_cols=25 Identities=32% Similarity=0.798 Sum_probs=16.8
Q ss_pred CCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 71 SCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 71 ~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.|.|..|..=|.+ .+.||+|...+.
T Consensus 1161 ~CkH~a~~~EIs~-----y~~CPLCHs~~~ 1185 (1189)
T KOG2041|consen 1161 RCKHRAHQHEISK-----YNCCPLCHSMES 1185 (1189)
T ss_pred ccccccccccccc-----cccCccccChhh
Confidence 5888777654432 467999977653
No 174
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=40.00 E-value=29 Score=27.60 Aligned_cols=24 Identities=21% Similarity=0.407 Sum_probs=15.0
Q ss_pred CcccccccccccccCCCceEEeCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCH 73 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~ 73 (132)
..++.|++|-++... -....|.|.
T Consensus 13 dl~ElCPVCGDkVSG-YHYGLLTCE 36 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSG-YHYGLLTCE 36 (475)
T ss_pred ccccccccccCcccc-ceeeeeehh
Confidence 356789999887542 444545443
No 175
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=39.75 E-value=16 Score=17.41 Aligned_cols=10 Identities=40% Similarity=1.175 Sum_probs=7.8
Q ss_pred CCCCCCCCCC
Q 042112 91 ICPVCHDSIA 100 (132)
Q Consensus 91 ~CP~Cr~~~~ 100 (132)
.||+|.+.+.
T Consensus 3 ~CPiC~~~v~ 12 (26)
T smart00734 3 QCPVCFREVP 12 (26)
T ss_pred cCCCCcCccc
Confidence 6999987763
No 176
>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=38.89 E-value=25 Score=20.47 Aligned_cols=10 Identities=30% Similarity=1.371 Sum_probs=5.3
Q ss_pred CCCCCCCCCC
Q 042112 90 AICPVCHDSI 99 (132)
Q Consensus 90 ~~CP~Cr~~~ 99 (132)
..||+|+..+
T Consensus 3 ~~CPlCkt~~ 12 (61)
T PF05715_consen 3 SLCPLCKTTL 12 (61)
T ss_pred ccCCcccchh
Confidence 3456665544
No 177
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=38.51 E-value=36 Score=25.10 Aligned_cols=23 Identities=17% Similarity=0.143 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhc
Q 042112 4 YLIRFLRCLKWACNLLLHFSFFG 26 (132)
Q Consensus 4 ~li~~~~~l~~~~~~~~~~~~~~ 26 (132)
.|.++++++.++++++.+..|+.
T Consensus 15 iLNiaI~IV~lLIiiva~~lf~~ 37 (217)
T PF07423_consen 15 ILNIAIGIVSLLIIIVAYQLFFG 37 (217)
T ss_pred hHHHHHHHHHHHHHHHhhhheec
Confidence 45556666666666666666664
No 178
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=38.00 E-value=3 Score=31.72 Aligned_cols=43 Identities=28% Similarity=0.492 Sum_probs=18.0
Q ss_pred cccccccccccccCC-----C--ceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEG-----E--EIRELSCHHLFHAVCLDTWISNNYAICPVCHDS 98 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~-----~--~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~ 98 (132)
....||||-..-.-+ + ..+ |.+|..|-..|--.+ ..||.|-..
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R-----~L~Cs~C~t~W~~~R-~~Cp~Cg~~ 220 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKR-----YLHCSLCGTEWRFVR-IKCPYCGNT 220 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EE-----EEEETTT--EEE--T-TS-TTT---
T ss_pred cCCcCCCCCCcCceEEEecCCCCccE-----EEEcCCCCCeeeecC-CCCcCCCCC
Confidence 346899998764321 1 122 455666777786533 689999654
No 179
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=37.32 E-value=36 Score=22.01 Aligned_cols=34 Identities=24% Similarity=0.293 Sum_probs=26.1
Q ss_pred cccccccccccCCCceEEeCCCCcccHHhHHHHHh
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWIS 86 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~ 86 (132)
-.|.||-+++..|+.-..++= -..|..|+..=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~k-G~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKK-GPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEecC-CcEeHHHHHHHHh
Confidence 369999999999887665533 5689999987653
No 180
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.66 E-value=29 Score=26.53 Aligned_cols=9 Identities=33% Similarity=1.051 Sum_probs=6.4
Q ss_pred CCCCCCCCC
Q 042112 90 AICPVCHDS 98 (132)
Q Consensus 90 ~~CP~Cr~~ 98 (132)
..||.|.+.
T Consensus 270 ~~C~~Cgt~ 278 (279)
T TIGR00627 270 PICKTCKTA 278 (279)
T ss_pred CCCCCCCCC
Confidence 578888764
No 181
>PRK01343 zinc-binding protein; Provisional
Probab=35.50 E-value=24 Score=20.38 Aligned_cols=12 Identities=25% Similarity=0.609 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCC
Q 042112 89 YAICPVCHDSIA 100 (132)
Q Consensus 89 ~~~CP~Cr~~~~ 100 (132)
...||+|++++.
T Consensus 9 ~~~CP~C~k~~~ 20 (57)
T PRK01343 9 TRPCPECGKPST 20 (57)
T ss_pred CCcCCCCCCcCc
Confidence 357999998764
No 182
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.34 E-value=19 Score=27.89 Aligned_cols=51 Identities=24% Similarity=0.541 Sum_probs=37.4
Q ss_pred CcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 49 AEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
.....|-+|...+..+.. .-.|.|.|+..|-..|.... ..||.|+....+.
T Consensus 103 ~~~~~~~~~~g~l~vpt~--~qg~w~qf~~~~p~~~~~~~-~~~~d~~~~~~pv 153 (324)
T KOG0824|consen 103 QDHDICYICYGKLTVPTR--IQGCWHQFCYVCPKSNFAMG-NDCPDCRGKISPV 153 (324)
T ss_pred CCccceeeeeeeEEeccc--ccCceeeeeecCCchhhhhh-hccchhhcCcCce
Confidence 356689999888776432 12489999999999999653 6899998765433
No 183
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=35.30 E-value=27 Score=19.01 Aligned_cols=34 Identities=26% Similarity=0.447 Sum_probs=23.1
Q ss_pred cccccccccccc--cCCCceEEeCCCCcccHHhHHH
Q 042112 50 EAVECAVCLSHI--EEGEEIRELSCHHLFHAVCLDT 83 (132)
Q Consensus 50 ~~~~C~IC~~~~--~~~~~~~~l~C~H~fh~~Ci~~ 83 (132)
....|.+|.+.+ ...+..+-..|+-..|..|+..
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 456799999988 3334455558999999999764
No 184
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=34.76 E-value=24 Score=29.76 Aligned_cols=37 Identities=22% Similarity=0.480 Sum_probs=25.5
Q ss_pred CcccccccccccccCC-----C-----ceEEeCCCCcccHHhHHHHH
Q 042112 49 AEAVECAVCLSHIEEG-----E-----EIRELSCHHLFHAVCLDTWI 85 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~-----~-----~~~~l~C~H~fh~~Ci~~wl 85 (132)
+....|+||.|+|+.- + ....+.=|-+||..|+..-.
T Consensus 511 e~~~~C~IC~EkFe~v~d~e~~~Wm~kdaV~le~G~ifH~~Cl~e~~ 557 (579)
T KOG2071|consen 511 ERQASCPICQEKFEVVFDQEEDLWMYKDAVYLEFGRIFHSKCLSEKR 557 (579)
T ss_pred ccccCCcccccccceeecchhhheeecceeeeccCceeeccccchHH
Confidence 4567899999999541 1 12334458899999987643
No 185
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.73 E-value=23 Score=22.49 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=10.7
Q ss_pred cccHHhHHHHHh
Q 042112 75 LFHAVCLDTWIS 86 (132)
Q Consensus 75 ~fh~~Ci~~wl~ 86 (132)
-||+.|+..|..
T Consensus 42 gFCRNCLs~Wy~ 53 (104)
T COG3492 42 GFCRNCLSNWYR 53 (104)
T ss_pred HHHHHHHHHHHH
Confidence 499999999984
No 186
>smart00746 TRASH metallochaperone-like domain.
Probab=34.05 E-value=33 Score=15.93 Aligned_cols=9 Identities=33% Similarity=0.922 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q 042112 92 CPVCHDSIA 100 (132)
Q Consensus 92 CP~Cr~~~~ 100 (132)
||+|...+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 788887775
No 187
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=33.62 E-value=23 Score=20.80 Aligned_cols=11 Identities=27% Similarity=0.924 Sum_probs=9.1
Q ss_pred CCCCCCCCCCC
Q 042112 90 AICPVCHDSIA 100 (132)
Q Consensus 90 ~~CP~Cr~~~~ 100 (132)
..||.|++++.
T Consensus 7 v~CP~C~k~~~ 17 (62)
T PRK00418 7 VNCPTCGKPVE 17 (62)
T ss_pred ccCCCCCCccc
Confidence 57999999874
No 188
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.82 E-value=23 Score=18.53 Aligned_cols=13 Identities=38% Similarity=1.009 Sum_probs=9.1
Q ss_pred CCCCCCCCCCCCC
Q 042112 91 ICPVCHDSIAPSR 103 (132)
Q Consensus 91 ~CP~Cr~~~~~~~ 103 (132)
.||.|+..+....
T Consensus 1 ~CP~C~~~l~~~~ 13 (41)
T PF13453_consen 1 KCPRCGTELEPVR 13 (41)
T ss_pred CcCCCCcccceEE
Confidence 4999988765433
No 189
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=31.30 E-value=34 Score=19.91 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=12.3
Q ss_pred CCCCCCCCCCCCCCCC
Q 042112 89 YAICPVCHDSIAPSRW 104 (132)
Q Consensus 89 ~~~CP~Cr~~~~~~~~ 104 (132)
++-||+|-+++++.+.
T Consensus 8 H~HC~VCg~aIp~de~ 23 (64)
T COG4068 8 HRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CccccccCCcCCCccc
Confidence 5679999998876543
No 190
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=31.24 E-value=19 Score=26.26 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=14.3
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 042112 89 YAICPVCHDSIAPSRWLTGH 108 (132)
Q Consensus 89 ~~~CP~Cr~~~~~~~~~~~~ 108 (132)
..+||+|.+.+..+...+..
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~ 24 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGK 24 (214)
T ss_pred ceECCCCCCeeeeeEEEcCC
Confidence 46799999888766655544
No 191
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=31.00 E-value=35 Score=25.43 Aligned_cols=25 Identities=20% Similarity=0.395 Sum_probs=15.7
Q ss_pred cccccccccccCCCceEEeCCCCcc
Q 042112 52 VECAVCLSHIEEGEEIRELSCHHLF 76 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~~~~l~C~H~f 76 (132)
..||+|.+++...+..-.-+.+|.|
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCCCCCC
Confidence 3699999999754432212446776
No 192
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=30.91 E-value=40 Score=24.85 Aligned_cols=26 Identities=15% Similarity=0.082 Sum_probs=19.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhhc
Q 042112 1 MFGYLIRFLRCLKWACNLLLHFSFFG 26 (132)
Q Consensus 1 ~~~~li~~~~~l~~~~~~~~~~~~~~ 26 (132)
+++++|.++.+|.+++...+||.-..
T Consensus 15 iLNiaI~IV~lLIiiva~~lf~~~~~ 40 (217)
T PF07423_consen 15 ILNIAIGIVSLLIIIVAYQLFFGGDD 40 (217)
T ss_pred hHHHHHHHHHHHHHHHhhhheecCCC
Confidence 46788888888888888888885544
No 193
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.80 E-value=15 Score=28.57 Aligned_cols=42 Identities=24% Similarity=0.488 Sum_probs=25.9
Q ss_pred cccccccccccccCC-------CceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEG-------EEIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~-------~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
....||+|-..-... +..+. ..|..|-..|--. ...||.|-.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~Ry-----L~CslC~teW~~~-R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRY-----LHCNLCESEWHVV-RVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceE-----EEcCCCCCccccc-CccCCCCCC
Confidence 356899998864221 22333 3444567778653 368999965
No 194
>TIGR02652 conserved hypothetical protein TIGR02652, cyanobacterial. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end.
Probab=30.11 E-value=19 Score=24.83 Aligned_cols=14 Identities=29% Similarity=0.657 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCCC
Q 042112 89 YAICPVCHDSIAPS 102 (132)
Q Consensus 89 ~~~CP~Cr~~~~~~ 102 (132)
...||.||+.++.-
T Consensus 9 ei~CPhCRQ~ipAL 22 (163)
T TIGR02652 9 EIRCPHCRQNIPAL 22 (163)
T ss_pred cCcCchhhcccchh
Confidence 36799999988744
No 195
>PF09654 DUF2396: Protein of unknown function (DUF2396); InterPro: IPR013472 These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N terminus.
Probab=30.01 E-value=19 Score=24.73 Aligned_cols=14 Identities=29% Similarity=0.683 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCCCC
Q 042112 89 YAICPVCHDSIAPS 102 (132)
Q Consensus 89 ~~~CP~Cr~~~~~~ 102 (132)
...||.||+.++.-
T Consensus 6 ei~CPhCRq~ipAL 19 (161)
T PF09654_consen 6 EIQCPHCRQTIPAL 19 (161)
T ss_pred cCcCchhhcccchh
Confidence 35799999988744
No 196
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=29.93 E-value=30 Score=23.50 Aligned_cols=21 Identities=24% Similarity=0.673 Sum_probs=16.1
Q ss_pred eCCCCcccHHhHHHHHhcCCCCCCCCCCCC
Q 042112 70 LSCHHLFHAVCLDTWISNNYAICPVCHDSI 99 (132)
Q Consensus 70 l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~ 99 (132)
-.|||.|+. .+..||.|.++.
T Consensus 33 ~~CG~v~~P---------Pr~~Cp~C~~~~ 53 (140)
T COG1545 33 KKCGRVYFP---------PRAYCPKCGSET 53 (140)
T ss_pred CCCCeEEcC---------CcccCCCCCCCC
Confidence 368999875 456899998874
No 197
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=29.46 E-value=38 Score=19.69 Aligned_cols=16 Identities=31% Similarity=0.654 Sum_probs=11.4
Q ss_pred CcccccccccccccCC
Q 042112 49 AEAVECAVCLSHIEEG 64 (132)
Q Consensus 49 ~~~~~C~IC~~~~~~~ 64 (132)
++...|++|..++..+
T Consensus 37 ~~~p~CPlC~s~M~~~ 52 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVSG 52 (59)
T ss_pred CCCccCCCcCCccccc
Confidence 3457788888877665
No 198
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=29.44 E-value=40 Score=18.75 Aligned_cols=7 Identities=43% Similarity=0.980 Sum_probs=5.3
Q ss_pred CCCCCCC
Q 042112 89 YAICPVC 95 (132)
Q Consensus 89 ~~~CP~C 95 (132)
...||.|
T Consensus 49 ~~~CP~C 55 (55)
T PF14311_consen 49 GKGCPYC 55 (55)
T ss_pred CCCCCCC
Confidence 4679988
No 199
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=28.61 E-value=51 Score=25.19 Aligned_cols=44 Identities=20% Similarity=0.306 Sum_probs=24.4
Q ss_pred cccccccccccCCCc-eEEe-CCCCcccHHhHHHHHhcCCCCCCCC
Q 042112 52 VECAVCLSHIEEGEE-IREL-SCHHLFHAVCLDTWISNNYAICPVC 95 (132)
Q Consensus 52 ~~C~IC~~~~~~~~~-~~~l-~C~H~fh~~Ci~~wl~~~~~~CP~C 95 (132)
.-|.||++---++.. ...| .=+=.=|++|+.+|--..+..||--
T Consensus 31 sfChiCfEl~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~prs 76 (285)
T PF06937_consen 31 SFCHICFELSIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCPRS 76 (285)
T ss_pred eecceeeccccccCccccccccccccchHHHHHHHHHHHcCCCCcc
Confidence 456666664433322 1112 1112457999999974445789943
No 200
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=28.60 E-value=28 Score=15.26 Aligned_cols=8 Identities=13% Similarity=0.322 Sum_probs=3.2
Q ss_pred hhHHHHHH
Q 042112 2 FGYLIRFL 9 (132)
Q Consensus 2 ~~~li~~~ 9 (132)
.++.++++
T Consensus 2 Mk~vIIlv 9 (19)
T PF13956_consen 2 MKLVIILV 9 (19)
T ss_pred ceehHHHH
Confidence 34444433
No 201
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=28.38 E-value=47 Score=21.22 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=4.3
Q ss_pred HHHHHHHHHH
Q 042112 6 IRFLRCLKWA 15 (132)
Q Consensus 6 i~~~~~l~~~ 15 (132)
++++++++++
T Consensus 63 iili~lls~v 72 (101)
T PF06024_consen 63 IILISLLSFV 72 (101)
T ss_pred chHHHHHHHH
Confidence 3444444444
No 202
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.30 E-value=1.2e+02 Score=18.21 Aligned_cols=25 Identities=20% Similarity=0.093 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhc
Q 042112 2 FGYLIRFLRCLKWACNLLLHFSFFG 26 (132)
Q Consensus 2 ~~~li~~~~~l~~~~~~~~~~~~~~ 26 (132)
..++.+++.++..++.+++-|++.+
T Consensus 2 ~l~lail~ivl~ll~G~~~G~fiar 26 (71)
T COG3763 2 SLWLAILLIVLALLAGLIGGFFIAR 26 (71)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666666655555444443
No 203
>PF15353 HECA: Headcase protein family homologue
Probab=27.90 E-value=42 Score=21.90 Aligned_cols=15 Identities=20% Similarity=0.718 Sum_probs=12.8
Q ss_pred CCCCcccHHhHHHHH
Q 042112 71 SCHHLFHAVCLDTWI 85 (132)
Q Consensus 71 ~C~H~fh~~Ci~~wl 85 (132)
|.++..|.+|++.|-
T Consensus 39 p~~~~MH~~CF~~wE 53 (107)
T PF15353_consen 39 PFGQYMHRECFEKWE 53 (107)
T ss_pred CCCCchHHHHHHHHH
Confidence 457999999999995
No 204
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=27.67 E-value=1e+02 Score=21.47 Aligned_cols=6 Identities=0% Similarity=-0.291 Sum_probs=2.2
Q ss_pred HHHHHH
Q 042112 10 RCLKWA 15 (132)
Q Consensus 10 ~~l~~~ 15 (132)
+++.++
T Consensus 38 IvVlii 43 (189)
T PF05568_consen 38 IVVLII 43 (189)
T ss_pred HHHHHH
Confidence 333333
No 205
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=27.54 E-value=1e+02 Score=16.10 Aligned_cols=14 Identities=14% Similarity=0.107 Sum_probs=6.1
Q ss_pred hHHHHHHHHHHHHH
Q 042112 3 GYLIRFLRCLKWAC 16 (132)
Q Consensus 3 ~~li~~~~~l~~~~ 16 (132)
+|+++.+.++.+.+
T Consensus 15 ~Wi~F~l~mi~vFi 28 (38)
T PF09125_consen 15 GWIAFALAMILVFI 28 (38)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHH
Confidence 35444444443333
No 206
>PF15122 TMEM206: TMEM206 protein family
Probab=27.49 E-value=70 Score=24.24 Aligned_cols=12 Identities=33% Similarity=0.636 Sum_probs=9.4
Q ss_pred eEEeCCCCcccH
Q 042112 67 IRELSCHHLFHA 78 (132)
Q Consensus 67 ~~~l~C~H~fh~ 78 (132)
...+.|.|.||.
T Consensus 70 a~llsCkhhyyd 81 (298)
T PF15122_consen 70 AQLLSCKHHYYD 81 (298)
T ss_pred chhccccccccc
Confidence 455789999886
No 207
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.03 E-value=42 Score=23.47 Aligned_cols=26 Identities=27% Similarity=0.539 Sum_probs=20.0
Q ss_pred CCcccHHhHHHHHhcCCCCCCCCCCCCCCC
Q 042112 73 HHLFHAVCLDTWISNNYAICPVCHDSIAPS 102 (132)
Q Consensus 73 ~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~ 102 (132)
.+.||..|-.+-.. .||.|..++...
T Consensus 27 ~~~fC~kCG~~tI~----~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 27 REKFCSKCGAKTIT----SCPNCSTPIRGD 52 (158)
T ss_pred HHHHHHHhhHHHHH----HCcCCCCCCCCc
Confidence 36799999887553 699999988644
No 208
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=26.74 E-value=19 Score=17.51 Aligned_cols=10 Identities=40% Similarity=1.182 Sum_probs=5.2
Q ss_pred CCCCCCCCCC
Q 042112 91 ICPVCHDSIA 100 (132)
Q Consensus 91 ~CP~Cr~~~~ 100 (132)
.||+|-+++.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899988775
No 209
>PF10717 ODV-E18: Occlusion-derived virus envelope protein ODV-E18; InterPro: IPR019655 Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles []. ; GO: 0019031 viral envelope
Probab=26.64 E-value=1.1e+02 Score=19.01 Aligned_cols=8 Identities=25% Similarity=0.521 Sum_probs=3.1
Q ss_pred HHHHhhhc
Q 042112 19 LLHFSFFG 26 (132)
Q Consensus 19 ~~~~~~~~ 26 (132)
++.+.+|+
T Consensus 38 iLlImlfq 45 (85)
T PF10717_consen 38 ILLIMLFQ 45 (85)
T ss_pred HHHHHHHh
Confidence 33333444
No 210
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=26.16 E-value=33 Score=20.01 Aligned_cols=11 Identities=36% Similarity=1.090 Sum_probs=8.8
Q ss_pred CCCCCCCCCCC
Q 042112 90 AICPVCHDSIA 100 (132)
Q Consensus 90 ~~CP~Cr~~~~ 100 (132)
-.||+||.++.
T Consensus 9 LaCP~~kg~L~ 19 (60)
T COG2835 9 LACPVCKGPLV 19 (60)
T ss_pred eeccCcCCcce
Confidence 36999999864
No 211
>PRK11827 hypothetical protein; Provisional
Probab=25.93 E-value=36 Score=19.82 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=9.8
Q ss_pred CCCCCCCCCCCC
Q 042112 90 AICPVCHDSIAP 101 (132)
Q Consensus 90 ~~CP~Cr~~~~~ 101 (132)
-.||.|+.++..
T Consensus 9 LaCP~ckg~L~~ 20 (60)
T PRK11827 9 IACPVCNGKLWY 20 (60)
T ss_pred eECCCCCCcCeE
Confidence 579999998854
No 212
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=25.83 E-value=1.2e+02 Score=16.43 Aligned_cols=7 Identities=14% Similarity=-0.007 Sum_probs=2.6
Q ss_pred HHHHHHH
Q 042112 9 LRCLKWA 15 (132)
Q Consensus 9 ~~~l~~~ 15 (132)
.+++.++
T Consensus 14 ~~v~~~~ 20 (49)
T PF05545_consen 14 GTVLFFV 20 (49)
T ss_pred HHHHHHH
Confidence 3333333
No 213
>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=25.30 E-value=3.5 Score=23.33 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=14.2
Q ss_pred ccccc--ccccccCCCceE---Ee-C-CCCcccHHhHHHH
Q 042112 52 VECAV--CLSHIEEGEEIR---EL-S-CHHLFHAVCLDTW 84 (132)
Q Consensus 52 ~~C~I--C~~~~~~~~~~~---~l-~-C~H~fh~~Ci~~w 84 (132)
.-|+- |-..+...+... .. + |++.||..|-..|
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 36766 766554433211 12 3 7777777665555
No 214
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=24.96 E-value=37 Score=25.70 Aligned_cols=45 Identities=13% Similarity=0.239 Sum_probs=30.7
Q ss_pred ccccccccccccCCCceEEeCCCCcccHHhHHHHHhcC-CCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNN-YAICPVCHD 97 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~ 97 (132)
+..|||=..++..+ ++--.|||+|=++-|...+... ...||+=-.
T Consensus 176 s~rdPis~~~I~nP--viSkkC~HvydrDsI~~~l~~~~~i~CPv~gC 221 (262)
T KOG2979|consen 176 SNRDPISKKPIVNP--VISKKCGHVYDRDSIMQILCDEITIRCPVLGC 221 (262)
T ss_pred cccCchhhhhhhch--hhhcCcCcchhhhhHHHHhccCceeecccccC
Confidence 55788876666652 2223899999999999988532 246887433
No 215
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.77 E-value=1.3e+02 Score=18.26 Aligned_cols=28 Identities=18% Similarity=0.236 Sum_probs=14.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhhccCc
Q 042112 2 FGYLIRFLRCLKWACNLLLHFSFFGHRI 29 (132)
Q Consensus 2 ~~~li~~~~~l~~~~~~~~~~~~~~~~~ 29 (132)
-.|++.|..++.+++..-+-+.+.+..+
T Consensus 2 ~t~lltFg~Fllvi~gMsiG~I~krk~I 29 (77)
T COG2991 2 TTFLLTFGIFLLVIAGMSIGYIFKRKSI 29 (77)
T ss_pred ccHHHHHHHHHHHHHHHhHhhheecccc
Confidence 3466666666666655444443333333
No 216
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=24.30 E-value=11 Score=21.15 Aligned_cols=15 Identities=27% Similarity=0.623 Sum_probs=12.3
Q ss_pred CCCCcccHHhHHHHH
Q 042112 71 SCHHLFHAVCLDTWI 85 (132)
Q Consensus 71 ~C~H~fh~~Ci~~wl 85 (132)
.|++.||..|...|-
T Consensus 45 ~C~~~fC~~C~~~~H 59 (64)
T smart00647 45 KCGFSFCFRCKVPWH 59 (64)
T ss_pred CCCCeECCCCCCcCC
Confidence 588999998888773
No 217
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=24.27 E-value=27 Score=32.70 Aligned_cols=53 Identities=25% Similarity=0.458 Sum_probs=37.9
Q ss_pred CCCcccccccccccccCCCceEEeCCCCcccHHhHHHHHhcCC---CCCCCCCCCC
Q 042112 47 SRAEAVECAVCLSHIEEGEEIRELSCHHLFHAVCLDTWISNNY---AICPVCHDSI 99 (132)
Q Consensus 47 ~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~wl~~~~---~~CP~Cr~~~ 99 (132)
.+.....|.+|..............|.-.||..|++.-+.... =.||-||..-
T Consensus 1104 ~s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1104 RSAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEH 1159 (1404)
T ss_pred cccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhh
Confidence 3345678999998876644333347889999999999884322 2699998765
No 218
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.80 E-value=28 Score=19.41 Aligned_cols=11 Identities=45% Similarity=1.241 Sum_probs=7.9
Q ss_pred CCCCCCCCCCC
Q 042112 90 AICPVCHDSIA 100 (132)
Q Consensus 90 ~~CP~Cr~~~~ 100 (132)
..||+|..++.
T Consensus 13 KICpvCqRPFs 23 (54)
T COG4338 13 KICPVCQRPFS 23 (54)
T ss_pred hhhhhhcCchH
Confidence 46888887764
No 219
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=23.64 E-value=32 Score=26.60 Aligned_cols=33 Identities=24% Similarity=0.515 Sum_probs=23.9
Q ss_pred cccccccccccccCCCceEEeCCCCcccHHhHH
Q 042112 50 EAVECAVCLSHIEEGEEIRELSCHHLFHAVCLD 82 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 82 (132)
+-..|.||..+-.+.+.+..=-|..-||..|+.
T Consensus 313 ~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVG 345 (381)
T KOG1512|consen 313 SCELCRICLGPVIESEHLFCDVCDRGPHTLCVG 345 (381)
T ss_pred ccHhhhccCCcccchheeccccccCCCCccccc
Confidence 456799999887776554433688888888874
No 220
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=23.44 E-value=46 Score=17.50 Aligned_cols=33 Identities=27% Similarity=0.414 Sum_probs=22.2
Q ss_pred ccccccccccccCC--CceEEeCCCCcccHHhHHH
Q 042112 51 AVECAVCLSHIEEG--EEIRELSCHHLFHAVCLDT 83 (132)
Q Consensus 51 ~~~C~IC~~~~~~~--~~~~~l~C~H~fh~~Ci~~ 83 (132)
...|.+|.+.+... ...+-..|+-..|..|...
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 45699998887642 2233346888888888764
No 221
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=23.44 E-value=13 Score=30.14 Aligned_cols=17 Identities=29% Similarity=0.583 Sum_probs=11.8
Q ss_pred CCCCCCCCCCCCCCCCC
Q 042112 90 AICPVCHDSIAPSRWLT 106 (132)
Q Consensus 90 ~~CP~Cr~~~~~~~~~~ 106 (132)
..|-+|..+|.+.+..+
T Consensus 395 PrCs~C~~PI~P~~G~~ 411 (468)
T KOG1701|consen 395 PRCSVCGNPILPRDGKD 411 (468)
T ss_pred cchhhccCCccCCCCCc
Confidence 47888888887655444
No 222
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=23.41 E-value=62 Score=16.78 Aligned_cols=33 Identities=24% Similarity=0.445 Sum_probs=22.8
Q ss_pred ccccccccccccCCC-ceEEeCCCCcccHHhHHH
Q 042112 51 AVECAVCLSHIEEGE-EIRELSCHHLFHAVCLDT 83 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~-~~~~l~C~H~fh~~Ci~~ 83 (132)
...|.+|.+.+.... ..+-..|+=..|..|...
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 456999988876532 233346888889998775
No 223
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=23.21 E-value=23 Score=20.66 Aligned_cols=26 Identities=27% Similarity=0.468 Sum_probs=13.9
Q ss_pred CCCCcccHHhHHHHHhcCCCCCCCCC
Q 042112 71 SCHHLFHAVCLDTWISNNYAICPVCH 96 (132)
Q Consensus 71 ~C~H~fh~~Ci~~wl~~~~~~CP~Cr 96 (132)
|||..|-..--+--.......||.|.
T Consensus 26 PCGDRFeIsLeDl~~GE~VArCPSCS 51 (67)
T COG5216 26 PCGDRFEISLEDLRNGEVVARCPSCS 51 (67)
T ss_pred CCCCEeEEEHHHhhCCceEEEcCCce
Confidence 67887765332222121224699994
No 224
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=23.16 E-value=53 Score=28.24 Aligned_cols=49 Identities=20% Similarity=0.519 Sum_probs=29.5
Q ss_pred ccccccccccccCCC--ceEEeCCCCcccHHhHHHHHhcC----CCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEEGE--EIRELSCHHLFHAVCLDTWISNN----YAICPVCHDSI 99 (132)
Q Consensus 51 ~~~C~IC~~~~~~~~--~~~~l~C~H~fh~~Ci~~wl~~~----~~~CP~Cr~~~ 99 (132)
...|++|-..=.... .+..-.|+-.+|..|+..|++.. .-.||-||.-.
T Consensus 18 ~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 18 CLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred hhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 345666654322211 12223788999999999998421 13599888644
No 225
>PRK01844 hypothetical protein; Provisional
Probab=23.05 E-value=1.8e+02 Score=17.62 Aligned_cols=18 Identities=11% Similarity=0.110 Sum_probs=8.0
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 042112 3 GYLIRFLRCLKWACNLLL 20 (132)
Q Consensus 3 ~~li~~~~~l~~~~~~~~ 20 (132)
.++.+++.++.++..+++
T Consensus 3 ~~~~I~l~I~~li~G~~~ 20 (72)
T PRK01844 3 IWLGILVGVVALVAGVAL 20 (72)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344444444444433333
No 226
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.96 E-value=1.3e+02 Score=18.28 Aligned_cols=44 Identities=20% Similarity=0.578 Sum_probs=28.2
Q ss_pred ccccccccccCCCceEEeCC--CCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 53 ECAVCLSHIEEGEEIRELSC--HHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C--~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.|--|-.++-.+..-. +-| .|.||.+|...-+. ..||.|--.+.
T Consensus 7 nCECCDrDLpp~s~dA-~ICtfEcTFCadCae~~l~---g~CPnCGGelv 52 (84)
T COG3813 7 NCECCDRDLPPDSTDA-RICTFECTFCADCAENRLH---GLCPNCGGELV 52 (84)
T ss_pred CCcccCCCCCCCCCce-eEEEEeeehhHhHHHHhhc---CcCCCCCchhh
Confidence 4555655554433211 224 48899999987663 58999976664
No 227
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=22.80 E-value=1.2e+02 Score=15.20 Aligned_cols=14 Identities=14% Similarity=0.176 Sum_probs=6.8
Q ss_pred hHHHHHHHHHHHHH
Q 042112 3 GYLIRFLRCLKWAC 16 (132)
Q Consensus 3 ~~li~~~~~l~~~~ 16 (132)
-|+.+++..+++++
T Consensus 5 ~Ytfll~~tlgiiF 18 (31)
T PRK11875 5 AYILILTLALVTLF 18 (31)
T ss_pred HHHHHHHHHHHHHH
Confidence 35555555444443
No 228
>PF12292 DUF3624: Protein of unknown function (DUF3624); InterPro: IPR022072 This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
Probab=22.64 E-value=20 Score=22.01 Aligned_cols=21 Identities=19% Similarity=0.551 Sum_probs=15.9
Q ss_pred cHHhHHHHHhcCCCCCCCCCC
Q 042112 77 HAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 77 h~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
|.+|-..|+.++-..|..|-.
T Consensus 3 C~~C~~~~F~~KiGRC~rCM~ 23 (77)
T PF12292_consen 3 CNDCQESWFWQKIGRCQRCMW 23 (77)
T ss_pred hhhHHHHHHHHHhccHHHHHH
Confidence 567889999666678988854
No 229
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.44 E-value=47 Score=16.09 Aligned_cols=28 Identities=25% Similarity=0.424 Sum_probs=15.0
Q ss_pred ccccccccccCCCceEEeCCCCcccHHh
Q 042112 53 ECAVCLSHIEEGEEIRELSCHHLFHAVC 80 (132)
Q Consensus 53 ~C~IC~~~~~~~~~~~~l~C~H~fh~~C 80 (132)
.|.+|.++......-.-..|.-.+|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 4778876655431112235666666655
No 230
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.17 E-value=47 Score=25.76 Aligned_cols=41 Identities=22% Similarity=0.464 Sum_probs=25.2
Q ss_pred ccccccccccccC--------CCceEEeCCCCcccHHhHHHHHhcCCCCCCCCCC
Q 042112 51 AVECAVCLSHIEE--------GEEIRELSCHHLFHAVCLDTWISNNYAICPVCHD 97 (132)
Q Consensus 51 ~~~C~IC~~~~~~--------~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~ 97 (132)
...||+|-..-.. .+..+.+ .|..|-..|--. ...||.|-.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL-----~CslC~teW~~~-R~~C~~Cg~ 232 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYL-----SCSLCATEWHYV-RVKCSHCEE 232 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEE-----EcCCCCCccccc-CccCCCCCC
Confidence 4579999886421 1223444 444566778653 368999965
No 231
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=21.86 E-value=49 Score=28.79 Aligned_cols=51 Identities=18% Similarity=0.406 Sum_probs=33.3
Q ss_pred cccccccccccccCCCc-------eEEeCCCCcccHHhHHHHH---h-c-----CCCCCCCCCCCCC
Q 042112 50 EAVECAVCLSHIEEGEE-------IRELSCHHLFHAVCLDTWI---S-N-----NYAICPVCHDSIA 100 (132)
Q Consensus 50 ~~~~C~IC~~~~~~~~~-------~~~l~C~H~fh~~Ci~~wl---~-~-----~~~~CP~Cr~~~~ 100 (132)
....|.||-|.=++.+. +-.-.|...||..|....- . . +.+-|-+|+..+.
T Consensus 116 fnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~Hfs 182 (900)
T KOG0956|consen 116 FNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYHFS 182 (900)
T ss_pred hcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHHHH
Confidence 46789999987555432 1123577899999987641 1 1 1235999986553
No 232
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=21.75 E-value=70 Score=21.60 Aligned_cols=22 Identities=27% Similarity=0.721 Sum_probs=15.4
Q ss_pred eCCCCcccHHhHHHHHhcCCCCCCCCCCCCCC
Q 042112 70 LSCHHLFHAVCLDTWISNNYAICPVCHDSIAP 101 (132)
Q Consensus 70 l~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~ 101 (132)
.-|++.|| +.+-||.|+.-+-.
T Consensus 101 v~C~~~Y~----------GeK~C~~C~tGiYS 122 (128)
T PF11682_consen 101 VMCGNHYH----------GEKYCPKCGTGIYS 122 (128)
T ss_pred ecCCCccC----------cCEecCCCCCcccc
Confidence 34777776 34689999886643
No 233
>CHL00031 psbT photosystem II protein T
Probab=21.64 E-value=1.2e+02 Score=15.47 Aligned_cols=13 Identities=15% Similarity=0.140 Sum_probs=6.2
Q ss_pred hHHHHHHHHHHHH
Q 042112 3 GYLIRFLRCLKWA 15 (132)
Q Consensus 3 ~~li~~~~~l~~~ 15 (132)
-|+.+++..++++
T Consensus 5 vYtfll~~tlgil 17 (33)
T CHL00031 5 VYTFLLVSTLGII 17 (33)
T ss_pred HHHHHHHHHHHHH
Confidence 3555555444444
No 234
>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=21.11 E-value=55 Score=21.35 Aligned_cols=14 Identities=29% Similarity=0.857 Sum_probs=10.5
Q ss_pred CCCCCCCCCCCCCC
Q 042112 89 YAICPVCHDSIAPS 102 (132)
Q Consensus 89 ~~~CP~Cr~~~~~~ 102 (132)
...||.|-+.+...
T Consensus 26 PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 26 PIVCPKCGTEFPPE 39 (108)
T ss_pred CccCCCCCCccCcc
Confidence 35699998877655
No 235
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=21.05 E-value=71 Score=14.62 Aligned_cols=10 Identities=40% Similarity=1.006 Sum_probs=7.4
Q ss_pred CCCCCCCCCC
Q 042112 92 CPVCHDSIAP 101 (132)
Q Consensus 92 CP~Cr~~~~~ 101 (132)
||.|-+++..
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 8888877753
No 236
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.96 E-value=37 Score=23.53 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=17.7
Q ss_pred ccHHhHHHHHhcC---CCCCCCCCCCCCCCC
Q 042112 76 FHAVCLDTWISNN---YAICPVCHDSIAPSR 103 (132)
Q Consensus 76 fh~~Ci~~wl~~~---~~~CP~Cr~~~~~~~ 103 (132)
||..|+++=++.- .=.||.|+..-....
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~ 32 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKSGQS 32 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCCCCc
Confidence 7888887766321 126999987554333
No 237
>PLN02248 cellulose synthase-like protein
Probab=20.91 E-value=1.1e+02 Score=28.09 Aligned_cols=29 Identities=21% Similarity=0.494 Sum_probs=23.3
Q ss_pred CCCCcccHHhHHHHHhcCCCCCCCCCCCCC
Q 042112 71 SCHHLFHAVCLDTWISNNYAICPVCHDSIA 100 (132)
Q Consensus 71 ~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~ 100 (132)
.|+...|++|...-++. ...||-|+.+..
T Consensus 149 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 177 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKS-GGICPGCKEPYK 177 (1135)
T ss_pred cccchhHHhHhhhhhhc-CCCCCCCccccc
Confidence 45688899999888875 478999998773
No 238
>KOG3726 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.90 E-value=58 Score=28.12 Aligned_cols=41 Identities=24% Similarity=0.477 Sum_probs=28.0
Q ss_pred cccccccccccc-CCCceEEeCCCCcccHHhHHHHHhcCCCCCCCC
Q 042112 51 AVECAVCLSHIE-EGEEIRELSCHHLFHAVCLDTWISNNYAICPVC 95 (132)
Q Consensus 51 ~~~C~IC~~~~~-~~~~~~~l~C~H~fh~~Ci~~wl~~~~~~CP~C 95 (132)
...|.+|..+=. +.+.++.+.|+-.||..|-... ++.||+|
T Consensus 654 ~r~C~vcq~pedse~~v~rt~~C~~~~C~~c~~~~----~~~~~vC 695 (717)
T KOG3726|consen 654 IRTCKVCQLPEDSETDVCRTTFCYTPYCVACSLDY----ASISEVC 695 (717)
T ss_pred HHHHHHhcCCcCccccccCccccCCcchHhhhhhh----hccCccc
Confidence 567888876532 2334566689999988875443 3579999
Done!