Query 046177
Match_columns 272
No_of_seqs 287 out of 1596
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 09:26:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046177.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046177hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3002 Zn finger protein [Gen 100.0 2.8E-46 6.1E-51 338.0 12.8 223 49-271 41-264 (299)
2 PF03145 Sina: Seven in absent 100.0 1.3E-38 2.8E-43 274.9 10.5 171 101-271 1-171 (198)
3 cd03829 Sina Seven in absentia 99.9 1.9E-29 4.1E-34 196.4 1.3 96 174-272 2-98 (127)
4 KOG0297 TNF receptor-associate 99.4 4.3E-13 9.4E-18 126.9 7.2 118 51-173 16-140 (391)
5 TIGR00599 rad18 DNA repair pro 98.7 1.1E-08 2.4E-13 96.4 2.7 78 34-113 5-88 (397)
6 PF14835 zf-RING_6: zf-RING of 98.6 8.5E-09 1.8E-13 72.2 0.8 58 52-109 3-64 (65)
7 PF15227 zf-C3HC4_4: zinc fing 98.6 1.1E-08 2.4E-13 66.4 0.7 35 59-94 1-42 (42)
8 smart00504 Ubox Modified RING 98.6 2.8E-08 6E-13 69.7 2.6 56 56-112 1-62 (63)
9 PLN03208 E3 ubiquitin-protein 98.5 2.9E-08 6.3E-13 84.6 1.9 47 53-100 15-80 (193)
10 KOG0287 Postreplication repair 98.5 1.1E-08 2.3E-13 93.0 -1.7 67 46-113 13-85 (442)
11 KOG0823 Predicted E3 ubiquitin 98.5 5.2E-08 1.1E-12 84.6 2.6 48 52-100 43-96 (230)
12 PF13923 zf-C3HC4_2: Zinc fing 98.4 6.2E-08 1.4E-12 61.7 0.7 36 59-94 1-39 (39)
13 PF13920 zf-C3HC4_3: Zinc fing 98.3 1.1E-07 2.4E-12 63.9 0.6 43 56-99 2-48 (50)
14 PF02176 zf-TRAF: TRAF-type zi 98.3 3.5E-07 7.5E-12 63.6 1.6 53 112-166 7-60 (60)
15 PF04564 U-box: U-box domain; 98.2 3.9E-07 8.4E-12 66.3 1.5 59 54-113 2-67 (73)
16 PF13639 zf-RING_2: Ring finge 98.2 2.8E-07 6.1E-12 60.2 0.2 38 58-95 2-44 (44)
17 KOG0320 Predicted E3 ubiquitin 98.2 5.1E-07 1.1E-11 75.4 1.4 46 54-99 129-178 (187)
18 PHA02929 N1R/p28-like protein; 98.1 9.9E-07 2.1E-11 78.0 1.1 48 53-100 171-228 (238)
19 KOG0317 Predicted E3 ubiquitin 98.0 1.2E-06 2.5E-11 78.5 0.6 47 53-100 236-285 (293)
20 PF14634 zf-RING_5: zinc-RING 98.0 1.2E-06 2.5E-11 57.4 0.3 38 58-96 1-44 (44)
21 PF00097 zf-C3HC4: Zinc finger 97.9 2.9E-06 6.3E-11 54.3 1.0 36 59-94 1-41 (41)
22 COG5432 RAD18 RING-finger-cont 97.9 1.9E-06 4.2E-11 77.0 0.1 52 47-99 16-70 (391)
23 cd00162 RING RING-finger (Real 97.9 4.1E-06 8.9E-11 53.6 0.6 41 58-98 1-45 (45)
24 PHA02926 zinc finger-like prot 97.8 4.1E-06 8.9E-11 72.6 -0.5 48 52-100 166-231 (242)
25 PF13445 zf-RING_UBOX: RING-ty 97.6 1.1E-05 2.4E-10 52.5 -0.4 27 59-87 1-31 (43)
26 TIGR00570 cdk7 CDK-activating 97.5 4.7E-05 1E-09 69.5 2.4 46 55-100 2-55 (309)
27 KOG2164 Predicted E3 ubiquitin 97.5 2.5E-05 5.5E-10 74.9 0.6 44 56-100 186-237 (513)
28 COG5574 PEX10 RING-finger-cont 97.5 3.1E-05 6.8E-10 68.6 1.0 45 54-99 213-262 (271)
29 smart00184 RING Ring finger. E 97.5 2.8E-05 6.1E-10 47.9 0.3 35 59-94 1-39 (39)
30 KOG2177 Predicted E3 ubiquitin 97.4 2.9E-05 6.3E-10 68.9 -0.4 67 50-117 7-77 (386)
31 KOG0311 Predicted E3 ubiquitin 97.3 1.2E-05 2.6E-10 73.8 -4.1 50 51-100 38-91 (381)
32 KOG4159 Predicted E3 ubiquitin 97.3 6.7E-05 1.5E-09 71.1 0.3 64 36-100 64-130 (398)
33 PLN03086 PRLI-interacting fact 97.0 0.00086 1.9E-08 66.2 4.9 106 52-169 403-536 (567)
34 PF07800 DUF1644: Protein of u 97.0 0.00096 2.1E-08 55.1 4.1 28 144-173 107-134 (162)
35 KOG0978 E3 ubiquitin ligase in 97.0 0.00016 3.5E-09 72.4 -0.5 50 50-100 637-690 (698)
36 PF12678 zf-rbx1: RING-H2 zinc 96.9 0.00036 7.8E-09 50.7 0.9 38 58-95 21-73 (73)
37 COG5152 Uncharacterized conser 96.4 0.00093 2E-08 57.0 0.5 56 56-112 196-256 (259)
38 KOG2660 Locus-specific chromos 96.2 0.00099 2.2E-08 60.9 -0.7 51 50-100 9-62 (331)
39 PF12861 zf-Apc11: Anaphase-pr 96.2 0.0016 3.4E-08 48.5 0.5 41 59-99 35-82 (85)
40 KOG1813 Predicted E3 ubiquitin 96.1 0.0039 8.4E-08 56.4 2.7 46 57-103 242-290 (313)
41 PLN03086 PRLI-interacting fact 96.0 0.02 4.4E-07 56.7 7.2 39 124-168 459-497 (567)
42 PF14570 zf-RING_4: RING/Ubox 96.0 0.0021 4.5E-08 42.7 0.3 40 59-98 1-47 (48)
43 KOG4172 Predicted E3 ubiquitin 96.0 0.00076 1.6E-08 45.7 -1.9 42 57-99 8-54 (62)
44 KOG2879 Predicted E3 ubiquitin 95.9 0.005 1.1E-07 55.1 2.6 47 53-99 236-287 (298)
45 PF02176 zf-TRAF: TRAF-type zi 95.7 0.0044 9.5E-08 42.7 1.1 37 136-174 1-37 (60)
46 KOG0824 Predicted E3 ubiquitin 95.6 0.0053 1.1E-07 55.6 1.4 44 56-100 7-54 (324)
47 KOG0802 E3 ubiquitin ligase [P 95.4 0.0036 7.9E-08 62.1 -0.6 44 54-98 289-340 (543)
48 COG5222 Uncharacterized conser 95.3 0.0069 1.5E-07 54.8 1.0 40 57-96 275-318 (427)
49 PF11789 zf-Nse: Zinc-finger o 95.0 0.0059 1.3E-07 42.2 -0.2 35 53-87 8-42 (57)
50 COG5175 MOT2 Transcriptional r 94.9 0.0066 1.4E-07 55.9 -0.2 48 51-99 10-64 (480)
51 COG5540 RING-finger-containing 94.7 0.012 2.5E-07 53.6 0.9 43 57-99 324-372 (374)
52 KOG4739 Uncharacterized protei 94.7 0.017 3.6E-07 51.0 1.8 44 56-99 3-48 (233)
53 KOG4265 Predicted E3 ubiquitin 94.6 0.01 2.2E-07 55.1 0.2 45 54-99 288-336 (349)
54 KOG4275 Predicted E3 ubiquitin 94.5 0.0061 1.3E-07 55.0 -1.5 42 55-98 299-341 (350)
55 PF14447 Prok-RING_4: Prokaryo 93.9 0.06 1.3E-06 36.7 2.7 43 56-99 7-50 (55)
56 KOG1002 Nucleotide excision re 93.5 0.023 5E-07 55.2 0.3 50 49-99 529-586 (791)
57 PF11793 FANCL_C: FANCL C-term 93.5 0.018 3.8E-07 41.4 -0.4 44 56-99 2-66 (70)
58 PF05290 Baculo_IE-1: Baculovi 93.0 0.039 8.4E-07 44.4 0.8 45 55-100 79-133 (140)
59 KOG1785 Tyrosine kinase negati 92.8 0.025 5.4E-07 53.2 -0.6 42 58-100 371-417 (563)
60 PF05605 zf-Di19: Drought indu 92.4 0.16 3.5E-06 34.3 3.2 49 115-172 3-54 (54)
61 COG5236 Uncharacterized conser 91.3 0.064 1.4E-06 49.7 0.2 49 49-98 54-107 (493)
62 KOG1571 Predicted E3 ubiquitin 91.0 0.055 1.2E-06 50.3 -0.5 46 52-99 301-347 (355)
63 KOG1039 Predicted E3 ubiquitin 90.8 0.098 2.1E-06 48.9 0.9 47 54-100 159-222 (344)
64 COG5219 Uncharacterized conser 90.7 0.044 9.6E-07 56.6 -1.5 46 54-99 1467-1523(1525)
65 KOG4367 Predicted Zn-finger pr 90.0 0.079 1.7E-06 50.5 -0.4 33 54-87 2-34 (699)
66 PF07975 C1_4: TFIIH C1-like d 89.4 0.2 4.3E-06 33.8 1.3 37 59-95 2-50 (51)
67 COG5243 HRD1 HRD ubiquitin lig 88.9 0.18 3.9E-06 47.2 1.1 44 54-98 285-344 (491)
68 KOG3039 Uncharacterized conser 88.5 0.23 4.9E-06 44.1 1.3 46 55-100 220-271 (303)
69 KOG0825 PHD Zn-finger protein 87.9 0.076 1.6E-06 53.9 -2.2 42 58-99 125-171 (1134)
70 PF13909 zf-H2C2_5: C2H2-type 87.8 0.33 7.2E-06 26.9 1.3 24 145-172 1-24 (24)
71 PF07191 zinc-ribbons_6: zinc- 87.3 0.19 4.2E-06 36.0 0.2 38 57-99 2-41 (70)
72 KOG1814 Predicted E3 ubiquitin 87.2 0.24 5.2E-06 47.0 0.8 103 53-159 181-322 (445)
73 PF04641 Rtf2: Rtf2 RING-finge 87.0 0.47 1E-05 42.6 2.6 50 51-100 108-162 (260)
74 KOG0804 Cytoplasmic Zn-finger 86.6 0.24 5.1E-06 47.5 0.4 48 52-99 171-222 (493)
75 KOG4692 Predicted E3 ubiquitin 85.4 0.23 4.9E-06 46.3 -0.3 45 54-99 420-467 (489)
76 PF10571 UPF0547: Uncharacteri 85.3 0.42 9.1E-06 27.6 0.9 22 58-79 2-24 (26)
77 KOG4628 Predicted E3 ubiquitin 84.3 0.73 1.6E-05 43.2 2.4 44 57-100 230-279 (348)
78 KOG4185 Predicted E3 ubiquitin 83.9 0.69 1.5E-05 42.1 2.1 57 56-113 3-77 (296)
79 COG5194 APC11 Component of SCF 83.6 0.29 6.3E-06 35.9 -0.4 43 57-99 21-81 (88)
80 KOG1645 RING-finger-containing 83.0 0.35 7.5E-06 45.9 -0.2 42 57-98 5-55 (463)
81 PF13913 zf-C2HC_2: zinc-finge 82.6 0.88 1.9E-05 25.8 1.4 23 115-141 3-25 (25)
82 KOG3800 Predicted E3 ubiquitin 80.6 0.72 1.6E-05 41.9 0.9 42 58-99 2-51 (300)
83 KOG3161 Predicted E3 ubiquitin 80.3 0.34 7.3E-06 48.4 -1.4 40 52-92 7-51 (861)
84 KOG1001 Helicase-like transcri 79.3 0.45 9.7E-06 48.5 -0.9 40 57-98 455-499 (674)
85 PF02891 zf-MIZ: MIZ/SP-RING z 79.1 0.68 1.5E-05 30.9 0.2 42 56-97 2-50 (50)
86 smart00647 IBR In Between Ring 77.2 1.3 2.8E-05 30.2 1.2 33 56-88 18-59 (64)
87 KOG2462 C2H2-type Zn-finger pr 76.9 8.3 0.00018 34.9 6.4 73 89-169 162-237 (279)
88 COG3813 Uncharacterized protei 76.5 1.3 2.7E-05 32.0 1.0 30 71-100 23-53 (84)
89 PF01485 IBR: IBR domain; Int 75.6 2.2 4.7E-05 29.0 2.0 34 55-88 17-59 (64)
90 PF05605 zf-Di19: Drought indu 75.3 3 6.4E-05 28.0 2.5 27 144-174 2-28 (54)
91 KOG2932 E3 ubiquitin ligase in 74.9 1.7 3.8E-05 39.9 1.7 83 49-137 82-167 (389)
92 KOG3002 Zn finger protein [Gen 74.7 1.6 3.4E-05 40.2 1.4 77 89-169 49-131 (299)
93 KOG2231 Predicted E3 ubiquitin 73.5 1.8 3.8E-05 43.9 1.5 41 58-99 2-52 (669)
94 KOG2817 Predicted E3 ubiquitin 73.4 1.3 2.8E-05 41.9 0.5 45 52-97 330-383 (394)
95 COG4306 Uncharacterized protei 72.8 1 2.2E-05 36.0 -0.3 48 79-132 30-82 (160)
96 KOG0826 Predicted E3 ubiquitin 72.3 1.7 3.6E-05 40.3 0.9 45 53-97 297-344 (357)
97 TIGR00622 ssl1 transcription f 72.1 3.1 6.7E-05 32.7 2.3 38 58-95 57-110 (112)
98 PRK14890 putative Zn-ribbon RN 72.1 5.5 0.00012 27.6 3.2 14 142-159 46-59 (59)
99 PF06906 DUF1272: Protein of u 71.0 2.4 5.2E-05 29.0 1.2 43 58-100 7-53 (57)
100 KOG1734 Predicted RING-contain 70.7 0.9 1.9E-05 40.9 -1.1 45 55-99 223-281 (328)
101 KOG3608 Zn finger proteins [Ge 67.5 3.2 7E-05 38.9 1.7 113 53-171 204-345 (467)
102 COG2888 Predicted Zn-ribbon RN 67.4 4.8 0.0001 27.9 2.1 36 113-159 26-61 (61)
103 PF10083 DUF2321: Uncharacteri 66.9 1.5 3.2E-05 36.3 -0.5 22 78-99 29-50 (158)
104 PF13894 zf-C2H2_4: C2H2-type 66.7 5 0.00011 21.2 1.8 22 146-171 2-24 (24)
105 PRK11088 rrmA 23S rRNA methylt 66.3 2.7 6E-05 37.6 1.0 24 56-79 2-27 (272)
106 PRK04023 DNA polymerase II lar 66.0 6.2 0.00014 41.8 3.6 44 55-100 625-675 (1121)
107 PLN02436 cellulose synthase A 65.8 4.9 0.00011 42.9 2.8 42 58-99 38-89 (1094)
108 KOG0828 Predicted E3 ubiquitin 65.3 1.7 3.8E-05 42.3 -0.5 47 53-99 568-634 (636)
109 KOG2462 C2H2-type Zn-finger pr 64.8 3.7 7.9E-05 37.2 1.5 75 89-173 188-269 (279)
110 PF14446 Prok-RING_1: Prokaryo 62.0 3.9 8.6E-05 27.8 0.9 36 57-93 6-44 (54)
111 KOG4362 Transcriptional regula 61.9 1.9 4.2E-05 43.7 -0.9 48 51-99 16-69 (684)
112 KOG3039 Uncharacterized conser 60.7 4.1 8.9E-05 36.4 1.0 36 51-87 38-73 (303)
113 PF01363 FYVE: FYVE zinc finge 60.4 5.8 0.00013 27.7 1.6 33 55-87 8-43 (69)
114 KOG0297 TNF receptor-associate 59.8 4.5 9.7E-05 38.7 1.2 34 113-149 113-147 (391)
115 PF15616 TerY-C: TerY-C metal 59.6 5.3 0.00011 32.3 1.4 45 51-99 72-116 (131)
116 KOG1812 Predicted E3 ubiquitin 58.7 3.8 8.3E-05 39.0 0.5 33 55-87 145-180 (384)
117 KOG2807 RNA polymerase II tran 58.5 5.3 0.00012 37.0 1.4 37 59-95 333-374 (378)
118 smart00154 ZnF_AN1 AN1-like Zi 58.2 6.4 0.00014 24.8 1.3 24 59-83 1-26 (39)
119 PF03145 Sina: Seven in absent 58.1 5.9 0.00013 33.9 1.6 47 94-140 24-70 (198)
120 PF01428 zf-AN1: AN1-like Zinc 57.6 8.3 0.00018 24.6 1.8 33 59-92 1-36 (43)
121 PLN02400 cellulose synthase 57.5 9.2 0.0002 41.0 3.1 42 58-99 38-89 (1085)
122 PF10272 Tmpp129: Putative tra 56.7 4.8 0.0001 38.0 0.8 29 71-99 307-351 (358)
123 PF10367 Vps39_2: Vacuolar sor 56.2 7.1 0.00015 29.4 1.6 33 54-86 76-109 (109)
124 PF04216 FdhE: Protein involve 56.0 4.9 0.00011 36.6 0.7 42 56-97 172-220 (290)
125 PF04606 Ogr_Delta: Ogr/Delta- 54.8 3.6 7.8E-05 26.9 -0.2 38 90-129 1-38 (47)
126 KOG1100 Predicted E3 ubiquitin 54.2 8.5 0.00018 33.5 1.9 39 59-99 161-200 (207)
127 PF05253 zf-U11-48K: U11-48K-l 54.1 4.2 9.2E-05 23.4 0.0 24 115-141 3-26 (27)
128 KOG3579 Predicted E3 ubiquitin 53.8 6.9 0.00015 35.7 1.3 33 54-86 266-301 (352)
129 PRK14714 DNA polymerase II lar 53.8 15 0.00033 40.0 4.0 43 56-100 667-721 (1337)
130 PF13834 DUF4193: Domain of un 53.2 13 0.00028 28.5 2.5 37 47-83 61-98 (99)
131 PF14569 zf-UDP: Zinc-binding 53.0 4.8 0.0001 29.5 0.1 43 57-99 10-62 (80)
132 KOG0298 DEAD box-containing he 51.0 1.9 4E-05 46.5 -3.1 66 32-99 1128-1199(1394)
133 PF14445 Prok-RING_2: Prokaryo 50.7 1.2 2.5E-05 29.9 -3.0 44 55-98 6-51 (57)
134 PF13240 zinc_ribbon_2: zinc-r 50.5 7.9 0.00017 21.5 0.7 7 90-96 15-21 (23)
135 KOG2789 Putative Zn-finger pro 49.9 9.1 0.0002 36.4 1.5 71 16-87 27-106 (482)
136 TIGR01562 FdhE formate dehydro 49.4 12 0.00027 34.5 2.2 42 55-96 183-232 (305)
137 PF12756 zf-C2H2_2: C2H2 type 48.8 13 0.00028 27.2 1.9 35 134-172 40-76 (100)
138 COG1198 PriA Primosomal protei 47.5 14 0.00029 38.3 2.4 10 90-99 446-455 (730)
139 cd00065 FYVE FYVE domain; Zinc 47.4 9.5 0.00021 25.4 0.9 30 58-87 4-36 (57)
140 KOG1493 Anaphase-promoting com 47.0 2.8 6.2E-05 30.6 -1.8 26 74-99 50-81 (84)
141 smart00064 FYVE Protein presen 46.6 11 0.00025 26.1 1.2 32 56-87 10-44 (68)
142 PHA00616 hypothetical protein 46.3 30 0.00065 22.5 3.1 27 144-174 1-28 (44)
143 KOG3268 Predicted E3 ubiquitin 45.9 7.1 0.00015 33.2 0.1 25 75-99 190-228 (234)
144 KOG1812 Predicted E3 ubiquitin 45.5 7.9 0.00017 36.9 0.3 33 55-87 305-341 (384)
145 PF00096 zf-C2H2: Zinc finger, 45.0 12 0.00026 19.9 0.9 20 146-169 2-22 (23)
146 PF05502 Dynactin_p62: Dynacti 44.9 12 0.00026 36.8 1.5 45 53-100 2-64 (483)
147 cd00350 rubredoxin_like Rubred 44.5 17 0.00037 21.8 1.7 9 89-97 18-26 (33)
148 PLN02189 cellulose synthase 43.8 13 0.00029 39.7 1.7 42 58-99 36-87 (1040)
149 PF08209 Sgf11: Sgf11 (transcr 41.5 9.8 0.00021 23.2 0.2 18 124-141 10-27 (33)
150 PF08882 Acetone_carb_G: Aceto 41.2 12 0.00027 29.2 0.8 13 70-82 24-36 (112)
151 COG5220 TFB3 Cdk activating ki 40.7 3.8 8.3E-05 36.4 -2.3 43 56-98 10-63 (314)
152 TIGR00416 sms DNA repair prote 40.6 13 0.00029 36.1 1.1 24 69-97 6-30 (454)
153 COG4647 AcxC Acetone carboxyla 40.0 11 0.00024 30.3 0.4 21 61-82 62-82 (165)
154 smart00301 DM Doublesex DNA-bi 39.6 17 0.00036 24.8 1.1 39 124-166 8-46 (54)
155 PF15135 UPF0515: Uncharacteri 39.6 23 0.00049 31.8 2.3 91 8-99 60-166 (278)
156 PLN02638 cellulose synthase A 39.1 17 0.00038 38.9 1.7 42 58-99 19-70 (1079)
157 PRK09678 DNA-binding transcrip 39.0 17 0.00037 26.2 1.2 45 90-136 3-47 (72)
158 KOG2930 SCF ubiquitin ligase, 39.0 3.1 6.6E-05 32.2 -2.8 44 55-98 45-107 (114)
159 PRK03564 formate dehydrogenase 38.2 22 0.00048 32.9 2.1 42 55-96 186-234 (309)
160 PRK11823 DNA repair protein Ra 37.8 17 0.00037 35.3 1.4 24 69-97 6-30 (446)
161 smart00734 ZnF_Rad18 Rad18-lik 37.7 31 0.00067 19.6 1.9 21 145-169 2-22 (26)
162 PF09297 zf-NADH-PPase: NADH p 37.6 10 0.00022 22.6 -0.2 20 77-96 3-29 (32)
163 PLN02195 cellulose synthase A 36.7 22 0.00047 37.9 1.9 42 58-99 8-59 (977)
164 PF13248 zf-ribbon_3: zinc-rib 36.3 18 0.00038 20.5 0.8 7 90-96 18-24 (26)
165 PHA03096 p28-like protein; Pro 35.6 9.1 0.0002 35.0 -0.9 40 57-96 179-231 (284)
166 PF03854 zf-P11: P-11 zinc fin 35.5 10 0.00022 25.2 -0.4 39 59-99 5-46 (50)
167 PF00412 LIM: LIM domain; Int 35.4 15 0.00032 24.3 0.4 32 55-86 25-56 (58)
168 PF02318 FYVE_2: FYVE-type zin 35.3 25 0.00054 27.5 1.7 41 56-96 54-102 (118)
169 KOG2114 Vacuolar assembly/sort 35.2 17 0.00036 38.0 0.8 50 49-98 833-882 (933)
170 cd00729 rubredoxin_SM Rubredox 35.1 33 0.00071 20.8 1.9 9 89-97 19-27 (34)
171 PF13717 zinc_ribbon_4: zinc-r 35.0 28 0.0006 21.4 1.5 13 57-69 3-15 (36)
172 PRK00420 hypothetical protein; 34.0 25 0.00053 27.7 1.4 25 57-85 24-48 (112)
173 PRK14892 putative transcriptio 34.0 43 0.00093 25.7 2.8 35 49-84 14-49 (99)
174 PRK14559 putative protein seri 33.8 31 0.00067 35.3 2.5 43 57-99 2-52 (645)
175 COG5109 Uncharacterized conser 33.6 18 0.00039 33.6 0.7 43 52-95 332-383 (396)
176 PF05883 Baculo_RING: Baculovi 32.8 7.7 0.00017 31.4 -1.6 31 56-87 26-65 (134)
177 COG1645 Uncharacterized Zn-fin 32.6 24 0.00051 28.5 1.2 23 57-84 29-51 (131)
178 KOG2068 MOT2 transcription fac 32.3 32 0.00068 32.1 2.1 43 57-99 250-298 (327)
179 cd01121 Sms Sms (bacterial rad 31.4 22 0.00047 33.8 0.9 13 85-97 11-23 (372)
180 KOG3113 Uncharacterized conser 31.3 29 0.00062 31.2 1.6 49 51-99 106-158 (293)
181 COG4357 Zinc finger domain con 30.9 28 0.00061 26.6 1.3 23 78-100 63-92 (105)
182 PF06676 DUF1178: Protein of u 30.5 30 0.00066 28.5 1.5 22 71-97 6-41 (148)
183 PF00301 Rubredoxin: Rubredoxi 30.4 30 0.00066 22.7 1.2 20 45-65 24-43 (47)
184 KOG2186 Cell growth-regulating 30.2 26 0.00056 31.5 1.1 43 123-169 8-50 (276)
185 KOG3899 Uncharacterized conser 29.9 13 0.00027 34.2 -0.9 27 73-99 323-365 (381)
186 PLN02915 cellulose synthase A 29.0 30 0.00066 37.1 1.6 44 56-99 15-68 (1044)
187 PF10426 zf-RAG1: Recombinatio 28.6 38 0.00082 20.2 1.3 23 145-169 3-25 (30)
188 COG1592 Rubrerythrin [Energy p 28.2 37 0.0008 28.6 1.7 11 56-66 134-144 (166)
189 TIGR00373 conserved hypothetic 28.1 46 0.001 27.5 2.2 16 88-103 128-143 (158)
190 PF12660 zf-TFIIIC: Putative z 27.7 26 0.00057 26.7 0.6 40 58-98 16-65 (99)
191 KOG3993 Transcription factor ( 27.7 12 0.00026 36.0 -1.4 49 47-99 258-306 (500)
192 KOG0827 Predicted E3 ubiquitin 27.4 18 0.0004 34.4 -0.3 37 57-96 5-53 (465)
193 PF13912 zf-C2H2_6: C2H2-type 27.2 46 0.001 18.3 1.5 24 145-172 2-26 (27)
194 COG5242 TFB4 RNA polymerase II 27.0 28 0.00061 30.8 0.8 16 55-70 259-274 (296)
195 KOG3576 Ovo and related transc 27.0 60 0.0013 28.4 2.8 109 52-174 113-239 (267)
196 PF06677 Auto_anti-p27: Sjogre 26.4 47 0.001 21.2 1.5 22 58-83 19-40 (41)
197 PF06750 DiS_P_DiS: Bacterial 26.3 47 0.001 25.0 1.8 12 88-99 58-69 (92)
198 PF03833 PolC_DP2: DNA polymer 26.0 23 0.00049 37.1 0.0 43 55-99 654-703 (900)
199 PRK06266 transcription initiat 25.7 65 0.0014 27.3 2.7 16 88-103 136-151 (178)
200 PF03604 DNA_RNApol_7kD: DNA d 25.6 53 0.0012 19.8 1.6 7 59-65 3-9 (32)
201 KOG2272 Focal adhesion protein 25.0 38 0.00082 30.5 1.2 52 47-99 152-206 (332)
202 PF01286 XPA_N: XPA protein N- 24.8 50 0.0011 20.2 1.4 30 56-85 3-32 (34)
203 PF09723 Zn-ribbon_8: Zinc rib 24.6 52 0.0011 20.8 1.5 8 89-96 27-34 (42)
204 TIGR00595 priA primosomal prot 24.4 50 0.0011 32.6 2.1 22 77-100 213-234 (505)
205 TIGR00595 priA primosomal prot 24.3 72 0.0016 31.5 3.2 42 54-97 211-262 (505)
206 PF13719 zinc_ribbon_5: zinc-r 24.1 67 0.0014 19.7 1.9 13 57-69 3-15 (37)
207 PF03107 C1_2: C1 domain; Int 23.8 62 0.0013 18.8 1.6 17 58-74 2-19 (30)
208 PF10497 zf-4CXXC_R1: Zinc-fin 23.7 40 0.00087 26.0 1.0 29 58-86 9-47 (105)
209 smart00661 RPOL9 RNA polymeras 23.5 59 0.0013 21.0 1.7 11 59-69 3-13 (52)
210 PF12907 zf-met2: Zinc-binding 23.3 48 0.001 21.1 1.1 17 158-174 15-31 (40)
211 KOG1952 Transcription factor N 23.1 27 0.00057 36.6 -0.1 43 54-96 189-244 (950)
212 PHA00733 hypothetical protein 23.1 1.2E+02 0.0026 24.1 3.7 26 144-173 99-125 (128)
213 cd00730 rubredoxin Rubredoxin; 22.3 45 0.00098 22.2 0.9 14 51-64 29-42 (50)
214 KOG1815 Predicted E3 ubiquitin 22.2 40 0.00087 32.7 0.9 25 71-95 180-206 (444)
215 PRK14559 putative protein seri 21.9 60 0.0013 33.2 2.1 22 77-98 15-37 (645)
216 PF14319 Zn_Tnp_IS91: Transpos 21.7 49 0.0011 25.7 1.2 44 70-120 42-88 (111)
217 COG5151 SSL1 RNA polymerase II 21.7 34 0.00074 31.7 0.3 9 90-98 390-398 (421)
218 KOG1356 Putative transcription 21.7 31 0.00068 36.0 0.1 32 56-87 229-261 (889)
219 PF01690 PLRV_ORF5: Potato lea 21.6 2.7E+02 0.0059 27.3 6.3 34 233-266 200-235 (465)
220 PRK00398 rpoP DNA-directed RNA 21.2 22 0.00048 22.9 -0.7 11 89-99 22-32 (46)
221 PF02148 zf-UBP: Zn-finger in 21.2 60 0.0013 22.3 1.4 23 59-82 1-24 (63)
222 PRK05580 primosome assembly pr 21.1 72 0.0016 32.7 2.6 41 55-97 380-430 (679)
223 KOG2807 RNA polymerase II tran 21.1 55 0.0012 30.6 1.5 12 54-65 274-285 (378)
224 PF11781 RRN7: RNA polymerase 21.0 40 0.00086 20.8 0.4 25 56-84 8-32 (36)
225 PRK11827 hypothetical protein; 20.9 48 0.001 23.0 0.9 17 51-67 3-19 (60)
226 PF14353 CpXC: CpXC protein 20.7 66 0.0014 25.3 1.7 10 90-99 3-12 (128)
227 KOG3183 Predicted Zn-finger pr 20.6 65 0.0014 28.7 1.8 52 58-110 10-77 (250)
228 COG1198 PriA Primosomal protei 20.4 70 0.0015 33.3 2.2 42 54-97 433-484 (730)
229 COG2835 Uncharacterized conser 20.3 74 0.0016 22.1 1.6 16 52-67 4-19 (60)
230 PF09237 GAGA: GAGA factor; I 20.1 80 0.0017 21.3 1.7 27 143-173 23-50 (54)
No 1
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=100.00 E-value=2.8e-46 Score=338.05 Aligned_cols=223 Identities=45% Similarity=0.862 Sum_probs=209.5
Q ss_pred cccCCCCeeeeccccccCcCCcccccCCceeccCcccccCCCCCCcccCCCcccchhHHHHhhhcCCCcccccCCCCcee
Q 046177 49 VSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVHNRCPTCRHELGNIRCLALEKVAASLELPCKYQSYGCMGIY 128 (272)
Q Consensus 49 ~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~~~CP~Cr~~~~~~r~~~le~~~~~l~v~C~~~~~GC~~~~ 128 (272)
......++|+||||++.+.+||+||.+||+.|++|..++.+.||.||.+++++|+++||++++++.++|+|...||++.+
T Consensus 41 ~~~~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~ 120 (299)
T KOG3002|consen 41 VTLLDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSF 120 (299)
T ss_pred ccccchhhccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccccHHHHHHHHHHHhceecccccccCCceee
Confidence 44556789999999999999999999999999999988889999999999999999999999999999999999999999
Q ss_pred ccCcHHhhhhcCCCccccCCCCCCCCccccChhHHHHHhhhcCCCCCcCCceEEEEEeecCCcccccceeEEEEEeecCe
Q 046177 129 PYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPYLVAHLKDDHKVDMHNGSTFNHRYVKQNPHEVENATWMLTVFSCFGQ 208 (272)
Q Consensus 129 ~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~~~~~~g~~~~~~~~~s~~~~v~~~~~~l~v~~~~~~ 208 (272)
+|.+..+||+.|.|+|+.||.++..|+|.|..+++..|+...|+.++..+..++++|..+++..+...+|++.+..++++
T Consensus 121 ~Y~~~~~HE~~C~f~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 (299)
T KOG3002|consen 121 PYGEKSKHEKVCEFRPCSCPVPGAECKYTGSYKDLYAHLNDTHKSDIITLTGFDFVFVATDENLLGAATWTLKTSVCFGR 200 (299)
T ss_pred ccccccccccccccCCcCCCCCcccCCccCcHHHHHHHHHhhChhhhhhccccceecccCCccccccchhheeeeecCcE
Confidence 99999999999999999999998889999999999999999999988888888889999988888888998877779999
Q ss_pred eEEEEEeeeeeCCc-cEEEEEEEEeCCccCCCCcEEEEEEecCCceEEEEeeccchhccccccc
Q 046177 209 YFCLHFEAFQLGMA-PVYIAFLRFMGDDNESKNYSYSLEVGGNGRKMSWQGVPRSIRDSHKKVR 271 (272)
Q Consensus 209 ~F~l~~~~~~~~~~-~~~~a~v~~iG~~~~a~~f~Y~l~~~~~~r~l~~~s~~~si~~~~~~~~ 271 (272)
.|++++..+..+.. ++|+++++++|.+++|++|+|+|++.+++++|+||+.|+|+++++.+++
T Consensus 201 ~~~~~~~~q~~~~~~~~y~tv~~i~~~~~e~~~fsy~L~~~~~~~klt~~s~~~s~~~kvs~~~ 264 (299)
T KOG3002|consen 201 EFGLLFEVQCFREPHGVYVTVNRIAPSAPEAGEFSYSLALGGSGRKLTWQSPPRSIIQKVSKVR 264 (299)
T ss_pred EEeeeeeehhhcCCCceEEEeehhccCCCcccccceeeecCCCCceEeecCCcceeecccceec
Confidence 99999999887554 8999999999999999999999999999999999999999999998765
No 2
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=100.00 E-value=1.3e-38 Score=274.94 Aligned_cols=171 Identities=42% Similarity=0.850 Sum_probs=127.7
Q ss_pred ccchhHHHHhhhcCCCcccccCCCCceeccCcHHhhhhcCCCccccCCCCCCCCccccChhHHHHHhhhcCCCCCcCCce
Q 046177 101 IRCLALEKVAASLELPCKYQSYGCMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPYLVAHLKDDHKVDMHNGST 180 (272)
Q Consensus 101 ~r~~~le~~~~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~~~~~~g~~ 180 (272)
+||++||++++++++||+|+..||++.+++.++.+||++|+|+|+.||.++.+|+|.|+.++|..|+..+|.+.+..+..
T Consensus 1 iR~~alE~v~~~~~~pC~~~~~GC~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~~~~~~ 80 (198)
T PF03145_consen 1 IRNRALEKVAESIKFPCKNAKYGCTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNVTDNGT 80 (198)
T ss_dssp --------------EE-CCGGGT---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSEEEESS
T ss_pred CCcHHHHHHHhhceecCCCCCCCCcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCccccCcc
Confidence 48999999999999999999999999999999999999999999999997667999999999999999999998877677
Q ss_pred EEEEEeecCCcccccceeEEEEEeecCeeEEEEEeeeeeCCccEEEEEEEEeCCccCCCCcEEEEEEecCCceEEEEeec
Q 046177 181 FNHRYVKQNPHEVENATWMLTVFSCFGQYFCLHFEAFQLGMAPVYIAFLRFMGDDNESKNYSYSLEVGGNGRKMSWQGVP 260 (272)
Q Consensus 181 ~~~~~~~s~~~~v~~~~~~l~v~~~~~~~F~l~~~~~~~~~~~~~~a~v~~iG~~~~a~~f~Y~l~~~~~~r~l~~~s~~ 260 (272)
+.++|..++.......+|+++.++|+|++|+|+++.+......+|+++||++|++++|++|+|+|++.+++|||+||++|
T Consensus 81 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~F~l~~~~~~~~~~~v~~~~v~~~G~~~~a~~f~Yel~~~~~~rkl~~~~~p 160 (198)
T PF03145_consen 81 FSISFLHSDINSVESPDWVLVQFSCFGKLFLLYVQKFELEGNAVYFAVVCYIGPAEEASNFSYELEVRSNGRKLTWQSFP 160 (198)
T ss_dssp -EEEEEECTTT-SSSEEEEEEE-EETTEEEEEEEEEEEEETEEEEEEEEEESS-HHHHTTEEEEEEEEETTEEEEEEE--
T ss_pred ceEEEeeecccccCCceEEEeecccCCccEEEEEEEEccCCceEEEEEEEEccCchhhhceEEEEEEecCCcEEEEEEcC
Confidence 77888887776556678988666999999999998887655679999999999999999999999999999999999999
Q ss_pred cchhccccccc
Q 046177 261 RSIRDSHKKVR 271 (272)
Q Consensus 261 ~si~~~~~~~~ 271 (272)
+||+++++.++
T Consensus 161 ~si~~~~~~~~ 171 (198)
T PF03145_consen 161 RSIREDIDDAI 171 (198)
T ss_dssp EETTT-SHHHH
T ss_pred cchhhhHHhhc
Confidence 99999998764
No 3
>cd03829 Sina Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins that function as E3 ubiquitin ligases, acting either as single proteins or as a part of multiprotein complexes. Sina is expressed in many cells in the developing eye but is essential specifically for R7 photoreceptor cell development. Sina cooperates with Phyllopod (Phyl), Ebi and the E2 ubiquitin-conjugating enzyme Ubcd1 to catalyze the ubiquitination and subsequent degradation of Tramtrack (Ttk88); Ttk88 is a transcriptional repressor that blocks photoreceptor differentiation. Similarly, the mammalian homologue Siah1 cooperates with SIP (Siah-interacting protein), Ebi and the adaptor protein Skp1, to target beta-catenin for ubiquitination and degradation via a p53-dependent mechanism. SINAT5 targets NAC1 for ubiquitin-medi
Probab=99.95 E-value=1.9e-29 Score=196.39 Aligned_cols=96 Identities=31% Similarity=0.626 Sum_probs=89.4
Q ss_pred CCcCCceEEEEEeecCCcccccceeEEEEEeecCeeEEEEEeeeee-CCccEEEEEEEEeCCccCCCCcEEEEEEecCCc
Q 046177 174 DMHNGSTFNHRYVKQNPHEVENATWMLTVFSCFGQYFCLHFEAFQL-GMAPVYIAFLRFMGDDNESKNYSYSLEVGGNGR 252 (272)
Q Consensus 174 ~~~~g~~~~~~~~~s~~~~v~~~~~~l~v~~~~~~~F~l~~~~~~~-~~~~~~~a~v~~iG~~~~a~~f~Y~l~~~~~~r 252 (272)
++++|+ +++|++++++.++ +.|.+++++|||++|||+++++++ +.+++|+|++|+||+.++|++|+|+||+.+|+|
T Consensus 2 ~~~~G~--di~fl~t~~~~~~-a~~w~mv~sCfG~~F~L~~Ek~~l~~~~~~y~A~~~~iG~~~eA~nf~Y~Lel~~n~R 78 (127)
T cd03829 2 TTLQGE--DIVFLATDINLPG-ATDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGTEKQAENFTYRLELNGNRR 78 (127)
T ss_pred ccccCc--cEEEEecCCCCcc-ceeeeehhhhcCceEEEEEehhhhcCCcHHHHHHHHHHcCHhHHhcceEEEEEcCCCc
Confidence 567898 6799999999887 666677999999999999999999 778999999999999999999999999999999
Q ss_pred eEEEEeeccchhcccccccC
Q 046177 253 KMSWQGVPRSIRDSHKKVRD 272 (272)
Q Consensus 253 ~l~~~s~~~si~~~~~~~~~ 272 (272)
||+||++||||||+|++|+|
T Consensus 79 kL~we~~PRSIrds~~~~~~ 98 (127)
T cd03829 79 RLTWEATPRSIREGHASVID 98 (127)
T ss_pred EEEeecCCccHHHhhHHHhh
Confidence 99999999999999999985
No 4
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=99.40 E-value=4.3e-13 Score=126.90 Aligned_cols=118 Identities=31% Similarity=0.638 Sum_probs=103.5
Q ss_pred cCCCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCcc----cchhHHHHhhhcCCCcccccCC
Q 046177 51 SSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGNI----RCLALEKVAASLELPCKYQSYG 123 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~~----r~~~le~~~~~l~v~C~~~~~G 123 (272)
..+.+++.||+|..++.+|+..-.|||.||..|+..+ ...||.|+..+... ....+.+.+.++.+.|.+...|
T Consensus 16 ~~~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~~~~~~~~~~~l~i~c~~~~~G 95 (391)
T KOG0297|consen 16 RPLDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPVPRALRRELLKLPIRCIFASRG 95 (391)
T ss_pred CCCcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccCchHHHHHHHHhcccccccCCCC
Confidence 3478889999999999999743479999999999998 36899999887642 2467889999999999999999
Q ss_pred CCceeccCcHHhhhhcCCCccccCCCCCCCCccccChhHHHHHhhhcCCC
Q 046177 124 CMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPYLVAHLKDDHKV 173 (272)
Q Consensus 124 C~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~~ 173 (272)
|.|.+.+..+..|+..| .+.+||+ +|+..+.++++.+|++.....
T Consensus 96 C~~~~~l~~~~~Hl~~c--~~~~C~~---~C~~~~~~~d~~~hl~~~C~~ 140 (391)
T KOG0297|consen 96 CRADLELEALQGHLSTC--DPLKCPH---RCGVQVPRDDLEDHLEAECPR 140 (391)
T ss_pred ccccccHHHHHhHhccC--CcccCcc---ccccccchHHHHHHHhccccc
Confidence 99999999999999999 9999998 399999999999999776553
No 5
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.66 E-value=1.1e-08 Score=96.44 Aligned_cols=78 Identities=23% Similarity=0.473 Sum_probs=57.3
Q ss_pred CCCCccccccCCCcccccCCCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc---ccchhHH
Q 046177 34 SVNDPAQIALKPNLTVSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN---IRCLALE 107 (272)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~---~r~~~le 107 (272)
++.|++.-... .+...+.+.+.+.|+||.+++..|+.+ .|||.||..|+..+ ...||.|+..+.. .+|..++
T Consensus 5 di~D~tDw~~t-~~~~l~~Le~~l~C~IC~d~~~~Pvit-pCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~ 82 (397)
T TIGR00599 5 DITDSSDWLTT-PIPSLYPLDTSLRCHICKDFFDVPVLT-SCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVS 82 (397)
T ss_pred cCCCchhhccC-CcccccccccccCCCcCchhhhCccCC-CCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHH
Confidence 33444443333 233457888999999999999999865 89999999999876 3579999998764 4567676
Q ss_pred HHhhhc
Q 046177 108 KVAASL 113 (272)
Q Consensus 108 ~~~~~l 113 (272)
++++.+
T Consensus 83 ~iVe~~ 88 (397)
T TIGR00599 83 EIVESF 88 (397)
T ss_pred HHHHHH
Confidence 666543
No 6
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.63 E-value=8.5e-09 Score=72.16 Aligned_cols=58 Identities=24% Similarity=0.602 Sum_probs=30.7
Q ss_pred CCCCeeeeccccccCcCCcccccCCceeccCccccc-CCCCCCcccCCC--c-ccchhHHHH
Q 046177 52 SVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV-HNRCPTCRHELG--N-IRCLALEKV 109 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-~~~CP~Cr~~~~--~-~r~~~le~~ 109 (272)
.+++.|.|++|.++|+.|+..-.|.|+||+.|+..- ...||.|..|.- . ..|+.++.+
T Consensus 3 ~le~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~NrqLd~~ 64 (65)
T PF14835_consen 3 RLEELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQLDSM 64 (65)
T ss_dssp HHHHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS----HHHHHH
T ss_pred HHHHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhhhhcc
Confidence 456778999999999999865579999999998774 467999999863 2 345555544
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.60 E-value=1.1e-08 Score=66.45 Aligned_cols=35 Identities=37% Similarity=1.090 Sum_probs=26.9
Q ss_pred eccccccCcCCcccccCCceeccCcccccC-------CCCCCc
Q 046177 59 CPVCLNAMYPPIHQCSNGHTLCSGCKPRVH-------NRCPTC 94 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~-------~~CP~C 94 (272)
||||+++|++|+.. .|||+||..|+.++. ..||.|
T Consensus 1 CpiC~~~~~~Pv~l-~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSL-PCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE--SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchhhCCcccc-CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 89999999999865 899999999999871 358876
No 8
>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=98.59 E-value=2.8e-08 Score=69.66 Aligned_cols=56 Identities=25% Similarity=0.380 Sum_probs=46.3
Q ss_pred eeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc---ccchhHHHHhhh
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN---IRCLALEKVAAS 112 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~---~r~~~le~~~~~ 112 (272)
.|.||||.++|.+|+.. .|||+||..|+.++ ...||.|+.+++. .+|..+.+.++.
T Consensus 1 ~~~Cpi~~~~~~~Pv~~-~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~ 62 (63)
T smart00504 1 EFLCPISLEVMKDPVIL-PSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE 62 (63)
T ss_pred CcCCcCCCCcCCCCEEC-CCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence 36899999999999865 79999999999987 4689999999853 567777776653
No 9
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.54 E-value=2.9e-08 Score=84.58 Aligned_cols=47 Identities=23% Similarity=0.721 Sum_probs=39.8
Q ss_pred CCCeeeeccccccCcCCcccccCCceeccCcccccC-------------------CCCCCcccCCCc
Q 046177 53 VRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH-------------------NRCPTCRHELGN 100 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~-------------------~~CP~Cr~~~~~ 100 (272)
..+.+.|+||++.+++|+.+ .|||.||..|+.+|. ..||.||.++..
T Consensus 15 ~~~~~~CpICld~~~dPVvT-~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 15 SGGDFDCNICLDQVRDPVVT-LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCCccCCccCCCcCCCcEEc-CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 34568999999999999865 899999999998761 479999998863
No 10
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.51 E-value=1.1e-08 Score=92.99 Aligned_cols=67 Identities=25% Similarity=0.584 Sum_probs=54.1
Q ss_pred CcccccCCCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc---ccchhHHHHhhhc
Q 046177 46 NLTVSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN---IRCLALEKVAASL 113 (272)
Q Consensus 46 ~~~~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~---~r~~~le~~~~~l 113 (272)
.+.....+.+.|.|.||+++|+.|+.+ +|||.||+-|+.+. ++.||.|+.++.. ..|+.++.++.++
T Consensus 13 sipslk~lD~lLRC~IC~eyf~ip~it-pCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 13 SIPSLKTLDDLLRCGICFEYFNIPMIT-PCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred cCchhhhhHHHHHHhHHHHHhcCceec-cccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence 355677888999999999999999877 79999999999886 5899999998764 3355666655544
No 11
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=5.2e-08 Score=84.58 Aligned_cols=48 Identities=25% Similarity=0.663 Sum_probs=42.1
Q ss_pred CCCCeeeeccccccCcCCcccccCCceeccCccccc------CCCCCCcccCCCc
Q 046177 52 SVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV------HNRCPTCRHELGN 100 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~------~~~CP~Cr~~~~~ 100 (272)
.....|+|.||++..++||+++ |||+||-.|+.+| ...||+|+..++.
T Consensus 43 ~~~~~FdCNICLd~akdPVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAKDPVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCCCceeeeeeccccCCCEEee-cccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 4567899999999999999884 9999999999999 3679999998764
No 12
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.42 E-value=6.2e-08 Score=61.75 Aligned_cols=36 Identities=33% Similarity=1.077 Sum_probs=29.5
Q ss_pred eccccccCcCCcccccCCceeccCccccc---CCCCCCc
Q 046177 59 CPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTC 94 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~C 94 (272)
|+||++.+.+|+..-.|||+||..|+.++ ..+||.|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 89999999999655589999999999987 4678876
No 13
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.35 E-value=1.1e-07 Score=63.91 Aligned_cols=43 Identities=30% Similarity=0.832 Sum_probs=36.7
Q ss_pred eeeeccccccCcCCcccccCCce-eccCccccc---CCCCCCcccCCC
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHT-LCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~-~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
+..|+||++...++++. +|||. +|..|..++ ...||.||+++.
T Consensus 2 ~~~C~iC~~~~~~~~~~-pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRDVVLL-PCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSSEEEE-TTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCccCCceEEe-CCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 56899999999998877 89999 999999998 479999999875
No 14
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=98.27 E-value=3.5e-07 Score=63.59 Aligned_cols=53 Identities=26% Similarity=0.423 Sum_probs=38.2
Q ss_pred hcCCCcccccCCCCceeccCcHHhhhh-cCCCccccCCCCCCCCccccChhHHHHH
Q 046177 112 SLELPCKYQSYGCMGIYPYYSKLKHES-QCIFRPYNCPYAGSECTVMGDIPYLVAH 166 (272)
Q Consensus 112 ~l~v~C~~~~~GC~~~~~~~~~~~He~-~C~~~~~~CP~~~~~C~~~g~~~~l~~H 166 (272)
...+.|+| .||...++..++.+|.+ +|+++++.||+...||++.+.+.+|.+|
T Consensus 7 ~~~v~C~~--~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 7 FRPVPCPN--GCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp TSEEE-TT----S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEHHHHHHC
T ss_pred CCEeeCCC--CCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccchhHHhCC
Confidence 45688987 46778899999999999 9999999999977789999999999987
No 15
>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=98.25 E-value=3.9e-07 Score=66.27 Aligned_cols=59 Identities=24% Similarity=0.305 Sum_probs=44.9
Q ss_pred CCeeeeccccccCcCCcccccCCceeccCcccccC----CCCCCcccCCCc---ccchhHHHHhhhc
Q 046177 54 RELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH----NRCPTCRHELGN---IRCLALEKVAASL 113 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~----~~CP~Cr~~~~~---~r~~~le~~~~~l 113 (272)
++.|.|||+.++|.+||.. .+||+|++.++.+|. ..||.++.++.. .+|.+|.+.++.+
T Consensus 2 P~~f~CpIt~~lM~dPVi~-~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~ 67 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVIL-PSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW 67 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEE-TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred CcccCCcCcCcHhhCceeC-CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence 5789999999999999866 799999999999982 679999998875 6788888877654
No 16
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=98.21 E-value=2.8e-07 Score=60.20 Aligned_cols=38 Identities=34% Similarity=0.876 Sum_probs=31.3
Q ss_pred eeccccccCc--CCcccccCCceeccCccccc---CCCCCCcc
Q 046177 58 ECPVCLNAMY--PPIHQCSNGHTLCSGCKPRV---HNRCPTCR 95 (272)
Q Consensus 58 ~CpiC~~~l~--~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr 95 (272)
.|+||++.+. ..++...|||.||.+|+.+| ..+||.||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 5999999994 34556679999999999998 47999997
No 17
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.20 E-value=5.1e-07 Score=75.43 Aligned_cols=46 Identities=33% Similarity=0.881 Sum_probs=37.1
Q ss_pred CCeeeeccccccCcCCc-ccccCCceeccCccccc---CCCCCCcccCCC
Q 046177 54 RELLECPVCLNAMYPPI-HQCSNGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv-~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
...+.||||++....-+ +...|||+||+.|+... ...||+|+..+.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 46699999999986543 34479999999999886 378999998664
No 18
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.09 E-value=9.9e-07 Score=78.03 Aligned_cols=48 Identities=27% Similarity=0.638 Sum_probs=38.1
Q ss_pred CCCeeeeccccccCcCC-c------ccccCCceeccCccccc---CCCCCCcccCCCc
Q 046177 53 VRELLECPVCLNAMYPP-I------HQCSNGHTLCSGCKPRV---HNRCPTCRHELGN 100 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~P-v------~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~ 100 (272)
..+...|+||++.+..+ + ....|||.||..|+.+| ...||.||.++..
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 34568999999987653 1 23479999999999998 4789999998764
No 19
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=98.04 E-value=1.2e-06 Score=78.48 Aligned_cols=47 Identities=26% Similarity=0.632 Sum_probs=40.7
Q ss_pred CCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc
Q 046177 53 VRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN 100 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~ 100 (272)
.+....|.+|++....|-.+ +|||+||-+|+..| +..||.||..+..
T Consensus 236 ~~a~~kC~LCLe~~~~pSaT-pCGHiFCWsCI~~w~~ek~eCPlCR~~~~p 285 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSNPSAT-PCGHIFCWSCILEWCSEKAECPLCREKFQP 285 (293)
T ss_pred CCCCCceEEEecCCCCCCcC-cCcchHHHHHHHHHHccccCCCcccccCCC
Confidence 45668999999999999644 79999999999999 5789999998764
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.03 E-value=1.2e-06 Score=57.36 Aligned_cols=38 Identities=32% Similarity=0.905 Sum_probs=30.9
Q ss_pred eeccccccC---cCCcccccCCceeccCcccccC---CCCCCccc
Q 046177 58 ECPVCLNAM---YPPIHQCSNGHTLCSGCKPRVH---NRCPTCRH 96 (272)
Q Consensus 58 ~CpiC~~~l---~~Pv~qC~cGH~~C~~C~~~~~---~~CP~Cr~ 96 (272)
+|++|++.+ ..|++. +|||+||..|+.++. ..||.|++
T Consensus 1 ~C~~C~~~~~~~~~~~l~-~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLT-SCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEc-ccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 499999999 244444 899999999999874 58999974
No 21
>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=97.95 E-value=2.9e-06 Score=54.33 Aligned_cols=36 Identities=33% Similarity=0.988 Sum_probs=30.3
Q ss_pred eccccccCcCCcccccCCceeccCccccc-----CCCCCCc
Q 046177 59 CPVCLNAMYPPIHQCSNGHTLCSGCKPRV-----HNRCPTC 94 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-----~~~CP~C 94 (272)
|+||.+.+..|+..-+|||.||..|+.++ ...||.|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 89999999999834489999999999887 2568876
No 22
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=97.94 E-value=1.9e-06 Score=77.05 Aligned_cols=52 Identities=29% Similarity=0.650 Sum_probs=44.4
Q ss_pred cccccCCCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCC
Q 046177 47 LTVSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 47 ~~~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
+.+...+...+.|-||.+.++.|+.+ +|||.||+-|+.+. ++.||.||.+..
T Consensus 16 IPSL~~LDs~lrC~IC~~~i~ip~~T-tCgHtFCslCIR~hL~~qp~CP~Cr~~~~ 70 (391)
T COG5432 16 IPSLKGLDSMLRCRICDCRISIPCET-TCGHTFCSLCIRRHLGTQPFCPVCREDPC 70 (391)
T ss_pred CcchhcchhHHHhhhhhheeecceec-ccccchhHHHHHHHhcCCCCCccccccHH
Confidence 34466778889999999999999866 89999999999886 478999998764
No 23
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.86 E-value=4.1e-06 Score=53.63 Aligned_cols=41 Identities=37% Similarity=0.983 Sum_probs=33.3
Q ss_pred eeccccccCcCCcccccCCceeccCccccc----CCCCCCcccCC
Q 046177 58 ECPVCLNAMYPPIHQCSNGHTLCSGCKPRV----HNRCPTCRHEL 98 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~ 98 (272)
.|+||.+.+..|+..-.|||.||..|+.++ ...||.|+..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999999778655459999999999876 25799998753
No 24
>PHA02926 zinc finger-like protein; Provisional
Probab=97.79 E-value=4.1e-06 Score=72.56 Aligned_cols=48 Identities=31% Similarity=0.742 Sum_probs=37.2
Q ss_pred CCCCeeeeccccccCcC---------CcccccCCceeccCcccccC---------CCCCCcccCCCc
Q 046177 52 SVRELLECPVCLNAMYP---------PIHQCSNGHTLCSGCKPRVH---------NRCPTCRHELGN 100 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~---------Pv~qC~cGH~~C~~C~~~~~---------~~CP~Cr~~~~~ 100 (272)
...++.+|+||++.... ++.. .|+|.||..|+.+|. ..||.||..+..
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~-~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLD-SCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN 231 (242)
T ss_pred hccCCCCCccCccccccccccccccccccC-CCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence 44567899999998643 2433 799999999999993 239999998764
No 25
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.60 E-value=1.1e-05 Score=52.55 Aligned_cols=27 Identities=30% Similarity=0.955 Sum_probs=18.0
Q ss_pred eccccccCcC----CcccccCCceeccCccccc
Q 046177 59 CPVCLNAMYP----PIHQCSNGHTLCSGCKPRV 87 (272)
Q Consensus 59 CpiC~~~l~~----Pv~qC~cGH~~C~~C~~~~ 87 (272)
||||.+ +.. |+.. .|||+||..|+.++
T Consensus 1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE--SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHH
Confidence 899999 777 8766 69999999999987
No 26
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.52 E-value=4.7e-05 Score=69.54 Aligned_cols=46 Identities=30% Similarity=0.685 Sum_probs=34.1
Q ss_pred Ceeeeccccc--cCcCCc--ccccCCceeccCccccc----CCCCCCcccCCCc
Q 046177 55 ELLECPVCLN--AMYPPI--HQCSNGHTLCSGCKPRV----HNRCPTCRHELGN 100 (272)
Q Consensus 55 ~~l~CpiC~~--~l~~Pv--~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~~ 100 (272)
+...||+|.. ++.+-+ +.-.|||.||.+|+..+ ...||.|+.++..
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 3468999999 444431 22269999999999985 3579999988753
No 27
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.52 E-value=2.5e-05 Score=74.89 Aligned_cols=44 Identities=30% Similarity=0.799 Sum_probs=37.4
Q ss_pred eeeeccccccCcCCcccccCCceeccCccccc--------CCCCCCcccCCCc
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV--------HNRCPTCRHELGN 100 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~--------~~~CP~Cr~~~~~ 100 (272)
...||||++...-|+.+ .|||+||..|+-.. -..||+|+..+..
T Consensus 186 ~~~CPICL~~~~~p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCCccccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 78899999999988766 79999999998763 2579999998764
No 28
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.51 E-value=3.1e-05 Score=68.60 Aligned_cols=45 Identities=27% Similarity=0.540 Sum_probs=38.6
Q ss_pred CCeeeeccccccCcCCcccccCCceeccCcccc-c---C-CCCCCcccCCC
Q 046177 54 RELLECPVCLNAMYPPIHQCSNGHTLCSGCKPR-V---H-NRCPTCRHELG 99 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~-~---~-~~CP~Cr~~~~ 99 (272)
..++.|++|.+....|... .|||+||-.|+.. | + ..||.||.-..
T Consensus 213 ~~d~kC~lC~e~~~~ps~t-~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 213 LADYKCFLCLEEPEVPSCT-PCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred ccccceeeeecccCCcccc-cccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 6789999999999999866 7999999999888 6 2 45999998654
No 29
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.49 E-value=2.8e-05 Score=47.86 Aligned_cols=35 Identities=40% Similarity=1.108 Sum_probs=29.2
Q ss_pred eccccccCcCCcccccCCceeccCccccc----CCCCCCc
Q 046177 59 CPVCLNAMYPPIHQCSNGHTLCSGCKPRV----HNRCPTC 94 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~----~~~CP~C 94 (272)
|+||.+....++.. .|||.||..|+.++ ...||.|
T Consensus 1 C~iC~~~~~~~~~~-~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVL-PCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEe-cCCChHHHHHHHHHHHhCcCCCCCC
Confidence 79999998888766 79999999999876 2568876
No 30
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.41 E-value=2.9e-05 Score=68.86 Aligned_cols=67 Identities=28% Similarity=0.585 Sum_probs=50.0
Q ss_pred ccCCCCeeeeccccccCcCCcccccCCceeccCcccccC---CCCCCcccCCCc-ccchhHHHHhhhcCCCc
Q 046177 50 SSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH---NRCPTCRHELGN-IRCLALEKVAASLELPC 117 (272)
Q Consensus 50 ~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~---~~CP~Cr~~~~~-~r~~~le~~~~~l~v~C 117 (272)
...+.+.+.||||++.+..|... .|||.||..|+..+. ..||.||..... .+|..+.+++..+....
T Consensus 7 ~~~~~~~~~C~iC~~~~~~p~~l-~C~H~~c~~C~~~~~~~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~~~~ 77 (386)
T KOG2177|consen 7 LEVLQEELTCPICLEYFREPVLL-PCGHNFCRACLTRSWEGPLSCPVCRPPSRNLRPNVLLANLVERLRQLR 77 (386)
T ss_pred hhhccccccChhhHHHhhcCccc-cccchHhHHHHHHhcCCCcCCcccCCchhccCccHHHHHHHHHHHhcC
Confidence 45567889999999999999544 699999999998864 689999951111 35666777766665443
No 31
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.32 E-value=1.2e-05 Score=73.85 Aligned_cols=50 Identities=28% Similarity=0.638 Sum_probs=42.4
Q ss_pred cCCCCeeeeccccccCcCCcccccCCceeccCccccc----CCCCCCcccCCCc
Q 046177 51 SSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV----HNRCPTCRHELGN 100 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~~ 100 (272)
..+...+.||||+.+|+..+.+=.|+|.||..|+-+. .+.||+||+.+..
T Consensus 38 ~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S 91 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS 91 (381)
T ss_pred HHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence 4566788999999999988766569999999998875 4789999998765
No 32
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.28 E-value=6.7e-05 Score=71.09 Aligned_cols=64 Identities=36% Similarity=0.729 Sum_probs=50.5
Q ss_pred CCccccccCCCcccccCCCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc
Q 046177 36 NDPAQIALKPNLTVSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN 100 (272)
Q Consensus 36 ~~~~~~~~~~~~~~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~ 100 (272)
.+.+...+....+....+...|.|.||...+.+|+.+ +|||.+|..|+.+. ...||.||.++..
T Consensus 64 e~~~~~~~~~~~s~~~~~~sef~c~vc~~~l~~pv~t-pcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 64 ETMADSTPKALLSGPEEIRSEFECCVCSRALYPPVVT-PCGHSFCLECLDRSLDQETECPLCRDELVE 130 (398)
T ss_pred hhhhhhhhhhhhccCccccchhhhhhhHhhcCCCccc-cccccccHHHHHHHhccCCCCccccccccc
Confidence 3333345555555566778999999999999999977 99999999997775 3689999998863
No 33
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.00 E-value=0.00086 Score=66.20 Aligned_cols=106 Identities=21% Similarity=0.432 Sum_probs=59.8
Q ss_pred CCCCeeeeccccccCcCCcc-----cccCCceeccC--ccccc-------CCCCCCcccCCCcccchhHHHHhh--hcCC
Q 046177 52 SVRELLECPVCLNAMYPPIH-----QCSNGHTLCSG--CKPRV-------HNRCPTCRHELGNIRCLALEKVAA--SLEL 115 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~Pv~-----qC~cGH~~C~~--C~~~~-------~~~CP~Cr~~~~~~r~~~le~~~~--~l~v 115 (272)
...+...|+-|......--+ .|...-+.|.. |...+ ...|+.|...+.. ..+++-.. ..++
T Consensus 403 ~~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~---s~LekH~~~~Hkpv 479 (567)
T PLN03086 403 MDVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQ---GEMEKHMKVFHEPL 479 (567)
T ss_pred CCCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeeccccccCccCCCCCCccch---HHHHHHHHhcCCCc
Confidence 34566789999887643211 24333334432 43332 2468888776642 22222222 3456
Q ss_pred CcccccCCCCceeccCcHHhhhh-cCCCccccCCCCCCCCccccC-----------hhHHHHHhhh
Q 046177 116 PCKYQSYGCMGIYPYYSKLKHES-QCIFRPYNCPYAGSECTVMGD-----------IPYLVAHLKD 169 (272)
Q Consensus 116 ~C~~~~~GC~~~~~~~~~~~He~-~C~~~~~~CP~~~~~C~~~g~-----------~~~l~~Hl~~ 169 (272)
.|+ |+..+...++..|.. .|+.+++.|++ |+.... ...|..|...
T Consensus 480 ~Cp-----Cg~~~~R~~L~~H~~thCp~Kpi~C~f----C~~~v~~g~~~~d~~d~~s~Lt~HE~~ 536 (567)
T PLN03086 480 QCP-----CGVVLEKEQMVQHQASTCPLRLITCRF----CGDMVQAGGSAMDVRDRLRGMSEHESI 536 (567)
T ss_pred cCC-----CCCCcchhHHHhhhhccCCCCceeCCC----CCCccccCccccchhhhhhhHHHHHHh
Confidence 675 666666677777765 68778888876 666553 2356677655
No 34
>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=96.96 E-value=0.00096 Score=55.08 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=23.5
Q ss_pred cccCCCCCCCCccccChhHHHHHhhhcCCC
Q 046177 144 PYNCPYAGSECTVMGDIPYLVAHLKDDHKV 173 (272)
Q Consensus 144 ~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~~ 173 (272)
+-.|+.- +|.|.|+..+|..|.+.+|..
T Consensus 107 ~RsC~~e--~C~F~GtY~eLrKHar~~HP~ 134 (162)
T PF07800_consen 107 KRSCSQE--SCSFSGTYSELRKHARSEHPS 134 (162)
T ss_pred CccCccc--ccccccCHHHHHHHHHhhCCC
Confidence 3466663 599999999999999999984
No 35
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.00016 Score=72.38 Aligned_cols=50 Identities=28% Similarity=0.717 Sum_probs=41.7
Q ss_pred ccCCCCeeeeccccccCcCCcccccCCceeccCccccc----CCCCCCcccCCCc
Q 046177 50 SSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV----HNRCPTCRHELGN 100 (272)
Q Consensus 50 ~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~~ 100 (272)
..+....|.||+|..=.++-|.. .|||.||..|+.+. ..+||.|..+|+.
T Consensus 637 lk~yK~~LkCs~Cn~R~Kd~vI~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 637 LKEYKELLKCSVCNTRWKDAVIT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred HHHHHhceeCCCccCchhhHHHH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 34567889999999777777765 79999999998875 4789999999874
No 36
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=96.89 E-value=0.00036 Score=50.66 Aligned_cols=38 Identities=29% Similarity=0.703 Sum_probs=29.6
Q ss_pred eeccccccCcCCc------------ccccCCceeccCccccc---CCCCCCcc
Q 046177 58 ECPVCLNAMYPPI------------HQCSNGHTLCSGCKPRV---HNRCPTCR 95 (272)
Q Consensus 58 ~CpiC~~~l~~Pv------------~qC~cGH~~C~~C~~~~---~~~CP~Cr 95 (272)
.|+||++.|.+|. ..-.|||.|-..|+.+| ...||+||
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 3999999995442 22259999999999998 47899997
No 37
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.43 E-value=0.00093 Score=57.05 Aligned_cols=56 Identities=23% Similarity=0.486 Sum_probs=42.2
Q ss_pred eeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc--ccchhHHHHhhh
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN--IRCLALEKVAAS 112 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~--~r~~~le~~~~~ 112 (272)
-|.|.||..-+..||.+ .|||.||+.|..+- ...|-.|....-. .-...+++++.+
T Consensus 196 PF~C~iCKkdy~spvvt-~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL~~ 256 (259)
T COG5152 196 PFLCGICKKDYESPVVT-ECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKMLNK 256 (259)
T ss_pred ceeehhchhhccchhhh-hcchhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHHhh
Confidence 37899999999999866 89999999997653 3679889776432 234456666654
No 38
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.19 E-value=0.00099 Score=60.95 Aligned_cols=51 Identities=20% Similarity=0.481 Sum_probs=42.2
Q ss_pred ccCCCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCc
Q 046177 50 SSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGN 100 (272)
Q Consensus 50 ~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~ 100 (272)
..++.....|.+|..+|.++-..-.|=|+||++|+-+. ...||.|...+..
T Consensus 9 ~~~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~ 62 (331)
T KOG2660|consen 9 LTELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHK 62 (331)
T ss_pred hhhcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence 35667889999999999999555469999999998875 4789999887653
No 39
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=96.18 E-value=0.0016 Score=48.52 Aligned_cols=41 Identities=24% Similarity=0.536 Sum_probs=30.8
Q ss_pred eccccccCcC-CcccccCCceeccCccccc------CCCCCCcccCCC
Q 046177 59 CPVCLNAMYP-PIHQCSNGHTLCSGCKPRV------HNRCPTCRHELG 99 (272)
Q Consensus 59 CpiC~~~l~~-Pv~qC~cGH~~C~~C~~~~------~~~CP~Cr~~~~ 99 (272)
||.|..+-.+ |+....|+|.|=..|+.+| ++.||+||++..
T Consensus 35 Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 35 CPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 5555554433 5556689999999999998 378999999764
No 40
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.12 E-value=0.0039 Score=56.35 Aligned_cols=46 Identities=22% Similarity=0.608 Sum_probs=38.3
Q ss_pred eeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCCcccc
Q 046177 57 LECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELGNIRC 103 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~~r~ 103 (272)
+.|-||...+..||.+ .|||.||..|..+- ...|++|.+++-..-|
T Consensus 242 f~c~icr~~f~~pVvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~ 290 (313)
T KOG1813|consen 242 FKCFICRKYFYRPVVT-KCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFN 290 (313)
T ss_pred ccccccccccccchhh-cCCceeehhhhccccccCCcceecccccccccc
Confidence 6799999999999976 89999999997664 2689999998754333
No 41
>PLN03086 PRLI-interacting factor K; Provisional
Probab=95.98 E-value=0.02 Score=56.73 Aligned_cols=39 Identities=26% Similarity=0.458 Sum_probs=18.4
Q ss_pred CCceeccCcHHhhhhcCCCccccCCCCCCCCccccChhHHHHHhh
Q 046177 124 CMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPYLVAHLK 168 (272)
Q Consensus 124 C~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~l~~Hl~ 168 (272)
|...+...++.+|+..| +.++.|| |+....+.+|..|+.
T Consensus 459 Cgk~f~~s~LekH~~~~-Hkpv~Cp-----Cg~~~~R~~L~~H~~ 497 (567)
T PLN03086 459 CGQAFQQGEMEKHMKVF-HEPLQCP-----CGVVLEKEQMVQHQA 497 (567)
T ss_pred CCCccchHHHHHHHHhc-CCCccCC-----CCCCcchhHHHhhhh
Confidence 44444444455555554 3455554 333334445555543
No 42
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.97 E-value=0.0021 Score=42.72 Aligned_cols=40 Identities=30% Similarity=0.840 Sum_probs=20.4
Q ss_pred eccccccCcC---CcccccCCceeccCccccc----CCCCCCcccCC
Q 046177 59 CPVCLNAMYP---PIHQCSNGHTLCSGCKPRV----HNRCPTCRHEL 98 (272)
Q Consensus 59 CpiC~~~l~~---Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~ 98 (272)
||+|.+.+.. -++-|.||..+|..|..++ .+.||.||.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 7889888832 2456999999999997776 37899999864
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.95 E-value=0.00076 Score=45.73 Aligned_cols=42 Identities=31% Similarity=0.794 Sum_probs=33.7
Q ss_pred eeeccccccCcCCcccccCCce-eccCccccc----CCCCCCcccCCC
Q 046177 57 LECPVCLNAMYPPIHQCSNGHT-LCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~-~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
-+|-||++-..+-|.. .|||. .|..|-.++ +..||.||.++.
T Consensus 8 dECTICye~pvdsVlY-tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 8 DECTICYEHPVDSVLY-TCGHMCMCYACGLRLKKALHGCCPICRAPIK 54 (62)
T ss_pred cceeeeccCcchHHHH-HcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence 4799999987777654 59996 899996664 478999999874
No 44
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.95 E-value=0.005 Score=55.10 Aligned_cols=47 Identities=28% Similarity=0.497 Sum_probs=37.4
Q ss_pred CCCeeeeccccccCcCCcccccCCceeccCccccc-----CCCCCCcccCCC
Q 046177 53 VRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV-----HNRCPTCRHELG 99 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-----~~~CP~Cr~~~~ 99 (272)
-...-+||+|.+....|...-.|||++|..|+..- ...||.|.++..
T Consensus 236 ~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 236 GTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 34667999999999999533249999999998874 258999988764
No 45
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=95.74 E-value=0.0044 Score=42.67 Aligned_cols=37 Identities=35% Similarity=0.635 Sum_probs=28.3
Q ss_pred hhhcCCCccccCCCCCCCCccccChhHHHHHhhhcCCCC
Q 046177 136 HESQCIFRPYNCPYAGSECTVMGDIPYLVAHLKDDHKVD 174 (272)
Q Consensus 136 He~~C~~~~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~~~ 174 (272)
|+..|+++++.||+.+ |.....+.+|.+|+.+.-...
T Consensus 1 H~~~C~~~~v~C~~~c--c~~~i~r~~l~~H~~~~C~~~ 37 (60)
T PF02176_consen 1 HEEECPFRPVPCPNGC--CNEMIPRKELDDHLENECPKR 37 (60)
T ss_dssp HHTTSTTSEEE-TT----S-BEEECCCHHHHHHTTSTTS
T ss_pred CcccCCCCEeeCCCCC--cccceeHHHHHHHHHccCCCC
Confidence 8889999999999843 667788999999999766543
No 46
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.0053 Score=55.65 Aligned_cols=44 Identities=25% Similarity=0.557 Sum_probs=37.2
Q ss_pred eeeeccccccCcCCcccccCCceeccCccccc----CCCCCCcccCCCc
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV----HNRCPTCRHELGN 100 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~~ 100 (272)
.-+|+||+.-..-|+.. .|+|.||.-|+... +..|++||.++..
T Consensus 7 ~~eC~IC~nt~n~Pv~l-~C~HkFCyiCiKGsy~ndk~~CavCR~pids 54 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNL-YCFHKFCYICIKGSYKNDKKTCAVCRFPIDS 54 (324)
T ss_pred CCcceeeeccCCcCccc-cccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence 34799999999999755 79999999998875 3579999999863
No 47
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.35 E-value=0.0036 Score=62.08 Aligned_cols=44 Identities=30% Similarity=0.618 Sum_probs=37.0
Q ss_pred CCeeeeccccccCcC-----CcccccCCceeccCccccc---CCCCCCcccCC
Q 046177 54 RELLECPVCLNAMYP-----PIHQCSNGHTLCSGCKPRV---HNRCPTCRHEL 98 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~-----Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~ 98 (272)
.....|+||.+.|.. |... .|||+|+..|+.+| ++.||.||..+
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL-~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRL-PCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hcCCeeeeechhhcccccccccee-ecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 346689999999977 5445 79999999999999 58999999944
No 48
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.28 E-value=0.0069 Score=54.84 Aligned_cols=40 Identities=33% Similarity=0.884 Sum_probs=34.9
Q ss_pred eeeccccccCcCCcccccCCceeccCccccc----CCCCCCccc
Q 046177 57 LECPVCLNAMYPPIHQCSNGHTLCSGCKPRV----HNRCPTCRH 96 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~ 96 (272)
|.||.|..+++.|+.+-.|||.||..|+... ...||.|..
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence 8999999999999877339999999999864 378999976
No 49
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=95.00 E-value=0.0059 Score=42.16 Aligned_cols=35 Identities=23% Similarity=0.370 Sum_probs=24.2
Q ss_pred CCCeeeeccccccCcCCcccccCCceeccCccccc
Q 046177 53 VRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV 87 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~ 87 (272)
....+.|||...++.+||..-.|||+|.+..+..+
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~ 42 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQY 42 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHH
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHH
Confidence 34568999999999999866569999988887776
No 50
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=94.90 E-value=0.0066 Score=55.86 Aligned_cols=48 Identities=31% Similarity=0.794 Sum_probs=38.3
Q ss_pred cCCCCeeeeccccccCcC---CcccccCCceeccCccccc----CCCCCCcccCCC
Q 046177 51 SSVRELLECPVCLNAMYP---PIHQCSNGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~---Pv~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
++.++++ ||.|.+.|.. -.+-|+||-.+|.-|+..+ .+.||.||....
T Consensus 10 sedeed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 10 SEDEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred ccccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcc
Confidence 4445555 9999999853 3678999999999998876 489999998654
No 51
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.74 E-value=0.012 Score=53.58 Aligned_cols=43 Identities=26% Similarity=0.756 Sum_probs=35.1
Q ss_pred eeeccccccCcCC--cccccCCceeccCccccc----CCCCCCcccCCC
Q 046177 57 LECPVCLNAMYPP--IHQCSNGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l~~P--v~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.+|.||.+-+..- +..-+|.|.|=..|+++| +.+||+||.++.
T Consensus 324 veCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred ceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 7999999877422 333479999999999999 479999999875
No 52
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.71 E-value=0.017 Score=50.95 Aligned_cols=44 Identities=20% Similarity=0.616 Sum_probs=34.9
Q ss_pred eeeeccccccC-cCCcccccCCceeccCcccccCC-CCCCcccCCC
Q 046177 56 LLECPVCLNAM-YPPIHQCSNGHTLCSGCKPRVHN-RCPTCRHELG 99 (272)
Q Consensus 56 ~l~CpiC~~~l-~~Pv~qC~cGH~~C~~C~~~~~~-~CP~Cr~~~~ 99 (272)
-..|..|..-- .+|.+...|+|+||..|.....+ .||.|+.++.
T Consensus 3 ~VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 3 FVHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred eEEeccccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 45788887644 56777778999999999877654 9999999864
No 53
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.64 E-value=0.01 Score=55.08 Aligned_cols=45 Identities=33% Similarity=0.759 Sum_probs=38.1
Q ss_pred CCeeeeccccccCcCCcccccCCce-eccCccccc---CCCCCCcccCCC
Q 046177 54 RELLECPVCLNAMYPPIHQCSNGHT-LCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC~cGH~-~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
+.--+|-||+.-.++-+.. +|.|+ .|+.|...+ .+.||+||+++.
T Consensus 288 ~~gkeCVIClse~rdt~vL-PCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVL-PCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecCCcceEEe-cchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 3457899999999998766 89997 999998877 378999999885
No 54
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.45 E-value=0.0061 Score=55.01 Aligned_cols=42 Identities=31% Similarity=0.771 Sum_probs=36.4
Q ss_pred CeeeeccccccCcCCcccccCCce-eccCcccccCCCCCCcccCC
Q 046177 55 ELLECPVCLNAMYPPIHQCSNGHT-LCSGCKPRVHNRCPTCRHEL 98 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC~cGH~-~C~~C~~~~~~~CP~Cr~~~ 98 (272)
....|.||++...+=++. .|||. .|..|-.++ +.||+||+.+
T Consensus 299 ~~~LC~ICmDaP~DCvfL-eCGHmVtCt~CGkrm-~eCPICRqyi 341 (350)
T KOG4275|consen 299 TRRLCAICMDAPRDCVFL-ECGHMVTCTKCGKRM-NECPICRQYI 341 (350)
T ss_pred HHHHHHHHhcCCcceEEe-ecCcEEeehhhcccc-ccCchHHHHH
Confidence 367899999999998887 89995 799998887 6999999865
No 55
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=93.90 E-value=0.06 Score=36.72 Aligned_cols=43 Identities=26% Similarity=0.515 Sum_probs=31.9
Q ss_pred eeeeccccccCcCCcccccCCceeccCcccccC-CCCCCcccCCC
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH-NRCPTCRHELG 99 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~-~~CP~Cr~~~~ 99 (272)
...|-.|...-...++. +|||++|..|+.-.. +-||.|..++.
T Consensus 7 ~~~~~~~~~~~~~~~~~-pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 7 EQPCVFCGFVGTKGTVL-PCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred ceeEEEccccccccccc-cccceeeccccChhhccCCCCCCCccc
Confidence 34566666665545444 799999999988764 78999999875
No 56
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=93.51 E-value=0.023 Score=55.22 Aligned_cols=50 Identities=24% Similarity=0.533 Sum_probs=41.3
Q ss_pred cccCCCCeeeeccccccCcCCcccccCCceeccCccccc--------CCCCCCcccCCC
Q 046177 49 VSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV--------HNRCPTCRHELG 99 (272)
Q Consensus 49 ~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~--------~~~CP~Cr~~~~ 99 (272)
+.++......|.+|.++..++|.. .|.|.||+-|+... .-.||.|...++
T Consensus 529 ~~~enk~~~~C~lc~d~aed~i~s-~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls 586 (791)
T KOG1002|consen 529 LPDENKGEVECGLCHDPAEDYIES-SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS 586 (791)
T ss_pred CCccccCceeecccCChhhhhHhh-hhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence 345566788999999999999855 89999999999664 358999988775
No 57
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=93.50 E-value=0.018 Score=41.42 Aligned_cols=44 Identities=25% Similarity=0.568 Sum_probs=19.4
Q ss_pred eeeeccccccCc----CCccccc---CCceeccCccccc--------------CCCCCCcccCCC
Q 046177 56 LLECPVCLNAMY----PPIHQCS---NGHTLCSGCKPRV--------------HNRCPTCRHELG 99 (272)
Q Consensus 56 ~l~CpiC~~~l~----~Pv~qC~---cGH~~C~~C~~~~--------------~~~CP~Cr~~~~ 99 (272)
.+.|+||+..+. .|...|. |+..|=..|+.+| .+.||.|+.++.
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 468999999764 3666673 7777767788887 145999988774
No 58
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=92.98 E-value=0.039 Score=44.39 Aligned_cols=45 Identities=24% Similarity=0.748 Sum_probs=36.6
Q ss_pred CeeeeccccccCcCCcc----cccCCceeccCccccc------CCCCCCcccCCCc
Q 046177 55 ELLECPVCLNAMYPPIH----QCSNGHTLCSGCKPRV------HNRCPTCRHELGN 100 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~----qC~cGH~~C~~C~~~~------~~~CP~Cr~~~~~ 100 (272)
..++|.||.+.-.++.+ .| ||-..|..|...+ .+.||.|+..+..
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneC-CgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNEC-CGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccccchhhcCCcccc-cchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 88999999998766544 34 9999999997764 3789999998754
No 59
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=92.85 E-value=0.025 Score=53.23 Aligned_cols=42 Identities=29% Similarity=0.674 Sum_probs=34.6
Q ss_pred eeccccccCcCCcccccCCceeccCcccccC-----CCCCCcccCCCc
Q 046177 58 ECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH-----NRCPTCRHELGN 100 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~-----~~CP~Cr~~~~~ 100 (272)
.|-||-+-=++--.. +|||+.|..|+..|+ +.||.||..+..
T Consensus 371 LCKICaendKdvkIE-PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG 417 (563)
T KOG1785|consen 371 LCKICAENDKDVKIE-PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG 417 (563)
T ss_pred HHHHhhccCCCcccc-cccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence 499999977765334 799999999999993 689999998753
No 60
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=92.38 E-value=0.16 Score=34.30 Aligned_cols=49 Identities=24% Similarity=0.502 Sum_probs=33.3
Q ss_pred CCcccccCCCCceeccCcHHhhhhc--CC-CccccCCCCCCCCccccChhHHHHHhhhcCC
Q 046177 115 LPCKYQSYGCMGIYPYYSKLKHESQ--CI-FRPYNCPYAGSECTVMGDIPYLVAHLKDDHK 172 (272)
Q Consensus 115 v~C~~~~~GC~~~~~~~~~~~He~~--C~-~~~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~ 172 (272)
++||| |...+....|..|... .. -..+.||. |..... .+|..|+...|+
T Consensus 3 f~CP~----C~~~~~~~~L~~H~~~~H~~~~~~v~CPi----C~~~~~-~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 3 FTCPY----CGKGFSESSLVEHCEDEHRSESKNVVCPI----CSSRVT-DNLIRHLNSQHR 54 (54)
T ss_pred cCCCC----CCCccCHHHHHHHHHhHCcCCCCCccCCC----chhhhh-hHHHHHHHHhcC
Confidence 56777 7776666677777543 11 23688997 765433 589999998884
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.32 E-value=0.064 Score=49.70 Aligned_cols=49 Identities=27% Similarity=0.695 Sum_probs=37.4
Q ss_pred cccCCCCeeeeccccccCcCCcccccCCceeccCccccc-----CCCCCCcccCC
Q 046177 49 VSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV-----HNRCPTCRHEL 98 (272)
Q Consensus 49 ~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-----~~~CP~Cr~~~ 98 (272)
..+..++...|.||-+-+.---.. +|+|..|.-|.-++ ...||.||...
T Consensus 54 addtDEen~~C~ICA~~~TYs~~~-PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 54 ADDTDEENMNCQICAGSTTYSARY-PCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred ccccccccceeEEecCCceEEEec-cCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 345567888999999877533223 69999999998776 47899999864
No 62
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.03 E-value=0.055 Score=50.34 Aligned_cols=46 Identities=26% Similarity=0.663 Sum_probs=34.0
Q ss_pred CCCCeeeeccccccCcCCcccccCCceeccC-cccccCCCCCCcccCCC
Q 046177 52 SVRELLECPVCLNAMYPPIHQCSNGHTLCSG-CKPRVHNRCPTCRHELG 99 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~-C~~~~~~~CP~Cr~~~~ 99 (272)
+++....|.||.+-.++.++. +|||+-|.. |... ..+||.||+.+.
T Consensus 301 ~~~~p~lcVVcl~e~~~~~fv-pcGh~ccct~cs~~-l~~CPvCR~rI~ 347 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDEPKSAVFV-PCGHVCCCTLCSKH-LPQCPVCRQRIR 347 (355)
T ss_pred ccCCCCceEEecCCccceeee-cCCcEEEchHHHhh-CCCCchhHHHHH
Confidence 334556799999999998887 899997622 3333 368999998764
No 63
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.79 E-value=0.098 Score=48.94 Aligned_cols=47 Identities=21% Similarity=0.542 Sum_probs=37.7
Q ss_pred CCeeeeccccccCcCCc-----c--cccCCceeccCcccccC----------CCCCCcccCCCc
Q 046177 54 RELLECPVCLNAMYPPI-----H--QCSNGHTLCSGCKPRVH----------NRCPTCRHELGN 100 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv-----~--qC~cGH~~C~~C~~~~~----------~~CP~Cr~~~~~ 100 (272)
...-.|.||.+....+. + .-.|-|.||..|+.+|. ..||.||.....
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~ 222 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF 222 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence 45678999999987765 3 12589999999999993 679999997653
No 64
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.66 E-value=0.044 Score=56.61 Aligned_cols=46 Identities=24% Similarity=0.655 Sum_probs=37.1
Q ss_pred CCeeeeccccccCc-----CCccccc-CCceeccCccccc-----CCCCCCcccCCC
Q 046177 54 RELLECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV-----HNRCPTCRHELG 99 (272)
Q Consensus 54 ~~~l~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~-----~~~CP~Cr~~~~ 99 (272)
.-.-+|+||+.++. -|-..|. |.|-|=.+|+-+| ...||.||..++
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 44558999999986 4655676 8899999999998 478999998765
No 65
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.96 E-value=0.079 Score=50.47 Aligned_cols=33 Identities=36% Similarity=0.759 Sum_probs=29.3
Q ss_pred CCeeeeccccccCcCCcccccCCceeccCccccc
Q 046177 54 RELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV 87 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~ 87 (272)
++.|.||||...+++||.. +|||..|..|....
T Consensus 2 eeelkc~vc~~f~~epiil-~c~h~lc~~ca~~~ 34 (699)
T KOG4367|consen 2 EEELKCPVCGSFYREPIIL-PCSHNLCQACARNI 34 (699)
T ss_pred cccccCceehhhccCceEe-ecccHHHHHHHHhh
Confidence 5789999999999999877 89999999997654
No 66
>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=89.38 E-value=0.2 Score=33.75 Aligned_cols=37 Identities=22% Similarity=0.601 Sum_probs=20.0
Q ss_pred eccccccCcCC--------ccccc-CCceeccCcccc---cCCCCCCcc
Q 046177 59 CPVCLNAMYPP--------IHQCS-NGHTLCSGCKPR---VHNRCPTCR 95 (272)
Q Consensus 59 CpiC~~~l~~P--------v~qC~-cGH~~C~~C~~~---~~~~CP~Cr 95 (272)
|--|...+..+ .++|+ |++.||..|-.= ....||-|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 55666666553 67887 999999999433 246899884
No 67
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=88.87 E-value=0.18 Score=47.20 Aligned_cols=44 Identities=27% Similarity=0.651 Sum_probs=34.7
Q ss_pred CCeeeeccccccC-cCC------------cccccCCceeccCccccc---CCCCCCcccCC
Q 046177 54 RELLECPVCLNAM-YPP------------IHQCSNGHTLCSGCKPRV---HNRCPTCRHEL 98 (272)
Q Consensus 54 ~~~l~CpiC~~~l-~~P------------v~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~ 98 (272)
.++-.|.||.+-| .+| -.. +|||++=-.|...| ++.||.||.++
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrL-pCGHilHl~CLknW~ERqQTCPICr~p~ 344 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRL-PCGHILHLHCLKNWLERQQTCPICRRPV 344 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccc-cccceeeHHHHHHHHHhccCCCcccCcc
Confidence 3556899999974 443 223 69999999999988 58999999994
No 68
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.49 E-value=0.23 Score=44.13 Aligned_cols=46 Identities=17% Similarity=0.334 Sum_probs=37.5
Q ss_pred CeeeeccccccCcCCc---ccccCCceeccCccccc---CCCCCCcccCCCc
Q 046177 55 ELLECPVCLNAMYPPI---HQCSNGHTLCSGCKPRV---HNRCPTCRHELGN 100 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv---~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~~ 100 (272)
..+.||+|.+.|...+ +.=++||+||..|.+++ ...||+|..++..
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd 271 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD 271 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence 6799999999998753 22269999999999997 3689999888763
No 69
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=87.87 E-value=0.076 Score=53.93 Aligned_cols=42 Identities=29% Similarity=0.708 Sum_probs=30.3
Q ss_pred eeccccccCcCCccc--ccCCceeccCccccc---CCCCCCcccCCC
Q 046177 58 ECPVCLNAMYPPIHQ--CSNGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~q--C~cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
.||+|..-..+-... -.|+|.||..|+..| .+.||+||..+.
T Consensus 125 ~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~ 171 (1134)
T KOG0825|consen 125 QCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFG 171 (1134)
T ss_pred hhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhh
Confidence 467776554433211 149999999999998 479999999875
No 70
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.76 E-value=0.33 Score=26.87 Aligned_cols=24 Identities=38% Similarity=0.732 Sum_probs=18.2
Q ss_pred ccCCCCCCCCccccChhHHHHHhhhcCC
Q 046177 145 YNCPYAGSECTVMGDIPYLVAHLKDDHK 172 (272)
Q Consensus 145 ~~CP~~~~~C~~~g~~~~l~~Hl~~~H~ 172 (272)
+.|+. |+|......|..|++..|.
T Consensus 1 y~C~~----C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPH----CSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SS----SS-EESHHHHHHHHHHHHS
T ss_pred CCCCC----CCCcCCHHHHHHHHHhhCc
Confidence 46776 9999988899999998773
No 71
>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=87.27 E-value=0.19 Score=36.03 Aligned_cols=38 Identities=29% Similarity=0.728 Sum_probs=23.4
Q ss_pred eeeccccccCcCCcccccCCceeccCccccc--CCCCCCcccCCC
Q 046177 57 LECPVCLNAMYPPIHQCSNGHTLCSGCKPRV--HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~--~~~CP~Cr~~~~ 99 (272)
+.||.|...|.. ..|+..|..|-... ...||.|..++.
T Consensus 2 ~~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEE-----eCCEEECccccccceecccCCCcccHHH
Confidence 689999998643 24899999997765 368999998874
No 72
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.19 E-value=0.24 Score=46.98 Aligned_cols=103 Identities=19% Similarity=0.374 Sum_probs=62.0
Q ss_pred CCCeeeeccccccCcCC---cccccCCceeccCccccc-----------CCCCCCcccC--CCc--------------cc
Q 046177 53 VRELLECPVCLNAMYPP---IHQCSNGHTLCSGCKPRV-----------HNRCPTCRHE--LGN--------------IR 102 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~P---v~qC~cGH~~C~~C~~~~-----------~~~CP~Cr~~--~~~--------------~r 102 (272)
+..++.|.||++-.... +++ +|+|+||.+|.... .-+||.+.-. ... ..
T Consensus 181 ~~slf~C~ICf~e~~G~~c~~~l-pC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe 259 (445)
T KOG1814|consen 181 VNSLFDCCICFEEQMGQHCFKFL-PCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYE 259 (445)
T ss_pred HhhcccceeeehhhcCcceeeec-ccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence 46789999999987653 345 79999999997663 2468865432 111 01
Q ss_pred chhHHHHhhhcC--CCcccccCCCCceeccCcHHhhhhcCC---Ccccc-CCC---CCCCCccccC
Q 046177 103 CLALEKVAASLE--LPCKYQSYGCMGIYPYYSKLKHESQCI---FRPYN-CPY---AGSECTVMGD 159 (272)
Q Consensus 103 ~~~le~~~~~l~--v~C~~~~~GC~~~~~~~~~~~He~~C~---~~~~~-CP~---~~~~C~~~g~ 159 (272)
...+++.+..+. +.||++ -|+... ..+...-+..|. |+-+. |-. .++.|++.+.
T Consensus 260 ~l~lqk~l~~msdv~yCPr~--~Cq~p~-~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~ 322 (445)
T KOG1814|consen 260 KLMLQKTLELMSDVVYCPRA--CCQLPV-KQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVKAE 322 (445)
T ss_pred HHHHHHHHHhhcccccCChh--hccCcc-ccCchhhhhhhccCccHHHHHHHHhhcCCCcccCchH
Confidence 123445555555 899985 466554 445555555554 43321 321 1256888764
No 73
>PF04641 Rtf2: Rtf2 RING-finger
Probab=86.98 E-value=0.47 Score=42.65 Aligned_cols=50 Identities=14% Similarity=0.343 Sum_probs=39.9
Q ss_pred cCCCCeeeeccccccCcC--C-cccccCCceeccCcccccC--CCCCCcccCCCc
Q 046177 51 SSVRELLECPVCLNAMYP--P-IHQCSNGHTLCSGCKPRVH--NRCPTCRHELGN 100 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~--P-v~qC~cGH~~C~~C~~~~~--~~CP~Cr~~~~~ 100 (272)
+.....|.|||....|.. + ++.=+|||+|+..++..+. ..||.|..++..
T Consensus 108 ~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 108 DNSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTE 162 (260)
T ss_pred ccCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcccc
Confidence 345788999999999954 2 4444699999999999985 479999999863
No 74
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=86.65 E-value=0.24 Score=47.46 Aligned_cols=48 Identities=29% Similarity=0.593 Sum_probs=37.8
Q ss_pred CCCCeeeeccccccCcCCc---ccccCCceeccCcccccC-CCCCCcccCCC
Q 046177 52 SVRELLECPVCLNAMYPPI---HQCSNGHTLCSGCKPRVH-NRCPTCRHELG 99 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~Pv---~qC~cGH~~C~~C~~~~~-~~CP~Cr~~~~ 99 (272)
.+.++-.||||++=|-+-+ ..-.|.|.|=.+|..+|. .+||.||--..
T Consensus 171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q~ 222 (493)
T KOG0804|consen 171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQS 222 (493)
T ss_pred CcccCCCcchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhcC
Confidence 4456779999999987653 444599999999999994 78999986443
No 75
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.41 E-value=0.23 Score=46.27 Aligned_cols=45 Identities=24% Similarity=0.554 Sum_probs=35.7
Q ss_pred CCeeeeccccccCcCCcccccCCceeccCcccccC---CCCCCcccCCC
Q 046177 54 RELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH---NRCPTCRHELG 99 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~---~~CP~Cr~~~~ 99 (272)
.++-.||||+--....+++ +|+|.-|+.|+.+.. +.|=.|+..+.
T Consensus 420 sEd~lCpICyA~pi~Avf~-PC~H~SC~~CI~qHlmN~k~CFfCktTv~ 467 (489)
T KOG4692|consen 420 SEDNLCPICYAGPINAVFA-PCSHRSCYGCITQHLMNCKRCFFCKTTVI 467 (489)
T ss_pred cccccCcceecccchhhcc-CCCCchHHHHHHHHHhcCCeeeEecceee
Confidence 3556799999888888888 899999999999873 46767766553
No 76
>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=85.27 E-value=0.42 Score=27.56 Aligned_cols=22 Identities=23% Similarity=0.546 Sum_probs=12.7
Q ss_pred eeccccccCcCCccccc-CCcee
Q 046177 58 ECPVCLNAMYPPIHQCS-NGHTL 79 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~qC~-cGH~~ 79 (272)
.||.|...+..-...|+ |||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 46777766644444555 66654
No 77
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.27 E-value=0.73 Score=43.16 Aligned_cols=44 Identities=18% Similarity=0.523 Sum_probs=34.9
Q ss_pred eeeccccccCcCC--cccccCCceeccCccccc----CCCCCCcccCCCc
Q 046177 57 LECPVCLNAMYPP--IHQCSNGHTLCSGCKPRV----HNRCPTCRHELGN 100 (272)
Q Consensus 57 l~CpiC~~~l~~P--v~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~~ 100 (272)
..|.||++-+.+= +..=+|+|.|=..|+..| ...||.|++.+..
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 6999999988643 333379999999999999 2459999997643
No 78
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.87 E-value=0.69 Score=42.07 Aligned_cols=57 Identities=26% Similarity=0.594 Sum_probs=39.6
Q ss_pred eeeeccccccCc------CCcccccCCceeccCcccccC----CCCCCcccCC--Cc------ccchhHHHHhhhc
Q 046177 56 LLECPVCLNAMY------PPIHQCSNGHTLCSGCKPRVH----NRCPTCRHEL--GN------IRCLALEKVAASL 113 (272)
Q Consensus 56 ~l~CpiC~~~l~------~Pv~qC~cGH~~C~~C~~~~~----~~CP~Cr~~~--~~------~r~~~le~~~~~l 113 (272)
.+.|-||.+.+. .|... .|||.+|..|..++. ..||.||.+. .. ..|.++-..+...
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l-~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~~~~~~~l~kNf~ll~~~~~~ 77 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVL-KCGHTICQNCASKLLGNSRILCPFCRETTEIPDGDVKSLQKNFALLQAIEHM 77 (296)
T ss_pred CCceeecCccccccCcccCCccc-ccCceehHhHHHHHhcCceeeccCCCCcccCCchhHhhhhhhHHHHHHHHHH
Confidence 467888888764 35323 499999999999872 5699999984 22 3456655555543
No 79
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=83.56 E-value=0.29 Score=35.92 Aligned_cols=43 Identities=23% Similarity=0.482 Sum_probs=30.8
Q ss_pred eeeccccccCcCCccccc---------------CCceeccCccccc---CCCCCCcccCCC
Q 046177 57 LECPVCLNAMYPPIHQCS---------------NGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~---------------cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
-.|.||...+..+-.+|+ |.|.|=..|+.+| ++.||++++...
T Consensus 21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~ 81 (88)
T COG5194 21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81 (88)
T ss_pred chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence 357777777666544443 5577777888888 588999998764
No 80
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.05 E-value=0.35 Score=45.85 Aligned_cols=42 Identities=26% Similarity=0.644 Sum_probs=34.0
Q ss_pred eeeccccccCcCCcccc----cCCceeccCccccc-----CCCCCCcccCC
Q 046177 57 LECPVCLNAMYPPIHQC----SNGHTLCSGCKPRV-----HNRCPTCRHEL 98 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC----~cGH~~C~~C~~~~-----~~~CP~Cr~~~ 98 (272)
-.||||++-..-|.-.| .|||.|=++|+++| ...||.|...-
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka 55 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA 55 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence 47999999887774333 59999999999999 36899997754
No 81
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=82.59 E-value=0.88 Score=25.83 Aligned_cols=23 Identities=30% Similarity=0.553 Sum_probs=15.4
Q ss_pred CCcccccCCCCceeccCcHHhhhhcCC
Q 046177 115 LPCKYQSYGCMGIYPYYSKLKHESQCI 141 (272)
Q Consensus 115 v~C~~~~~GC~~~~~~~~~~~He~~C~ 141 (272)
++|++ |...+....+..|+..|.
T Consensus 3 ~~C~~----CgR~F~~~~l~~H~~~C~ 25 (25)
T PF13913_consen 3 VPCPI----CGRKFNPDRLEKHEKICK 25 (25)
T ss_pred CcCCC----CCCEECHHHHHHHHHhcC
Confidence 45665 777777777777777663
No 82
>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=80.59 E-value=0.72 Score=41.89 Aligned_cols=42 Identities=33% Similarity=0.812 Sum_probs=30.7
Q ss_pred eecccccc-CcCC-c--ccccCCceeccCccccc----CCCCCCcccCCC
Q 046177 58 ECPVCLNA-MYPP-I--HQCSNGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~-l~~P-v--~qC~cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.||+|.-- +..| + +.-.|||..|.+|..++ ...||.|...+.
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR 51 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR 51 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence 48888753 3444 2 22269999999999987 478999987653
No 83
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.33 E-value=0.34 Score=48.40 Aligned_cols=40 Identities=35% Similarity=0.797 Sum_probs=31.8
Q ss_pred CCCCeeeeccccccC----cCCcccccCCceeccCccccc-CCCCC
Q 046177 52 SVRELLECPVCLNAM----YPPIHQCSNGHTLCSGCKPRV-HNRCP 92 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l----~~Pv~qC~cGH~~C~~C~~~~-~~~CP 92 (272)
.+.+.|.|+||++.+ ..|+.. .|||+.|+.|.+.+ ..+||
T Consensus 7 ~w~~~l~c~ic~n~f~~~~~~Pvsl-~cghtic~~c~~~lyn~scp 51 (861)
T KOG3161|consen 7 KWVLLLLCDICLNLFVVQRLEPVSL-QCGHTICGHCVQLLYNASCP 51 (861)
T ss_pred hhHHHhhchHHHHHHHHHhcCcccc-cccchHHHHHHHhHhhccCC
Confidence 456788999997655 467755 69999999999987 46898
No 84
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=79.33 E-value=0.45 Score=48.52 Aligned_cols=40 Identities=28% Similarity=0.708 Sum_probs=33.2
Q ss_pred eeeccccccCcCCcccccCCceeccCccccc-----CCCCCCcccCC
Q 046177 57 LECPVCLNAMYPPIHQCSNGHTLCSGCKPRV-----HNRCPTCRHEL 98 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-----~~~CP~Cr~~~ 98 (272)
+.|++|.+ ...++.. .|||.+|..|+... ...||.||..+
T Consensus 455 ~~c~ic~~-~~~~~it-~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFIT-RCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred cccccccc-cccceee-cccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 89999999 7777655 89999999998876 24699998755
No 85
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=79.06 E-value=0.68 Score=30.91 Aligned_cols=42 Identities=21% Similarity=0.554 Sum_probs=21.9
Q ss_pred eeeeccccccCcCCcccccCCceeccCccccc-------CCCCCCcccC
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV-------HNRCPTCRHE 97 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-------~~~CP~Cr~~ 97 (272)
.|.||+-...+..|+.--.|.|.-|.+=..-+ .-.||.|.++
T Consensus 2 sL~CPls~~~i~~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 2 SLRCPLSFQRIRIPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp ESB-TTTSSB-SSEEEETT--SS--EEHHHHHHHHHHS---B-TTT---
T ss_pred eeeCCCCCCEEEeCccCCcCcccceECHHHHHHHhhccCCeECcCCcCc
Confidence 37899999999999877679999765431111 2469999764
No 86
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=77.25 E-value=1.3 Score=30.20 Aligned_cols=33 Identities=33% Similarity=0.623 Sum_probs=23.7
Q ss_pred eeeec--cccccCc------CCcccc-cCCceeccCcccccC
Q 046177 56 LLECP--VCLNAMY------PPIHQC-SNGHTLCSGCKPRVH 88 (272)
Q Consensus 56 ~l~Cp--iC~~~l~------~Pv~qC-~cGH~~C~~C~~~~~ 88 (272)
..-|| -|..++. .+..+| .||+.||..|...|.
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H 59 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWH 59 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCC
Confidence 33577 7765543 335689 699999999998874
No 87
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=76.88 E-value=8.3 Score=34.94 Aligned_cols=73 Identities=21% Similarity=0.347 Sum_probs=42.8
Q ss_pred CCCCCcccCCCcccchhHHHHhhhcCCCcccccCCCCceeccCcH-Hhhhh-cCCCccccCCCCCCCCcccc-ChhHHHH
Q 046177 89 NRCPTCRHELGNIRCLALEKVAASLELPCKYQSYGCMGIYPYYSK-LKHES-QCIFRPYNCPYAGSECTVMG-DIPYLVA 165 (272)
Q Consensus 89 ~~CP~Cr~~~~~~r~~~le~~~~~l~v~C~~~~~GC~~~~~~~~~-~~He~-~C~~~~~~CP~~~~~C~~~g-~~~~l~~ 165 (272)
..|+.|.........+.|-...-.+...|.. |...+..--| .-|.+ .=.-.|+.||. |+-.. .+..|-.
T Consensus 162 ~~C~~C~K~YvSmpALkMHirTH~l~c~C~i----CGKaFSRPWLLQGHiRTHTGEKPF~C~h----C~kAFADRSNLRA 233 (279)
T KOG2462|consen 162 FSCKYCGKVYVSMPALKMHIRTHTLPCECGI----CGKAFSRPWLLQGHIRTHTGEKPFSCPH----CGKAFADRSNLRA 233 (279)
T ss_pred ccCCCCCceeeehHHHhhHhhccCCCccccc----ccccccchHHhhcccccccCCCCccCCc----ccchhcchHHHHH
Confidence 5677777665544445554455555556654 6666654433 35554 22346777776 55544 5667777
Q ss_pred Hhhh
Q 046177 166 HLKD 169 (272)
Q Consensus 166 Hl~~ 169 (272)
|++.
T Consensus 234 HmQT 237 (279)
T KOG2462|consen 234 HMQT 237 (279)
T ss_pred HHHh
Confidence 7765
No 88
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.53 E-value=1.3 Score=31.99 Aligned_cols=30 Identities=37% Similarity=0.863 Sum_probs=24.9
Q ss_pred ccccCCceeccCccc-ccCCCCCCcccCCCc
Q 046177 71 HQCSNGHTLCSGCKP-RVHNRCPTCRHELGN 100 (272)
Q Consensus 71 ~qC~cGH~~C~~C~~-~~~~~CP~Cr~~~~~ 100 (272)
..|.-.++||..|.+ ++.+.||.|...+..
T Consensus 23 ~ICtfEcTFCadCae~~l~g~CPnCGGelv~ 53 (84)
T COG3813 23 RICTFECTFCADCAENRLHGLCPNCGGELVA 53 (84)
T ss_pred eEEEEeeehhHhHHHHhhcCcCCCCCchhhc
Confidence 357888999999988 457899999998764
No 89
>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=75.65 E-value=2.2 Score=29.02 Aligned_cols=34 Identities=26% Similarity=0.583 Sum_probs=20.6
Q ss_pred Ceeeecc--ccccCcCC------ccccc-CCceeccCcccccC
Q 046177 55 ELLECPV--CLNAMYPP------IHQCS-NGHTLCSGCKPRVH 88 (272)
Q Consensus 55 ~~l~Cpi--C~~~l~~P------v~qC~-cGH~~C~~C~~~~~ 88 (272)
+..-||- |..++..+ .++|. ||+.||..|...|.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H 59 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWH 59 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESC
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccC
Confidence 3348988 98887532 25898 99999999988874
No 90
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=75.28 E-value=3 Score=28.02 Aligned_cols=27 Identities=33% Similarity=0.742 Sum_probs=22.7
Q ss_pred cccCCCCCCCCccccChhHHHHHhhhcCCCC
Q 046177 144 PYNCPYAGSECTVMGDIPYLVAHLKDDHKVD 174 (272)
Q Consensus 144 ~~~CP~~~~~C~~~g~~~~l~~Hl~~~H~~~ 174 (272)
.+.||+ |+...+...|..|+...|..+
T Consensus 2 ~f~CP~----C~~~~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPY----CGKGFSESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCC----CCCccCHHHHHHHHHhHCcCC
Confidence 468998 777667889999999999864
No 91
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=74.93 E-value=1.7 Score=39.88 Aligned_cols=83 Identities=16% Similarity=0.293 Sum_probs=50.8
Q ss_pred cccCCCC-eeeeccccccCcCCcccccCCceeccCccccc-CCCCCCcccCCCcccchhHHHHhhhcCCCcccccCCCCc
Q 046177 49 VSSSVRE-LLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV-HNRCPTCRHELGNIRCLALEKVAASLELPCKYQSYGCMG 126 (272)
Q Consensus 49 ~~~~~~~-~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~-~~~CP~Cr~~~~~~r~~~le~~~~~l~v~C~~~~~GC~~ 126 (272)
.+..+.. .-.|--|-.++..==..=.|.|+||..|...- .+.||.|...+ .-+|+....-.+-|. ...||..
T Consensus 82 gek~l~p~VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~V-----qrIeq~~~g~iFmC~-~~~GC~R 155 (389)
T KOG2932|consen 82 GEKQLGPRVHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRV-----QRIEQIMMGGIFMCA-APHGCLR 155 (389)
T ss_pred cccccCcceEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHH-----HHHHHhcccceEEee-cchhHHH
Confidence 3444444 55688888876532111269999999996543 36899997655 345555555556676 4567765
Q ss_pred e-eccCcHHhhh
Q 046177 127 I-YPYYSKLKHE 137 (272)
Q Consensus 127 ~-~~~~~~~~He 137 (272)
+ +.-.++..|.
T Consensus 156 TyLsqrDlqAHI 167 (389)
T KOG2932|consen 156 TYLSQRDLQAHI 167 (389)
T ss_pred HHhhHHHHHHHh
Confidence 3 3444566654
No 92
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=74.75 E-value=1.6 Score=40.23 Aligned_cols=77 Identities=19% Similarity=0.108 Sum_probs=51.3
Q ss_pred CCCCCcccCCCc---ccc---hhHHHHhhhcCCCcccccCCCCceeccCcHHhhhhcCCCccccCCCCCCCCccccChhH
Q 046177 89 NRCPTCRHELGN---IRC---LALEKVAASLELPCKYQSYGCMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPY 162 (272)
Q Consensus 89 ~~CP~Cr~~~~~---~r~---~~le~~~~~l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~ 162 (272)
..||.|..++.. ..+ .+-..=-..+...||. |...++..--..=|+.++-..++||+...||++.++..+
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~----Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~ 124 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPT----CRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGE 124 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhcccCCc----cccccccHHHHHHHHHHHhceecccccccCCceeecccc
Confidence 468888887753 111 2222223366778886 877666332234456899999999999899999998766
Q ss_pred HHHHhhh
Q 046177 163 LVAHLKD 169 (272)
Q Consensus 163 l~~Hl~~ 169 (272)
-..|.+.
T Consensus 125 ~~~HE~~ 131 (299)
T KOG3002|consen 125 KSKHEKV 131 (299)
T ss_pred ccccccc
Confidence 5666544
No 93
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.49 E-value=1.8 Score=43.94 Aligned_cols=41 Identities=34% Similarity=0.762 Sum_probs=32.1
Q ss_pred eeccccccCcCCcccccCCc-eeccCcccccC---------CCCCCcccCCC
Q 046177 58 ECPVCLNAMYPPIHQCSNGH-TLCSGCKPRVH---------NRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~qC~cGH-~~C~~C~~~~~---------~~CP~Cr~~~~ 99 (272)
.|+||..-+.-+.+- .||| .+|..|..++. ..||.|+..+.
T Consensus 2 ~c~ic~~s~~~~~~~-s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~~ 52 (669)
T KOG2231|consen 2 SCAICAFSPDFVGRG-SCGHNEVCATCVVRLRFELNNRKCSNECPVCRREVE 52 (669)
T ss_pred CcceeecCccccccc-cccccccchhhhhhhhhhcccccccccCccccccee
Confidence 488998887777655 7999 89999988861 45799988654
No 94
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.40 E-value=1.3 Score=41.95 Aligned_cols=45 Identities=27% Similarity=0.586 Sum_probs=33.9
Q ss_pred CCCCeeeeccccccC---cCCcccccCCceeccCcccccC------CCCCCcccC
Q 046177 52 SVRELLECPVCLNAM---YPPIHQCSNGHTLCSGCKPRVH------NRCPTCRHE 97 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l---~~Pv~qC~cGH~~C~~C~~~~~------~~CP~Cr~~ 97 (272)
.....|.|||=.+.- .||+.. .|||+.++.-+.++. .+||+|-..
T Consensus 330 ~fHSvF~CPVlKeqtsdeNPPm~L-~CGHVISkdAlnrLS~ng~~sfKCPYCP~e 383 (394)
T KOG2817|consen 330 HFHSVFICPVLKEQTSDENPPMML-ICGHVISKDALNRLSKNGSQSFKCPYCPVE 383 (394)
T ss_pred cccceeecccchhhccCCCCCeee-eccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence 456889999977764 478755 799999999888872 468888543
No 95
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.80 E-value=1 Score=36.04 Aligned_cols=48 Identities=23% Similarity=0.556 Sum_probs=29.4
Q ss_pred eccCcccccCCCCCCcccCCCcccchhHHHHhh-----hcCCCcccccCCCCceeccCc
Q 046177 79 LCSGCKPRVHNRCPTCRHELGNIRCLALEKVAA-----SLELPCKYQSYGCMGIYPYYS 132 (272)
Q Consensus 79 ~C~~C~~~~~~~CP~Cr~~~~~~r~~~le~~~~-----~l~v~C~~~~~GC~~~~~~~~ 132 (272)
||+.|-+....+||.|..++.. +..+|.++. ..+-.|.| |...+|+.+
T Consensus 30 fcskcgeati~qcp~csasirg--d~~vegvlglg~dye~psfchn----cgs~fpwte 82 (160)
T COG4306 30 FCSKCGEATITQCPICSASIRG--DYYVEGVLGLGGDYEPPSFCHN----CGSRFPWTE 82 (160)
T ss_pred HHhhhchHHHhcCCccCCcccc--cceeeeeeccCCCCCCcchhhc----CCCCCCcHH
Confidence 8999987766789999988742 333444432 22334554 655555543
No 96
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=72.30 E-value=1.7 Score=40.25 Aligned_cols=45 Identities=24% Similarity=0.445 Sum_probs=33.6
Q ss_pred CCCeeeeccccccCcCCcccccCCceeccCccccc---CCCCCCcccC
Q 046177 53 VRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHE 97 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~ 97 (272)
..+.-.||+|..--..|-..-..|-+||..|+... .+.||.=.-+
T Consensus 297 ~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p 344 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYP 344 (357)
T ss_pred CCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCc
Confidence 34566899999998888433357999999998875 3789864433
No 97
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.15 E-value=3.1 Score=32.67 Aligned_cols=38 Identities=26% Similarity=0.602 Sum_probs=28.7
Q ss_pred eeccccccCcCC------------ccccc-CCceeccCccccc---CCCCCCcc
Q 046177 58 ECPVCLNAMYPP------------IHQCS-NGHTLCSGCKPRV---HNRCPTCR 95 (272)
Q Consensus 58 ~CpiC~~~l~~P------------v~qC~-cGH~~C~~C~~~~---~~~CP~Cr 95 (272)
.|-.|...+..+ .++|. |++.||.+|-.-+ ...||-|.
T Consensus 57 ~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred cccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 599999877543 46787 9999999995443 36799885
No 98
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=72.07 E-value=5.5 Score=27.61 Aligned_cols=14 Identities=43% Similarity=1.066 Sum_probs=11.0
Q ss_pred CccccCCCCCCCCccccC
Q 046177 142 FRPYNCPYAGSECTVMGD 159 (272)
Q Consensus 142 ~~~~~CP~~~~~C~~~g~ 159 (272)
..+|.||. |+|.|+
T Consensus 46 ~~~Y~CP~----CGF~GP 59 (59)
T PRK14890 46 SNPYTCPK----CGFEGP 59 (59)
T ss_pred CCceECCC----CCCcCc
Confidence 36889996 999884
No 99
>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=71.01 E-value=2.4 Score=29.03 Aligned_cols=43 Identities=30% Similarity=0.715 Sum_probs=31.2
Q ss_pred eeccccccCcCC---cccccCCceeccCccccc-CCCCCCcccCCCc
Q 046177 58 ECPVCLNAMYPP---IHQCSNGHTLCSGCKPRV-HNRCPTCRHELGN 100 (272)
Q Consensus 58 ~CpiC~~~l~~P---v~qC~cGH~~C~~C~~~~-~~~CP~Cr~~~~~ 100 (272)
.|-.|-.-|.+. -+.|+-..+||..|.+.. .+.||.|...+..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcccc
Confidence 355565555322 356777789999999887 7899999988753
No 100
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.71 E-value=0.9 Score=40.94 Aligned_cols=45 Identities=20% Similarity=0.400 Sum_probs=34.5
Q ss_pred CeeeeccccccCcCC---------cccccCCceeccCccccc-----CCCCCCcccCCC
Q 046177 55 ELLECPVCLNAMYPP---------IHQCSNGHTLCSGCKPRV-----HNRCPTCRHELG 99 (272)
Q Consensus 55 ~~l~CpiC~~~l~~P---------v~qC~cGH~~C~~C~~~~-----~~~CP~Cr~~~~ 99 (272)
++-.|.||..-+..- +++=+|+|+|=..|+.-| ++.||.|++.+.
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence 445799998876433 355579999999998887 589999988764
No 101
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=67.52 E-value=3.2 Score=38.92 Aligned_cols=113 Identities=17% Similarity=0.318 Sum_probs=57.8
Q ss_pred CCCeeeeccccccCcCCc--c-----cc--cCCceeccCccccc---------------CCCCCCcccCCCc---ccchh
Q 046177 53 VRELLECPVCLNAMYPPI--H-----QC--SNGHTLCSGCKPRV---------------HNRCPTCRHELGN---IRCLA 105 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv--~-----qC--~cGH~~C~~C~~~~---------------~~~CP~Cr~~~~~---~r~~~ 105 (272)
-+..+-||-|.+.+..-- + |. .-.+-.|+.|..+. ..+||.|....+. .++-.
T Consensus 204 ~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 204 NEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred CCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHH
Confidence 356788999999876421 1 11 12366788887664 2579999776543 22223
Q ss_pred HHHHhhhcCCCcccccCCCCce-eccCcHHhhhhcCCCccccCCCCCCCCcccc-ChhHHHHHhhhcC
Q 046177 106 LEKVAASLELPCKYQSYGCMGI-YPYYSKLKHESQCIFRPYNCPYAGSECTVMG-DIPYLVAHLKDDH 171 (272)
Q Consensus 106 le~~~~~l~v~C~~~~~GC~~~-~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g-~~~~l~~Hl~~~H 171 (272)
+-+-..+-.+.|.- |... +...++.+|...=.-..+.|-++. |.+.. ...+|..|+...|
T Consensus 284 r~rHs~dkpfKCd~----Cd~~c~~esdL~kH~~~HS~~~y~C~h~~--C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 284 RYRHSKDKPFKCDE----CDTRCVRESDLAKHVQVHSKTVYQCEHPD--CHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred HhhhccCCCccccc----hhhhhccHHHHHHHHHhccccceecCCCC--CcHHHHHHHHHHHHHHHhc
Confidence 33344455555543 3332 233456666542223334444432 44433 2334444444444
No 102
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.44 E-value=4.8 Score=27.94 Aligned_cols=36 Identities=28% Similarity=0.692 Sum_probs=20.0
Q ss_pred cCCCcccccCCCCceeccCcHHhhhhcCCCccccCCCCCCCCccccC
Q 046177 113 LELPCKYQSYGCMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGD 159 (272)
Q Consensus 113 l~v~C~~~~~GC~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~ 159 (272)
..++||| |.+..-+.-..--. .-.+|.||. |+|.|+
T Consensus 26 v~F~CPn----CGe~~I~Rc~~CRk---~g~~Y~Cp~----CGF~GP 61 (61)
T COG2888 26 VKFPCPN----CGEVEIYRCAKCRK---LGNPYRCPK----CGFEGP 61 (61)
T ss_pred eEeeCCC----CCceeeehhhhHHH---cCCceECCC----cCccCC
Confidence 3567776 66444333221000 235788986 889874
No 103
>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=66.93 E-value=1.5 Score=36.32 Aligned_cols=22 Identities=27% Similarity=0.880 Sum_probs=19.0
Q ss_pred eeccCcccccCCCCCCcccCCC
Q 046177 78 TLCSGCKPRVHNRCPTCRHELG 99 (272)
Q Consensus 78 ~~C~~C~~~~~~~CP~Cr~~~~ 99 (272)
-||..|-.+....||.|..++.
T Consensus 29 ~fC~kCG~~tI~~Cp~C~~~Ir 50 (158)
T PF10083_consen 29 KFCSKCGAKTITSCPNCSTPIR 50 (158)
T ss_pred HHHHHhhHHHHHHCcCCCCCCC
Confidence 4899998887789999999885
No 104
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=66.67 E-value=5 Score=21.19 Aligned_cols=22 Identities=27% Similarity=0.561 Sum_probs=15.2
Q ss_pred cCCCCCCCCcccc-ChhHHHHHhhhcC
Q 046177 146 NCPYAGSECTVMG-DIPYLVAHLKDDH 171 (272)
Q Consensus 146 ~CP~~~~~C~~~g-~~~~l~~Hl~~~H 171 (272)
.|+. |+... ...+|..|+...|
T Consensus 2 ~C~~----C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 2 QCPI----CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp E-SS----TS-EESSHHHHHHHHHHHS
T ss_pred CCcC----CCCcCCcHHHHHHHHHhhC
Confidence 5765 77766 5678999998776
No 105
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=66.32 E-value=2.7 Score=37.63 Aligned_cols=24 Identities=21% Similarity=0.654 Sum_probs=19.2
Q ss_pred eeeeccccccCc--CCcccccCCcee
Q 046177 56 LLECPVCLNAMY--PPIHQCSNGHTL 79 (272)
Q Consensus 56 ~l~CpiC~~~l~--~Pv~qC~cGH~~ 79 (272)
.|.||+|...|. +.-+.|.+||.|
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCC
Confidence 378999999995 344678999987
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=65.98 E-value=6.2 Score=41.83 Aligned_cols=44 Identities=25% Similarity=0.594 Sum_probs=34.3
Q ss_pred CeeeeccccccCcCCccccc-CCc-----eeccCcccccC-CCCCCcccCCCc
Q 046177 55 ELLECPVCLNAMYPPIHQCS-NGH-----TLCSGCKPRVH-NRCPTCRHELGN 100 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC~-cGH-----~~C~~C~~~~~-~~CP~Cr~~~~~ 100 (272)
....||-|.... +.+.|+ ||. .+|..|..... ..||.|......
T Consensus 625 g~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 625 GRRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred cCccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 445799999986 556898 984 59999977763 679999987754
No 107
>PLN02436 cellulose synthase A
Probab=65.83 E-value=4.9 Score=42.87 Aligned_cols=42 Identities=21% Similarity=0.720 Sum_probs=33.4
Q ss_pred eeccccccCc-----CCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 58 ECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.|.||.+-+- +|..-|. ||--+|+.|.+-- .+.||.|++...
T Consensus 38 iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~ 89 (1094)
T PLN02436 38 TCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYK 89 (1094)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 7999998752 4656787 9999999998654 478999998764
No 108
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.26 E-value=1.7 Score=42.27 Aligned_cols=47 Identities=23% Similarity=0.460 Sum_probs=34.3
Q ss_pred CCCeeeeccccccCcC-----C-----------cccccCCceeccCcccccC----CCCCCcccCCC
Q 046177 53 VRELLECPVCLNAMYP-----P-----------IHQCSNGHTLCSGCKPRVH----NRCPTCRHELG 99 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~-----P-----------v~qC~cGH~~C~~C~~~~~----~~CP~Cr~~~~ 99 (272)
....-.|+||.....- | ....+|.|+|=..|+.+|. -.||.||.++.
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP 634 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence 3455689999876531 1 1123799999999999983 38999999875
No 109
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=64.76 E-value=3.7 Score=37.17 Aligned_cols=75 Identities=17% Similarity=0.299 Sum_probs=49.7
Q ss_pred CCCCCcccCCCcccchhHHHHh----hhcCCCcccccCCCCcee-ccCcHHhhhhc-CCCccccCCCCCCCCccccChh-
Q 046177 89 NRCPTCRHELGNIRCLALEKVA----ASLELPCKYQSYGCMGIY-PYYSKLKHESQ-CIFRPYNCPYAGSECTVMGDIP- 161 (272)
Q Consensus 89 ~~CP~Cr~~~~~~r~~~le~~~----~~l~v~C~~~~~GC~~~~-~~~~~~~He~~-C~~~~~~CP~~~~~C~~~g~~~- 161 (272)
-.|+.|...|. |...|+.-+ .+-++.|+. |...+ ...+|+.|+.+ =...++.|+. |+-...++
T Consensus 188 c~C~iCGKaFS--RPWLLQGHiRTHTGEKPF~C~h----C~kAFADRSNLRAHmQTHS~~K~~qC~~----C~KsFsl~S 257 (279)
T KOG2462|consen 188 CECGICGKAFS--RPWLLQGHIRTHTGEKPFSCPH----CGKAFADRSNLRAHMQTHSDVKKHQCPR----CGKSFALKS 257 (279)
T ss_pred ccccccccccc--chHHhhcccccccCCCCccCCc----ccchhcchHHHHHHHHhhcCCccccCcc----hhhHHHHHH
Confidence 46888888774 444444433 455788885 77655 45678899873 3456888985 87777654
Q ss_pred HHHHHhhhcCCC
Q 046177 162 YLVAHLKDDHKV 173 (272)
Q Consensus 162 ~l~~Hl~~~H~~ 173 (272)
.|-.|++.....
T Consensus 258 yLnKH~ES~C~~ 269 (279)
T KOG2462|consen 258 YLNKHSESACLK 269 (279)
T ss_pred HHHHhhhhcccc
Confidence 567787776543
No 110
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=62.03 E-value=3.9 Score=27.83 Aligned_cols=36 Identities=25% Similarity=0.557 Sum_probs=26.2
Q ss_pred eeeccccccC--cCCccccc-CCceeccCcccccCCCCCC
Q 046177 57 LECPVCLNAM--YPPIHQCS-NGHTLCSGCKPRVHNRCPT 93 (272)
Q Consensus 57 l~CpiC~~~l--~~Pv~qC~-cGH~~C~~C~~~~~~~CP~ 93 (272)
-.|++|.+.+ .+.+++|+ ||-.+=+.|..+. +.|-.
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~-g~C~~ 44 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA-GGCIN 44 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhC-CceEe
Confidence 4799999999 67788887 8866666676664 45544
No 111
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=61.87 E-value=1.9 Score=43.68 Aligned_cols=48 Identities=23% Similarity=0.683 Sum_probs=38.4
Q ss_pred cCCCCeeeeccccccCcCCcccccCCceeccCccccc------CCCCCCcccCCC
Q 046177 51 SSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV------HNRCPTCRHELG 99 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~------~~~CP~Cr~~~~ 99 (272)
......++||||......|+.. .|-|.||..|+... ...||+|+..+.
T Consensus 16 ~~~~k~lEc~ic~~~~~~p~~~-kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e 69 (684)
T KOG4362|consen 16 NAMQKILECPICLEHVKEPSLL-KCDHIFLKFCLNKLFESKKGPKQCALCKSDIE 69 (684)
T ss_pred HHHhhhccCCceeEEeeccchh-hhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence 3445678999999999999655 79999999998775 257999986553
No 112
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.67 E-value=4.1 Score=36.37 Aligned_cols=36 Identities=14% Similarity=0.233 Sum_probs=29.7
Q ss_pred cCCCCeeeeccccccCcCCcccccCCceeccCccccc
Q 046177 51 SSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRV 87 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~ 87 (272)
+.+.+.-.|..|+.+..+|| .|.-||+||+.||.+.
T Consensus 38 DsiK~FdcCsLtLqPc~dPv-it~~GylfdrEaILe~ 73 (303)
T KOG3039|consen 38 DSIKPFDCCSLTLQPCRDPV-ITPDGYLFDREAILEY 73 (303)
T ss_pred cccCCcceeeeecccccCCc-cCCCCeeeeHHHHHHH
Confidence 44556667999999999998 4689999999998763
No 113
>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=60.37 E-value=5.8 Score=27.72 Aligned_cols=33 Identities=27% Similarity=0.670 Sum_probs=16.5
Q ss_pred CeeeeccccccCcC--Cccccc-CCceeccCccccc
Q 046177 55 ELLECPVCLNAMYP--PIHQCS-NGHTLCSGCKPRV 87 (272)
Q Consensus 55 ~~l~CpiC~~~l~~--Pv~qC~-cGH~~C~~C~~~~ 87 (272)
+.-.|.+|...+.- --..|. ||++||..|....
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 34579999988732 234676 9999999997653
No 114
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=59.76 E-value=4.5 Score=38.66 Aligned_cols=34 Identities=24% Similarity=0.363 Sum_probs=27.0
Q ss_pred cCCCcccccCCCCceeccCcHHhhh-hcCCCccccCCC
Q 046177 113 LELPCKYQSYGCMGIYPYYSKLKHE-SQCIFRPYNCPY 149 (272)
Q Consensus 113 l~v~C~~~~~GC~~~~~~~~~~~He-~~C~~~~~~CP~ 149 (272)
-.+.|++ +|...++..++.+|. ..|+++...|..
T Consensus 113 ~~~~C~~---~C~~~~~~~d~~~hl~~~C~~~~~~c~~ 147 (391)
T KOG0297|consen 113 DPLKCPH---RCGVQVPRDDLEDHLEAECPRRSLKCSL 147 (391)
T ss_pred CcccCcc---ccccccchHHHHHHHhcccccccccchh
Confidence 4678887 488888888888886 588888887776
No 115
>PF15616 TerY-C: TerY-C metal binding domain
Probab=59.57 E-value=5.3 Score=32.30 Aligned_cols=45 Identities=27% Similarity=0.492 Sum_probs=32.2
Q ss_pred cCCCCeeeeccccccCcCCcccccCCceeccCcccccCCCCCCcccCCC
Q 046177 51 SSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVHNRCPTCRHELG 99 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~~~CP~Cr~~~~ 99 (272)
+++...--||-|....-- ..|.||+++|-.=-.. ..||.|.....
T Consensus 72 seL~g~PgCP~CGn~~~f--a~C~CGkl~Ci~g~~~--~~CPwCg~~g~ 116 (131)
T PF15616_consen 72 SELIGAPGCPHCGNQYAF--AVCGCGKLFCIDGEGE--VTCPWCGNEGS 116 (131)
T ss_pred HHhcCCCCCCCCcChhcE--EEecCCCEEEeCCCCC--EECCCCCCeee
Confidence 344555689999987653 4689999998554333 58999987653
No 116
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.65 E-value=3.8 Score=39.03 Aligned_cols=33 Identities=21% Similarity=0.467 Sum_probs=23.0
Q ss_pred Ceeeecccc-ccCcCCc--ccccCCceeccCccccc
Q 046177 55 ELLECPVCL-NAMYPPI--HQCSNGHTLCSGCKPRV 87 (272)
Q Consensus 55 ~~l~CpiC~-~~l~~Pv--~qC~cGH~~C~~C~~~~ 87 (272)
....|.||. +.....- ....|+|.||..|..+.
T Consensus 145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ 180 (384)
T KOG1812|consen 145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQH 180 (384)
T ss_pred ccccCccCccccccHhhhHHHhcccchhhhHHhHHH
Confidence 356899999 4433321 23459999999998864
No 117
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=58.49 E-value=5.3 Score=37.02 Aligned_cols=37 Identities=22% Similarity=0.672 Sum_probs=22.2
Q ss_pred eccccc-cCcCCccccc-CCceeccCccccc---CCCCCCcc
Q 046177 59 CPVCLN-AMYPPIHQCS-NGHTLCSGCKPRV---HNRCPTCR 95 (272)
Q Consensus 59 CpiC~~-~l~~Pv~qC~-cGH~~C~~C~~~~---~~~CP~Cr 95 (272)
|-.|.. .+..+.|+|. |.+.||.+|-.-+ ...||.|.
T Consensus 333 Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 333 CFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred eeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcC
Confidence 667733 3445567776 7777777773322 24677764
No 118
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=58.19 E-value=6.4 Score=24.81 Aligned_cols=24 Identities=21% Similarity=0.614 Sum_probs=16.8
Q ss_pred eccccccCcC-Cccccc-CCceeccCc
Q 046177 59 CPVCLNAMYP-PIHQCS-NGHTLCSGC 83 (272)
Q Consensus 59 CpiC~~~l~~-Pv~qC~-cGH~~C~~C 83 (272)
|.+|.....- |+ .|. |+..||..=
T Consensus 1 C~~C~~~~~l~~f-~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRKKVGLTGF-KCRHCGNLFCGEH 26 (39)
T ss_pred CcccCCcccccCe-ECCccCCcccccc
Confidence 5567765544 74 788 999998753
No 119
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=58.12 E-value=5.9 Score=33.87 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=29.9
Q ss_pred cccCCCcccchhHHHHhhhcCCCcccccCCCCceeccCcHHhhhhcC
Q 046177 94 CRHELGNIRCLALEKVAASLELPCKYQSYGCMGIYPYYSKLKHESQC 140 (272)
Q Consensus 94 Cr~~~~~~r~~~le~~~~~l~v~C~~~~~GC~~~~~~~~~~~He~~C 140 (272)
|...+....-..-|+...--+..||....||.|.+.+.++..|...-
T Consensus 24 C~~~~~~~~~~~HE~~C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~ 70 (198)
T PF03145_consen 24 CTETFPYSEKREHEEECPFRPCSCPFPGSGCDWQGSYKELLDHLRDK 70 (198)
T ss_dssp ---EE-GGGHHHHHHT-TTSEEE-SSSSTT---EEECCCHHHHHHHH
T ss_pred CcccccccChhhHhccCCCcCCcCCCCCCCccccCCHHHHHHHHHHH
Confidence 55555555555667777788899998778999999999999998764
No 120
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=57.57 E-value=8.3 Score=24.64 Aligned_cols=33 Identities=21% Similarity=0.713 Sum_probs=18.6
Q ss_pred ecc--ccccCcCCccccc-CCceeccCcccccCCCCC
Q 046177 59 CPV--CLNAMYPPIHQCS-NGHTLCSGCKPRVHNRCP 92 (272)
Q Consensus 59 Cpi--C~~~l~~Pv~qC~-cGH~~C~~C~~~~~~~CP 92 (272)
|.. |.....-|+ .|. |+..||..=+..-.-.|+
T Consensus 1 C~~~~C~~~~~~~~-~C~~C~~~FC~~Hr~~e~H~C~ 36 (43)
T PF01428_consen 1 CSFPGCKKKDFLPF-KCKHCGKSFCLKHRLPEDHNCS 36 (43)
T ss_dssp -SSTTT--BCTSHE-E-TTTS-EE-TTTHSTTTCT-S
T ss_pred CccCcCcCccCCCe-ECCCCCcccCccccCccccCCc
Confidence 455 888777775 788 999999987665444454
No 121
>PLN02400 cellulose synthase
Probab=57.52 E-value=9.2 Score=40.96 Aligned_cols=42 Identities=19% Similarity=0.580 Sum_probs=32.8
Q ss_pred eeccccccCc-----CCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 58 ECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.|.||.+-+- +|..-|. |+--+|+.|.+-- .+.||.|++...
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYk 89 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYR 89 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccc
Confidence 7999998753 4655676 9999999997643 478999998764
No 122
>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=56.65 E-value=4.8 Score=37.97 Aligned_cols=29 Identities=31% Similarity=0.708 Sum_probs=21.4
Q ss_pred ccccCCceeccCccccc----------------CCCCCCcccCCC
Q 046177 71 HQCSNGHTLCSGCKPRV----------------HNRCPTCRHELG 99 (272)
Q Consensus 71 ~qC~cGH~~C~~C~~~~----------------~~~CP~Cr~~~~ 99 (272)
.+|.|.=.-|-+|..+| +..||+||..+-
T Consensus 307 ~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 307 QQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC 351 (358)
T ss_pred ccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence 35666677788898888 246999998763
No 123
>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=56.15 E-value=7.1 Score=29.36 Aligned_cols=33 Identities=24% Similarity=0.439 Sum_probs=24.9
Q ss_pred CCeeeeccccccCcCC-cccccCCceeccCcccc
Q 046177 54 RELLECPVCLNAMYPP-IHQCSNGHTLCSGCKPR 86 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~P-v~qC~cGH~~C~~C~~~ 86 (272)
.+.-.|++|...+... +...+|||++-..|..+
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 3445699999999755 44557999999998753
No 124
>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=55.98 E-value=4.9 Score=36.60 Aligned_cols=42 Identities=26% Similarity=0.526 Sum_probs=20.1
Q ss_pred eeeeccccccCcCCcccccC--C--ceeccCccccc---CCCCCCcccC
Q 046177 56 LLECPVCLNAMYPPIHQCSN--G--HTLCSGCKPRV---HNRCPTCRHE 97 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~c--G--H~~C~~C~~~~---~~~CP~Cr~~ 97 (272)
.-.||||.....--++.=.- | +.+|+-|-..| ...||.|...
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 45899999975444333122 4 67999999999 3689999764
No 125
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=54.77 E-value=3.6 Score=26.93 Aligned_cols=38 Identities=21% Similarity=0.438 Sum_probs=27.4
Q ss_pred CCCCcccCCCcccchhHHHHhhhcCCCcccccCCCCceec
Q 046177 90 RCPTCRHELGNIRCLALEKVAASLELPCKYQSYGCMGIYP 129 (272)
Q Consensus 90 ~CP~Cr~~~~~~r~~~le~~~~~l~v~C~~~~~GC~~~~~ 129 (272)
.||.|...........+...+..+-..|.|.. |.+.+.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~--Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPE--CGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCc--CCCEEE
Confidence 49999887765556667777788888899864 555543
No 126
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.23 E-value=8.5 Score=33.52 Aligned_cols=39 Identities=26% Similarity=0.565 Sum_probs=27.4
Q ss_pred eccccccCcCCcccccCCc-eeccCcccccCCCCCCcccCCC
Q 046177 59 CPVCLNAMYPPIHQCSNGH-TLCSGCKPRVHNRCPTCRHELG 99 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~cGH-~~C~~C~~~~~~~CP~Cr~~~~ 99 (272)
|-.|.+--..=+.. +|.| .+|..|-..+ ..||+|+.+..
T Consensus 161 Cr~C~~~~~~Vlll-PCrHl~lC~~C~~~~-~~CPiC~~~~~ 200 (207)
T KOG1100|consen 161 CRKCGEREATVLLL-PCRHLCLCGICDESL-RICPICRSPKT 200 (207)
T ss_pred ceecCcCCceEEee-cccceEecccccccC-ccCCCCcChhh
Confidence 88887754442333 6776 5999998764 68999998653
No 127
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=54.15 E-value=4.2 Score=23.42 Aligned_cols=24 Identities=25% Similarity=0.384 Sum_probs=14.3
Q ss_pred CCcccccCCCCceeccCcHHhhhhcCC
Q 046177 115 LPCKYQSYGCMGIYPYYSKLKHESQCI 141 (272)
Q Consensus 115 v~C~~~~~GC~~~~~~~~~~~He~~C~ 141 (272)
+.||| .-.-.++..++..|+..|+
T Consensus 3 v~CPy---n~~H~v~~~~l~~Hi~~C~ 26 (27)
T PF05253_consen 3 VRCPY---NPSHRVPASELQKHIKKCP 26 (27)
T ss_dssp EE-TT---TSS-EEEGGGHHHHHHHHH
T ss_pred eeCCC---CCCcCcCHHHHHHHHHHcC
Confidence 45665 3456677777777777664
No 128
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.82 E-value=6.9 Score=35.66 Aligned_cols=33 Identities=24% Similarity=0.613 Sum_probs=27.2
Q ss_pred CCeeeeccccccCcCC-ccccc--CCceeccCcccc
Q 046177 54 RELLECPVCLNAMYPP-IHQCS--NGHTLCSGCKPR 86 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~P-v~qC~--cGH~~C~~C~~~ 86 (272)
.+-|.|-+|.+-|.+- ++||. ..|-||..|-.+
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 3459999999999887 66887 789999999544
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.79 E-value=15 Score=40.00 Aligned_cols=43 Identities=33% Similarity=0.824 Sum_probs=32.6
Q ss_pred eeeeccccccCcCCccccc-CCce-----eccCcccccC------CCCCCcccCCCc
Q 046177 56 LLECPVCLNAMYPPIHQCS-NGHT-----LCSGCKPRVH------NRCPTCRHELGN 100 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~-cGH~-----~C~~C~~~~~------~~CP~Cr~~~~~ 100 (272)
.+.||-|...... ..|+ ||.. .|..|-.++. ..||.|..++..
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcccc
Confidence 4899999997544 3687 9965 4999988752 279999988754
No 130
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=53.18 E-value=13 Score=28.48 Aligned_cols=37 Identities=16% Similarity=0.517 Sum_probs=26.3
Q ss_pred cccccCCCCeeeeccccccCcCC-cccccCCceeccCc
Q 046177 47 LTVSSSVRELLECPVCLNAMYPP-IHQCSNGHTLCSGC 83 (272)
Q Consensus 47 ~~~~~~~~~~l~CpiC~~~l~~P-v~qC~cGH~~C~~C 83 (272)
++..-...+.|.|..|+.+-..- +-.-..|+.+|..|
T Consensus 61 V~ViP~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 61 VRVIPKQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred EEEecCCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 34445567899999999987443 22224799999998
No 131
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=52.97 E-value=4.8 Score=29.47 Aligned_cols=43 Identities=19% Similarity=0.559 Sum_probs=17.3
Q ss_pred eeeccccccCc-----CCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 57 LECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
-.|.||.+-+- .+..-|. |+-.+|+.|.+-- ...||.|+.+..
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk 62 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK 62 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred cccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence 36999988652 4555565 8889999997643 378999998764
No 132
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=50.96 E-value=1.9 Score=46.53 Aligned_cols=66 Identities=27% Similarity=0.617 Sum_probs=47.0
Q ss_pred cCCCCCccccccC-CCcccccCCCCeeeeccccccCcCC--cccccCCceeccCccccc---CCCCCCcccCCC
Q 046177 32 ESSVNDPAQIALK-PNLTVSSSVRELLECPVCLNAMYPP--IHQCSNGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 32 ~~~~~~~~~~~~~-~~~~~~~~~~~~l~CpiC~~~l~~P--v~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
+.++.++.+++.. -+.....++.....|++|.+++..- |+ .|||.+|..|...| +..||.|....+
T Consensus 1128 e~~~~~~~~i~~~es~~~y~~~~~~~~~c~ic~dil~~~~~I~--~cgh~~c~~c~~~~l~~~s~~~~~ksi~~ 1199 (1394)
T KOG0298|consen 1128 ESKADTPCKIAQTESDVRYLMNLSGHFVCEICLDILRNQGGIA--GCGHEPCCRCDELWLYASSRCPICKSIKG 1199 (1394)
T ss_pred HHhccCccccCCccchHHHHHHhhcccchHHHHHHHHhcCCee--eechhHhhhHHHHHHHHhccCcchhhhhh
Confidence 4455555554433 2345566777788999999999743 43 59999999999887 478999986543
No 133
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=50.73 E-value=1.2 Score=29.88 Aligned_cols=44 Identities=20% Similarity=0.527 Sum_probs=31.6
Q ss_pred CeeeeccccccCcCC-ccccc-CCceeccCcccccCCCCCCcccCC
Q 046177 55 ELLECPVCLNAMYPP-IHQCS-NGHTLCSGCKPRVHNRCPTCRHEL 98 (272)
Q Consensus 55 ~~l~CpiC~~~l~~P-v~qC~-cGH~~C~~C~~~~~~~CP~Cr~~~ 98 (272)
..+.|..|....... +.||. ||...|.+|+..---.|-.|..-+
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~Gii 51 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCKSCNGII 51 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhchh
Confidence 346788888765333 67998 999999999876435677775543
No 134
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=50.48 E-value=7.9 Score=21.47 Aligned_cols=7 Identities=43% Similarity=1.265 Sum_probs=3.3
Q ss_pred CCCCccc
Q 046177 90 RCPTCRH 96 (272)
Q Consensus 90 ~CP~Cr~ 96 (272)
.||.|..
T Consensus 15 fC~~CG~ 21 (23)
T PF13240_consen 15 FCPNCGT 21 (23)
T ss_pred chhhhCC
Confidence 4555544
No 135
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=49.94 E-value=9.1 Score=36.44 Aligned_cols=71 Identities=17% Similarity=0.307 Sum_probs=41.7
Q ss_pred CcCCCCCCchhhhhhhcCCCCCccccccCC-------CcccccCCCCeeeeccccccCcCC--cccccCCceeccCcccc
Q 046177 16 EVIDPPESEDLVEIVSESSVNDPAQIALKP-------NLTVSSSVRELLECPVCLNAMYPP--IHQCSNGHTLCSGCKPR 86 (272)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~l~CpiC~~~l~~P--v~qC~cGH~~C~~C~~~ 86 (272)
+-.++-.++.++++|-+..+....-.-.++ +....+......+||||+.+.-.. ..-| |...+|+.|+..
T Consensus 27 qgvy~~~d~~~s~~vRkl~~es~l~p~y~G~d~~~~ts~Hlls~~rr~~ecpicflyyps~~n~~rc-C~~~Ic~ecf~~ 105 (482)
T KOG2789|consen 27 QGVYKQYDEEASSRVRKLRTESLLNPIYNGNDARTKTSSHLLSTSRRKTECPICFLYYPSAKNLVRC-CSETICGECFAP 105 (482)
T ss_pred cceeecCcHHHHHHHHHHHHHHhhccccCCcccccccccchhhhccccccCceeeeecccccchhhh-hccchhhhheec
Confidence 334445667777777665543322211111 122233334567899999876443 2344 889999999988
Q ss_pred c
Q 046177 87 V 87 (272)
Q Consensus 87 ~ 87 (272)
.
T Consensus 106 ~ 106 (482)
T KOG2789|consen 106 F 106 (482)
T ss_pred c
Confidence 6
No 136
>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=49.38 E-value=12 Score=34.52 Aligned_cols=42 Identities=24% Similarity=0.545 Sum_probs=28.5
Q ss_pred CeeeeccccccCcCCcccc---cCC--ceeccCcccccC---CCCCCccc
Q 046177 55 ELLECPVCLNAMYPPIHQC---SNG--HTLCSGCKPRVH---NRCPTCRH 96 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC---~cG--H~~C~~C~~~~~---~~CP~Cr~ 96 (272)
..-.||||.....--+..= ..| +..|+-|-..|. ..||.|..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEE 232 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 3458999999754332221 244 678999999983 67888865
No 137
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=48.80 E-value=13 Score=27.18 Aligned_cols=35 Identities=26% Similarity=0.527 Sum_probs=19.6
Q ss_pred HhhhhcCCCccccCCCCCCCCcccc-ChhHHHHHhhhc-CC
Q 046177 134 LKHESQCIFRPYNCPYAGSECTVMG-DIPYLVAHLKDD-HK 172 (272)
Q Consensus 134 ~~He~~C~~~~~~CP~~~~~C~~~g-~~~~l~~Hl~~~-H~ 172 (272)
..+...-......|+. |+... +...|..|++.. |.
T Consensus 40 ~~~~~~~~~~~~~C~~----C~~~f~s~~~l~~Hm~~~~H~ 76 (100)
T PF12756_consen 40 LNYLRKKVKESFRCPY----CNKTFRSREALQEHMRSKHHK 76 (100)
T ss_dssp ---------SSEEBSS----SS-EESSHHHHHHHHHHTTTT
T ss_pred ccccccccCCCCCCCc----cCCCCcCHHHHHHHHcCccCC
Confidence 3444444444788987 77666 778999999976 54
No 138
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.49 E-value=14 Score=38.32 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=5.3
Q ss_pred CCCCcccCCC
Q 046177 90 RCPTCRHELG 99 (272)
Q Consensus 90 ~CP~Cr~~~~ 99 (272)
.||.|..+++
T Consensus 446 ~Cp~Cd~~lt 455 (730)
T COG1198 446 ECPNCDSPLT 455 (730)
T ss_pred cCCCCCcceE
Confidence 4555555544
No 139
>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=47.43 E-value=9.5 Score=25.41 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=20.6
Q ss_pred eeccccccCcC--Cccccc-CCceeccCccccc
Q 046177 58 ECPVCLNAMYP--PIHQCS-NGHTLCSGCKPRV 87 (272)
Q Consensus 58 ~CpiC~~~l~~--Pv~qC~-cGH~~C~~C~~~~ 87 (272)
.|++|...|.. .-..|. ||++||..|....
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence 57788765532 234676 9999999997654
No 140
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=46.97 E-value=2.8 Score=30.57 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=19.8
Q ss_pred cCCceeccCccccc------CCCCCCcccCCC
Q 046177 74 SNGHTLCSGCKPRV------HNRCPTCRHELG 99 (272)
Q Consensus 74 ~cGH~~C~~C~~~~------~~~CP~Cr~~~~ 99 (272)
.|-|.|=..|+.+| +..||.||+...
T Consensus 50 ~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~ 81 (84)
T KOG1493|consen 50 YCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ 81 (84)
T ss_pred HHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence 36677777888887 368999998653
No 141
>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 PHA00616 hypothetical protein
Probab=46.26 E-value=30 Score=22.52 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=21.1
Q ss_pred cccCCCCCCCCcccc-ChhHHHHHhhhcCCCC
Q 046177 144 PYNCPYAGSECTVMG-DIPYLVAHLKDDHKVD 174 (272)
Q Consensus 144 ~~~CP~~~~~C~~~g-~~~~l~~Hl~~~H~~~ 174 (272)
|+.||. |+... ..++|..|+...|..+
T Consensus 1 pYqC~~----CG~~F~~~s~l~~H~r~~hg~~ 28 (44)
T PHA00616 1 MYQCLR----CGGIFRKKKEVIEHLLSVHKQN 28 (44)
T ss_pred CCccch----hhHHHhhHHHHHHHHHHhcCCC
Confidence 467876 77666 5679999999999864
No 143
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.86 E-value=7.1 Score=33.17 Aligned_cols=25 Identities=20% Similarity=0.546 Sum_probs=17.1
Q ss_pred CCceeccCccccc--------------CCCCCCcccCCC
Q 046177 75 NGHTLCSGCKPRV--------------HNRCPTCRHELG 99 (272)
Q Consensus 75 cGH~~C~~C~~~~--------------~~~CP~Cr~~~~ 99 (272)
||..|=.-|+..| -+.||.|..++.
T Consensus 190 CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 190 CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 6666656677776 156888888764
No 144
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.45 E-value=7.9 Score=36.93 Aligned_cols=33 Identities=24% Similarity=0.533 Sum_probs=23.9
Q ss_pred CeeeeccccccCcCC----cccccCCceeccCccccc
Q 046177 55 ELLECPVCLNAMYPP----IHQCSNGHTLCSGCKPRV 87 (272)
Q Consensus 55 ~~l~CpiC~~~l~~P----v~qC~cGH~~C~~C~~~~ 87 (272)
.-..||.|.-.+.-- .++|.|||-||..|...|
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~ 341 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDW 341 (384)
T ss_pred hcCcCcccceeeeecCCcceEEeeccccchhhcCcch
Confidence 346799998876321 347888888888888666
No 145
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=44.95 E-value=12 Score=19.92 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=13.9
Q ss_pred cCCCCCCCCcccc-ChhHHHHHhhh
Q 046177 146 NCPYAGSECTVMG-DIPYLVAHLKD 169 (272)
Q Consensus 146 ~CP~~~~~C~~~g-~~~~l~~Hl~~ 169 (272)
.||. |+... ....|..|++.
T Consensus 2 ~C~~----C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPI----CGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETT----TTEEESSHHHHHHHHHH
T ss_pred CCCC----CCCccCCHHHHHHHHhH
Confidence 5664 77766 45688888775
No 146
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=44.85 E-value=12 Score=36.81 Aligned_cols=45 Identities=29% Similarity=0.617 Sum_probs=27.2
Q ss_pred CCCeeeeccccccCcCCcccccC---CceeccCccccc------------C---CCCCCcccCCCc
Q 046177 53 VRELLECPVCLNAMYPPIHQCSN---GHTLCSGCKPRV------------H---NRCPTCRHELGN 100 (272)
Q Consensus 53 ~~~~l~CpiC~~~l~~Pv~qC~c---GH~~C~~C~~~~------------~---~~CP~Cr~~~~~ 100 (272)
+.++|-|..|..+-- |. |.. .-.||..|+..+ . ..||.|..++..
T Consensus 2 l~~L~fC~~C~~irc-~~--c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 2 LEELYFCEHCHKIRC-PR--CVSEEIDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred cccceecccccccCC-hh--hcccccceeECccccccCChhhheeccceeccccccCCCCCCccee
Confidence 456677887777543 31 221 245777776554 0 469999888753
No 147
>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=44.54 E-value=17 Score=21.78 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=6.6
Q ss_pred CCCCCcccC
Q 046177 89 NRCPTCRHE 97 (272)
Q Consensus 89 ~~CP~Cr~~ 97 (272)
..||.|..+
T Consensus 18 ~~CP~Cg~~ 26 (33)
T cd00350 18 WVCPVCGAP 26 (33)
T ss_pred CcCcCCCCc
Confidence 479999764
No 148
>PLN02189 cellulose synthase
Probab=43.82 E-value=13 Score=39.67 Aligned_cols=42 Identities=21% Similarity=0.656 Sum_probs=33.5
Q ss_pred eeccccccCc-----CCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 58 ECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.|.||.+-+- .|..-|. ||--+|+.|.+-- .+.||.|++...
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~ 87 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK 87 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence 7999999754 4656787 9999999998654 478999998764
No 149
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=41.47 E-value=9.8 Score=23.18 Aligned_cols=18 Identities=17% Similarity=0.244 Sum_probs=9.8
Q ss_pred CCceeccCcHHhhhhcCC
Q 046177 124 CMGIYPYYSKLKHESQCI 141 (272)
Q Consensus 124 C~~~~~~~~~~~He~~C~ 141 (272)
|.-.+.-..+..|++.|.
T Consensus 10 C~R~v~a~RfA~HLekCm 27 (33)
T PF08209_consen 10 CGRPVAASRFAPHLEKCM 27 (33)
T ss_dssp TSSEEEGGGHHHHHHHHT
T ss_pred CcCCcchhhhHHHHHHHH
Confidence 555555555555555553
No 150
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=41.21 E-value=12 Score=29.19 Aligned_cols=13 Identities=31% Similarity=1.020 Sum_probs=11.1
Q ss_pred cccccCCceeccC
Q 046177 70 IHQCSNGHTLCSG 82 (272)
Q Consensus 70 v~qC~cGH~~C~~ 82 (272)
+.+|.|||.||..
T Consensus 24 ~vkc~CGh~f~d~ 36 (112)
T PF08882_consen 24 VVKCDCGHEFCDA 36 (112)
T ss_pred eeeccCCCeecCh
Confidence 6799999999864
No 151
>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=40.70 E-value=3.8 Score=36.38 Aligned_cols=43 Identities=33% Similarity=0.731 Sum_probs=29.7
Q ss_pred eeeecccccc-CcCC-c--cccc-CCceeccCccccc----CCCCC--CcccCC
Q 046177 56 LLECPVCLNA-MYPP-I--HQCS-NGHTLCSGCKPRV----HNRCP--TCRHEL 98 (272)
Q Consensus 56 ~l~CpiC~~~-l~~P-v--~qC~-cGH~~C~~C~~~~----~~~CP--~Cr~~~ 98 (272)
+-.||+|..- ...| + +.-+ |=|..|.+|..++ ...|| -|..-+
T Consensus 10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 3479999863 3344 2 2223 8899999999987 36899 576543
No 152
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=40.57 E-value=13 Score=36.12 Aligned_cols=24 Identities=25% Similarity=0.681 Sum_probs=16.4
Q ss_pred Cccccc-CCceeccCcccccCCCCCCcccC
Q 046177 69 PIHQCS-NGHTLCSGCKPRVHNRCPTCRHE 97 (272)
Q Consensus 69 Pv~qC~-cGH~~C~~C~~~~~~~CP~Cr~~ 97 (272)
+.|+|+ ||+.. .+|..+||.|+.-
T Consensus 6 ~~y~C~~Cg~~~-----~~~~g~Cp~C~~w 30 (454)
T TIGR00416 6 SKFVCQHCGADS-----PKWQGKCPACHAW 30 (454)
T ss_pred CeEECCcCCCCC-----ccccEECcCCCCc
Confidence 456776 66653 5667889999764
No 153
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.04 E-value=11 Score=30.34 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=15.3
Q ss_pred cccccCcCCcccccCCceeccC
Q 046177 61 VCLNAMYPPIHQCSNGHTLCSG 82 (272)
Q Consensus 61 iC~~~l~~Pv~qC~cGH~~C~~ 82 (272)
||...-.. |..|.|||.||..
T Consensus 62 i~qs~~~r-v~rcecghsf~d~ 82 (165)
T COG4647 62 ICQSAQKR-VIRCECGHSFGDY 82 (165)
T ss_pred EEeccccc-EEEEeccccccCh
Confidence 45665555 6789999999764
No 154
>smart00301 DM Doublesex DNA-binding motif.
Probab=39.59 E-value=17 Score=24.79 Aligned_cols=39 Identities=26% Similarity=0.428 Sum_probs=29.8
Q ss_pred CCceeccCcHHhhhhcCCCccccCCCCCCCCccccChhHHHHH
Q 046177 124 CMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPYLVAH 166 (272)
Q Consensus 124 C~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~l~~H 166 (272)
|.-.+....++-|-..|+|+.+.|+. |..+..+..+...
T Consensus 8 CrnHg~~~~lKGHKr~C~~r~C~C~k----C~Li~~Rq~vma~ 46 (54)
T smart00301 8 CENHGVKVPLKGHKPECPFRDCECEK----CTLVEKRRALMAL 46 (54)
T ss_pred HhcCCCeeccCCcCCCCCCCCCcCCC----CcChHHHHHHHHH
Confidence 44445566778899999999999985 9888877766554
No 155
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=39.57 E-value=23 Score=31.75 Aligned_cols=91 Identities=21% Similarity=0.389 Sum_probs=47.1
Q ss_pred hhhhhCCCCcCCCCCCchhhhhhhcCCCCCccccccCCCccc----ccCCCCeeeeccccccCcCCcccccCCceeccCc
Q 046177 8 YDDLRNKPEVIDPPESEDLVEIVSESSVNDPAQIALKPNLTV----SSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGC 83 (272)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C 83 (272)
++..|+..+-.+.+.+.+...+-+..+..+.++.....--+. .-.....|-|..|..+-..-+-| .-.-.-|..|
T Consensus 60 ~~~~~~~~~~~~~~~d~dIq~va~~~~~lPLTe~Nlrm~d~a~~~~ip~~drqFaC~~Cd~~WwRrvp~-rKeVSRCr~C 138 (278)
T PF15135_consen 60 NKAKREDMKQNEMSADQDIQAVASKTSVLPLTEENLRMFDDAQENLIPSVDRQFACSSCDHMWWRRVPQ-RKEVSRCRKC 138 (278)
T ss_pred cchhhcccccccCCCcccHHHHHhhhccCCchHHHHHHhhhhhhccccccceeeeccccchHHHhccCc-cccccccccc
Confidence 333334444444444555555433344444444222211111 12234678999997764433333 3445567777
Q ss_pred cccc------------CCCCCCcccCCC
Q 046177 84 KPRV------------HNRCPTCRHELG 99 (272)
Q Consensus 84 ~~~~------------~~~CP~Cr~~~~ 99 (272)
..+. ...||.|+..+.
T Consensus 139 ~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 139 RKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccccCCCccccccceeeeecccccccch
Confidence 7663 257999988774
No 156
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=39.13 E-value=17 Score=38.94 Aligned_cols=42 Identities=21% Similarity=0.692 Sum_probs=33.1
Q ss_pred eeccccccCc-----CCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 58 ECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.|.||.+-+- +|..-|. ||--+|+.|.+-- .+.||.|++...
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 7999998753 4656776 9999999997543 478999998764
No 157
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=39.03 E-value=17 Score=26.23 Aligned_cols=45 Identities=16% Similarity=0.426 Sum_probs=27.6
Q ss_pred CCCCcccCCCcccchhHHHHhhhcCCCcccccCCCCceeccCcHHhh
Q 046177 90 RCPTCRHELGNIRCLALEKVAASLELPCKYQSYGCMGIYPYYSKLKH 136 (272)
Q Consensus 90 ~CP~Cr~~~~~~r~~~le~~~~~l~v~C~~~~~GC~~~~~~~~~~~H 136 (272)
.||.|+........+.+...+..+...|.|- .|...+...+-..|
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~--eCg~tF~t~es~s~ 47 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERYHQCQNV--NCSATFITYESVQR 47 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheeeeecCCC--CCCCEEEEEEEEEE
Confidence 6999988764344455555567777778874 35555554443333
No 158
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=38.99 E-value=3.1 Score=32.16 Aligned_cols=44 Identities=25% Similarity=0.514 Sum_probs=31.3
Q ss_pred CeeeeccccccCcCCccccc----------------CCceeccCccccc---CCCCCCcccCC
Q 046177 55 ELLECPVCLNAMYPPIHQCS----------------NGHTLCSGCKPRV---HNRCPTCRHEL 98 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC~----------------cGH~~C~~C~~~~---~~~CP~Cr~~~ 98 (272)
..-.|.||..-+.++-..|+ |.|.|=..|+.+| .+.||+|...-
T Consensus 45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW 107 (114)
T KOG2930|consen 45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW 107 (114)
T ss_pred eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence 44469999987766533442 5577777788888 47899997754
No 159
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.22 E-value=22 Score=32.94 Aligned_cols=42 Identities=26% Similarity=0.625 Sum_probs=28.5
Q ss_pred CeeeeccccccCcCCccc--ccCC--ceeccCcccccC---CCCCCccc
Q 046177 55 ELLECPVCLNAMYPPIHQ--CSNG--HTLCSGCKPRVH---NRCPTCRH 96 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~q--C~cG--H~~C~~C~~~~~---~~CP~Cr~ 96 (272)
..-.||||.....--+.. -.-| +..|+-|-..|. ..||.|..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence 456899999975332211 1244 578999999883 67988864
No 160
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.83 E-value=17 Score=35.27 Aligned_cols=24 Identities=29% Similarity=0.617 Sum_probs=16.0
Q ss_pred Cccccc-CCceeccCcccccCCCCCCcccC
Q 046177 69 PIHQCS-NGHTLCSGCKPRVHNRCPTCRHE 97 (272)
Q Consensus 69 Pv~qC~-cGH~~C~~C~~~~~~~CP~Cr~~ 97 (272)
+.|.|+ ||+.. .+|..+||.|+.-
T Consensus 6 ~~y~C~~Cg~~~-----~~~~g~Cp~C~~w 30 (446)
T PRK11823 6 TAYVCQECGAES-----PKWLGRCPECGAW 30 (446)
T ss_pred CeEECCcCCCCC-----cccCeeCcCCCCc
Confidence 456676 66653 5666789999763
No 161
>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=37.72 E-value=31 Score=19.62 Aligned_cols=21 Identities=24% Similarity=0.445 Sum_probs=16.6
Q ss_pred ccCCCCCCCCccccChhHHHHHhhh
Q 046177 145 YNCPYAGSECTVMGDIPYLVAHLKD 169 (272)
Q Consensus 145 ~~CP~~~~~C~~~g~~~~l~~Hl~~ 169 (272)
+.||. |.+..+...+-.|+..
T Consensus 2 v~CPi----C~~~v~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPV----CFREVPENLINSHLDS 22 (26)
T ss_pred CcCCC----CcCcccHHHHHHHHHH
Confidence 57886 8888888888888863
No 162
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=37.59 E-value=10 Score=22.57 Aligned_cols=20 Identities=40% Similarity=1.162 Sum_probs=9.8
Q ss_pred ceeccCccccc-------CCCCCCccc
Q 046177 77 HTLCSGCKPRV-------HNRCPTCRH 96 (272)
Q Consensus 77 H~~C~~C~~~~-------~~~CP~Cr~ 96 (272)
|.||..|-... ...||.|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 66777775554 245777754
No 163
>PLN02195 cellulose synthase A
Probab=36.71 E-value=22 Score=37.89 Aligned_cols=42 Identities=19% Similarity=0.473 Sum_probs=33.0
Q ss_pred eeccccccC-----cCCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 58 ECPVCLNAM-----YPPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 58 ~CpiC~~~l-----~~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.|.||.+-+ -+|..-|. ||--+|+.|.+-- .+.||.|++...
T Consensus 8 ~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 8 ICATCGEEVGVDSNGEAFVACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred cceecccccCcCCCCCeEEEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 699999854 35666776 9999999997543 478999998875
No 164
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=36.32 E-value=18 Score=20.49 Aligned_cols=7 Identities=43% Similarity=1.241 Sum_probs=3.3
Q ss_pred CCCCccc
Q 046177 90 RCPTCRH 96 (272)
Q Consensus 90 ~CP~Cr~ 96 (272)
.||.|..
T Consensus 18 fC~~CG~ 24 (26)
T PF13248_consen 18 FCPNCGA 24 (26)
T ss_pred cChhhCC
Confidence 4555543
No 165
>PHA03096 p28-like protein; Provisional
Probab=35.64 E-value=9.1 Score=35.02 Aligned_cols=40 Identities=20% Similarity=0.257 Sum_probs=27.5
Q ss_pred eeeccccccCcC-Ccc------cccCCceeccCccccc------CCCCCCccc
Q 046177 57 LECPVCLNAMYP-PIH------QCSNGHTLCSGCKPRV------HNRCPTCRH 96 (272)
Q Consensus 57 l~CpiC~~~l~~-Pv~------qC~cGH~~C~~C~~~~------~~~CP~Cr~ 96 (272)
-.|.||.+.... |.. .-.|.|.||..|+..| ...||.|+.
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 679999997642 111 1258999999999988 234655554
No 166
>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=35.50 E-value=10 Score=25.17 Aligned_cols=39 Identities=33% Similarity=0.801 Sum_probs=21.9
Q ss_pred eccccccCcCCcccccCCceeccCccccc---CCCCCCcccCCC
Q 046177 59 CPVCLNAMYPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
|--|--.-+. ...| ..|-.|-.|+..+ ...||.|..++.
T Consensus 5 CKsCWf~~k~-Li~C-~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 5 CKSCWFANKG-LIKC-SDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp --SS-S--SS-EEE--SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred ChhhhhcCCC-eeee-cchhHHHHHHHHHhccccCCCcccCcCc
Confidence 4444433333 3355 5799999998876 478999998875
No 167
>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=35.36 E-value=15 Score=24.29 Aligned_cols=32 Identities=19% Similarity=0.495 Sum_probs=21.9
Q ss_pred CeeeeccccccCcCCcccccCCceeccCcccc
Q 046177 55 ELLECPVCLNAMYPPIHQCSNGHTLCSGCKPR 86 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~ 86 (272)
+=|.|..|...|.+.-+.-..|..+|..|..+
T Consensus 25 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp TTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 45778888888876633325778888877643
No 168
>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=35.29 E-value=25 Score=27.55 Aligned_cols=41 Identities=20% Similarity=0.445 Sum_probs=24.6
Q ss_pred eeeeccccccCc---CCccccc-CCceeccCcccccC----CCCCCccc
Q 046177 56 LLECPVCLNAMY---PPIHQCS-NGHTLCSGCKPRVH----NRCPTCRH 96 (272)
Q Consensus 56 ~l~CpiC~~~l~---~Pv~qC~-cGH~~C~~C~~~~~----~~CP~Cr~ 96 (272)
.-.|.+|...+. .+-..|. |+|.+|+.|..... -.|..|..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 348999987642 2223566 99999999966531 23666643
No 169
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.24 E-value=17 Score=37.99 Aligned_cols=50 Identities=24% Similarity=0.582 Sum_probs=38.7
Q ss_pred cccCCCCeeeeccccccCcCCcccccCCceeccCcccccCCCCCCcccCC
Q 046177 49 VSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVHNRCPTCRHEL 98 (272)
Q Consensus 49 ~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~~~CP~Cr~~~ 98 (272)
....+...-.|..|...|.-|.+-=.|||.|=..|.++-...||.|+...
T Consensus 833 ~sa~i~q~skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 833 TSAQIFQVSKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPEL 882 (933)
T ss_pred cccceeeeeeecccCCccccceeeeecccHHHHHhhccCcccCCccchhh
Confidence 34445555689999999999954336999999999985557899998744
No 170
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=35.09 E-value=33 Score=20.81 Aligned_cols=9 Identities=33% Similarity=1.158 Sum_probs=6.6
Q ss_pred CCCCCcccC
Q 046177 89 NRCPTCRHE 97 (272)
Q Consensus 89 ~~CP~Cr~~ 97 (272)
..||.|..+
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 478888764
No 171
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.95 E-value=28 Score=21.41 Aligned_cols=13 Identities=23% Similarity=0.580 Sum_probs=8.6
Q ss_pred eeeccccccCcCC
Q 046177 57 LECPVCLNAMYPP 69 (272)
Q Consensus 57 l~CpiC~~~l~~P 69 (272)
+.||-|.-.+..|
T Consensus 3 i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 3 ITCPNCQAKYEID 15 (36)
T ss_pred EECCCCCCEEeCC
Confidence 5677777766544
No 172
>PRK00420 hypothetical protein; Validated
Probab=33.99 E-value=25 Score=27.67 Aligned_cols=25 Identities=24% Similarity=0.627 Sum_probs=16.3
Q ss_pred eeeccccccCcCCcccccCCceeccCccc
Q 046177 57 LECPVCLNAMYPPIHQCSNGHTLCSGCKP 85 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~ 85 (272)
-.||+|..+|..- ..|..+|..|-.
T Consensus 24 ~~CP~Cg~pLf~l----k~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFEL----KDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceec----CCCceECCCCCC
Confidence 4899999776432 466776555544
No 173
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=33.96 E-value=43 Score=25.69 Aligned_cols=35 Identities=20% Similarity=0.496 Sum_probs=20.3
Q ss_pred cccCCCCeeeeccccccC-cCCcccccCCceeccCcc
Q 046177 49 VSSSVRELLECPVCLNAM-YPPIHQCSNGHTLCSGCK 84 (272)
Q Consensus 49 ~~~~~~~~l~CpiC~~~l-~~Pv~qC~cGH~~C~~C~ 84 (272)
....+...+.||-|.+.. .-|+-. .-+|+.|..|-
T Consensus 14 ~k~klpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG 49 (99)
T PRK14892 14 PKPKLPKIFECPRCGKVSISVKIKK-NIAIITCGNCG 49 (99)
T ss_pred cccCCCcEeECCCCCCeEeeeecCC-CcceEECCCCC
Confidence 345667889999999632 223322 23566555553
No 174
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.79 E-value=31 Score=35.27 Aligned_cols=43 Identities=33% Similarity=0.723 Sum_probs=21.2
Q ss_pred eeeccccccCcCCccccc-CCce----eccCccccc---CCCCCCcccCCC
Q 046177 57 LECPVCLNAMYPPIHQCS-NGHT----LCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~-cGH~----~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
+.||-|.....+--..|. ||.. .|..|-... ...||.|..++.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCCCcccccccccCCccc
Confidence 357777765432222333 4432 455554443 145666665554
No 175
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.65 E-value=18 Score=33.56 Aligned_cols=43 Identities=26% Similarity=0.580 Sum_probs=29.7
Q ss_pred CCCCeeeeccccccC---cCCcccccCCceeccCccccc------CCCCCCcc
Q 046177 52 SVRELLECPVCLNAM---YPPIHQCSNGHTLCSGCKPRV------HNRCPTCR 95 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l---~~Pv~qC~cGH~~C~~C~~~~------~~~CP~Cr 95 (272)
.....|.|||=.+.- .+|+.. .|||++=..-..++ ..+||.|-
T Consensus 332 hfHs~FiCPVlKe~~t~ENpP~ml-~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 332 HFHSLFICPVLKELCTDENPPVML-ECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred cccceeeccccHhhhcccCCCeee-eccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 557889999977765 467755 79999866555544 14577763
No 176
>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=32.75 E-value=7.7 Score=31.42 Aligned_cols=31 Identities=23% Similarity=0.739 Sum_probs=24.0
Q ss_pred eeeeccccccCcC--C-cccccCC------ceeccCccccc
Q 046177 56 LLECPVCLNAMYP--P-IHQCSNG------HTLCSGCKPRV 87 (272)
Q Consensus 56 ~l~CpiC~~~l~~--P-v~qC~cG------H~~C~~C~~~~ 87 (272)
..+|.||++-+.. = |.. ++| |.||..|..+|
T Consensus 26 ~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 26 TVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred CeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHH
Confidence 6899999998876 2 222 344 78999999999
No 177
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=32.61 E-value=24 Score=28.54 Aligned_cols=23 Identities=26% Similarity=0.842 Sum_probs=17.8
Q ss_pred eeeccccccCcCCcccccCCceeccCcc
Q 046177 57 LECPVCLNAMYPPIHQCSNGHTLCSGCK 84 (272)
Q Consensus 57 l~CpiC~~~l~~Pv~qC~cGH~~C~~C~ 84 (272)
.+||.|..+| |. ..|-+||..|-
T Consensus 29 ~hCp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcc----ee-eCCeEECCCCC
Confidence 4799999865 56 78888877765
No 178
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=32.30 E-value=32 Score=32.05 Aligned_cols=43 Identities=30% Similarity=0.841 Sum_probs=33.7
Q ss_pred eeeccccccC---cCCcccccCCceeccCccccc---CCCCCCcccCCC
Q 046177 57 LECPVCLNAM---YPPIHQCSNGHTLCSGCKPRV---HNRCPTCRHELG 99 (272)
Q Consensus 57 l~CpiC~~~l---~~Pv~qC~cGH~~C~~C~~~~---~~~CP~Cr~~~~ 99 (272)
-.||+|.+++ ..+..-|+||+..|-.|.... ...||.||.+..
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 4699999977 234456889999999998776 478999997653
No 179
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=31.37 E-value=22 Score=33.79 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=9.8
Q ss_pred cccCCCCCCcccC
Q 046177 85 PRVHNRCPTCRHE 97 (272)
Q Consensus 85 ~~~~~~CP~Cr~~ 97 (272)
.+|..+||.|+.-
T Consensus 11 ~~~~g~cp~c~~w 23 (372)
T cd01121 11 PKWLGKCPECGEW 23 (372)
T ss_pred CCccEECcCCCCc
Confidence 5667889999763
No 180
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.31 E-value=29 Score=31.23 Aligned_cols=49 Identities=18% Similarity=0.350 Sum_probs=37.2
Q ss_pred cCCCCeeeeccccccCcCCcccc---cCCceeccCcccccC-CCCCCcccCCC
Q 046177 51 SSVRELLECPVCLNAMYPPIHQC---SNGHTLCSGCKPRVH-NRCPTCRHELG 99 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~~Pv~qC---~cGH~~C~~C~~~~~-~~CP~Cr~~~~ 99 (272)
+.....|.|||=...|..-...| .|||+|=.+-+.+++ ..|+.|..++.
T Consensus 106 D~~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeikas~C~~C~a~y~ 158 (293)
T KOG3113|consen 106 DTQRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIKASVCHVCGAAYQ 158 (293)
T ss_pred ccccceeecccccceecceEEEEEEeccceeccHHHHHHhhhccccccCCccc
Confidence 33467899999999987763323 499999777777664 68999999875
No 181
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=30.89 E-value=28 Score=26.57 Aligned_cols=23 Identities=22% Similarity=0.781 Sum_probs=15.3
Q ss_pred eeccCccccc-------CCCCCCcccCCCc
Q 046177 78 TLCSGCKPRV-------HNRCPTCRHELGN 100 (272)
Q Consensus 78 ~~C~~C~~~~-------~~~CP~Cr~~~~~ 100 (272)
+.|+.|+..+ ...||.|+.++.+
T Consensus 63 iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp 92 (105)
T COG4357 63 IICGVCRKLLTRAEYGMCGSCPYCQSPFNP 92 (105)
T ss_pred EEhhhhhhhhhHHHHhhcCCCCCcCCCCCc
Confidence 4566665554 2579999988853
No 182
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=30.46 E-value=30 Score=28.53 Aligned_cols=22 Identities=32% Similarity=0.765 Sum_probs=15.5
Q ss_pred ccccCCceeccCccccc--------------CCCCCCcccC
Q 046177 71 HQCSNGHTLCSGCKPRV--------------HNRCPTCRHE 97 (272)
Q Consensus 71 ~qC~cGH~~C~~C~~~~--------------~~~CP~Cr~~ 97 (272)
++|.+||.| +.| .-.||.|...
T Consensus 6 L~C~~gH~F-----EgWF~ss~~fd~Q~~~glv~CP~Cgs~ 41 (148)
T PF06676_consen 6 LRCENGHEF-----EGWFRSSAAFDRQQARGLVSCPVCGST 41 (148)
T ss_pred EecCCCCcc-----ceecCCHHHHHHHHHcCCccCCCCCCC
Confidence 478999998 555 1468888664
No 183
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=30.39 E-value=30 Score=22.74 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=10.7
Q ss_pred CCcccccCCCCeeeecccccc
Q 046177 45 PNLTVSSSVRELLECPVCLNA 65 (272)
Q Consensus 45 ~~~~~~~~~~~~l~CpiC~~~ 65 (272)
+++.| ++|.+.+.||+|...
T Consensus 24 pGt~F-~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 24 PGTPF-EDLPDDWVCPVCGAP 43 (47)
T ss_dssp TT--G-GGS-TT-B-TTTSSB
T ss_pred CCCCH-HHCCCCCcCcCCCCc
Confidence 33444 678899999999753
No 184
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=30.22 E-value=26 Score=31.50 Aligned_cols=43 Identities=21% Similarity=0.145 Sum_probs=37.1
Q ss_pred CCCceeccCcHHhhhhcCCCccccCCCCCCCCccccChhHHHHHhhh
Q 046177 123 GCMGIYPYYSKLKHESQCIFRPYNCPYAGSECTVMGDIPYLVAHLKD 169 (272)
Q Consensus 123 GC~~~~~~~~~~~He~~C~~~~~~CP~~~~~C~~~g~~~~l~~Hl~~ 169 (272)
-|++.++-..++.|...|.-.-++|-. |+-...+.++..|..-
T Consensus 8 vCgEsvKKp~vekH~srCrn~~fSCID----C~k~F~~~sYknH~kC 50 (276)
T KOG2186|consen 8 VCGESVKKPQVEKHMSRCRNAYFSCID----CGKTFERVSYKNHTKC 50 (276)
T ss_pred hhhhhccccchHHHHHhccCCeeEEee----cccccccchhhhhhhh
Confidence 499999999999999999999999975 8887777888888653
No 185
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.89 E-value=13 Score=34.16 Aligned_cols=27 Identities=30% Similarity=0.865 Sum_probs=19.5
Q ss_pred ccCCceeccCccccc----------------CCCCCCcccCCC
Q 046177 73 CSNGHTLCSGCKPRV----------------HNRCPTCRHELG 99 (272)
Q Consensus 73 C~cGH~~C~~C~~~~----------------~~~CP~Cr~~~~ 99 (272)
|-|.-..|.+|+.+| +.+||+||..+.
T Consensus 323 c~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc 365 (381)
T KOG3899|consen 323 CICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC 365 (381)
T ss_pred cccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence 446666777888776 357999998763
No 186
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=29.03 E-value=30 Score=37.08 Aligned_cols=44 Identities=25% Similarity=0.655 Sum_probs=33.6
Q ss_pred eeeeccccccCc-----CCccccc-CCceeccCccccc----CCCCCCcccCCC
Q 046177 56 LLECPVCLNAMY-----PPIHQCS-NGHTLCSGCKPRV----HNRCPTCRHELG 99 (272)
Q Consensus 56 ~l~CpiC~~~l~-----~Pv~qC~-cGH~~C~~C~~~~----~~~CP~Cr~~~~ 99 (272)
.-.|.||.+-+- +|..-|. ||--+|+.|.+-- ...||.|++...
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 347999998753 4656776 9999999998543 478999998764
No 187
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc-finger domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=28.59 E-value=38 Score=20.19 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=12.7
Q ss_pred ccCCCCCCCCccccChhHHHHHhhh
Q 046177 145 YNCPYAGSECTVMGDIPYLVAHLKD 169 (272)
Q Consensus 145 ~~CP~~~~~C~~~g~~~~l~~Hl~~ 169 (272)
++||..+ |...........|+.+
T Consensus 3 vrCPvkd--C~EEv~lgKY~~H~ss 25 (30)
T PF10426_consen 3 VRCPVKD--CDEEVSLGKYSHHLSS 25 (30)
T ss_dssp EE--STT-----EEEHHHHHHHHHT
T ss_pred ccccccc--Ccchhhhhhhcccccc
Confidence 5788754 8888877777777764
No 188
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.16 E-value=37 Score=28.58 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=7.4
Q ss_pred eeeeccccccC
Q 046177 56 LLECPVCLNAM 66 (272)
Q Consensus 56 ~l~CpiC~~~l 66 (272)
.+.|++|..+.
T Consensus 134 ~~vC~vCGy~~ 144 (166)
T COG1592 134 VWVCPVCGYTH 144 (166)
T ss_pred EEEcCCCCCcc
Confidence 67788775544
No 189
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=28.09 E-value=46 Score=27.54 Aligned_cols=16 Identities=25% Similarity=0.582 Sum_probs=11.4
Q ss_pred CCCCCCcccCCCcccc
Q 046177 88 HNRCPTCRHELGNIRC 103 (272)
Q Consensus 88 ~~~CP~Cr~~~~~~r~ 103 (272)
...||.|...+...-|
T Consensus 128 ~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 128 NFTCPRCGAMLDYLDN 143 (158)
T ss_pred CCcCCCCCCEeeeccC
Confidence 3689999888765444
No 190
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=27.75 E-value=26 Score=26.71 Aligned_cols=40 Identities=30% Similarity=0.728 Sum_probs=14.6
Q ss_pred eeccccccCc--CC-cccccCCceeccCccccc-------CCCCCCcccCC
Q 046177 58 ECPVCLNAMY--PP-IHQCSNGHTLCSGCKPRV-------HNRCPTCRHEL 98 (272)
Q Consensus 58 ~CpiC~~~l~--~P-v~qC~cGH~~C~~C~~~~-------~~~CP~Cr~~~ 98 (272)
.|++|...+. ++ +.+|..||.+ .+|.... ...|+.|....
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~GH~w-~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCENGHVW-PRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TTS-EE-EB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCCCCEE-eeeeeeeeeeccCCeeEcCCCCCEE
Confidence 6999999763 44 5689999996 5554432 15799998754
No 191
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=27.66 E-value=12 Score=35.95 Aligned_cols=49 Identities=22% Similarity=0.422 Sum_probs=32.4
Q ss_pred cccccCCCCeeeeccccccCcCCcccccCCceeccCcccccCCCCCCcccCCC
Q 046177 47 LTVSSSVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVHNRCPTCRHELG 99 (272)
Q Consensus 47 ~~~~~~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~~~CP~Cr~~~~ 99 (272)
+....+..-++.|..|...+.+|...-+ |. | .||..+..+||.|...++
T Consensus 258 l~~i~n~iGdyiCqLCK~kYeD~F~LAQ--Hr-C-~RIV~vEYrCPEC~KVFs 306 (500)
T KOG3993|consen 258 LAGIPNVIGDYICQLCKEKYEDAFALAQ--HR-C-PRIVHVEYRCPECDKVFS 306 (500)
T ss_pred hccCcccHHHHHHHHHHHhhhhHHHHhh--cc-C-CeeEEeeecCCccccccc
Confidence 3445677788999999999999954321 21 1 133344467888877664
No 192
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.35 E-value=18 Score=34.41 Aligned_cols=37 Identities=32% Similarity=0.846 Sum_probs=27.2
Q ss_pred eeeccccccCcC------CcccccCCceeccCccccc-----C-CCCCCccc
Q 046177 57 LECPVCLNAMYP------PIHQCSNGHTLCSGCKPRV-----H-NRCPTCRH 96 (272)
Q Consensus 57 l~CpiC~~~l~~------Pv~qC~cGH~~C~~C~~~~-----~-~~CP~Cr~ 96 (272)
-.|.||-+ +++ || -.|||+|=..|...| . ..||.|+-
T Consensus 5 A~C~Ic~d-~~p~~~~l~~i--~~cGhifh~~cl~qwfe~~Ps~R~cpic~i 53 (465)
T KOG0827|consen 5 AECHICID-GRPNDHELGPI--GTCGHIFHTTCLTQWFEGDPSNRGCPICQI 53 (465)
T ss_pred ceeeEecc-CCccccccccc--cchhhHHHHHHHHHHHccCCccCCCCceee
Confidence 47999954 333 33 149999999999998 2 47999983
No 193
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=27.20 E-value=46 Score=18.30 Aligned_cols=24 Identities=17% Similarity=0.373 Sum_probs=16.2
Q ss_pred ccCCCCCCCCcccc-ChhHHHHHhhhcCC
Q 046177 145 YNCPYAGSECTVMG-DIPYLVAHLKDDHK 172 (272)
Q Consensus 145 ~~CP~~~~~C~~~g-~~~~l~~Hl~~~H~ 172 (272)
+.|.. |+... ....|..|.+..|+
T Consensus 2 ~~C~~----C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDE----CGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETT----TTEEESSHHHHHHHHCTTTT
T ss_pred CCCCc----cCCccCChhHHHHHhHHhcC
Confidence 45654 66655 56789999876653
No 194
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=27.02 E-value=28 Score=30.82 Aligned_cols=16 Identities=31% Similarity=0.742 Sum_probs=12.4
Q ss_pred CeeeeccccccCcCCc
Q 046177 55 ELLECPVCLNAMYPPI 70 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv 70 (272)
--|.|+||+.++.+|+
T Consensus 259 ~GfvCsVCLsvfc~p~ 274 (296)
T COG5242 259 LGFVCSVCLSVFCRPV 274 (296)
T ss_pred EeeehhhhheeecCCc
Confidence 3478999999887775
No 195
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=27.01 E-value=60 Score=28.42 Aligned_cols=109 Identities=20% Similarity=0.333 Sum_probs=61.2
Q ss_pred CCCCeeeeccccccCcCCcccccCCceeccCcccccCCCCCCcccCCCcccchhHHHHhh----hcCCCcccccCCCCce
Q 046177 52 SVRELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVHNRCPTCRHELGNIRCLALEKVAA----SLELPCKYQSYGCMGI 127 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~~~CP~Cr~~~~~~r~~~le~~~~----~l~v~C~~~~~GC~~~ 127 (272)
...+.+.|-||..-+.-... -+.|+-|.+=+.+. .|..|...+... ..+.+-+. --++.|. -|...
T Consensus 113 sd~d~ftCrvCgK~F~lQRm--lnrh~kch~~vkr~--lct~cgkgfndt--fdlkrh~rthtgvrpykc~----~c~ka 182 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRM--LNRHLKCHSDVKRH--LCTFCGKGFNDT--FDLKRHTRTHTGVRPYKCS----LCEKA 182 (267)
T ss_pred CCCCeeeeehhhhhhhHHHH--HHHHhhhccHHHHH--HHhhccCcccch--hhhhhhhccccCccccchh----hhhHH
Confidence 34688999999988754322 26677766655553 577787766431 22222222 2233443 35554
Q ss_pred eccC-cHHhhhhcC-----C-------CccccCCCCCCCCccccC-hhHHHHHhhhcCCCC
Q 046177 128 YPYY-SKLKHESQC-----I-------FRPYNCPYAGSECTVMGD-IPYLVAHLKDDHKVD 174 (272)
Q Consensus 128 ~~~~-~~~~He~~C-----~-------~~~~~CP~~~~~C~~~g~-~~~l~~Hl~~~H~~~ 174 (272)
++.. .++.|.+.= . -..+-|- .|++.+. .+.+..|+...|...
T Consensus 183 ftqrcsleshl~kvhgv~~~yaykerr~kl~vce----dcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 183 FTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCE----DCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred HHhhccHHHHHHHHcCchHHHHHHHhhhheeeec----ccCCCCCChhHHHHHHHhcCCCC
Confidence 4432 355554311 1 1234564 3777774 457788999888753
No 196
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=26.41 E-value=47 Score=21.21 Aligned_cols=22 Identities=27% Similarity=0.842 Sum_probs=15.0
Q ss_pred eeccccccCcCCcccccCCceeccCc
Q 046177 58 ECPVCLNAMYPPIHQCSNGHTLCSGC 83 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~qC~cGH~~C~~C 83 (272)
.||.|..+| ++=..|.++|-.|
T Consensus 19 ~Cp~C~~PL----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL----MRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCee----EEecCCCEECCCC
Confidence 699996544 3324778888776
No 197
>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=26.32 E-value=47 Score=24.96 Aligned_cols=12 Identities=25% Similarity=0.689 Sum_probs=9.2
Q ss_pred CCCCCCcccCCC
Q 046177 88 HNRCPTCRHELG 99 (272)
Q Consensus 88 ~~~CP~Cr~~~~ 99 (272)
+++|..|+++++
T Consensus 58 rGrCr~C~~~I~ 69 (92)
T PF06750_consen 58 RGRCRYCGAPIP 69 (92)
T ss_pred CCCCcccCCCCC
Confidence 478888888775
No 198
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=25.98 E-value=23 Score=37.14 Aligned_cols=43 Identities=28% Similarity=0.752 Sum_probs=0.0
Q ss_pred CeeeeccccccCcCCccccc-CCc-----eeccCccccc-CCCCCCcccCCC
Q 046177 55 ELLECPVCLNAMYPPIHQCS-NGH-----TLCSGCKPRV-HNRCPTCRHELG 99 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC~-cGH-----~~C~~C~~~~-~~~CP~Cr~~~~ 99 (272)
....||-|...-... .|+ ||- .+|..|...+ ...||.|.....
T Consensus 654 ~~r~Cp~Cg~~t~~~--~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~ 703 (900)
T PF03833_consen 654 GRRRCPKCGKETFYN--RCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETT 703 (900)
T ss_dssp ----------------------------------------------------
T ss_pred ecccCcccCCcchhh--cCcccCCccccceeccccccccCccccccccccCc
Confidence 456899999875443 585 883 4899998887 368999988754
No 199
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.68 E-value=65 Score=27.29 Aligned_cols=16 Identities=31% Similarity=0.615 Sum_probs=11.8
Q ss_pred CCCCCCcccCCCcccc
Q 046177 88 HNRCPTCRHELGNIRC 103 (272)
Q Consensus 88 ~~~CP~Cr~~~~~~r~ 103 (272)
...||.|...+...-|
T Consensus 136 ~F~Cp~Cg~~L~~~dn 151 (178)
T PRK06266 136 GFRCPQCGEMLEEYDN 151 (178)
T ss_pred CCcCCCCCCCCeeccc
Confidence 3689999998875433
No 200
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=25.59 E-value=53 Score=19.76 Aligned_cols=7 Identities=29% Similarity=0.705 Sum_probs=3.0
Q ss_pred ecccccc
Q 046177 59 CPVCLNA 65 (272)
Q Consensus 59 CpiC~~~ 65 (272)
|.-|...
T Consensus 3 C~~Cg~~ 9 (32)
T PF03604_consen 3 CGECGAE 9 (32)
T ss_dssp ESSSSSS
T ss_pred CCcCCCe
Confidence 4444443
No 201
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=25.03 E-value=38 Score=30.49 Aligned_cols=52 Identities=19% Similarity=0.504 Sum_probs=36.2
Q ss_pred cccccCC--CCeeeeccccccCcCCcccccCCceeccCcccccC-CCCCCcccCCC
Q 046177 47 LTVSSSV--RELLECPVCLNAMYPPIHQCSNGHTLCSGCKPRVH-NRCPTCRHELG 99 (272)
Q Consensus 47 ~~~~~~~--~~~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~~~~-~~CP~Cr~~~~ 99 (272)
+.+.++. ...+.|..|...|...-.. ..|-++|..|..+.. +.|-.||.+|.
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaRe-vk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDARE-VKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred ccccCCCCCccceecccccccccchhhh-hccceeccccccccCCcccccccCchH
Confidence 3444433 5678899999988766544 588999999998863 44555666664
No 202
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=24.79 E-value=50 Score=20.25 Aligned_cols=30 Identities=13% Similarity=0.372 Sum_probs=14.8
Q ss_pred eeeeccccccCcCCcccccCCceeccCccc
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCKP 85 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~~ 85 (272)
...|--|...+.+..+.-.-++.+|-.|+.
T Consensus 3 ~~~C~eC~~~f~dSyL~~~F~~~VCD~CRD 32 (34)
T PF01286_consen 3 YPKCDECGKPFMDSYLLNNFDLPVCDKCRD 32 (34)
T ss_dssp -EE-TTT--EES-SSCCCCTS-S--TTT-S
T ss_pred CchHhHhCCHHHHHHHHHhCCccccccccC
Confidence 457888888888775543577888888864
No 203
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.56 E-value=52 Score=20.79 Aligned_cols=8 Identities=38% Similarity=1.090 Sum_probs=6.2
Q ss_pred CCCCCccc
Q 046177 89 NRCPTCRH 96 (272)
Q Consensus 89 ~~CP~Cr~ 96 (272)
..||.|+.
T Consensus 27 ~~CP~Cg~ 34 (42)
T PF09723_consen 27 VPCPECGS 34 (42)
T ss_pred CcCCCCCC
Confidence 57888877
No 204
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.40 E-value=50 Score=32.64 Aligned_cols=22 Identities=32% Similarity=0.766 Sum_probs=15.8
Q ss_pred ceeccCcccccCCCCCCcccCCCc
Q 046177 77 HTLCSGCKPRVHNRCPTCRHELGN 100 (272)
Q Consensus 77 H~~C~~C~~~~~~~CP~Cr~~~~~ 100 (272)
.+.|.+|-... .||.|..++..
T Consensus 213 ~~~C~~Cg~~~--~C~~C~~~l~~ 234 (505)
T TIGR00595 213 NLLCRSCGYIL--CCPNCDVSLTY 234 (505)
T ss_pred eeEhhhCcCcc--CCCCCCCceEE
Confidence 45788886554 78888887765
No 205
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.27 E-value=72 Score=31.53 Aligned_cols=42 Identities=29% Similarity=0.643 Sum_probs=27.7
Q ss_pred CCeeeeccccccCcCCccccc--------CCceeccCccccc--CCCCCCcccC
Q 046177 54 RELLECPVCLNAMYPPIHQCS--------NGHTLCSGCKPRV--HNRCPTCRHE 97 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC~--------cGH~~C~~C~~~~--~~~CP~Cr~~ 97 (272)
...+.|..|..++.=|. |. -+...|..|-... ...||.|...
T Consensus 211 a~~~~C~~Cg~~~~C~~--C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 211 SKNLLCRSCGYILCCPN--CDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCeeEhhhCcCccCCCC--CCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 34567777777765542 32 2356799996654 3689999875
No 206
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.14 E-value=67 Score=19.73 Aligned_cols=13 Identities=31% Similarity=0.897 Sum_probs=9.5
Q ss_pred eeeccccccCcCC
Q 046177 57 LECPVCLNAMYPP 69 (272)
Q Consensus 57 l~CpiC~~~l~~P 69 (272)
..||.|.-.+..|
T Consensus 3 i~CP~C~~~f~v~ 15 (37)
T PF13719_consen 3 ITCPNCQTRFRVP 15 (37)
T ss_pred EECCCCCceEEcC
Confidence 5688888777665
No 207
>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=23.81 E-value=62 Score=18.83 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=12.6
Q ss_pred eeccccccCcCC-ccccc
Q 046177 58 ECPVCLNAMYPP-IHQCS 74 (272)
Q Consensus 58 ~CpiC~~~l~~P-v~qC~ 74 (272)
.|.+|.+.+... .|.|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~ 19 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCS 19 (30)
T ss_pred CCCCCCCCcCCCEeEEeC
Confidence 578888877777 77764
No 208
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=23.72 E-value=40 Score=26.03 Aligned_cols=29 Identities=24% Similarity=0.551 Sum_probs=15.7
Q ss_pred eeccccccCcCCcccc------c-C---CceeccCcccc
Q 046177 58 ECPVCLNAMYPPIHQC------S-N---GHTLCSGCKPR 86 (272)
Q Consensus 58 ~CpiC~~~l~~Pv~qC------~-c---GH~~C~~C~~~ 86 (272)
.|..|..--.+....| . | .-.||..|+..
T Consensus 9 ~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ 47 (105)
T PF10497_consen 9 TCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRN 47 (105)
T ss_pred CchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHH
Confidence 4666666444444444 1 3 45577777443
No 209
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.50 E-value=59 Score=21.02 Aligned_cols=11 Identities=45% Similarity=1.111 Sum_probs=7.9
Q ss_pred eccccccCcCC
Q 046177 59 CPVCLNAMYPP 69 (272)
Q Consensus 59 CpiC~~~l~~P 69 (272)
||-|..+|..+
T Consensus 3 Cp~Cg~~l~~~ 13 (52)
T smart00661 3 CPKCGNMLIPK 13 (52)
T ss_pred CCCCCCccccc
Confidence 77888777555
No 210
>PF12907 zf-met2: Zinc-binding
Probab=23.31 E-value=48 Score=21.09 Aligned_cols=17 Identities=24% Similarity=0.417 Sum_probs=13.9
Q ss_pred cChhHHHHHhhhcCCCC
Q 046177 158 GDIPYLVAHLKDDHKVD 174 (272)
Q Consensus 158 g~~~~l~~Hl~~~H~~~ 174 (272)
.+...|.+|.+++|.-.
T Consensus 15 ~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 15 TNEPQLKEHAENKHPKN 31 (40)
T ss_pred CCHHHHHHHHHccCCCC
Confidence 35689999999999753
No 211
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=23.09 E-value=27 Score=36.56 Aligned_cols=43 Identities=26% Similarity=0.681 Sum_probs=35.7
Q ss_pred CCeeeeccccccC--cCCccccc-CCceeccCccccc----------CCCCCCccc
Q 046177 54 RELLECPVCLNAM--YPPIHQCS-NGHTLCSGCKPRV----------HNRCPTCRH 96 (272)
Q Consensus 54 ~~~l~CpiC~~~l--~~Pv~qC~-cGH~~C~~C~~~~----------~~~CP~Cr~ 96 (272)
...++|-||.+-+ ..|+..|. |=|+|=-.||.+| ...||.|+.
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 5779999999988 46788887 8898888899998 257999984
No 212
>PHA00733 hypothetical protein
Probab=23.06 E-value=1.2e+02 Score=24.14 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=19.8
Q ss_pred cccCCCCCCCCcccc-ChhHHHHHhhhcCCC
Q 046177 144 PYNCPYAGSECTVMG-DIPYLVAHLKDDHKV 173 (272)
Q Consensus 144 ~~~CP~~~~~C~~~g-~~~~l~~Hl~~~H~~ 173 (272)
++.|+. |+... ....|..|....|.+
T Consensus 99 ~~~C~~----CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 99 SKVCPV----CGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CccCCC----CCCccCCHHHHHHHHHHhcCc
Confidence 467775 76664 557899999999985
No 213
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=22.33 E-value=45 Score=22.22 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=11.8
Q ss_pred cCCCCeeeeccccc
Q 046177 51 SSVRELLECPVCLN 64 (272)
Q Consensus 51 ~~~~~~l~CpiC~~ 64 (272)
+++.+.+.||+|..
T Consensus 29 ~~Lp~~w~CP~C~a 42 (50)
T cd00730 29 EDLPDDWVCPVCGA 42 (50)
T ss_pred hHCCCCCCCCCCCC
Confidence 56888999999975
No 214
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.18 E-value=40 Score=32.67 Aligned_cols=25 Identities=32% Similarity=0.890 Sum_probs=19.2
Q ss_pred ccccCCceeccCcccccC--CCCCCcc
Q 046177 71 HQCSNGHTLCSGCKPRVH--NRCPTCR 95 (272)
Q Consensus 71 ~qC~cGH~~C~~C~~~~~--~~CP~Cr 95 (272)
+.|.|||.||..|...++ ..|+...
T Consensus 180 v~C~~g~~FC~~C~~~~H~p~~C~~~~ 206 (444)
T KOG1815|consen 180 VDCGCGHEFCFACGEESHSPVSCPGAK 206 (444)
T ss_pred eeCCCCchhHhhccccccCCCcccchH
Confidence 489999999999998884 3454443
No 215
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.88 E-value=60 Score=33.20 Aligned_cols=22 Identities=27% Similarity=0.908 Sum_probs=12.3
Q ss_pred ceeccCcccccC-CCCCCcccCC
Q 046177 77 HTLCSGCKPRVH-NRCPTCRHEL 98 (272)
Q Consensus 77 H~~C~~C~~~~~-~~CP~Cr~~~ 98 (272)
..||..|-.++. ..||.|...+
T Consensus 15 akFC~~CG~~l~~~~Cp~CG~~~ 37 (645)
T PRK14559 15 NRFCQKCGTSLTHKPCPQCGTEV 37 (645)
T ss_pred CccccccCCCCCCCcCCCCCCCC
Confidence 446666655542 4566666554
No 216
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=21.71 E-value=49 Score=25.72 Aligned_cols=44 Identities=34% Similarity=0.699 Sum_probs=24.1
Q ss_pred ccccc-CCc--eeccCcccccCCCCCCcccCCCcccchhHHHHhhhcCCCcccc
Q 046177 70 IHQCS-NGH--TLCSGCKPRVHNRCPTCRHELGNIRCLALEKVAASLELPCKYQ 120 (272)
Q Consensus 70 v~qC~-cGH--~~C~~C~~~~~~~CP~Cr~~~~~~r~~~le~~~~~l~v~C~~~ 120 (272)
++.|+ ||| .+..+|..+ .||.|...-+ ..=++++.+.+ ++|+|.
T Consensus 42 ~~~C~~Cg~~~~~~~SCk~R---~CP~C~~~~~---~~W~~~~~~~l-l~~~y~ 88 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSCKNR---HCPSCQAKAT---EQWIEKQREDL-LPVPYF 88 (111)
T ss_pred eeecCCCCceEEecCcccCc---CCCCCCChHH---HHHHHHHHhhC-CCCCeE
Confidence 34555 665 467777766 4888865322 12233344333 667774
No 217
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=21.69 E-value=34 Score=31.70 Aligned_cols=9 Identities=22% Similarity=1.003 Sum_probs=4.5
Q ss_pred CCCCcccCC
Q 046177 90 RCPTCRHEL 98 (272)
Q Consensus 90 ~CP~Cr~~~ 98 (272)
.|+.|+..+
T Consensus 390 ~Ce~CK~~F 398 (421)
T COG5151 390 QCELCKSTF 398 (421)
T ss_pred echhhhhhh
Confidence 355555544
No 218
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=21.67 E-value=31 Score=35.98 Aligned_cols=32 Identities=19% Similarity=0.521 Sum_probs=26.5
Q ss_pred eeeeccccccCcCCccccc-CCceeccCccccc
Q 046177 56 LLECPVCLNAMYPPIHQCS-NGHTLCSGCKPRV 87 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~-cGH~~C~~C~~~~ 87 (272)
.-.|..|..-+..-...|+ ||+.+|-.|...|
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKW 261 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhc
Confidence 3479999998876556787 9999999999887
No 219
>PF01690 PLRV_ORF5: Potato leaf roll virus readthrough protein; InterPro: IPR002929 This family consists mainly of the Potato leafroll virus (PLrV) read through protein otherwise known as the minor capsid protein. This is generated via a readthrough of open reading frame 3, the coat protein, allowing transcription of open reading frame 5 to give an extended coat protein with a large C-terminal addition or read through domain []. The read through protein is essential for the circulative aphid transmission of PLrV [] and Beet western yellows virus []. The N-terminal region of the luteovirus readthrough domain determines virus binding to Buchnera GroEL and is essential for virus persistence in the aphid [].; GO: 0019028 viral capsid
Probab=21.56 E-value=2.7e+02 Score=27.32 Aligned_cols=34 Identities=18% Similarity=0.520 Sum_probs=27.4
Q ss_pred CCc-cCCCCcEEEEEEec-CCceEEEEeeccchhcc
Q 046177 233 GDD-NESKNYSYSLEVGG-NGRKMSWQGVPRSIRDS 266 (272)
Q Consensus 233 G~~-~~a~~f~Y~l~~~~-~~r~l~~~s~~~si~~~ 266 (272)
||+ ....+|.|-+.+.+ -.|.+.|-++..+|.|.
T Consensus 200 aPpi~K~~kYNY~VSYG~~Tdk~mE~G~IsV~~DE~ 235 (465)
T PF01690_consen 200 APPIQKTSKYNYVVSYGGYTDKDMEFGSISVSLDEH 235 (465)
T ss_pred cCCcccccccceEEEeccccccceeeeeEEEEEecc
Confidence 554 45679999999976 66899999999888775
No 220
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.24 E-value=22 Score=22.86 Aligned_cols=11 Identities=36% Similarity=0.812 Sum_probs=7.4
Q ss_pred CCCCCcccCCC
Q 046177 89 NRCPTCRHELG 99 (272)
Q Consensus 89 ~~CP~Cr~~~~ 99 (272)
..||.|..++.
T Consensus 22 ~~Cp~CG~~~~ 32 (46)
T PRK00398 22 VRCPYCGYRIL 32 (46)
T ss_pred eECCCCCCeEE
Confidence 36888877654
No 221
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=21.21 E-value=60 Score=22.29 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=12.3
Q ss_pred eccccccCcCCccccc-CCceeccC
Q 046177 59 CPVCLNAMYPPIHQCS-NGHTLCSG 82 (272)
Q Consensus 59 CpiC~~~l~~Pv~qC~-cGH~~C~~ 82 (272)
|.+|... ...+..|- ||+++|.+
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5566654 34455564 77777763
No 222
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.11 E-value=72 Score=32.74 Aligned_cols=41 Identities=24% Similarity=0.517 Sum_probs=24.7
Q ss_pred CeeeeccccccCcCCcccc--------cCCceeccCccccc--CCCCCCcccC
Q 046177 55 ELLECPVCLNAMYPPIHQC--------SNGHTLCSGCKPRV--HNRCPTCRHE 97 (272)
Q Consensus 55 ~~l~CpiC~~~l~~Pv~qC--------~cGH~~C~~C~~~~--~~~CP~Cr~~ 97 (272)
..+.|.-|..+++=|- | .-+...|..|-... ...||.|...
T Consensus 380 ~~~~C~~Cg~~~~C~~--C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 380 PFLLCRDCGWVAECPH--CDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CceEhhhCcCccCCCC--CCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 3455666665544331 2 23446788886654 3689999775
No 223
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=21.10 E-value=55 Score=30.56 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=6.7
Q ss_pred CCeeeecccccc
Q 046177 54 RELLECPVCLNA 65 (272)
Q Consensus 54 ~~~l~CpiC~~~ 65 (272)
..-+.||.|.--
T Consensus 274 ~~Gy~CP~Ckak 285 (378)
T KOG2807|consen 274 GGGYFCPQCKAK 285 (378)
T ss_pred cCceeCCcccCe
Confidence 344666666543
No 224
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=20.96 E-value=40 Score=20.82 Aligned_cols=25 Identities=28% Similarity=0.716 Sum_probs=15.5
Q ss_pred eeeeccccccCcCCcccccCCceeccCcc
Q 046177 56 LLECPVCLNAMYPPIHQCSNGHTLCSGCK 84 (272)
Q Consensus 56 ~l~CpiC~~~l~~Pv~qC~cGH~~C~~C~ 84 (272)
...|++|...+..+ .-|..+|..|-
T Consensus 8 ~~~C~~C~~~~~~~----~dG~~yC~~cG 32 (36)
T PF11781_consen 8 NEPCPVCGSRWFYS----DDGFYYCDRCG 32 (36)
T ss_pred CCcCCCCCCeEeEc----cCCEEEhhhCc
Confidence 34599999984322 45666666553
No 225
>PRK11827 hypothetical protein; Provisional
Probab=20.94 E-value=48 Score=23.04 Aligned_cols=17 Identities=29% Similarity=0.907 Sum_probs=13.5
Q ss_pred cCCCCeeeeccccccCc
Q 046177 51 SSVRELLECPVCLNAMY 67 (272)
Q Consensus 51 ~~~~~~l~CpiC~~~l~ 67 (272)
..+.+.|.||+|...|.
T Consensus 3 ~~LLeILaCP~ckg~L~ 19 (60)
T PRK11827 3 HRLLEIIACPVCNGKLW 19 (60)
T ss_pred hHHHhheECCCCCCcCe
Confidence 35678899999998775
No 226
>PF14353 CpXC: CpXC protein
Probab=20.67 E-value=66 Score=25.28 Aligned_cols=10 Identities=50% Similarity=1.328 Sum_probs=7.2
Q ss_pred CCCCcccCCC
Q 046177 90 RCPTCRHELG 99 (272)
Q Consensus 90 ~CP~Cr~~~~ 99 (272)
+||.|+..+.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 6888877654
No 227
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=20.61 E-value=65 Score=28.72 Aligned_cols=52 Identities=21% Similarity=0.512 Sum_probs=35.2
Q ss_pred eec--cccccCcCCccccc-CCceeccCcccc--------c-----CCCCCCcccCCCcccchhHHHHh
Q 046177 58 ECP--VCLNAMYPPIHQCS-NGHTLCSGCKPR--------V-----HNRCPTCRHELGNIRCLALEKVA 110 (272)
Q Consensus 58 ~Cp--iC~~~l~~Pv~qC~-cGH~~C~~C~~~--------~-----~~~CP~Cr~~~~~~r~~~le~~~ 110 (272)
.|. .|..+=--|+ .|. |+++||..=+.. . ...||.|..++...+.....+++
T Consensus 10 HCs~~~CkqlDFLPf-~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~~de~~~~~v 77 (250)
T KOG3183|consen 10 HCSVPYCKQLDFLPF-KCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTKKDEAPDKVV 77 (250)
T ss_pred ccCcchhhhccccce-eeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCCCCcchhhhh
Confidence 466 7888766675 787 999999853222 1 26799999888765555544443
No 228
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.39 E-value=70 Score=33.26 Aligned_cols=42 Identities=31% Similarity=0.654 Sum_probs=29.8
Q ss_pred CCeeeeccccccCcCCcccc--------cCCceeccCccccc--CCCCCCcccC
Q 046177 54 RELLECPVCLNAMYPPIHQC--------SNGHTLCSGCKPRV--HNRCPTCRHE 97 (272)
Q Consensus 54 ~~~l~CpiC~~~l~~Pv~qC--------~cGH~~C~~C~~~~--~~~CP~Cr~~ 97 (272)
...+.|..|..++.=| .| .-+...|..|-..- ...||.|...
T Consensus 433 s~~l~C~~Cg~v~~Cp--~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 433 APLLLCRDCGYIAECP--NCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred cceeecccCCCcccCC--CCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4567788888776655 23 24678999996653 4789999887
No 229
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=20.28 E-value=74 Score=22.15 Aligned_cols=16 Identities=38% Similarity=0.918 Sum_probs=13.0
Q ss_pred CCCCeeeeccccccCc
Q 046177 52 SVRELLECPVCLNAMY 67 (272)
Q Consensus 52 ~~~~~l~CpiC~~~l~ 67 (272)
.+.+.+-||+|...|.
T Consensus 4 ~LLeiLaCP~~kg~L~ 19 (60)
T COG2835 4 RLLEILACPVCKGPLV 19 (60)
T ss_pred hhheeeeccCcCCcce
Confidence 4678899999999864
No 230
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=20.14 E-value=80 Score=21.35 Aligned_cols=27 Identities=30% Similarity=0.476 Sum_probs=17.4
Q ss_pred ccccCCCCCCCCccccC-hhHHHHHhhhcCCC
Q 046177 143 RPYNCPYAGSECTVMGD-IPYLVAHLKDDHKV 173 (272)
Q Consensus 143 ~~~~CP~~~~~C~~~g~-~~~l~~Hl~~~H~~ 173 (272)
.|-.||. |+.+.+ ..+|..|++..|..
T Consensus 23 ~PatCP~----C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPI----CGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TT----T--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCc----chhhccchhhHHHHHHHHhcc
Confidence 3567887 777764 56999999999964
Done!