Query 043988
Match_columns 151
No_of_seqs 119 out of 1261
Neff 9.6
Searched_HMMs 46136
Date Fri Mar 29 10:19:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043988.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043988hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 99.9 3.9E-26 8.4E-31 173.5 7.0 140 11-151 144-288 (384)
2 KOG1814 Predicted E3 ubiquitin 99.9 1.4E-25 3E-30 166.5 5.8 136 11-147 182-319 (445)
3 KOG1815 Predicted E3 ubiquitin 99.8 1.2E-20 2.5E-25 146.7 6.6 138 11-151 68-208 (444)
4 KOG0006 E3 ubiquitin-protein l 99.7 1.1E-16 2.5E-21 116.1 6.1 133 8-146 216-360 (446)
5 smart00647 IBR In Between Ring 99.6 1.7E-15 3.6E-20 87.8 3.5 62 84-145 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.5 1.9E-15 4.2E-20 87.5 0.0 62 84-145 1-64 (64)
7 PF15227 zf-C3HC4_4: zinc fing 98.9 4.5E-10 9.7E-15 59.3 1.0 40 16-61 1-40 (42)
8 KOG0320 Predicted E3 ubiquitin 98.9 1.6E-09 3.4E-14 73.1 3.4 57 9-75 127-183 (187)
9 PF00097 zf-C3HC4: Zinc finger 98.9 3.8E-09 8.2E-14 55.5 3.6 39 16-61 1-39 (41)
10 PF13639 zf-RING_2: Ring finge 98.8 1.1E-09 2.3E-14 58.5 0.9 41 15-62 2-42 (44)
11 PF13445 zf-RING_UBOX: RING-ty 98.8 4.6E-09 1E-13 55.5 2.8 42 16-61 1-43 (43)
12 PF13923 zf-C3HC4_2: Zinc fing 98.8 3.1E-09 6.7E-14 55.2 2.0 38 16-62 1-38 (39)
13 PLN03208 E3 ubiquitin-protein 98.7 1.8E-08 3.8E-13 69.6 4.2 65 11-80 16-89 (193)
14 PF14634 zf-RING_5: zinc-RING 98.7 1.9E-08 4E-13 53.7 3.0 41 15-62 1-41 (44)
15 cd00162 RING RING-finger (Real 98.6 1E-07 2.2E-12 50.4 3.6 44 15-68 1-44 (45)
16 KOG2177 Predicted E3 ubiquitin 98.4 1.1E-07 2.5E-12 70.3 2.3 112 7-145 7-122 (386)
17 PF13920 zf-C3HC4_3: Zinc fing 98.3 9.2E-07 2E-11 48.4 3.1 46 13-70 2-48 (50)
18 TIGR00599 rad18 DNA repair pro 98.2 1.2E-06 2.6E-11 67.3 4.0 70 6-87 19-89 (397)
19 PHA02929 N1R/p28-like protein; 98.2 1E-06 2.2E-11 63.3 3.4 51 11-70 172-227 (238)
20 smart00184 RING Ring finger. E 98.2 1.5E-06 3.3E-11 44.2 3.0 30 16-48 1-30 (39)
21 KOG0823 Predicted E3 ubiquitin 98.2 1.1E-06 2.3E-11 62.1 2.8 61 10-79 44-104 (230)
22 PHA02926 zinc finger-like prot 98.2 1.9E-06 4.1E-11 60.5 3.4 57 11-70 168-230 (242)
23 smart00504 Ubox Modified RING 98.1 4.9E-06 1.1E-10 47.5 4.2 50 14-75 2-51 (63)
24 KOG2164 Predicted E3 ubiquitin 98.1 1.4E-06 3E-11 67.8 2.1 59 13-78 186-244 (513)
25 TIGR00570 cdk7 CDK-activating 98.1 5.3E-06 1.1E-10 61.5 5.0 54 14-75 4-59 (309)
26 KOG0317 Predicted E3 ubiquitin 98.0 3.6E-06 7.8E-11 61.2 2.1 52 11-74 237-288 (293)
27 KOG0006 E3 ubiquitin-protein l 97.9 7E-06 1.5E-10 60.5 2.1 95 33-141 341-437 (446)
28 PF11789 zf-Nse: Zinc-finger o 97.8 1.7E-05 3.6E-10 44.5 2.5 52 8-66 6-57 (57)
29 KOG1002 Nucleotide excision re 97.7 2.5E-05 5.4E-10 61.3 2.8 58 8-72 531-588 (791)
30 COG5540 RING-finger-containing 97.6 4.5E-05 9.7E-10 56.0 2.9 54 10-71 320-373 (374)
31 KOG0287 Postreplication repair 97.4 8.5E-05 1.8E-09 55.4 2.2 63 12-86 22-85 (442)
32 KOG0978 E3 ubiquitin ligase in 97.4 8E-05 1.7E-09 60.7 1.7 55 12-77 642-696 (698)
33 KOG1812 Predicted E3 ubiquitin 97.3 0.00015 3.2E-09 56.0 2.4 39 100-142 306-344 (384)
34 KOG1814 Predicted E3 ubiquitin 97.3 0.00013 2.8E-09 55.7 1.8 111 12-139 272-404 (445)
35 COG5574 PEX10 RING-finger-cont 97.3 0.0002 4.4E-09 51.7 2.5 52 12-74 214-266 (271)
36 PF12678 zf-rbx1: RING-H2 zinc 97.3 0.00013 2.8E-09 43.1 1.3 42 14-62 20-71 (73)
37 KOG2879 Predicted E3 ubiquitin 97.3 0.00047 1E-08 50.1 4.2 51 11-70 237-287 (298)
38 PF14835 zf-RING_6: zf-RING of 97.2 4.3E-05 9.2E-10 43.4 -1.1 50 13-75 7-56 (65)
39 KOG4628 Predicted E3 ubiquitin 97.2 0.00029 6.3E-09 53.2 2.7 46 14-67 230-275 (348)
40 PF11793 FANCL_C: FANCL C-term 97.0 0.00063 1.4E-08 39.8 2.3 58 13-72 2-68 (70)
41 PF04564 U-box: U-box domain; 96.9 0.00085 1.8E-08 39.5 2.6 51 13-74 4-54 (73)
42 KOG2660 Locus-specific chromos 96.7 0.00086 1.9E-08 49.9 1.8 49 10-69 12-60 (331)
43 COG5432 RAD18 RING-finger-cont 96.1 0.0034 7.3E-08 46.2 1.8 52 11-74 23-74 (391)
44 KOG1039 Predicted E3 ubiquitin 96.1 0.0052 1.1E-07 46.7 2.8 54 11-66 159-217 (344)
45 KOG0311 Predicted E3 ubiquitin 96.0 0.00064 1.4E-08 51.1 -2.2 47 12-68 42-88 (381)
46 PF12861 zf-Apc11: Anaphase-pr 95.9 0.0059 1.3E-07 36.8 1.9 51 13-69 21-81 (85)
47 KOG4185 Predicted E3 ubiquitin 95.6 0.035 7.5E-07 41.4 5.6 117 13-139 3-126 (296)
48 PF14570 zf-RING_4: RING/Ubox 95.6 0.013 2.9E-07 31.4 2.3 44 16-68 1-46 (48)
49 COG5152 Uncharacterized conser 95.4 0.0077 1.7E-07 41.9 1.4 32 11-45 194-225 (259)
50 KOG0802 E3 ubiquitin ligase [P 95.4 0.011 2.5E-07 47.8 2.6 44 12-62 290-335 (543)
51 COG5220 TFB3 Cdk activating ki 95.4 0.0036 7.9E-08 44.8 -0.3 52 14-71 11-65 (314)
52 KOG4159 Predicted E3 ubiquitin 95.4 0.018 3.9E-07 44.7 3.4 48 11-70 82-129 (398)
53 KOG1428 Inhibitor of type V ad 95.3 0.03 6.5E-07 49.8 4.6 70 9-80 3482-3554(3738)
54 KOG4445 Uncharacterized conser 95.2 0.0093 2E-07 44.1 1.3 47 4-50 106-152 (368)
55 COG5243 HRD1 HRD ubiquitin lig 95.1 0.028 6E-07 42.9 3.6 49 11-68 285-343 (491)
56 PF13719 zinc_ribbon_5: zinc-r 95.1 0.014 3E-07 29.6 1.3 29 101-131 3-35 (37)
57 KOG4739 Uncharacterized protei 95.0 0.0097 2.1E-07 42.7 0.8 47 12-70 2-48 (233)
58 KOG0824 Predicted E3 ubiquitin 95.0 0.015 3.3E-07 43.0 1.8 53 11-74 5-57 (324)
59 PF04641 Rtf2: Rtf2 RING-finge 95.0 0.063 1.4E-06 39.4 5.1 73 8-90 108-182 (260)
60 KOG1815 Predicted E3 ubiquitin 94.9 0.015 3.2E-07 46.0 1.8 38 101-141 227-268 (444)
61 KOG2817 Predicted E3 ubiquitin 94.9 0.031 6.7E-07 42.9 3.4 59 12-76 333-391 (394)
62 PF13717 zinc_ribbon_4: zinc-r 94.9 0.016 3.6E-07 29.2 1.4 29 101-131 3-35 (36)
63 KOG1645 RING-finger-containing 94.4 0.032 6.8E-07 43.0 2.4 54 13-74 4-60 (463)
64 KOG0297 TNF receptor-associate 94.4 0.032 6.9E-07 43.4 2.4 38 10-49 18-55 (391)
65 KOG1734 Predicted RING-contain 94.2 0.017 3.8E-07 42.1 0.6 62 9-78 220-290 (328)
66 PF10571 UPF0547: Uncharacteri 94.1 0.025 5.4E-07 26.3 0.8 23 102-131 2-24 (26)
67 KOG0828 Predicted E3 ubiquitin 94.1 0.036 7.9E-07 43.8 2.2 52 11-70 569-634 (636)
68 KOG4265 Predicted E3 ubiquitin 93.7 0.076 1.6E-06 40.3 3.2 49 9-69 286-335 (349)
69 PF05883 Baculo_RING: Baculovi 93.7 0.034 7.3E-07 36.5 1.2 36 12-48 25-67 (134)
70 PF02150 RNA_POL_M_15KD: RNA p 93.3 0.025 5.5E-07 28.3 0.1 28 101-130 2-29 (35)
71 KOG3002 Zn finger protein [Gen 93.3 0.077 1.7E-06 39.8 2.7 44 11-70 46-91 (299)
72 TIGR02098 MJ0042_CXXC MJ0042 f 93.1 0.058 1.2E-06 27.3 1.3 29 101-131 3-35 (38)
73 KOG3039 Uncharacterized conser 92.9 0.083 1.8E-06 38.2 2.2 57 11-76 219-276 (303)
74 KOG1785 Tyrosine kinase negati 92.7 0.049 1.1E-06 42.0 0.9 46 13-66 369-414 (563)
75 KOG4692 Predicted E3 ubiquitin 92.6 0.1 2.2E-06 39.7 2.4 35 12-49 421-455 (489)
76 smart00744 RINGv The RING-vari 92.2 0.19 4.2E-06 27.0 2.7 41 15-61 1-46 (49)
77 smart00661 RPOL9 RNA polymeras 92.0 0.081 1.8E-06 28.6 1.1 27 102-130 2-29 (52)
78 PF07975 C1_4: TFIIH C1-like d 91.9 0.032 6.9E-07 30.4 -0.7 36 107-142 4-42 (51)
79 COG5222 Uncharacterized conser 91.5 0.24 5.1E-06 36.9 3.2 43 14-66 275-317 (427)
80 KOG3800 Predicted E3 ubiquitin 91.5 0.27 5.9E-06 36.4 3.5 52 15-74 2-55 (300)
81 KOG1952 Transcription factor N 90.9 0.29 6.3E-06 41.3 3.6 54 11-66 189-243 (950)
82 COG5175 MOT2 Transcriptional r 90.8 0.39 8.4E-06 36.5 3.8 58 15-81 16-76 (480)
83 PRK00398 rpoP DNA-directed RNA 90.7 0.15 3.3E-06 27.0 1.2 29 101-132 4-32 (46)
84 PHA03096 p28-like protein; Pro 90.4 0.19 4E-06 37.5 1.9 39 14-52 179-222 (284)
85 PF14803 Nudix_N_2: Nudix N-te 90.0 0.11 2.4E-06 25.8 0.3 26 102-129 2-30 (34)
86 PRK14890 putative Zn-ribbon RN 89.8 0.21 4.5E-06 27.9 1.3 28 100-129 25-56 (59)
87 PF12773 DZR: Double zinc ribb 89.6 0.21 4.7E-06 26.7 1.3 27 99-129 11-37 (50)
88 KOG1001 Helicase-like transcri 88.1 0.13 2.9E-06 42.7 -0.3 50 14-74 455-504 (674)
89 KOG3579 Predicted E3 ubiquitin 87.8 0.94 2E-05 33.6 3.9 62 11-74 266-332 (352)
90 PF13240 zinc_ribbon_2: zinc-r 87.5 0.26 5.7E-06 22.1 0.6 22 102-130 1-22 (23)
91 TIGR00373 conserved hypothetic 87.2 0.65 1.4E-05 31.5 2.7 30 99-130 108-137 (158)
92 KOG1813 Predicted E3 ubiquitin 87.2 0.23 5E-06 36.8 0.5 35 11-48 239-273 (313)
93 PF14353 CpXC: CpXC protein 87.0 0.31 6.8E-06 31.7 1.0 14 118-131 35-48 (128)
94 PRK06266 transcription initiat 86.8 0.7 1.5E-05 32.0 2.7 30 99-130 116-145 (178)
95 COG2888 Predicted Zn-ribbon RN 86.6 0.42 9.2E-06 26.7 1.2 27 101-129 28-58 (61)
96 KOG0804 Cytoplasmic Zn-finger 86.4 0.53 1.2E-05 37.0 2.1 38 10-47 172-210 (493)
97 KOG0826 Predicted E3 ubiquitin 86.3 0.64 1.4E-05 35.1 2.4 47 12-67 299-345 (357)
98 smart00531 TFIIE Transcription 86.2 0.79 1.7E-05 30.7 2.7 30 99-130 98-132 (147)
99 COG5236 Uncharacterized conser 86.1 0.72 1.6E-05 35.2 2.6 40 4-46 51-91 (493)
100 PF13248 zf-ribbon_3: zinc-rib 85.6 0.39 8.5E-06 22.1 0.7 22 101-129 3-24 (26)
101 COG5109 Uncharacterized conser 85.3 1.2 2.6E-05 33.6 3.4 57 12-74 335-391 (396)
102 PF05290 Baculo_IE-1: Baculovi 85.2 1.2 2.7E-05 29.2 3.0 53 12-70 79-132 (140)
103 PF10367 Vps39_2: Vacuolar sor 84.8 0.34 7.4E-06 30.2 0.4 31 13-44 78-108 (109)
104 PF14369 zf-RING_3: zinc-finge 83.9 0.89 1.9E-05 22.6 1.6 30 100-131 2-31 (35)
105 KOG2807 RNA polymerase II tran 83.1 0.2 4.2E-06 37.8 -1.4 26 118-143 342-367 (378)
106 KOG2906 RNA polymerase III sub 83.1 0.52 1.1E-05 29.1 0.6 29 101-131 2-31 (105)
107 cd00021 BBOX B-Box-type zinc f 81.8 0.77 1.7E-05 22.9 0.9 27 119-145 10-36 (39)
108 COG5151 SSL1 RNA polymerase II 81.6 0.47 1E-05 35.6 0.1 39 102-142 364-409 (421)
109 KOG4172 Predicted E3 ubiquitin 81.6 0.66 1.4E-05 25.5 0.6 44 14-68 8-52 (62)
110 PF06844 DUF1244: Protein of u 80.9 1.4 3E-05 25.2 1.8 17 37-53 11-27 (68)
111 KOG1940 Zn-finger protein [Gen 80.9 0.89 1.9E-05 33.7 1.3 48 11-67 156-204 (276)
112 KOG0825 PHD Zn-finger protein 80.8 0.36 7.7E-06 40.6 -0.8 43 10-52 93-139 (1134)
113 KOG0827 Predicted E3 ubiquitin 80.6 1.1 2.3E-05 34.8 1.7 38 13-50 4-42 (465)
114 TIGR00622 ssl1 transcription f 80.3 0.95 2.1E-05 28.9 1.1 39 102-142 57-102 (112)
115 PLN00209 ribosomal protein S27 80.2 1.2 2.6E-05 26.9 1.4 31 101-133 37-67 (86)
116 PHA00626 hypothetical protein 79.4 1.1 2.5E-05 24.7 1.1 29 102-132 2-34 (59)
117 PF01428 zf-AN1: AN1-like Zinc 79.3 0.85 1.8E-05 23.7 0.6 29 120-150 12-40 (43)
118 COG1594 RPB9 DNA-directed RNA 78.3 1.2 2.6E-05 28.5 1.2 29 101-131 3-32 (113)
119 COG2051 RPS27A Ribosomal prote 78.2 1 2.2E-05 25.8 0.7 30 101-132 20-49 (67)
120 KOG2034 Vacuolar sorting prote 78.1 1.4 3.1E-05 37.6 1.8 40 11-51 815-854 (911)
121 PTZ00083 40S ribosomal protein 78.1 1.6 3.4E-05 26.3 1.5 31 101-133 36-66 (85)
122 PF09297 zf-NADH-PPase: NADH p 76.4 0.97 2.1E-05 21.8 0.3 27 101-130 4-30 (32)
123 KOG4367 Predicted Zn-finger pr 76.0 1.3 2.8E-05 34.9 1.0 34 12-48 3-36 (699)
124 KOG0825 PHD Zn-finger protein 75.8 2.9 6.2E-05 35.5 2.9 51 14-73 124-174 (1134)
125 PF08271 TF_Zn_Ribbon: TFIIB z 75.1 1.4 3E-05 22.8 0.7 26 102-129 2-27 (43)
126 smart00834 CxxC_CXXC_SSSS Puta 74.7 2.6 5.6E-05 21.2 1.6 27 101-129 6-34 (41)
127 KOG0317 Predicted E3 ubiquitin 74.2 0.5 1.1E-05 35.0 -1.5 19 121-139 251-269 (293)
128 PF09538 FYDLN_acid: Protein o 73.7 2.1 4.5E-05 27.2 1.3 29 99-131 8-36 (108)
129 PRK00415 rps27e 30S ribosomal 73.7 2.2 4.7E-05 23.9 1.3 31 101-133 12-42 (59)
130 smart00336 BBOX B-Box-type zin 73.1 2 4.4E-05 21.6 1.0 27 118-144 12-38 (42)
131 COG1579 Zn-ribbon protein, pos 72.9 4.4 9.5E-05 29.5 3.0 56 73-130 167-230 (239)
132 PRK00420 hypothetical protein; 71.8 7.6 0.00016 24.8 3.5 26 101-130 24-49 (112)
133 PF00643 zf-B_box: B-box zinc 71.8 0.37 8E-06 24.7 -2.1 26 119-144 13-38 (42)
134 KOG1941 Acetylcholine receptor 71.3 1.3 2.9E-05 34.4 0.0 49 12-67 364-413 (518)
135 PF14446 Prok-RING_1: Prokaryo 71.2 5.8 0.00013 21.8 2.5 34 12-45 4-38 (54)
136 PF09723 Zn-ribbon_8: Zinc rib 70.9 3.5 7.6E-05 21.2 1.6 27 101-129 6-34 (42)
137 PRK00432 30S ribosomal protein 70.6 2.1 4.5E-05 23.1 0.7 26 101-131 21-47 (50)
138 PF09788 Tmemb_55A: Transmembr 68.6 2.9 6.3E-05 30.6 1.3 17 9-25 61-77 (256)
139 PF08746 zf-RING-like: RING-li 68.6 3 6.5E-05 21.7 1.0 41 16-61 1-41 (43)
140 COG1675 TFA1 Transcription ini 68.3 4.9 0.00011 27.9 2.3 31 98-130 111-141 (176)
141 PRK03824 hypA hydrogenase nick 67.4 10 0.00022 25.0 3.6 14 100-115 70-83 (135)
142 COG5219 Uncharacterized conser 67.2 2.8 6E-05 36.5 1.1 52 12-70 1468-1523(1525)
143 PF06906 DUF1272: Protein of u 67.1 3.9 8.5E-05 22.6 1.3 46 14-71 6-53 (57)
144 PF14447 Prok-RING_4: Prokaryo 67.1 1.9 4.1E-05 23.8 0.1 47 13-73 7-53 (55)
145 KOG2907 RNA polymerase I trans 66.9 2.2 4.8E-05 27.1 0.4 88 37-131 8-112 (116)
146 TIGR00686 phnA alkylphosphonat 66.9 3.1 6.8E-05 26.3 1.0 27 102-132 4-30 (109)
147 PF11023 DUF2614: Protein of u 66.5 3.3 7.2E-05 26.4 1.1 10 131-140 87-96 (114)
148 PF00098 zf-CCHC: Zinc knuckle 66.5 3.9 8.4E-05 17.0 1.0 16 131-146 2-17 (18)
149 PF10426 zf-RAG1: Recombinatio 66.1 0.96 2.1E-05 21.6 -1.1 21 57-77 2-22 (30)
150 PF08274 PhnA_Zn_Ribbon: PhnA 65.9 1.8 3.8E-05 20.8 -0.2 25 103-131 5-29 (30)
151 PF14445 Prok-RING_2: Prokaryo 64.5 1.1 2.4E-05 24.2 -1.1 34 12-45 6-39 (57)
152 PF01599 Ribosomal_S27: Riboso 64.4 3.2 6.9E-05 22.2 0.6 29 100-129 18-46 (47)
153 PRK14892 putative transcriptio 63.9 6.2 0.00013 24.6 1.9 33 97-131 18-52 (99)
154 TIGR01384 TFS_arch transcripti 63.7 3.7 8E-05 25.6 0.9 24 102-130 2-25 (104)
155 TIGR01206 lysW lysine biosynth 62.5 4.2 9.1E-05 22.4 0.9 29 101-131 3-32 (54)
156 PF07754 DUF1610: Domain of un 62.3 5.7 0.00012 18.0 1.2 10 119-128 14-23 (24)
157 PF01667 Ribosomal_S27e: Ribos 62.2 3.8 8.3E-05 22.6 0.7 31 101-133 8-38 (55)
158 KOG2462 C2H2-type Zn-finger pr 62.0 13 0.00029 27.6 3.6 103 11-133 128-255 (279)
159 KOG3161 Predicted E3 ubiquitin 61.5 2.4 5.1E-05 35.1 -0.3 35 13-48 11-47 (861)
160 PRK10220 hypothetical protein; 61.2 4.7 0.0001 25.5 1.0 27 102-132 5-31 (111)
161 PF14471 DUF4428: Domain of un 60.9 9.2 0.0002 20.7 2.1 30 15-46 1-30 (51)
162 PRK03681 hypA hydrogenase nick 60.8 19 0.0004 23.0 3.8 26 100-129 70-95 (114)
163 KOG2789 Putative Zn-finger pro 60.5 3.1 6.7E-05 32.4 0.2 43 3-46 64-106 (482)
164 COG3492 Uncharacterized protei 60.0 9 0.0002 23.4 2.1 17 37-53 42-58 (104)
165 smart00249 PHD PHD zinc finger 59.7 3.9 8.5E-05 20.7 0.5 31 16-46 2-32 (47)
166 KOG3039 Uncharacterized conser 59.4 10 0.00022 27.8 2.6 35 14-51 44-78 (303)
167 PRK14559 putative protein seri 59.4 5.9 0.00013 33.2 1.6 32 98-138 13-50 (645)
168 PF13913 zf-C2HC_2: zinc-finge 59.0 3.6 7.8E-05 18.6 0.2 10 122-131 3-12 (25)
169 smart00064 FYVE Protein presen 58.7 8.4 0.00018 21.8 1.8 37 13-49 10-47 (68)
170 COG2816 NPY1 NTP pyrophosphohy 58.4 18 0.0004 27.0 3.9 49 78-130 90-138 (279)
171 PF05715 zf-piccolo: Piccolo Z 58.3 8 0.00017 21.7 1.5 36 102-139 4-40 (61)
172 PF02891 zf-MIZ: MIZ/SP-RING z 58.1 18 0.0004 19.3 3.0 47 14-67 3-49 (50)
173 PF01363 FYVE: FYVE zinc finge 58.1 3.1 6.7E-05 23.7 -0.1 34 12-45 8-42 (69)
174 TIGR02605 CxxC_CxxC_SSSS putat 58.0 8.2 0.00018 20.6 1.6 27 101-129 6-34 (52)
175 PF02148 zf-UBP: Zn-finger in 58.0 14 0.00031 20.7 2.6 32 16-49 1-36 (63)
176 PRK12380 hydrogenase nickel in 57.8 22 0.00048 22.6 3.8 25 100-129 70-94 (113)
177 PF14569 zf-UDP: Zinc-binding 57.5 12 0.00026 22.2 2.2 50 12-69 8-61 (80)
178 PRK12286 rpmF 50S ribosomal pr 57.5 8.5 0.00018 21.4 1.6 27 96-130 23-49 (57)
179 TIGR00100 hypA hydrogenase nic 57.4 23 0.0005 22.6 3.8 25 100-129 70-94 (115)
180 cd00065 FYVE FYVE domain; Zinc 56.9 8.3 0.00018 20.9 1.5 36 14-49 3-39 (57)
181 KOG2930 SCF ubiquitin ligase, 56.8 7.6 0.00016 24.4 1.4 23 33-62 80-102 (114)
182 KOG0309 Conserved WD40 repeat- 56.1 10 0.00022 32.4 2.4 47 11-66 1026-1072(1081)
183 TIGR02300 FYDLN_acid conserved 55.7 7.9 0.00017 25.3 1.4 29 99-131 8-36 (129)
184 smart00659 RPOLCX RNA polymera 55.7 10 0.00022 19.8 1.6 25 102-130 4-28 (44)
185 PF06677 Auto_anti-p27: Sjogre 55.6 8.1 0.00018 19.9 1.2 23 102-128 19-41 (41)
186 PF12760 Zn_Tnp_IS1595: Transp 55.5 8.7 0.00019 20.1 1.4 29 99-129 17-45 (46)
187 PLN03086 PRLI-interacting fact 55.2 12 0.00026 30.9 2.6 58 56-131 406-463 (567)
188 KOG1493 Anaphase-promoting com 55.1 2.2 4.8E-05 25.2 -1.1 49 14-68 21-79 (84)
189 PF00628 PHD: PHD-finger; Int 55.1 8.8 0.00019 20.2 1.4 34 15-48 1-34 (51)
190 KOG3053 Uncharacterized conser 55.0 18 0.00039 26.7 3.2 56 8-66 15-78 (293)
191 smart00154 ZnF_AN1 AN1-like Zi 54.0 7.1 0.00015 19.8 0.8 19 121-139 12-30 (39)
192 KOG2979 Protein involved in DN 53.8 14 0.0003 27.2 2.5 46 14-66 177-222 (262)
193 PF03604 DNA_RNApol_7kD: DNA d 52.7 8.7 0.00019 18.7 1.0 22 107-130 5-26 (32)
194 PF01155 HypA: Hydrogenase exp 52.5 16 0.00035 23.2 2.5 25 100-129 70-94 (113)
195 smart00734 ZnF_Rad18 Rad18-lik 52.3 8.4 0.00018 17.6 0.9 20 58-79 2-21 (26)
196 COG1645 Uncharacterized Zn-fin 52.1 7.5 0.00016 25.6 0.9 24 101-129 29-52 (131)
197 PF07191 zinc-ribbons_6: zinc- 51.8 5.4 0.00012 23.2 0.2 9 107-115 6-14 (70)
198 PF12906 RINGv: RING-variant d 51.2 19 0.00042 18.9 2.3 34 16-50 1-39 (47)
199 KOG3268 Predicted E3 ubiquitin 51.1 18 0.00038 25.2 2.6 61 9-71 161-229 (234)
200 PRK00564 hypA hydrogenase nick 50.3 33 0.00072 22.0 3.7 26 100-129 71-96 (117)
201 KOG2932 E3 ubiquitin ligase in 49.1 13 0.00029 28.1 1.9 32 13-46 90-121 (389)
202 PF10497 zf-4CXXC_R1: Zinc-fin 48.9 42 0.0009 21.1 3.9 31 35-67 37-69 (105)
203 PF08273 Prim_Zn_Ribbon: Zinc- 48.0 9.1 0.0002 19.6 0.7 25 14-42 4-32 (40)
204 TIGR00515 accD acetyl-CoA carb 47.4 6.3 0.00014 29.5 0.0 28 101-130 27-54 (285)
205 KOG4684 Uncharacterized conser 47.2 10 0.00022 27.2 1.0 34 98-131 136-180 (275)
206 COG1198 PriA Primosomal protei 47.0 11 0.00024 32.0 1.4 60 78-138 405-484 (730)
207 COG3813 Uncharacterized protei 46.2 15 0.00032 21.5 1.4 48 15-74 7-56 (84)
208 PF07282 OrfB_Zn_ribbon: Putat 46.0 9 0.00019 21.8 0.5 27 101-130 29-55 (69)
209 PF08792 A2L_zn_ribbon: A2L zi 45.6 14 0.0003 18.0 1.1 27 101-130 4-30 (33)
210 PF10122 Mu-like_Com: Mu-like 45.6 7.9 0.00017 21.0 0.2 27 102-130 6-33 (51)
211 TIGR01031 rpmF_bact ribosomal 45.0 15 0.00033 20.2 1.3 26 96-129 22-47 (55)
212 PRK05654 acetyl-CoA carboxylas 45.0 7 0.00015 29.4 -0.1 28 102-131 29-56 (292)
213 CHL00174 accD acetyl-CoA carbo 44.7 6.5 0.00014 29.6 -0.2 26 102-129 40-65 (296)
214 PF02748 PyrI_C: Aspartate car 44.0 9.5 0.00021 20.8 0.4 31 100-130 6-44 (52)
215 PF01783 Ribosomal_L32p: Ribos 43.7 22 0.00047 19.6 1.8 24 98-129 24-47 (56)
216 PF14319 Zn_Tnp_IS91: Transpos 43.5 55 0.0012 20.8 3.9 49 78-137 19-68 (111)
217 KOG3970 Predicted E3 ubiquitin 43.0 34 0.00074 24.8 3.1 58 13-73 50-109 (299)
218 PF00412 LIM: LIM domain; Int 42.8 22 0.00047 19.1 1.8 31 14-46 27-57 (58)
219 KOG4275 Predicted E3 ubiquitin 42.6 11 0.00024 28.3 0.6 29 13-44 300-329 (350)
220 KOG0957 PHD finger protein [Ge 42.5 9.8 0.00021 30.8 0.4 48 1-48 532-579 (707)
221 KOG2807 RNA polymerase II tran 42.4 17 0.00036 27.8 1.6 31 15-45 332-362 (378)
222 PF02318 FYVE_2: FYVE-type zin 42.4 31 0.00068 22.0 2.7 35 100-138 54-88 (118)
223 PF14169 YdjO: Cold-inducible 42.2 19 0.00041 20.2 1.4 28 102-129 20-47 (59)
224 PRK12495 hypothetical protein; 42.0 35 0.00076 24.6 3.0 26 99-129 41-66 (226)
225 PRK02935 hypothetical protein; 41.9 15 0.00032 23.2 1.0 10 131-140 88-97 (110)
226 PF07649 C1_3: C1-like domain; 41.9 23 0.0005 16.5 1.6 28 15-42 2-29 (30)
227 PF14205 Cys_rich_KTR: Cystein 41.3 17 0.00036 20.0 1.1 28 101-130 5-37 (55)
228 COG4647 AcxC Acetone carboxyla 40.9 52 0.0011 21.6 3.5 56 74-133 26-81 (165)
229 KOG1779 40s ribosomal protein 40.8 23 0.0005 21.1 1.7 33 101-135 35-67 (84)
230 COG3677 Transposase and inacti 40.6 37 0.00079 22.2 2.8 32 99-132 29-64 (129)
231 PF01214 CK_II_beta: Casein ki 39.6 36 0.00078 23.8 2.8 10 102-111 101-110 (184)
232 PF14392 zf-CCHC_4: Zinc knuck 39.5 12 0.00025 19.9 0.3 17 130-146 32-48 (49)
233 PRK04023 DNA polymerase II lar 39.1 21 0.00045 31.6 1.8 33 99-140 625-662 (1121)
234 KOG2114 Vacuolar assembly/sort 37.7 23 0.00049 30.6 1.8 40 14-67 841-880 (933)
235 PF00096 zf-C2H2: Zinc finger, 37.5 6.5 0.00014 16.8 -0.8 8 123-130 2-9 (23)
236 PF13453 zf-TFIIB: Transcripti 36.8 13 0.00029 18.8 0.2 6 107-112 4-9 (41)
237 COG0777 AccD Acetyl-CoA carbox 36.2 12 0.00025 27.9 -0.0 27 102-130 30-56 (294)
238 PRK14714 DNA polymerase II lar 35.6 29 0.00063 31.5 2.2 11 100-112 667-677 (1337)
239 KOG4362 Transcriptional regula 34.2 9.7 0.00021 31.9 -0.8 58 10-76 18-75 (684)
240 PRK00893 aspartate carbamoyltr 33.7 22 0.00048 24.0 1.0 33 99-131 104-144 (152)
241 PF13465 zf-H2C2_2: Zinc-finge 33.0 12 0.00027 16.8 -0.2 9 122-130 15-23 (26)
242 COG0375 HybF Zn finger protein 32.9 21 0.00045 22.9 0.7 25 100-129 70-94 (115)
243 PTZ00396 Casein kinase II subu 32.9 65 0.0014 23.7 3.3 28 102-129 122-156 (251)
244 COG1998 RPS31 Ribosomal protei 32.9 25 0.00054 18.9 0.9 27 100-129 19-45 (51)
245 PF13894 zf-C2H2_4: C2H2-type 32.4 12 0.00027 15.6 -0.3 8 123-130 2-9 (24)
246 PF01396 zf-C4_Topoisom: Topoi 32.3 30 0.00066 17.4 1.2 21 102-124 3-24 (39)
247 TIGR00595 priA primosomal prot 31.8 29 0.00063 28.2 1.5 31 107-138 227-262 (505)
248 cd00729 rubredoxin_SM Rubredox 31.8 36 0.00077 16.6 1.3 23 102-129 4-26 (34)
249 KOG3799 Rab3 effector RIM1 and 31.1 22 0.00048 23.5 0.6 28 11-45 63-90 (169)
250 PRK09710 lar restriction allev 30.4 27 0.00058 19.9 0.8 31 100-130 6-36 (64)
251 KOG3623 Homeobox transcription 30.0 88 0.0019 27.0 3.9 30 100-131 281-319 (1007)
252 PF05502 Dynactin_p62: Dynacti 30.0 19 0.00041 29.1 0.2 35 36-72 26-65 (483)
253 cd00350 rubredoxin_like Rubred 29.8 40 0.00087 16.1 1.3 23 102-129 3-25 (33)
254 PRK09678 DNA-binding transcrip 29.5 23 0.00051 20.7 0.5 14 102-115 29-42 (72)
255 COG5194 APC11 Component of SCF 29.4 28 0.00061 20.8 0.8 18 33-50 53-70 (88)
256 PF01096 TFIIS_C: Transcriptio 29.2 15 0.00032 18.5 -0.3 13 119-131 26-38 (39)
257 COG1096 Predicted RNA-binding 29.0 30 0.00065 24.2 1.0 29 102-135 151-179 (188)
258 PHA00616 hypothetical protein 29.0 23 0.0005 18.6 0.4 12 122-133 2-13 (44)
259 PF05741 zf-nanos: Nanos RNA b 28.9 31 0.00068 19.0 0.9 11 119-129 31-41 (55)
260 PHA02825 LAP/PHD finger-like p 28.7 81 0.0018 21.6 3.0 53 10-71 5-60 (162)
261 PF03107 C1_2: C1 domain; Int 28.3 37 0.0008 15.9 1.0 24 15-38 2-25 (30)
262 PF05191 ADK_lid: Adenylate ki 28.2 51 0.0011 16.3 1.5 27 101-129 2-29 (36)
263 KOG3113 Uncharacterized conser 28.1 1.7E+02 0.0037 21.7 4.7 70 11-91 109-180 (293)
264 PRK05978 hypothetical protein; 28.1 36 0.00078 22.9 1.2 27 102-130 35-61 (148)
265 PF07503 zf-HYPF: HypF finger; 27.5 18 0.0004 17.9 -0.2 30 38-69 1-31 (35)
266 PF13834 DUF4193: Domain of un 27.4 31 0.00066 21.5 0.8 31 11-42 68-98 (99)
267 PF14949 ARF7EP_C: ARF7 effect 27.2 19 0.00042 22.6 -0.1 32 118-151 64-95 (103)
268 PRK12496 hypothetical protein; 27.0 27 0.00058 23.9 0.5 24 102-130 129-152 (164)
269 PF01530 zf-C2HC: Zinc finger, 26.9 39 0.00085 16.3 0.9 11 58-68 2-12 (31)
270 KOG1571 Predicted E3 ubiquitin 26.4 60 0.0013 25.1 2.3 31 10-45 302-332 (355)
271 PF01194 RNA_pol_N: RNA polyme 26.4 1.1E+02 0.0024 17.2 2.9 13 56-70 3-15 (60)
272 COG1571 Predicted DNA-binding 25.8 37 0.0008 27.0 1.1 26 102-131 352-377 (421)
273 COG4098 comFA Superfamily II D 25.8 37 0.00081 26.5 1.1 34 10-45 36-69 (441)
274 TIGR01053 LSD1 zinc finger dom 25.6 50 0.0011 15.8 1.2 25 102-129 3-27 (31)
275 COG2824 PhnA Uncharacterized Z 25.4 36 0.00078 21.5 0.8 23 107-131 8-30 (112)
276 COG5627 MMS21 DNA repair prote 25.1 53 0.0011 24.0 1.7 59 51-115 183-241 (275)
277 PF03854 zf-P11: P-11 zinc fin 24.9 59 0.0013 17.4 1.5 46 13-71 2-47 (50)
278 PRK00241 nudC NADH pyrophospha 24.9 1.4E+02 0.003 22.0 3.9 28 99-129 98-125 (256)
279 PF01927 Mut7-C: Mut7-C RNAse 24.6 73 0.0016 21.1 2.3 33 81-115 69-104 (147)
280 smart00440 ZnF_C2C2 C2C2 Zinc 24.3 32 0.00068 17.5 0.4 10 120-129 27-36 (40)
281 PF10764 Gin: Inhibitor of sig 23.9 38 0.00083 17.9 0.6 35 15-53 1-35 (46)
282 smart00355 ZnF_C2H2 zinc finge 23.8 36 0.00078 14.2 0.5 9 123-131 2-10 (26)
283 COG1592 Rubrerythrin [Energy p 23.6 1.3E+02 0.0029 20.7 3.4 24 100-129 134-157 (166)
284 COG3357 Predicted transcriptio 23.5 1.9E+02 0.0041 17.8 4.0 61 67-131 17-86 (97)
285 COG1996 RPC10 DNA-directed RNA 23.5 41 0.00089 18.1 0.7 25 102-129 8-32 (49)
286 KOG0298 DEAD box-containing he 23.4 34 0.00074 31.1 0.6 38 12-51 1152-1189(1394)
287 PLN02189 cellulose synthase 22.8 79 0.0017 28.3 2.6 49 12-68 33-85 (1040)
288 PF09943 DUF2175: Uncharacteri 22.8 1.2E+02 0.0026 19.0 2.8 39 13-52 2-40 (101)
289 PF13963 Transpos_assoc: Trans 22.3 1.4E+02 0.003 17.4 2.9 16 100-115 37-52 (77)
290 PRK00762 hypA hydrogenase nick 21.7 1.7E+02 0.0037 18.9 3.5 27 100-129 70-100 (124)
291 PF00569 ZZ: Zinc finger, ZZ t 20.9 1.1E+02 0.0025 15.7 2.2 33 13-45 4-37 (46)
292 PF04438 zf-HIT: HIT zinc fing 20.9 27 0.00059 16.6 -0.3 14 119-132 11-24 (30)
293 PF10058 DUF2296: Predicted in 20.8 1.1E+02 0.0024 16.7 2.1 27 101-129 23-52 (54)
294 PF06827 zf-FPG_IleRS: Zinc fi 20.7 42 0.00091 15.5 0.4 24 103-128 4-28 (30)
295 PF04606 Ogr_Delta: Ogr/Delta- 20.6 30 0.00065 18.2 -0.2 12 102-113 27-38 (47)
296 PF03811 Zn_Tnp_IS1: InsA N-te 20.6 78 0.0017 15.7 1.3 26 100-127 5-35 (36)
297 COG2023 RPR2 RNase P subunit R 20.6 87 0.0019 19.8 1.8 29 100-130 56-91 (105)
298 PF06044 DRP: Dam-replacing fa 20.4 32 0.0007 25.2 -0.1 30 100-131 31-63 (254)
299 PRK05580 primosome assembly pr 20.3 62 0.0013 27.4 1.5 31 107-138 395-430 (679)
300 PF02591 DUF164: Putative zinc 20.3 1.1E+02 0.0024 16.5 2.1 12 98-111 44-55 (56)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=3.9e-26 Score=173.51 Aligned_cols=140 Identities=36% Similarity=0.808 Sum_probs=122.7
Q ss_pred CCeeecccccccCC-CCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHH
Q 043988 11 TPSFVCEICVESRS-LYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLA 89 (151)
Q Consensus 11 ~~~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~ 89 (151)
.+..+|.||+.+.+ ..+++....|+|.||.+|+++|+..+ ......+.||..+|...++.+....+|++.+.+.|+..
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~-~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~ 222 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK-LLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQR 222 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh-hccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHH
Confidence 45779999995444 44677777899999999999999999 44455799999999999999999999999999999999
Q ss_pred HHhhhhcCCCeeecCcccCCccccccc----cccCcccCcccchhhhhcCCCCCCCCCCchhhhhC
Q 043988 90 LCESALVGHKKFYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151 (151)
Q Consensus 90 ~~~~~~~~~~~~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~ 151 (151)
+.+.++...+.+|||+|+|...+.... .......|+.|+..||..|+.+||.+++|++|++|
T Consensus 223 ~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~ 288 (384)
T KOG1812|consen 223 LKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKL 288 (384)
T ss_pred HHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHh
Confidence 999998887777999999998887663 44566789999999999999999999999999997
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=1.4e-25 Score=166.53 Aligned_cols=136 Identities=25% Similarity=0.575 Sum_probs=122.6
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCc-cccCCCCCCCCCccChhHHhhcCCHHHHHHHHHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNI-TNISCPQLGCEARLEFEDCRLILPDDVFARWGLA 89 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~ 89 (151)
...+.|.|||++..+..-+.+++|+|.||++|++.|+...|++|. ..++||.++|++..+...++.+|+.++++||+.+
T Consensus 182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l 261 (445)
T KOG1814|consen 182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL 261 (445)
T ss_pred hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence 456899999999988777788899999999999999999999874 5799999999999999999999999999999999
Q ss_pred HHhhhhcC-CCeeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCCCCchh
Q 043988 90 LCESALVG-HKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQ 147 (151)
Q Consensus 90 ~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~ 147 (151)
++++.+.. .+.+|||++.|+.++-. +.+...+.|.+|+..||..|+..||++..|.-
T Consensus 262 ~lqk~l~~msdv~yCPr~~Cq~p~~~-d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~ 319 (445)
T KOG1814|consen 262 MLQKTLELMSDVVYCPRACCQLPVKQ-DPGRALAICSKCNFAFCTLCKLTWHGVSPCKV 319 (445)
T ss_pred HHHHHHHhhcccccCChhhccCcccc-CchhhhhhhccCccHHHHHHHHhhcCCCcccC
Confidence 99988886 67789999999999844 45677899999999999999999999988863
No 3
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=1.2e-20 Score=146.75 Aligned_cols=138 Identities=24% Similarity=0.491 Sum_probs=119.3
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCcc-ccCCCCCCCCCccChhHHhhcCCH-HHHHHHHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNIT-NISCPQLGCEARLEFEDCRLILPD-DVFARWGL 88 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~-~i~CP~~~C~~~~~~~~i~~~l~~-~~~~~~~~ 88 (151)
....+|.||++..+. .++ .+.|+|.||..|+..|+..+|.++.. .|+||..+|...+....|..++++ ++.++|.+
T Consensus 68 ~~~~~c~ic~~~~~~-~~~-~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~ 145 (444)
T KOG1815|consen 68 KGDVQCGICVESYDG-EII-GLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQR 145 (444)
T ss_pred CccccCCcccCCCcc-hhh-hcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHH
Confidence 345899999998866 444 45899999999999999999987532 399999999999999999999988 49999999
Q ss_pred HHHhhhhcCC-CeeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCCCCchhhhhC
Q 043988 89 ALCESALVGH-KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151 (151)
Q Consensus 89 ~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~ 151 (151)
.+.++++... ...|||+|+|+..+.........+.| .|++.||+.|+.+||.|.+|..+.+|
T Consensus 146 ~i~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~w 208 (444)
T KOG1815|consen 146 YILRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKW 208 (444)
T ss_pred HHHHHHHhcCCccccCCCCCCCceeeccCCCccceeC-CCCchhHhhccccccCCCcccchHHH
Confidence 9999999875 45699999999988864445788999 58889999999999999999999887
No 4
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.67 E-value=1.1e-16 Score=116.06 Aligned_cols=133 Identities=26% Similarity=0.570 Sum_probs=110.7
Q ss_pred CCCCCeeecccccccCCCCCceecCCCC--CccchHHHHHHHHHHHhCC--------ccccCCCCCCCCCccChhHH-hh
Q 043988 8 DDGTPSFVCEICVESRSLYDSFDVKGCS--HFNCTSCIVRYIASKLEGN--------ITNISCPQLGCEARLEFEDC-RL 76 (151)
Q Consensus 8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~--------~~~i~CP~~~C~~~~~~~~i-~~ 76 (151)
..+.++.+|..|.+.. +.+...+|. |..|.+|++.|..+.+.+. .+.+.||. +|...+-.+.. -.
T Consensus 216 ~~N~~ni~C~~Ctdv~---~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~ 291 (446)
T KOG0006|consen 216 ATNSRNITCITCTDVR---SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFR 291 (446)
T ss_pred hcccccceeEEecCCc---cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhhe
Confidence 3567889999997543 445555787 9999999999999998653 24688987 88876654443 67
Q ss_pred cCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccccccccccCcccCcc-cchhhhhcCCCCCCCCCCch
Q 043988 77 ILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPH-CRRLFCVQCKVPWHSEFDCS 146 (151)
Q Consensus 77 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~ 146 (151)
||+.+.|.+|+++..+..+.....+.||+|+|+..+..+. +.++++|+. |++.||+.|++.+|.| .|.
T Consensus 292 ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EP-D~rkvtC~~gCgf~FCR~C~e~yh~g-eC~ 360 (446)
T KOG0006|consen 292 ILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEP-DQRKVTCEGGCGFAFCRECKEAYHEG-ECS 360 (446)
T ss_pred ecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCC-CCCcccCCCCchhHhHHHHHhhhccc-cce
Confidence 8999999999999999999888899999999999888865 689999986 9999999999999987 554
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.57 E-value=1.7e-15 Score=87.80 Aligned_cols=62 Identities=37% Similarity=0.835 Sum_probs=54.7
Q ss_pred HHHHHHHHhhhhcC-CCeeecCcccCCcccccc-ccccCcccCcccchhhhhcCCCCCCCCCCc
Q 043988 84 ARWGLALCESALVG-HKKFYCPYKDCSSMLIDE-GEAIRKSNCPHCRRLFCVQCKVPWHSEFDC 145 (151)
Q Consensus 84 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 145 (151)
++|++++.+.++.. .+.+|||+++|+.++... +.....+.|+.|+..||+.|+.+||.|++|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 47889999998887 466799999999999887 346788999999999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.51 E-value=1.9e-15 Score=87.48 Aligned_cols=62 Identities=26% Similarity=0.702 Sum_probs=42.1
Q ss_pred HHHHHHHHhhhhcCC-CeeecCcccCCccccccccccC-cccCcccchhhhhcCCCCCCCCCCc
Q 043988 84 ARWGLALCESALVGH-KKFYCPYKDCSSMLIDEGEAIR-KSNCPHCRRLFCVQCKVPWHSEFDC 145 (151)
Q Consensus 84 ~~~~~~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~-~~~C~~C~~~~C~~C~~~~H~~~~C 145 (151)
++|++++++.++..+ +.+|||+++|+.++..+..... .+.|+.|++.||+.|+.+||.|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 578888888888654 4579999999999998855333 3999999999999999999999987
No 7
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=98.90 E-value=4.5e-10 Score=59.28 Aligned_cols=40 Identities=33% Similarity=0.726 Sum_probs=27.2
Q ss_pred cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988 16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP 61 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 61 (151)
|+||++.+ .+++++ +|||.||.+|+..+++..- ...+.||
T Consensus 1 CpiC~~~~--~~Pv~l-~CGH~FC~~Cl~~~~~~~~---~~~~~CP 40 (42)
T PF15227_consen 1 CPICLDLF--KDPVSL-PCGHSFCRSCLERLWKEPS---GSGFSCP 40 (42)
T ss_dssp ETTTTSB---SSEEE--SSSSEEEHHHHHHHHCCSS---SST---S
T ss_pred CCccchhh--CCcccc-CCcCHHHHHHHHHHHHccC---CcCCCCc
Confidence 89999877 566665 8999999999999876532 1227888
No 8
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.88 E-value=1.6e-09 Score=73.12 Aligned_cols=57 Identities=23% Similarity=0.609 Sum_probs=44.7
Q ss_pred CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988 9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75 (151)
Q Consensus 9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~ 75 (151)
..+..+.||||++++....++.. .|||.||..|++.-++.. -+|| -|...|+..++-
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsT-kCGHvFC~~Cik~alk~~-------~~CP--~C~kkIt~k~~~ 183 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVST-KCGHVFCSQCIKDALKNT-------NKCP--TCRKKITHKQFH 183 (187)
T ss_pred ccccccCCCceecchhhcccccc-ccchhHHHHHHHHHHHhC-------CCCC--Ccccccchhhhe
Confidence 34566899999999876666654 899999999999877664 5899 577778777653
No 9
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=98.85 E-value=3.8e-09 Score=55.47 Aligned_cols=39 Identities=26% Similarity=0.744 Sum_probs=31.0
Q ss_pred cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988 16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP 61 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 61 (151)
|+||++.+.. ...+++|||.||..|+..+++. ...++||
T Consensus 1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~-----~~~~~CP 39 (41)
T PF00097_consen 1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLEN-----SGSVKCP 39 (41)
T ss_dssp ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHH-----TSSSBTT
T ss_pred CCcCCccccC--CCEEecCCCcchHHHHHHHHHh-----cCCccCC
Confidence 7999987743 4446699999999999999987 2246788
No 10
>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=98.82 E-value=1.1e-09 Score=58.52 Aligned_cols=41 Identities=29% Similarity=0.551 Sum_probs=32.5
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ 62 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 62 (151)
+|+||++++...+.+..++|+|.|+.+|+..|++.. .+||.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~ 42 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV 42 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence 699999999765555556899999999999999773 38883
No 11
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.80 E-value=4.6e-09 Score=55.47 Aligned_cols=42 Identities=29% Similarity=0.576 Sum_probs=23.0
Q ss_pred cccccccCC-CCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988 16 CEICVESRS-LYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP 61 (151)
Q Consensus 16 C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 61 (151)
|+||.+ +. ......++.|||+||++|+.++++... ...|+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence 899998 53 344555668999999999999988543 2357887
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=98.79 E-value=3.1e-09 Score=55.24 Aligned_cols=38 Identities=34% Similarity=0.860 Sum_probs=28.8
Q ss_pred cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988 16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ 62 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 62 (151)
|+||++.. .+++.++.|||.||.+|+.+|++.. .+||.
T Consensus 1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~ 38 (39)
T PF13923_consen 1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKN-------PKCPV 38 (39)
T ss_dssp ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence 89999877 4465667999999999999997662 57773
No 13
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=98.71 E-value=1.8e-08 Score=69.60 Aligned_cols=65 Identities=22% Similarity=0.451 Sum_probs=48.4
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHh---------CCccccCCCCCCCCCccChhHHhhcCCH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLE---------GNITNISCPQLGCEARLEFEDCRLILPD 80 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~i~CP~~~C~~~~~~~~i~~~l~~ 80 (151)
...++|+||++.. .+++. ..|||.||..|+..|+...-. .......|| -|+..++...+..+.+.
T Consensus 16 ~~~~~CpICld~~--~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiygr 89 (193)
T PLN03208 16 GGDFDCNICLDQV--RDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYGR 89 (193)
T ss_pred CCccCCccCCCcC--CCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeecc
Confidence 4568999999876 45554 489999999999999864321 122357999 69999998888766553
No 14
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.68 E-value=1.9e-08 Score=53.66 Aligned_cols=41 Identities=27% Similarity=0.648 Sum_probs=33.2
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ 62 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 62 (151)
.|++|++.+...+.+.+++|||.||..|+.... ...+.||.
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~ 41 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI 41 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC
Confidence 489999999655567777999999999999876 23578984
No 15
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.55 E-value=1e-07 Score=50.43 Aligned_cols=44 Identities=32% Similarity=0.763 Sum_probs=33.5
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
+|+||++.+ .+.+.+..|+|.||.+|+..+++. ....|| .|+..
T Consensus 1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp--~C~~~ 44 (45)
T cd00162 1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS------GKNTCP--LCRTP 44 (45)
T ss_pred CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh------CcCCCC--CCCCc
Confidence 589999877 345555569999999999999876 246788 57643
No 16
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.42 E-value=1.1e-07 Score=70.26 Aligned_cols=112 Identities=22% Similarity=0.359 Sum_probs=67.4
Q ss_pred cCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHH
Q 043988 7 TDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARW 86 (151)
Q Consensus 7 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~ 86 (151)
.........|+||++.+..+ .+++|+|.||+.|+...+. ..+.|| .|.. ... .+...-.....
T Consensus 7 ~~~~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp--~cr~-~~~----~~~~n~~l~~~ 69 (386)
T KOG2177|consen 7 LEVLQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCP--VCRP-PSR----NLRPNVLLANL 69 (386)
T ss_pred hhhccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCc--ccCC-chh----ccCccHHHHHH
Confidence 34456778999999998655 5568999999999999887 358999 6773 222 22222122222
Q ss_pred HHHHHhhhhcCC-C--eeecCcccCCccccccccccCcccCcccchhhhhcCC-CCCCCCCCc
Q 043988 87 GLALCESALVGH-K--KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCK-VPWHSEFDC 145 (151)
Q Consensus 87 ~~~~~~~~~~~~-~--~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C 145 (151)
............ . ...|+. ......+.|..|....|..|. ...|.++.-
T Consensus 70 ~~~~~~~~~~~~~~~~~~~c~~----------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~ 122 (386)
T KOG2177|consen 70 VERLRQLRLSRPLGSKEELCEK----------HGEELKLFCEEDEKLLCVLCRESGEHRGHPV 122 (386)
T ss_pred HHHHHhcCCcccccccchhhhh----------cCCcceEEecccccccCCCCCCcccccCCcc
Confidence 222222111110 0 112331 122267889899999999998 666776653
No 17
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.28 E-value=9.2e-07 Score=48.35 Aligned_cols=46 Identities=30% Similarity=0.709 Sum_probs=33.7
Q ss_pred eeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
...|.||++.. .+ +.+.+|||. ||.+|+..+++ ...+|| -|...+.
T Consensus 2 ~~~C~iC~~~~--~~-~~~~pCgH~~~C~~C~~~~~~-------~~~~CP--~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENP--RD-VVLLPCGHLCFCEECAERLLK-------RKKKCP--ICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSB--SS-EEEETTCEEEEEHHHHHHHHH-------TTSBBT--TTTBB-S
T ss_pred cCCCccCCccC--Cc-eEEeCCCChHHHHHHhHHhcc-------cCCCCC--cCChhhc
Confidence 35899999865 33 444589999 99999999987 246899 5877654
No 18
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.24 E-value=1.2e-06 Score=67.26 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=47.1
Q ss_pred ccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH-hhcCCHHHHH
Q 043988 6 ETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC-RLILPDDVFA 84 (151)
Q Consensus 6 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i-~~~l~~~~~~ 84 (151)
..+..+..+.|+||++.+. +++ +..|||.||..|+..++.. ...|| .|...+....+ .+.+=.++++
T Consensus 19 ~l~~Le~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~~-------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe 86 (397)
T TIGR00599 19 SLYPLDTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLSN-------QPKCP--LCRAEDQESKLRSNWLVSEIVE 86 (397)
T ss_pred cccccccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHhC-------CCCCC--CCCCccccccCccchHHHHHHH
Confidence 3455567789999998774 334 4589999999999998754 13799 68877765544 2222234445
Q ss_pred HHH
Q 043988 85 RWG 87 (151)
Q Consensus 85 ~~~ 87 (151)
.|.
T Consensus 87 ~~~ 89 (397)
T TIGR00599 87 SFK 89 (397)
T ss_pred HHH
Confidence 543
No 19
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.23 E-value=1e-06 Score=63.29 Aligned_cols=51 Identities=24% Similarity=0.500 Sum_probs=36.9
Q ss_pred CCeeecccccccCCCCC-----ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 11 TPSFVCEICVESRSLYD-----SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
.+..+|+||++.+.... ...+.+|+|.||.+|+..|++. ..+|| -|...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCP--lCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCP--VCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCC--CCCCEee
Confidence 34579999999865432 2345589999999999999764 24899 5776543
No 20
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=98.22 E-value=1.5e-06 Score=44.22 Aligned_cols=30 Identities=40% Similarity=0.825 Sum_probs=23.9
Q ss_pred cccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988 16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA 48 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 48 (151)
|+||++.. .. ...+.|+|.||..|+..++.
T Consensus 1 C~iC~~~~--~~-~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEEL--KD-PVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCC--CC-cEEecCCChHHHHHHHHHHH
Confidence 78998773 33 44458999999999999987
No 21
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.20 E-value=1.1e-06 Score=62.07 Aligned_cols=61 Identities=21% Similarity=0.582 Sum_probs=47.2
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCC
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILP 79 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~ 79 (151)
....++|.||++.. .+++.. .|||.||=.||-+|+..... .-.|| -|+..++.+.|--|.+
T Consensus 44 ~~~~FdCNICLd~a--kdPVvT-lCGHLFCWpClyqWl~~~~~----~~~cP--VCK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA--KDPVVT-LCGHLFCWPCLYQWLQTRPN----SKECP--VCKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeecccc--CCCEEe-ecccceehHHHHHHHhhcCC----CeeCC--ccccccccceEEeeec
Confidence 46789999999866 455554 69999999999999987643 24678 6998888888766654
No 22
>PHA02926 zinc finger-like protein; Provisional
Probab=98.16 E-value=1.9e-06 Score=60.53 Aligned_cols=57 Identities=25% Similarity=0.476 Sum_probs=39.2
Q ss_pred CCeeecccccccCCC-----C-CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 11 TPSFVCEICVESRSL-----Y-DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~-----~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
.+..+|+||++.... . .+-.+.+|+|.||..|+..|.+..-..+ ..-.|| -|...+.
T Consensus 168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~-~~rsCP--iCR~~f~ 230 (242)
T PHA02926 168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG-ASDNCP--ICRTRFR 230 (242)
T ss_pred cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC-cCCcCC--CCcceee
Confidence 345799999987522 1 2334568999999999999998653223 245799 5775443
No 23
>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=98.13 E-value=4.9e-06 Score=47.51 Aligned_cols=50 Identities=22% Similarity=0.251 Sum_probs=38.4
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~ 75 (151)
+.|+||.+.+. +++. ..|||.||++|+..|++. ..+|| -|+..++.+++.
T Consensus 2 ~~Cpi~~~~~~--~Pv~-~~~G~v~~~~~i~~~~~~-------~~~cP--~~~~~~~~~~l~ 51 (63)
T smart00504 2 FLCPISLEVMK--DPVI-LPSGQTYERRAIEKWLLS-------HGTDP--VTGQPLTHEDLI 51 (63)
T ss_pred cCCcCCCCcCC--CCEE-CCCCCEEeHHHHHHHHHH-------CCCCC--CCcCCCChhhce
Confidence 57999998774 4554 489999999999999976 24788 577777766653
No 24
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=1.4e-06 Score=67.82 Aligned_cols=59 Identities=27% Similarity=0.616 Sum_probs=44.8
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcC
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLIL 78 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l 78 (151)
...||||+++.+.. .+..|||.||-.|+.+|+...... ....|| -|...|...++..+.
T Consensus 186 ~~~CPICL~~~~~p---~~t~CGHiFC~~CiLqy~~~s~~~--~~~~CP--iC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 186 DMQCPICLEPPSVP---VRTNCGHIFCGPCILQYWNYSAIK--GPCSCP--ICRSTITLKDLLPVF 244 (513)
T ss_pred CCcCCcccCCCCcc---cccccCceeeHHHHHHHHhhhccc--CCccCC--chhhhccccceeeee
Confidence 67899999877543 334699999999999999987222 256888 488888887776554
No 25
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.11 E-value=5.3e-06 Score=61.46 Aligned_cols=54 Identities=24% Similarity=0.447 Sum_probs=38.2
Q ss_pred eecccccccCC-CCCceecC-CCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988 14 FVCEICVESRS-LYDSFDVK-GCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75 (151)
Q Consensus 14 ~~C~iC~~~~~-~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~ 75 (151)
..||+|..+.. .+++..+. .|||.||.+|+...+.. + +..|| .|...+....++
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~----~--~~~CP--~C~~~lrk~~fr 59 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G--SGSCP--ECDTPLRKNNFR 59 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC----C--CCCCC--CCCCccchhhcc
Confidence 57999998644 34432221 69999999999998632 2 35899 798888777653
No 26
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.98 E-value=3.6e-06 Score=61.19 Aligned_cols=52 Identities=29% Similarity=0.695 Sum_probs=41.0
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
.....|.+|++.... ++..+|||.||-+|+..|...+- .|| -|...+...++
T Consensus 237 ~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~-------eCP--lCR~~~~pskv 288 (293)
T KOG0317|consen 237 EATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKA-------ECP--LCREKFQPSKV 288 (293)
T ss_pred CCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHcccc-------CCC--cccccCCCcce
Confidence 445789999987743 34568999999999999988763 499 69888877665
No 27
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=7e-06 Score=60.54 Aligned_cols=95 Identities=23% Similarity=0.526 Sum_probs=62.0
Q ss_pred CCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccc
Q 043988 33 GCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML 112 (151)
Q Consensus 33 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~ 112 (151)
+||-.||++|+..|....-..+. .-. -...|...++.... ..++|..+..+. .+.....|| .|....
T Consensus 341 gCgf~FCR~C~e~yh~geC~~~~-~as-~t~tc~y~vde~~a-------~~arwd~as~~T--Ik~tTkpCP--kChvpt 407 (446)
T KOG0006|consen 341 GCGFAFCRECKEAYHEGECSAVF-EAS-GTTTCAYRVDERAA-------EQARWDAASKET--IKKTTKPCP--KCHVPT 407 (446)
T ss_pred CchhHhHHHHHhhhccccceeee-ccc-cccceeeecChhhh-------hhhhhhhhhhhh--hhhccCCCC--CccCcc
Confidence 49999999999998654332110 000 01145555555432 335666543332 233455788 999999
Q ss_pred cccccccCcccCcc--cchhhhhcCCCCCCC
Q 043988 113 IDEGEAIRKSNCPH--CRRLFCVQCKVPWHS 141 (151)
Q Consensus 113 ~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~ 141 (151)
.+++ ...+|.|+. |+.+|||.|+-+|..
T Consensus 408 ErnG-GCmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 408 ERNG-GCMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ccCC-ceEEeecCCCCCCceeEeccCChhhh
Confidence 9875 488999965 999999999999954
No 28
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.82 E-value=1.7e-05 Score=44.52 Aligned_cols=52 Identities=31% Similarity=0.578 Sum_probs=33.4
Q ss_pred CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
++....+.|||-...+ .+++.-..|+|.|-++-+.+|+ ++...+.||..+|.
T Consensus 6 ~~~~~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 6 EGGTISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN 57 (57)
T ss_dssp -SSB--SB-TTTSSB---SSEEEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred eccEeccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence 3456678999999776 6777766899999999999999 23346899998884
No 29
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=97.71 E-value=2.5e-05 Score=61.33 Aligned_cols=58 Identities=31% Similarity=0.755 Sum_probs=44.3
Q ss_pred CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988 8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE 72 (151)
Q Consensus 8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~ 72 (151)
+++....+|.+|-++. .+.+. ..|.|.||+-|++.|+.....+. .++|| .|...++.+
T Consensus 531 ~enk~~~~C~lc~d~a--ed~i~-s~ChH~FCrlCi~eyv~~f~~~~--nvtCP--~C~i~LsiD 588 (791)
T KOG1002|consen 531 DENKGEVECGLCHDPA--EDYIE-SSCHHKFCRLCIKEYVESFMENN--NVTCP--VCHIGLSID 588 (791)
T ss_pred ccccCceeecccCChh--hhhHh-hhhhHHHHHHHHHHHHHhhhccc--CCCCc--ccccccccc
Confidence 3456678999998765 45554 48999999999999998887654 38999 687665544
No 30
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.63 E-value=4.5e-05 Score=56.03 Aligned_cols=54 Identities=20% Similarity=0.490 Sum_probs=43.4
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF 71 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~ 71 (151)
.+...+|.||++++-..+-+..++|.|.|-..|+.+|+..- ..+|| .|...+++
T Consensus 320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y------~~~CP--vCrt~iPP 373 (374)
T COG5540 320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGY------SNKCP--VCRTAIPP 373 (374)
T ss_pred cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhh------cccCC--ccCCCCCC
Confidence 34568999999988766667777999999999999998643 46899 68877654
No 31
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.43 E-value=8.5e-05 Score=55.41 Aligned_cols=63 Identities=27% Similarity=0.568 Sum_probs=45.0
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh-cCCHHHHHHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL-ILPDDVFARW 86 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~~~~~~ 86 (151)
...-|.||++-+..+- +.+|+|+||.=|++.|+..+ ..|| .|...+...+++. .+-++.++-|
T Consensus 22 ~lLRC~IC~eyf~ip~---itpCsHtfCSlCIR~~L~~~-------p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~ 85 (442)
T KOG0287|consen 22 DLLRCGICFEYFNIPM---ITPCSHTFCSLCIRKFLSYK-------PQCP--TCCVTVTESDLRNNRILDEIVKSL 85 (442)
T ss_pred HHHHHhHHHHHhcCce---eccccchHHHHHHHHHhccC-------CCCC--ceecccchhhhhhhhHHHHHHHHH
Confidence 3467999998875432 34799999999999998764 5788 6888888888742 2333444444
No 32
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=8e-05 Score=60.69 Aligned_cols=55 Identities=25% Similarity=0.652 Sum_probs=42.2
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhc
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLI 77 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~ 77 (151)
....|++|.. .+ .+.+ +..|+|.||.+|++..+... .=+|| .|...|...+|..|
T Consensus 642 ~~LkCs~Cn~-R~-Kd~v-I~kC~H~FC~~Cvq~r~etR------qRKCP--~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 642 ELLKCSVCNT-RW-KDAV-ITKCGHVFCEECVQTRYETR------QRKCP--KCNAAFGANDVHRI 696 (698)
T ss_pred hceeCCCccC-ch-hhHH-HHhcchHHHHHHHHHHHHHh------cCCCC--CCCCCCCccccccc
Confidence 4579999983 22 3333 34799999999999988776 35999 89999998887543
No 33
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=0.00015 Score=55.98 Aligned_cols=39 Identities=26% Similarity=0.663 Sum_probs=33.5
Q ss_pred eeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCC
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSE 142 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~ 142 (151)
.+.|| .|.+.+...++ .++|+|. |++.||+.|+.+|+.+
T Consensus 306 wr~Cp--kC~~~ie~~~G-Cnhm~Cr-C~~~fcy~C~~~~~~~ 344 (384)
T KOG1812|consen 306 WRQCP--KCKFMIELSEG-CNHMTCR-CGHQFCYMCGGDWKTH 344 (384)
T ss_pred cCcCc--ccceeeeecCC-cceEEee-ccccchhhcCcchhhC
Confidence 45799 99998888765 9999998 9999999999999543
No 34
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.28 E-value=0.00013 Score=55.71 Aligned_cols=111 Identities=20% Similarity=0.435 Sum_probs=66.6
Q ss_pred Ceeeccc--ccccC---CCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcC-----CH-
Q 043988 12 PSFVCEI--CVESR---SLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLIL-----PD- 80 (151)
Q Consensus 12 ~~~~C~i--C~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l-----~~- 80 (151)
....||- |--+. +...+.....|.-.||.-|...|.- +. .|+.... +.++..+ |.
T Consensus 272 dv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG------~s-------~Ck~~~~-~~~~l~~~~~~~d~a 337 (445)
T KOG1814|consen 272 DVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG------VS-------PCKVKAE-KLIELYLEYLEADEA 337 (445)
T ss_pred ccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC------CC-------cccCchH-HHHHHHHHHhhcCHH
Confidence 3456766 43221 1233445557899999999877642 21 2554332 2221111 11
Q ss_pred ---HHHHHHHHHHHhhhh----c----CCCeeecCcccCCccccccccccCcccCcccchhhhhcCCCCC
Q 043988 81 ---DVFARWGLALCESAL----V----GHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPW 139 (151)
Q Consensus 81 ---~~~~~~~~~~~~~~~----~----~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~ 139 (151)
++.+||.+++.+..+ + ..+...|| .|...+.+.+ +.++|.|..|++.|||.|....
T Consensus 338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~e-GCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSE-GCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCC-Cccceeeccccccceeehhhhc
Confidence 344566644333322 2 12445799 9999998865 5899999999999999998843
No 35
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=0.0002 Score=51.65 Aligned_cols=52 Identities=25% Similarity=0.636 Sum_probs=38.5
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHH-HHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR-YIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~-~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
..+.|.||++.... +...+|||.||-.|+.. +-+.+ .-.|| -|...+.+.++
T Consensus 214 ~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k------~~~Cp--lCRak~~pk~v 266 (271)
T COG5574 214 ADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKK------YEFCP--LCRAKVYPKKV 266 (271)
T ss_pred cccceeeeecccCC---cccccccchhhHHHHHHHHHhhc------cccCc--hhhhhccchhh
Confidence 46789999976633 45568999999999998 43333 34688 68888777766
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=97.26 E-value=0.00013 Score=43.06 Aligned_cols=42 Identities=24% Similarity=0.441 Sum_probs=29.9
Q ss_pred eecccccccCCC----------CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988 14 FVCEICVESRSL----------YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ 62 (151)
Q Consensus 14 ~~C~iC~~~~~~----------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 62 (151)
-.|.||++++.. .-.+....|||.|...||.++++.. -+||.
T Consensus 20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~ 71 (73)
T PF12678_consen 20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPL 71 (73)
T ss_dssp SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TT
T ss_pred CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCC
Confidence 359999998832 1234445799999999999998553 28884
No 37
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.25 E-value=0.00047 Score=50.09 Aligned_cols=51 Identities=25% Similarity=0.542 Sum_probs=37.1
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
+...+|++|-++- .-++....|+|+||..|+..-+.... .++|| .|++...
T Consensus 237 t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~a-----sf~Cp--~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWDA-----SFTCP--LCGENVE 287 (298)
T ss_pred cCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcchh-----hcccC--ccCCCCc
Confidence 4467999998643 34555656999999999887655442 48999 6886654
No 38
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=97.21 E-value=4.3e-05 Score=43.37 Aligned_cols=50 Identities=30% Similarity=0.702 Sum_probs=22.1
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~ 75 (151)
..-|++|.+-+ .+++.+..|.|.||..|+...+. -.|| -|..+.-..+++
T Consensus 7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~---------~~CP--vC~~Paw~qD~~ 56 (65)
T PF14835_consen 7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG---------SECP--VCHTPAWIQDIQ 56 (65)
T ss_dssp TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT---------TB-S--SS--B-S-SS--
T ss_pred hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC---------CCCC--CcCChHHHHHHH
Confidence 45699999876 45556668999999999866321 2488 687666555553
No 39
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.18 E-value=0.00029 Score=53.22 Aligned_cols=46 Identities=28% Similarity=0.621 Sum_probs=38.9
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA 67 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 67 (151)
.+|-||+|++...+-+..++|.|.|-..|+..|+... .-.||. |+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPv--CK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPV--CKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCC--CCC
Confidence 7999999999988888888999999999999998775 236885 553
No 40
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.97 E-value=0.00063 Score=39.77 Aligned_cols=58 Identities=19% Similarity=0.348 Sum_probs=27.0
Q ss_pred eeecccccccCC-CCCcee--c--CCCCCccchHHHHHHHHHHHhCCc-c---ccCCCCCCCCCccChh
Q 043988 13 SFVCEICVESRS-LYDSFD--V--KGCSHFNCTSCIVRYIASKLEGNI-T---NISCPQLGCEARLEFE 72 (151)
Q Consensus 13 ~~~C~iC~~~~~-~~~~~~--~--~~C~H~fC~~Cl~~~~~~~i~~~~-~---~i~CP~~~C~~~~~~~ 72 (151)
..+|+||+.... ..+... . ..|+..|-..||.+|+...-.... + .=+|| .|...|...
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~~ 68 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISWS 68 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEGG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeEe
Confidence 468999998765 222211 1 368899999999999987765432 2 22699 688877543
No 41
>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=96.92 E-value=0.00085 Score=39.53 Aligned_cols=51 Identities=24% Similarity=0.235 Sum_probs=35.2
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
.+.|+|+.+.+ .+++.+ ++||+|.++++..|+.. ....|| -++..++..++
T Consensus 4 ~f~CpIt~~lM--~dPVi~-~~G~tyer~~I~~~l~~------~~~~~P--~t~~~l~~~~l 54 (73)
T PF04564_consen 4 EFLCPITGELM--RDPVIL-PSGHTYERSAIERWLEQ------NGGTDP--FTRQPLSESDL 54 (73)
T ss_dssp GGB-TTTSSB---SSEEEE-TTSEEEEHHHHHHHHCT------TSSB-T--TT-SB-SGGGS
T ss_pred ccCCcCcCcHh--hCceeC-CcCCEEcHHHHHHHHHc------CCCCCC--CCCCcCCcccc
Confidence 47899999877 566665 79999999999999877 135788 45677776554
No 42
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=96.73 E-value=0.00086 Score=49.94 Aligned_cols=49 Identities=31% Similarity=0.764 Sum_probs=37.2
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL 69 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~ 69 (151)
..+-.+|.+|-.-+ .+......|-|+||++|+..|+... ..|| .|...+
T Consensus 12 ~n~~itC~LC~GYl--iDATTI~eCLHTFCkSCivk~l~~~-------~~CP--~C~i~i 60 (331)
T KOG2660|consen 12 LNPHITCRLCGGYL--IDATTITECLHTFCKSCIVKYLEES-------KYCP--TCDIVI 60 (331)
T ss_pred cccceehhhcccee--ecchhHHHHHHHHHHHHHHHHHHHh-------ccCC--ccceec
Confidence 35668999997655 4555566899999999999999883 5899 465433
No 43
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.10 E-value=0.0034 Score=46.19 Aligned_cols=52 Identities=25% Similarity=0.450 Sum_probs=35.9
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
+...-|-||-+-+.. .....|||.||.=|++.|+..+ ..|| -|........+
T Consensus 23 Ds~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~q-------p~CP--~Cr~~~~esrl 74 (391)
T COG5432 23 DSMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQ-------PFCP--VCREDPCESRL 74 (391)
T ss_pred hhHHHhhhhhheeec---ceecccccchhHHHHHHHhcCC-------CCCc--cccccHHhhhc
Confidence 445679999776643 3335899999999999998664 4788 46654443333
No 44
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.06 E-value=0.0052 Score=46.67 Aligned_cols=54 Identities=26% Similarity=0.477 Sum_probs=37.4
Q ss_pred CCeeecccccccCCCCC-----ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 11 TPSFVCEICVESRSLYD-----SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
.+..+|.||++.....- +-.+++|.|.||..|++.|-...-.+....-.|| -|.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CR 217 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCR 217 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--ccc
Confidence 34679999998765433 3334689999999999998744433333456888 465
No 45
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.02 E-value=0.00064 Score=51.07 Aligned_cols=47 Identities=30% Similarity=0.692 Sum_probs=32.6
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
..+.|+||++-+.. ......|.|+||.+|+..-++.. .-.|| .|...
T Consensus 42 ~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~g------n~ecp--tcRk~ 88 (381)
T KOG0311|consen 42 IQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSG------NNECP--TCRKK 88 (381)
T ss_pred hhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhc------CCCCc--hHHhh
Confidence 45789999987643 33345899999999987755443 23788 56643
No 46
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=95.87 E-value=0.0059 Score=36.83 Aligned_cols=51 Identities=25% Similarity=0.502 Sum_probs=33.5
Q ss_pred eeecccccccCCC---------CC-ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988 13 SFVCEICVESRSL---------YD-SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL 69 (151)
Q Consensus 13 ~~~C~iC~~~~~~---------~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~ 69 (151)
.-.|+||...++. .+ ++..-.|+|.|-..|+.+++.++-. .-.||+ |...+
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~----~~~CPm--CR~~w 81 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS----KGQCPM--CRQPW 81 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC----CCCCCC--cCCee
Confidence 3467777665541 12 2334479999999999999987521 248995 66544
No 47
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.62 E-value=0.035 Score=41.43 Aligned_cols=117 Identities=19% Similarity=0.341 Sum_probs=63.0
Q ss_pred eeecccccccCCCC---CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc--cChhHHhhcCCH-HHHHHH
Q 043988 13 SFVCEICVESRSLY---DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR--LEFEDCRLILPD-DVFARW 86 (151)
Q Consensus 13 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--~~~~~i~~~l~~-~~~~~~ 86 (151)
...|.||-++++.. ..+..+.|||.+|..|+...+... .+.|| -|... +...+++.+-.. ..++..
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~------~i~cp--fcR~~~~~~~~~~~~l~kNf~ll~~~ 74 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNS------RILCP--FCRETTEIPDGDVKSLQKNFALLQAI 74 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCc------eeecc--CCCCcccCCchhHhhhhhhHHHHHHH
Confidence 46899999888743 345566899999999998876543 46777 67765 555555544321 222222
Q ss_pred HHHHHhhhhcCCCeeecCcccCCcccccc-ccccCcccCcccchhhhhcCCCCC
Q 043988 87 GLALCESALVGHKKFYCPYKDCSSMLIDE-GEAIRKSNCPHCRRLFCVQCKVPW 139 (151)
Q Consensus 87 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~ 139 (151)
+.. ....+.......+|. .|....... ......-.|+.-...+|..|...-
T Consensus 75 ~~~-~~~~~~~~~~~~~~~-~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~ 126 (296)
T KOG4185|consen 75 EHM-KKTTVEEKGEADSPP-KCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFG 126 (296)
T ss_pred HHH-hcccccccCcccCCc-ccccCcccccceeecCCCcchhhhhhhhhccchh
Confidence 222 111111111222331 244322221 111222246666777888887744
No 48
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=95.58 E-value=0.013 Score=31.41 Aligned_cols=44 Identities=25% Similarity=0.640 Sum_probs=20.3
Q ss_pred cccccccCCCCC--ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 16 CEICVESRSLYD--SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 16 C~iC~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
||+|.++++..+ +..- .|++.+|+.|+..-++ ++ .=.|| +|++.
T Consensus 1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~----~~--~g~CP--gCr~~ 46 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILE----NE--GGRCP--GCREP 46 (48)
T ss_dssp -TTTS-B--CCCTT--SS-TTS----HHHHHHHTT----SS---SB-T--TT--B
T ss_pred CCCcccccccCCCccccC-cCCCcHHHHHHHHHHh----cc--CCCCC--CCCCC
Confidence 789998886543 3333 7999999999887544 11 23788 67754
No 49
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.43 E-value=0.0077 Score=41.94 Aligned_cols=32 Identities=28% Similarity=0.730 Sum_probs=24.8
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
.-++.|.||-.++. .++. ..|||.||..|...
T Consensus 194 ~IPF~C~iCKkdy~--spvv-t~CGH~FC~~Cai~ 225 (259)
T COG5152 194 KIPFLCGICKKDYE--SPVV-TECGHSFCSLCAIR 225 (259)
T ss_pred CCceeehhchhhcc--chhh-hhcchhHHHHHHHH
Confidence 34689999998884 3333 48999999999665
No 50
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.42 E-value=0.011 Score=47.79 Aligned_cols=44 Identities=23% Similarity=0.504 Sum_probs=34.2
Q ss_pred CeeecccccccCCCCCc--eecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988 12 PSFVCEICVESRSLYDS--FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ 62 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 62 (151)
....|+||.++.....- ...+.|+|.|+..|++.|++.+ -+||.
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~ 335 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPT 335 (543)
T ss_pred cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCc
Confidence 35689999998864321 3456899999999999999984 47884
No 51
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=95.40 E-value=0.0036 Score=44.78 Aligned_cols=52 Identities=29% Similarity=0.501 Sum_probs=37.4
Q ss_pred eecccccccCC-CCCcee--cCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988 14 FVCEICVESRS-LYDSFD--VKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF 71 (151)
Q Consensus 14 ~~C~iC~~~~~-~~~~~~--~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~ 71 (151)
.-||||-.+.. .+++.. -+.|-|++|.+|+-..+... +-.||.++|..++-.
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~G------pAqCP~~gC~kILRK 65 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRG------PAQCPYKGCGKILRK 65 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCC------CCCCCCccHHHHHHH
Confidence 46999977654 455433 23599999999998866442 678999999866543
No 52
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.39 E-value=0.018 Score=44.71 Aligned_cols=48 Identities=27% Similarity=0.683 Sum_probs=34.4
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
...++|.||+..+ ..++.. +|||.||..|+.+-+. ....|| .|...+.
T Consensus 82 ~sef~c~vc~~~l--~~pv~t-pcghs~c~~Cl~r~ld-------~~~~cp--~Cr~~l~ 129 (398)
T KOG4159|consen 82 RSEFECCVCSRAL--YPPVVT-PCGHSFCLECLDRSLD-------QETECP--LCRDELV 129 (398)
T ss_pred cchhhhhhhHhhc--CCCccc-cccccccHHHHHHHhc-------cCCCCc--ccccccc
Confidence 5678999998776 445554 9999999999777322 135777 5776555
No 53
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=95.28 E-value=0.03 Score=49.78 Aligned_cols=70 Identities=21% Similarity=0.343 Sum_probs=54.1
Q ss_pred CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCc---cccCCCCCCCCCccChhHHhhcCCH
Q 043988 9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNI---TNISCPQLGCEARLEFEDCRLILPD 80 (151)
Q Consensus 9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~---~~i~CP~~~C~~~~~~~~i~~~l~~ 80 (151)
.++..-.|-|||.+....-+-..+.|+|.|-..|.+..++..-.+.. ..|.|| -|..++.-..++++|++
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP 3554 (3738)
T ss_pred hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH
Confidence 34455689999987765555444699999999999998877655432 258999 69999999999999986
No 54
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=95.20 E-value=0.0093 Score=44.11 Aligned_cols=47 Identities=26% Similarity=0.576 Sum_probs=39.3
Q ss_pred CcccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHH
Q 043988 4 NAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASK 50 (151)
Q Consensus 4 ~a~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~ 50 (151)
+..++++.+...|.||+.-+-..+.|....|-|.|-..||.+|+...
T Consensus 106 e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~ 152 (368)
T KOG4445|consen 106 EFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC 152 (368)
T ss_pred HHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence 45678888999999998877776767777999999999999998744
No 55
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=95.12 E-value=0.028 Score=42.91 Aligned_cols=49 Identities=18% Similarity=0.466 Sum_probs=36.1
Q ss_pred CCeeecccccccCCCC----------CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 11 TPSFVCEICVESRSLY----------DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~----------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
.....|.||+|+.-.+ ..++.++|||.+--+|++.|++.+ -+|| -|+.+
T Consensus 285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCP--ICr~p 343 (491)
T COG5243 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCP--ICRRP 343 (491)
T ss_pred CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCC--cccCc
Confidence 3456899999983321 123556999999999999999875 4888 46654
No 56
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.05 E-value=0.014 Score=29.61 Aligned_cols=29 Identities=31% Similarity=0.816 Sum_probs=22.3
Q ss_pred eecCcccCCccccccc----cccCcccCcccchhh
Q 043988 101 FYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~ 131 (151)
+.|| .|+..+...+ .....+.|+.|++.|
T Consensus 3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 5788 8998887763 346689999998865
No 57
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.97 E-value=0.0097 Score=42.66 Aligned_cols=47 Identities=26% Similarity=0.593 Sum_probs=33.2
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
..+.|..|+.--+ .+.+.+..|+|.||..|...-.. -.|| -|+..+.
T Consensus 2 ~~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~---------~~C~--lCkk~ir 48 (233)
T KOG4739|consen 2 DFVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSP---------DVCP--LCKKSIR 48 (233)
T ss_pred ceEEeccccccCC-CCceeeeechhhhhhhhcccCCc---------cccc--cccceee
Confidence 3578999987555 56677779999999999654211 1787 5775543
No 58
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.96 E-value=0.015 Score=42.99 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=37.1
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
....+|+||+.+-..+ +. +.|+|.||.-|++...... ...|+ -|...|+...+
T Consensus 5 ~~~~eC~IC~nt~n~P--v~-l~C~HkFCyiCiKGsy~nd------k~~Ca--vCR~pids~i~ 57 (324)
T KOG0824|consen 5 TKKKECLICYNTGNCP--VN-LYCFHKFCYICIKGSYKND------KKTCA--VCRFPIDSTID 57 (324)
T ss_pred ccCCcceeeeccCCcC--cc-ccccchhhhhhhcchhhcC------CCCCc--eecCCCCcchh
Confidence 4556899999877543 33 5899999999988754432 34688 47766665543
No 59
>PF04641 Rtf2: Rtf2 RING-finger
Probab=94.95 E-value=0.063 Score=39.43 Aligned_cols=73 Identities=14% Similarity=0.273 Sum_probs=52.0
Q ss_pred CCCCCeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCH-HHHHH
Q 043988 8 DDGTPSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPD-DVFAR 85 (151)
Q Consensus 8 ~~~~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~-~~~~~ 85 (151)
+.....|.|||...++.. ..++.+.+|||.|....+...- . .-.|| .|+..+...+|-.|.+. ++++.
T Consensus 108 ~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~----~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~ 177 (260)
T PF04641_consen 108 DNSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K----SKKCP--VCGKPFTEEDIIPLNPPEEELEK 177 (260)
T ss_pred ccCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c----ccccc--ccCCccccCCEEEecCCccHHHH
Confidence 345778999999988864 3456667999999999998871 1 13588 69999998887666553 34444
Q ss_pred HHHHH
Q 043988 86 WGLAL 90 (151)
Q Consensus 86 ~~~~~ 90 (151)
+.+.+
T Consensus 178 l~~~~ 182 (260)
T PF04641_consen 178 LRERM 182 (260)
T ss_pred HHHHH
Confidence 44443
No 60
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.94 E-value=0.015 Score=46.02 Aligned_cols=38 Identities=26% Similarity=0.735 Sum_probs=30.8
Q ss_pred eecCcccCCccccccccccCcccCcc--cchhhhhcCCCCC--CC
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPH--CRRLFCVQCKVPW--HS 141 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~--H~ 141 (151)
..|| .|...+..++ ..+++.|.. |++.|||.|.+.| |.
T Consensus 227 k~CP--~c~~~iek~~-gc~~~~~~~~~c~~~FCw~Cl~~~~~h~ 268 (444)
T KOG1815|consen 227 KECP--KCKVPIEKDG-GCNHMTCKSASCKHEFCWVCLASLSDHG 268 (444)
T ss_pred ccCC--CcccchhccC-CccccccccCCcCCeeceeeeccccccc
Confidence 3488 9998888865 477888865 9999999998887 64
No 61
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.93 E-value=0.031 Score=42.89 Aligned_cols=59 Identities=19% Similarity=0.319 Sum_probs=45.3
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL 76 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~ 76 (151)
..+.|||=-+.....+++..+.|||.++++=+.+..+ +|...++|| -|+.....++.+.
T Consensus 333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCP--YCP~e~~~~~~kq 391 (394)
T KOG2817|consen 333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCP--YCPVEQLASDTKQ 391 (394)
T ss_pred ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCC--CCCcccCHHhccc
Confidence 3579999888777777877889999999998887643 354579999 6987766665543
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.92 E-value=0.016 Score=29.15 Aligned_cols=29 Identities=28% Similarity=0.716 Sum_probs=21.9
Q ss_pred eecCcccCCccccccc----cccCcccCcccchhh
Q 043988 101 FYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~ 131 (151)
+.|| .|+..+..++ .....+.|+.|++.|
T Consensus 3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 5788 8988777662 345689999998865
No 63
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.39 E-value=0.032 Score=43.04 Aligned_cols=54 Identities=22% Similarity=0.575 Sum_probs=38.8
Q ss_pred eeecccccccCCCC---CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 13 SFVCEICVESRSLY---DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 13 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
..+||||++++... .+++ +.|||.|=.+|++.|+- .+....|| -|..+-....|
T Consensus 4 g~tcpiclds~~~~g~hr~vs-l~cghlFgs~cie~wl~-----k~~~~~cp--~c~~katkr~i 60 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVS-LQCGHLFGSQCIEKWLG-----KKTKMQCP--LCSGKATKRQI 60 (463)
T ss_pred cccCceeeeeeeecCceEEee-ecccccccHHHHHHHHh-----hhhhhhCc--ccCChhHHHHH
Confidence 35899999987632 2344 58999999999999993 23457899 57765555444
No 64
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=94.35 E-value=0.032 Score=43.43 Aligned_cols=38 Identities=21% Similarity=0.629 Sum_probs=29.6
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHH
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIAS 49 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 49 (151)
.+....|++|.... .+++....|||.||..|+..+...
T Consensus 18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~ 55 (391)
T KOG0297|consen 18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN 55 (391)
T ss_pred CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc
Confidence 35678999998766 455553489999999999988765
No 65
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.21 E-value=0.017 Score=42.10 Aligned_cols=62 Identities=16% Similarity=0.443 Sum_probs=44.6
Q ss_pred CCCCeeecccccccCCCC--------CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH-hhcC
Q 043988 9 DGTPSFVCEICVESRSLY--------DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC-RLIL 78 (151)
Q Consensus 9 ~~~~~~~C~iC~~~~~~~--------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i-~~~l 78 (151)
+....-.|.||-..+..+ +.++ ++|+|.|-..|++.|.... + .-+|| -|++.++...+ ++..
T Consensus 220 khl~d~vCaVCg~~~~~s~~eegvienty~-LsCnHvFHEfCIrGWcivG----K-kqtCP--YCKekVdl~rmfsnpW 290 (328)
T KOG1734|consen 220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYK-LSCNHVFHEFCIRGWCIVG----K-KQTCP--YCKEKVDLKRMFSNPW 290 (328)
T ss_pred CCCCcchhHhhcchheeecchhhhhhhhee-eecccchHHHhhhhheeec----C-CCCCc--hHHHHhhHhhhccCcc
Confidence 334556899998766543 3444 4899999999999997542 2 35899 79999988876 4433
No 66
>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=94.11 E-value=0.025 Score=26.33 Aligned_cols=23 Identities=35% Similarity=0.956 Sum_probs=16.0
Q ss_pred ecCcccCCccccccccccCcccCcccchhh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.|| +|+..+.. ....||.||+.|
T Consensus 2 ~CP--~C~~~V~~-----~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCP--ECGAEVPE-----SAKFCPHCGYDF 24 (26)
T ss_pred cCC--CCcCCchh-----hcCcCCCCCCCC
Confidence 477 88876643 235788888876
No 67
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.07 E-value=0.036 Score=43.76 Aligned_cols=52 Identities=21% Similarity=0.584 Sum_probs=37.1
Q ss_pred CCeeecccccccCCCC-----Cc---------eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 11 TPSFVCEICVESRSLY-----DS---------FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~-----~~---------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
+...+|+||+.+.+.. .+ +-+.+|.|.|-++|+..|+..- .+.||. |..+++
T Consensus 569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y------kl~CPv--CR~pLP 634 (636)
T KOG0828|consen 569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY------KLICPV--CRCPLP 634 (636)
T ss_pred hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh------cccCCc--cCCCCC
Confidence 3456899999887631 11 2245899999999999998753 478994 655554
No 68
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.70 E-value=0.076 Score=40.27 Aligned_cols=49 Identities=24% Similarity=0.579 Sum_probs=34.3
Q ss_pred CCCCeeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988 9 DGTPSFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARL 69 (151)
Q Consensus 9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~ 69 (151)
+++...+|.||+.+. .+ +.+++|.|. .|.+|.....-+ . =.||. |...+
T Consensus 286 ~~~~gkeCVIClse~--rd-t~vLPCRHLCLCs~Ca~~Lr~q---~----n~CPI--CRqpi 335 (349)
T KOG4265|consen 286 ESESGKECVICLSES--RD-TVVLPCRHLCLCSGCAKSLRYQ---T----NNCPI--CRQPI 335 (349)
T ss_pred cccCCCeeEEEecCC--cc-eEEecchhhehhHhHHHHHHHh---h----cCCCc--cccch
Confidence 346678999999655 34 455699999 999998876522 1 26884 77554
No 69
>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=93.67 E-value=0.034 Score=36.48 Aligned_cols=36 Identities=19% Similarity=0.368 Sum_probs=27.5
Q ss_pred CeeecccccccCCC-CCceecCCCC------CccchHHHHHHHH
Q 043988 12 PSFVCEICVESRSL-YDSFDVKGCS------HFNCTSCIVRYIA 48 (151)
Q Consensus 12 ~~~~C~iC~~~~~~-~~~~~~~~C~------H~fC~~Cl~~~~~ 48 (151)
...+|.||++.+.. ...+.+ .++ |.||.+|+.+|-.
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHHh
Confidence 36899999999877 333443 676 7799999999943
No 70
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=93.29 E-value=0.025 Score=28.27 Aligned_cols=28 Identities=21% Similarity=0.740 Sum_probs=19.6
Q ss_pred eecCcccCCccccccccccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.+|| .|+..+....+....+.|+.|++.
T Consensus 2 ~FCp--~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEETTTTEEESSSS-E
T ss_pred eeCC--CCCccceEcCCCccCcCCCCCCCc
Confidence 4789 999999887554444478888764
No 71
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=93.27 E-value=0.077 Score=39.76 Aligned_cols=44 Identities=25% Similarity=0.647 Sum_probs=31.7
Q ss_pred CCeeecccccccCCCCCceecCCC--CCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGC--SHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
...++||||++.+..+. + +| ||..|.+|-... .-+|| .|...++
T Consensus 46 ~~lleCPvC~~~l~~Pi---~-QC~nGHlaCssC~~~~----------~~~CP--~Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSPPI---F-QCDNGHLACSSCRTKV----------SNKCP--TCRLPIG 91 (299)
T ss_pred hhhccCchhhccCcccc---e-ecCCCcEehhhhhhhh----------cccCC--ccccccc
Confidence 45679999999886533 2 45 899999997521 35788 5877666
No 72
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=93.08 E-value=0.058 Score=27.29 Aligned_cols=29 Identities=21% Similarity=0.586 Sum_probs=20.1
Q ss_pred eecCcccCCccccccc----cccCcccCcccchhh
Q 043988 101 FYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~ 131 (151)
+.|| .|+..+.... .....+.||.|+..|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 4688 8988766652 223478999998764
No 73
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.87 E-value=0.083 Score=38.18 Aligned_cols=57 Identities=12% Similarity=0.248 Sum_probs=42.1
Q ss_pred CCeeecccccccCCCCCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988 11 TPSFVCEICVESRSLYDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL 76 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~ 76 (151)
...+.||||-+.+...-. ..+-+|||.++.+|+..+|... +.+| -+..++...+|-.
T Consensus 219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D-------~v~p--v~d~plkdrdiI~ 276 (303)
T KOG3039|consen 219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD-------MVDP--VTDKPLKDRDIIG 276 (303)
T ss_pred ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc-------cccc--CCCCcCcccceEe
Confidence 367999999998865433 3455899999999999988764 4567 4677777776643
No 74
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=92.67 E-value=0.049 Score=42.02 Aligned_cols=46 Identities=33% Similarity=0.809 Sum_probs=32.3
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
...|.||-+.. +.+...+|||..|..|+..|-.+. +| -.||-+.|.
T Consensus 369 FeLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd--~g---q~CPFCRcE 414 (563)
T KOG1785|consen 369 FELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSD--EG---QTCPFCRCE 414 (563)
T ss_pred HHHHHHhhccC---CCcccccccchHHHHHHHhhcccC--CC---CCCCceeeE
Confidence 34699998644 335667999999999999984332 22 378866664
No 75
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.59 E-value=0.1 Score=39.71 Aligned_cols=35 Identities=29% Similarity=0.703 Sum_probs=25.4
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIAS 49 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~ 49 (151)
+.-.|+||+. .++.-++ .+|+|+-|..|+.+|+-.
T Consensus 421 Ed~lCpICyA-~pi~Avf--~PC~H~SC~~CI~qHlmN 455 (489)
T KOG4692|consen 421 EDNLCPICYA-GPINAVF--APCSHRSCYGCITQHLMN 455 (489)
T ss_pred ccccCcceec-ccchhhc--cCCCCchHHHHHHHHHhc
Confidence 3458999984 2333333 489999999999998744
No 76
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=92.24 E-value=0.19 Score=27.03 Aligned_cols=41 Identities=24% Similarity=0.614 Sum_probs=28.5
Q ss_pred ecccccccCCCCCceecCCCC-----CccchHHHHHHHHHHHhCCccccCCC
Q 043988 15 VCEICVESRSLYDSFDVKGCS-----HFNCTSCIVRYIASKLEGNITNISCP 61 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP 61 (151)
.|-||++.....+.+. .+|. |.+-.+||..|+..+. ..+||
T Consensus 1 ~CrIC~~~~~~~~~l~-~PC~C~G~~~~vH~~Cl~~W~~~~~-----~~~C~ 46 (49)
T smart00744 1 ICRICHDEGDEGDPLV-SPCRCKGSLKYVHQECLERWINESG-----NKTCE 46 (49)
T ss_pred CccCCCCCCCCCCeeE-eccccCCchhHHHHHHHHHHHHHcC-----CCcCC
Confidence 3789998433444444 3675 7899999999998763 23777
No 77
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.00 E-value=0.081 Score=28.62 Aligned_cols=27 Identities=33% Similarity=0.803 Sum_probs=19.4
Q ss_pred ecCcccCCcccccccccc-CcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAI-RKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~-~~~~C~~C~~~ 130 (151)
+|| .|+..+....... ..+.|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence 688 8998887764332 47789888864
No 78
>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=91.88 E-value=0.032 Score=30.37 Aligned_cols=36 Identities=28% Similarity=0.747 Sum_probs=19.7
Q ss_pred cCCccccccc---cccCcccCcccchhhhhcCCCCCCCC
Q 043988 107 DCSSMLIDEG---EAIRKSNCPHCRRLFCVQCKVPWHSE 142 (151)
Q Consensus 107 ~C~~~~~~~~---~~~~~~~C~~C~~~~C~~C~~~~H~~ 142 (151)
+|...+.... .....+.||.|+..||..|-...|+-
T Consensus 4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence 4555444431 12467999999999999999988874
No 79
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.49 E-value=0.24 Score=36.93 Aligned_cols=43 Identities=23% Similarity=0.678 Sum_probs=31.6
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
+.|+.|-..+ .+......|+|.||.+|+..-+... .+.|| .|.
T Consensus 275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~ds------Df~Cp--nC~ 317 (427)
T COG5222 275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDS------DFKCP--NCS 317 (427)
T ss_pred ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhc------cccCC--Ccc
Confidence 6899997654 4555556799999999988654432 58999 465
No 80
>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=91.47 E-value=0.27 Score=36.35 Aligned_cols=52 Identities=27% Similarity=0.514 Sum_probs=34.3
Q ss_pred ecccccccCC-CCCceec-CCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 15 VCEICVESRS-LYDSFDV-KGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 15 ~C~iC~~~~~-~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
.||+|-.+.. .++++.+ ..|+|+.|.+|+-..+... +-.|| +|..++-...+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g------~~~Cp--eC~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLG------PAQCP--ECMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcC------CCCCC--cccchhhhccc
Confidence 4888865443 3343322 3799999999998766442 35788 89877665544
No 81
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=90.92 E-value=0.29 Score=41.28 Aligned_cols=54 Identities=24% Similarity=0.558 Sum_probs=42.6
Q ss_pred CCeeecccccccCCCC-CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 11 TPSFVCEICVESRSLY-DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
...++|-||++.+... .+++..+|-|.|-..|++.|.++.-+++...-.|| .|.
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP--~Cq 243 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP--ACQ 243 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC--ccc
Confidence 4679999999988754 45677789999999999999999555555556898 566
No 82
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=90.82 E-value=0.39 Score=36.47 Aligned_cols=58 Identities=29% Similarity=0.662 Sum_probs=39.1
Q ss_pred ecccccccCCCCC--ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh-cCCHH
Q 043988 15 VCEICVESRSLYD--SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL-ILPDD 81 (151)
Q Consensus 15 ~C~iC~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~ 81 (151)
.||.|++++++.+ ++.. +||-+.|+-|+.. |++.+ .=.|| -|....+.+.|+- -|+++
T Consensus 16 ~cplcie~mditdknf~pc-~cgy~ic~fc~~~-irq~l-----ngrcp--acrr~y~denv~~~~~s~e 76 (480)
T COG5175 16 YCPLCIEPMDITDKNFFPC-PCGYQICQFCYNN-IRQNL-----NGRCP--ACRRKYDDENVRYVTLSPE 76 (480)
T ss_pred cCcccccccccccCCcccC-CcccHHHHHHHHH-HHhhc-----cCCCh--HhhhhccccceeEEecCHH
Confidence 3999999988654 4443 7999999999864 34433 33788 5887766666642 24443
No 83
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.71 E-value=0.15 Score=26.99 Aligned_cols=29 Identities=17% Similarity=0.460 Sum_probs=20.9
Q ss_pred eecCcccCCccccccccccCcccCcccchhhh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFC 132 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C 132 (151)
+.|| +|+..+..+... ..+.||.||..+=
T Consensus 4 y~C~--~CG~~~~~~~~~-~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCA--RCGREVELDEYG-TGVRCPYCGYRIL 32 (46)
T ss_pred EECC--CCCCEEEECCCC-CceECCCCCCeEE
Confidence 4688 899888776433 2789999987553
No 84
>PHA03096 p28-like protein; Provisional
Probab=90.43 E-value=0.19 Score=37.48 Aligned_cols=39 Identities=21% Similarity=0.233 Sum_probs=29.7
Q ss_pred eecccccccCCC----C-CceecCCCCCccchHHHHHHHHHHHh
Q 043988 14 FVCEICVESRSL----Y-DSFDVKGCSHFNCTSCIVRYIASKLE 52 (151)
Q Consensus 14 ~~C~iC~~~~~~----~-~~~~~~~C~H~fC~~Cl~~~~~~~i~ 52 (151)
.+|.||++.... . .+-.+..|.|.||..|.+.|......
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~ 222 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY 222 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence 689999986552 2 22234579999999999999988763
No 85
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=90.01 E-value=0.11 Score=25.80 Aligned_cols=26 Identities=31% Similarity=0.864 Sum_probs=15.1
Q ss_pred ecCcccCCcccccc---ccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDE---GEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~---~~~~~~~~C~~C~~ 129 (151)
+|| .|+..+... ++......|+.|+.
T Consensus 2 fC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCP--QCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-T--TT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccc--cccChhhhhcCCCCCccceECCCCCC
Confidence 688 899877664 45677888888875
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=89.76 E-value=0.21 Score=27.93 Aligned_cols=28 Identities=32% Similarity=0.870 Sum_probs=13.1
Q ss_pred eeecCcccCCcccccc----ccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDE----GEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~----~~~~~~~~C~~C~~ 129 (151)
.+.|| +|+..++.. ....+.+.||+||.
T Consensus 25 ~F~CP--nCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCP--NCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeeCC--CCCCeeEeechhHHhcCCceECCCCCC
Confidence 34566 555543333 12334455555553
No 87
>PF12773 DZR: Double zinc ribbon
Probab=89.55 E-value=0.21 Score=26.74 Aligned_cols=27 Identities=30% Similarity=0.752 Sum_probs=15.8
Q ss_pred CeeecCcccCCccccccccccCcccCcccch
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
+..+|| .|+..+.. .....+.|+.|++
T Consensus 11 ~~~fC~--~CG~~l~~--~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCP--HCGTPLPP--PDQSKKICPNCGA 37 (50)
T ss_pred cccCCh--hhcCChhh--ccCCCCCCcCCcC
Confidence 345777 77776662 2234566777754
No 88
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=88.10 E-value=0.13 Score=42.72 Aligned_cols=50 Identities=28% Similarity=0.611 Sum_probs=35.6
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
+.|.+|.+ ....+. ..|+|.||.+|+...+...-. ..|| .|...+....+
T Consensus 455 ~~c~ic~~---~~~~~i-t~c~h~~c~~c~~~~i~~~~~-----~~~~--~cr~~l~~~~l 504 (674)
T KOG1001|consen 455 HWCHICCD---LDSFFI-TRCGHDFCVECLKKSIQQSEN-----APCP--LCRNVLKEKKL 504 (674)
T ss_pred cccccccc---ccccee-ecccchHHHHHHHhccccccC-----CCCc--HHHHHHHHHHH
Confidence 79999998 233444 479999999999998765431 2666 67766665554
No 89
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.82 E-value=0.94 Score=33.59 Aligned_cols=62 Identities=18% Similarity=0.358 Sum_probs=41.9
Q ss_pred CCeeecccccccCCCCCceecCC-CCCccchHHHHHHHHHHHhCCccccCCCC-CCCC---CccChhHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKG-CSHFNCTSCIVRYIASKLEGNITNISCPQ-LGCE---ARLEFEDC 74 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~-~~C~---~~~~~~~i 74 (151)
...+-|-+|-|-+...-+++... =.|.||.-|-++.|+.+-..+ .+.||. .+|. ..++...|
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg--evYCPSGdkCPLvgS~vPWAFM 332 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG--EVYCPSGDKCPLVGSNVPWAFM 332 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC--ceeCCCCCcCcccCCcccHHHh
Confidence 34588999988775444333211 169999999999999886544 689995 3565 34555544
No 90
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.47 E-value=0.26 Score=22.08 Aligned_cols=22 Identities=36% Similarity=1.097 Sum_probs=11.9
Q ss_pred ecCcccCCccccccccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
+|| .|+..+..+ ...|+.||+.
T Consensus 1 ~Cp--~CG~~~~~~-----~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDD-----AKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCc-----CcchhhhCCc
Confidence 466 777655432 2346666653
No 91
>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=87.25 E-value=0.65 Score=31.53 Aligned_cols=30 Identities=20% Similarity=0.464 Sum_probs=22.1
Q ss_pred CeeecCcccCCccccccccccCcccCcccchh
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
..+.|| .|+.-+...+.....+.||.||..
T Consensus 108 ~~Y~Cp--~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICP--NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CeEECC--CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345799 788777666555578999999864
No 92
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.17 E-value=0.23 Score=36.83 Aligned_cols=35 Identities=23% Similarity=0.526 Sum_probs=25.8
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA 48 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 48 (151)
.-++.|.||-.++. +++. ..|+|.||..|....+.
T Consensus 239 ~~Pf~c~icr~~f~--~pVv-t~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 239 LLPFKCFICRKYFY--RPVV-TKCGHYFCEVCALKPYQ 273 (313)
T ss_pred cCCccccccccccc--cchh-hcCCceeehhhhccccc
Confidence 34578999998874 4444 48999999999766543
No 93
>PF14353 CpXC: CpXC protein
Probab=87.03 E-value=0.31 Score=31.70 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=8.5
Q ss_pred ccCcccCcccchhh
Q 043988 118 AIRKSNCPHCRRLF 131 (151)
Q Consensus 118 ~~~~~~C~~C~~~~ 131 (151)
....++||.||+.+
T Consensus 35 ~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 35 SLFSFTCPSCGHKF 48 (128)
T ss_pred CcCEEECCCCCCce
Confidence 34566677666654
No 94
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=86.82 E-value=0.7 Score=32.04 Aligned_cols=30 Identities=23% Similarity=0.672 Sum_probs=21.9
Q ss_pred CeeecCcccCCccccccccccCcccCcccchh
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
..+.|| .|+.-+...+.....+.||.||..
T Consensus 116 ~~Y~Cp--~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCP--NCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred CEEECC--CCCcEEeHHHHhhcCCcCCCCCCC
Confidence 346799 688777666555678999988864
No 95
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.56 E-value=0.42 Score=26.71 Aligned_cols=27 Identities=30% Similarity=0.707 Sum_probs=12.9
Q ss_pred eecCcccCCcccccc----ccccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDE----GEAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~----~~~~~~~~C~~C~~ 129 (151)
+.|| +|+..++.. ....+...||+||.
T Consensus 28 F~CP--nCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 28 FPCP--NCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeCC--CCCceeeehhhhHHHcCCceECCCcCc
Confidence 4566 666444443 11234455665553
No 96
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=86.45 E-value=0.53 Score=36.98 Aligned_cols=38 Identities=21% Similarity=0.370 Sum_probs=27.7
Q ss_pred CCCeeecccccccCCCCC-ceecCCCCCccchHHHHHHH
Q 043988 10 GTPSFVCEICVESRSLYD-SFDVKGCSHFNCTSCIVRYI 47 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~ 47 (151)
..+.-+||||++-++.+- .+....|.|.|-..|+..|.
T Consensus 172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~ 210 (493)
T KOG0804|consen 172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW 210 (493)
T ss_pred cccCCCcchhHhhcCccccceeeeecccccchHHHhhcc
Confidence 355669999999876432 22223699999999998874
No 97
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=86.28 E-value=0.64 Score=35.10 Aligned_cols=47 Identities=26% Similarity=0.528 Sum_probs=34.0
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA 67 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 67 (151)
..-.||+|+-..-. +..+..-|-.||..|+..|+..- =.||..+++.
T Consensus 299 ~~~~CpvClk~r~N--ptvl~vSGyVfCY~Ci~~Yv~~~-------~~CPVT~~p~ 345 (357)
T KOG0826|consen 299 DREVCPVCLKKRQN--PTVLEVSGYVFCYPCIFSYVVNY-------GHCPVTGYPA 345 (357)
T ss_pred ccccChhHHhccCC--CceEEecceEEeHHHHHHHHHhc-------CCCCccCCcc
Confidence 34689999866533 33333579999999999999842 3788777664
No 98
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=86.19 E-value=0.79 Score=30.68 Aligned_cols=30 Identities=23% Similarity=0.508 Sum_probs=19.7
Q ss_pred CeeecCcccCCcccccccc-----ccCcccCcccchh
Q 043988 99 KKFYCPYKDCSSMLIDEGE-----AIRKSNCPHCRRL 130 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~-----~~~~~~C~~C~~~ 130 (151)
..+.|| .|+..+..... ....+.||.||..
T Consensus 98 ~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 98 AYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred cEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 456899 89876665422 2233899988864
No 99
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.14 E-value=0.72 Score=35.18 Aligned_cols=40 Identities=30% Similarity=0.624 Sum_probs=27.5
Q ss_pred CcccCCC-CCeeecccccccCCCCCceecCCCCCccchHHHHHH
Q 043988 4 NAETDDG-TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRY 46 (151)
Q Consensus 4 ~a~~~~~-~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 46 (151)
+|++++. +....|.||.+... ...+.+|+|++|.-|....
T Consensus 51 tsSaddtDEen~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~Rl 91 (493)
T COG5236 51 TSSADDTDEENMNCQICAGSTT---YSARYPCGHQICHACAVRL 91 (493)
T ss_pred cccccccccccceeEEecCCce---EEEeccCCchHHHHHHHHH
Confidence 3444443 45678999987552 2345689999999997654
No 100
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=85.58 E-value=0.39 Score=22.11 Aligned_cols=22 Identities=27% Similarity=0.966 Sum_probs=11.6
Q ss_pred eecCcccCCccccccccccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
+.|| .|+..+.. ....||.||+
T Consensus 3 ~~Cp--~Cg~~~~~-----~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCP--NCGAEIDP-----DAKFCPNCGA 24 (26)
T ss_pred CCCc--ccCCcCCc-----ccccChhhCC
Confidence 3577 77763322 2235666654
No 101
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=85.28 E-value=1.2 Score=33.59 Aligned_cols=57 Identities=16% Similarity=0.348 Sum_probs=41.1
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
+.+.||+=-+.....+++.++.|||.+=.+=+.. ..++|...++|| -|+..-..+.+
T Consensus 335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~----LS~nG~~~FKCP--YCP~~~~~~~~ 391 (396)
T COG5109 335 SLFICPVLKELCTDENPPVMLECGHVISKEALSV----LSQNGVLSFKCP--YCPEMSKYENI 391 (396)
T ss_pred ceeeccccHhhhcccCCCeeeeccceeeHHHHHH----HhhcCcEEeeCC--CCCcchhhhhh
Confidence 4578999777666677777889999987765544 345677789999 68865544443
No 102
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=85.22 E-value=1.2 Score=29.19 Aligned_cols=53 Identities=19% Similarity=0.425 Sum_probs=39.7
Q ss_pred CeeecccccccCCCCCceec-CCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 12 PSFVCEICVESRSLYDSFDV-KGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
+.++|.||-|......+..- .-||-..|.-|....++... .-..|| -|+..+.
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~----~ypvCP--vCkTSFK 132 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN----LYPVCP--VCKTSFK 132 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc----cCCCCC--ccccccc
Confidence 78999999987765555442 23899999999999988763 346899 5876554
No 103
>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=84.79 E-value=0.34 Score=30.17 Aligned_cols=31 Identities=32% Similarity=0.479 Sum_probs=24.1
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIV 44 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~ 44 (151)
...|++|...+..+. +.+.+|||.|...|+.
T Consensus 78 ~~~C~vC~k~l~~~~-f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSV-FVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCce-EEEeCCCeEEeccccc
Confidence 446999998887644 5555899999999974
No 104
>PF14369 zf-RING_3: zinc-finger
Probab=83.91 E-value=0.89 Score=22.63 Aligned_cols=30 Identities=20% Similarity=0.668 Sum_probs=19.0
Q ss_pred eeecCcccCCccccccccccCcccCcccchhh
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
..||- .|+..+.........+.||.|+..|
T Consensus 2 ~ywCh--~C~~~V~~~~~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 2 RYWCH--QCNRFVRIAPSPDSDVACPRCHGGF 31 (35)
T ss_pred CEeCc--cCCCEeEeCcCCCCCcCCcCCCCcE
Confidence 35787 8887777643223334788887654
No 105
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=83.13 E-value=0.2 Score=37.75 Aligned_cols=26 Identities=27% Similarity=0.844 Sum_probs=22.1
Q ss_pred ccCcccCcccchhhhhcCCCCCCCCC
Q 043988 118 AIRKSNCPHCRRLFCVQCKVPWHSEF 143 (151)
Q Consensus 118 ~~~~~~C~~C~~~~C~~C~~~~H~~~ 143 (151)
....+.|+.|+..||..|....|+-+
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHESL 367 (378)
T ss_pred CCCcEEchhccceeeccchHHHHhhh
Confidence 45678999999999999999888643
No 106
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=83.12 E-value=0.52 Score=29.14 Aligned_cols=29 Identities=34% Similarity=0.913 Sum_probs=21.5
Q ss_pred eecCcccCCccccccccc-cCcccCcccchhh
Q 043988 101 FYCPYKDCSSMLIDEGEA-IRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~-~~~~~C~~C~~~~ 131 (151)
.+|| .|+..++.+.+. .+.+.|+.|.+.+
T Consensus 2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred cccC--CCCCEEEEecCCeEeeEEcCCCCcee
Confidence 4788 899988887443 4788888887654
No 107
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=81.79 E-value=0.77 Score=22.86 Aligned_cols=27 Identities=30% Similarity=0.493 Sum_probs=22.8
Q ss_pred cCcccCcccchhhhhcCCCCCCCCCCc
Q 043988 119 IRKSNCPHCRRLFCVQCKVPWHSEFDC 145 (151)
Q Consensus 119 ~~~~~C~~C~~~~C~~C~~~~H~~~~C 145 (151)
...+.|..|+..+|..|....|.++.-
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H~~ 36 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGHRR 36 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCCCE
Confidence 567899999999999999877887653
No 108
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=81.65 E-value=0.47 Score=35.60 Aligned_cols=39 Identities=23% Similarity=0.581 Sum_probs=28.1
Q ss_pred ecCcccCCcccccc-------ccccCcccCcccchhhhhcCCCCCCCC
Q 043988 102 YCPYKDCSSMLIDE-------GEAIRKSNCPHCRRLFCVQCKVPWHSE 142 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~-------~~~~~~~~C~~C~~~~C~~C~~~~H~~ 142 (151)
.|- .|+..+... ......++|+.|+..||..|.+..|+.
T Consensus 364 ~Cf--~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~ 409 (421)
T COG5151 364 HCF--VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHET 409 (421)
T ss_pred cce--eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHH
Confidence 455 566655443 123567899999999999999988753
No 109
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.58 E-value=0.66 Score=25.52 Aligned_cols=44 Identities=34% Similarity=0.677 Sum_probs=28.9
Q ss_pred eecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
-+|.||++.-. +.+ +-.|||. +|.+|-.+..+.. .=.|| -|...
T Consensus 8 dECTICye~pv--dsV-lYtCGHMCmCy~Cg~rl~~~~------~g~CP--iCRap 52 (62)
T KOG4172|consen 8 DECTICYEHPV--DSV-LYTCGHMCMCYACGLRLKKAL------HGCCP--ICRAP 52 (62)
T ss_pred cceeeeccCcc--hHH-HHHcchHHhHHHHHHHHHHcc------CCcCc--chhhH
Confidence 58999997432 222 2369998 8999988776541 23677 46643
No 110
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=80.89 E-value=1.4 Score=25.18 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=12.4
Q ss_pred ccchHHHHHHHHHHHhC
Q 043988 37 FNCTSCIVRYIASKLEG 53 (151)
Q Consensus 37 ~fC~~Cl~~~~~~~i~~ 53 (151)
-||++||..|......+
T Consensus 11 gFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 11 GFCRNCLSKWYREAAEE 27 (68)
T ss_dssp S--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 39999999999887654
No 111
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=80.86 E-value=0.89 Score=33.70 Aligned_cols=48 Identities=29% Similarity=0.699 Sum_probs=34.6
Q ss_pred CCeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988 11 TPSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA 67 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 67 (151)
.....||||.+.+.. ...+..+.|||..-..|++.++... .+|| -|..
T Consensus 156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-------y~CP--~C~~ 204 (276)
T KOG1940|consen 156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-------YTCP--ICSK 204 (276)
T ss_pred cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-------CCCC--cccc
Confidence 334569999886553 3344556899999999998886542 6898 5777
No 112
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=80.78 E-value=0.36 Score=40.60 Aligned_cols=43 Identities=16% Similarity=0.216 Sum_probs=24.7
Q ss_pred CCCeeecccccccCCC----CCceecCCCCCccchHHHHHHHHHHHh
Q 043988 10 GTPSFVCEICVESRSL----YDSFDVKGCSHFNCTSCIVRYIASKLE 52 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 52 (151)
.....+|++|.-++.. .....+..|+|.+|..||..+....+.
T Consensus 93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~ 139 (1134)
T KOG0825|consen 93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE 139 (1134)
T ss_pred cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence 3444556666544443 112223357888888888887766654
No 113
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.62 E-value=1.1 Score=34.78 Aligned_cols=38 Identities=21% Similarity=0.618 Sum_probs=27.3
Q ss_pred eeecccccccCCCCCce-ecCCCCCccchHHHHHHHHHH
Q 043988 13 SFVCEICVESRSLYDSF-DVKGCSHFNCTSCIVRYIASK 50 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~ 50 (151)
+-.|.||-+-++...-. ..-.|||+|-..|+.+|+...
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~ 42 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGD 42 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccC
Confidence 45899996656543322 222599999999999998764
No 114
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.34 E-value=0.95 Score=28.87 Aligned_cols=39 Identities=26% Similarity=0.709 Sum_probs=29.1
Q ss_pred ecCcccCCccccccc-------cccCcccCcccchhhhhcCCCCCCCC
Q 043988 102 YCPYKDCSSMLIDEG-------EAIRKSNCPHCRRLFCVQCKVPWHSE 142 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~-------~~~~~~~C~~C~~~~C~~C~~~~H~~ 142 (151)
.|- +|...+.... .....+.|+.|+..||..|...+|+-
T Consensus 57 ~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~ 102 (112)
T TIGR00622 57 FCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES 102 (112)
T ss_pred ccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence 466 7777665321 23456889999999999999999874
No 115
>PLN00209 ribosomal protein S27; Provisional
Probab=80.20 E-value=1.2 Score=26.89 Aligned_cols=31 Identities=16% Similarity=0.474 Sum_probs=24.5
Q ss_pred eecCcccCCccccccccccCcccCcccchhhhh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCV 133 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~ 133 (151)
+.|| +|...-...+.....+.|..|+...+.
T Consensus 37 VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEecCceEEEccccCCEeec
Confidence 4699 999876666666788999999988764
No 116
>PHA00626 hypothetical protein
Probab=79.40 E-value=1.1 Score=24.70 Aligned_cols=29 Identities=24% Similarity=0.385 Sum_probs=17.6
Q ss_pred ecCcccCCcc-cccc---ccccCcccCcccchhhh
Q 043988 102 YCPYKDCSSM-LIDE---GEAIRKSNCPHCRRLFC 132 (151)
Q Consensus 102 ~Cp~~~C~~~-~~~~---~~~~~~~~C~~C~~~~C 132 (151)
.|| +|+.. +... ....+.+.|+.||+.|=
T Consensus 2 ~CP--~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCP--KCGSGNIAKEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCC--CCCCceeeeeceecccCcceEcCCCCCeec
Confidence 477 77763 3332 12356788888887663
No 117
>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=79.25 E-value=0.85 Score=23.72 Aligned_cols=29 Identities=34% Similarity=0.912 Sum_probs=16.9
Q ss_pred CcccCcccchhhhhcCCCCCCCCCCchhhhh
Q 043988 120 RKSNCPHCRRLFCVQCKVPWHSEFDCSQFQK 150 (151)
Q Consensus 120 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~ 150 (151)
.-+.|+.|+..||.....+. .+.|....+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~e--~H~C~~~~~ 40 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLPE--DHNCSKLQK 40 (43)
T ss_dssp SHEE-TTTS-EE-TTTHSTT--TCT-SSTTS
T ss_pred CCeECCCCCcccCccccCcc--ccCCcchhh
Confidence 45789999999999877643 335654443
No 118
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=78.29 E-value=1.2 Score=28.47 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=21.7
Q ss_pred eecCcccCCccccccc-cccCcccCcccchhh
Q 043988 101 FYCPYKDCSSMLIDEG-EAIRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~-~~~~~~~C~~C~~~~ 131 (151)
.+|| .|+.++.... .....+.|++||+..
T Consensus 3 ~FCp--~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCP--KCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccC--CccCeeEEeEcCCCcEEECCCCCcch
Confidence 4799 9999888862 234588999888764
No 119
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=78.15 E-value=1 Score=25.77 Aligned_cols=30 Identities=23% Similarity=0.499 Sum_probs=23.8
Q ss_pred eecCcccCCccccccccccCcccCcccchhhh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFC 132 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C 132 (151)
+.|| +|++.....+.....+.|..||...+
T Consensus 20 VkCp--dC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 20 VKCP--DCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EECC--CCCCEEEEeccCceEEEecccccEEE
Confidence 4799 99987766666678899999988765
No 120
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=78.10 E-value=1.4 Score=37.57 Aligned_cols=40 Identities=25% Similarity=0.489 Sum_probs=30.7
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL 51 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 51 (151)
++.-.|.+|.-++...-++ +.+|||.|-++|+..++....
T Consensus 815 ep~d~C~~C~~~ll~~pF~-vf~CgH~FH~~Cl~~~v~~~~ 854 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLIKPFY-VFPCGHCFHRDCLIRHVLSLL 854 (911)
T ss_pred cCccchHHhcchhhcCcce-eeeccchHHHHHHHHHHHccc
Confidence 4556899998777665444 458999999999999876554
No 121
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=78.08 E-value=1.6 Score=26.31 Aligned_cols=31 Identities=26% Similarity=0.541 Sum_probs=24.6
Q ss_pred eecCcccCCccccccccccCcccCcccchhhhh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCV 133 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~ 133 (151)
+.|| +|...-...+.....+.|..|+...|.
T Consensus 36 VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEecCceEEEccccCCEeec
Confidence 4699 999876666666788999999988774
No 122
>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=76.38 E-value=0.97 Score=21.83 Aligned_cols=27 Identities=19% Similarity=0.450 Sum_probs=15.8
Q ss_pred eecCcccCCccccccccccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.+|| .|+........ ...+.||.|+..
T Consensus 4 rfC~--~CG~~t~~~~~-g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCG--RCGAPTKPAPG-GWARRCPSCGHE 30 (32)
T ss_dssp SB-T--TT--BEEE-SS-SS-EEESSSS-E
T ss_pred cccC--cCCccccCCCC-cCEeECCCCcCE
Confidence 5888 89988887643 577888888764
No 123
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=76.00 E-value=1.3 Score=34.90 Aligned_cols=34 Identities=21% Similarity=0.530 Sum_probs=26.1
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA 48 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 48 (151)
+...|+||..-+ .+++.+ +|+|..|+-|.+..+.
T Consensus 3 eelkc~vc~~f~--~epiil-~c~h~lc~~ca~~~~~ 36 (699)
T KOG4367|consen 3 EELKCPVCGSFY--REPIIL-PCSHNLCQACARNILV 36 (699)
T ss_pred ccccCceehhhc--cCceEe-ecccHHHHHHHHhhcc
Confidence 457899997655 456655 8999999999886554
No 124
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=75.80 E-value=2.9 Score=35.54 Aligned_cols=51 Identities=18% Similarity=0.316 Sum_probs=34.7
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhH
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFED 73 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~ 73 (151)
-.|++|+-.........-..|+|.||..|+..|-+.. -+|| -|..+|..-.
T Consensus 124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~a-------qTCP--iDR~EF~~v~ 174 (1134)
T KOG0825|consen 124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCA-------QTCP--VDRGEFGEVK 174 (1134)
T ss_pred hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhc-------ccCc--hhhhhhheee
Confidence 3688887665543333344799999999999997654 3788 4665554433
No 125
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=75.06 E-value=1.4 Score=22.84 Aligned_cols=26 Identities=31% Similarity=0.616 Sum_probs=13.8
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|| .|+...+..+.....+.|+.||.
T Consensus 2 ~Cp--~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCP--NCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBT--TTSSSEEEEETTTTEEEETTT-B
T ss_pred CCc--CCcCCceEEcCCCCeEECCCCCC
Confidence 477 67765433333344556666654
No 126
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=74.67 E-value=2.6 Score=21.24 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=18.3
Q ss_pred eecCcccCCccccccc--cccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDEG--EAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~--~~~~~~~C~~C~~ 129 (151)
+.|+ .|+..+.... .......||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCE--DCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcC--CCCCEEEEEEecCCCCCCCCCCCCC
Confidence 4687 8998665542 1255678988886
No 127
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=74.18 E-value=0.5 Score=34.97 Aligned_cols=19 Identities=26% Similarity=0.990 Sum_probs=16.7
Q ss_pred cccCcccchhhhhcCCCCC
Q 043988 121 KSNCPHCRRLFCVQCKVPW 139 (151)
Q Consensus 121 ~~~C~~C~~~~C~~C~~~~ 139 (151)
+-.|..||+.|||.|-.+|
T Consensus 251 ~pSaTpCGHiFCWsCI~~w 269 (293)
T KOG0317|consen 251 NPSATPCGHIFCWSCILEW 269 (293)
T ss_pred CCCcCcCcchHHHHHHHHH
Confidence 4577789999999999988
No 128
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=73.74 E-value=2.1 Score=27.20 Aligned_cols=29 Identities=31% Similarity=0.730 Sum_probs=19.1
Q ss_pred CeeecCcccCCccccccccccCcccCcccchhh
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.++.|| .|+..|.--+. .-+.||+||..|
T Consensus 8 tKR~Cp--~CG~kFYDLnk--~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCP--SCGAKFYDLNK--DPIVCPKCGTEF 36 (108)
T ss_pred CcccCC--CCcchhccCCC--CCccCCCCCCcc
Confidence 345788 88876654332 337799888765
No 129
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=73.73 E-value=2.2 Score=23.93 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=23.7
Q ss_pred eecCcccCCccccccccccCcccCcccchhhhh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCV 133 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~ 133 (151)
+.|| +|+......+.....+.|..|+...+.
T Consensus 12 VkCp--~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCP--DCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECC--CCCCeEEEEecCCcEEECcccCCCccc
Confidence 4799 999876666556788999999887653
No 130
>smart00336 BBOX B-Box-type zinc finger.
Probab=73.12 E-value=2 Score=21.62 Aligned_cols=27 Identities=22% Similarity=0.494 Sum_probs=22.3
Q ss_pred ccCcccCcccchhhhhcCCCCCCCCCC
Q 043988 118 AIRKSNCPHCRRLFCVQCKVPWHSEFD 144 (151)
Q Consensus 118 ~~~~~~C~~C~~~~C~~C~~~~H~~~~ 144 (151)
....+.|..|....|..|....|.++.
T Consensus 12 ~~~~~~C~~c~~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 12 EPAEFFCEECGALLCRTCDEAEHRGHT 38 (42)
T ss_pred CceEEECCCCCcccccccChhhcCCCc
Confidence 456788999999999999987787764
No 131
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=72.85 E-value=4.4 Score=29.49 Aligned_cols=56 Identities=14% Similarity=0.255 Sum_probs=36.1
Q ss_pred HHhhcCCHHHHHHHHHHHHhh-hhcCC--CeeecCcccCCcccccc-----ccccCcccCcccchh
Q 043988 73 DCRLILPDDVFARWGLALCES-ALVGH--KKFYCPYKDCSSMLIDE-----GEAIRKSNCPHCRRL 130 (151)
Q Consensus 73 ~i~~~l~~~~~~~~~~~~~~~-~~~~~--~~~~Cp~~~C~~~~~~~-----~~~~~~~~C~~C~~~ 130 (151)
.+..-++++++..|++..... -+-.. ..-.|. +|.-.+... .....-++||.||..
T Consensus 167 ~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 167 ELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 456668889999999887765 22111 123577 887665554 124566899999874
No 132
>PRK00420 hypothetical protein; Validated
Probab=71.80 E-value=7.6 Score=24.83 Aligned_cols=26 Identities=23% Similarity=0.451 Sum_probs=17.8
Q ss_pred eecCcccCCccccccccccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
..|| .|+..+... ......||.||..
T Consensus 24 ~~CP--~Cg~pLf~l--k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCP--VCGLPLFEL--KDGEVVCPVHGKV 49 (112)
T ss_pred CCCC--CCCCcceec--CCCceECCCCCCe
Confidence 4799 899887763 2335678877763
No 133
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=71.76 E-value=0.37 Score=24.71 Aligned_cols=26 Identities=23% Similarity=0.548 Sum_probs=22.5
Q ss_pred cCcccCcccchhhhhcCCCCCCCCCC
Q 043988 119 IRKSNCPHCRRLFCVQCKVPWHSEFD 144 (151)
Q Consensus 119 ~~~~~C~~C~~~~C~~C~~~~H~~~~ 144 (151)
...+.|..|+..+|..|....|.++.
T Consensus 13 ~~~~~C~~C~~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 13 PLSLFCEDCNEPLCSECTVSGHKGHK 38 (42)
T ss_dssp BEEEEETTTTEEEEHHHHHTSTTTSE
T ss_pred ceEEEecCCCCccCccCCCCCCCCCE
Confidence 36789999999999999998898864
No 134
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=71.32 E-value=1.3 Score=34.35 Aligned_cols=49 Identities=27% Similarity=0.634 Sum_probs=35.8
Q ss_pred CeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988 12 PSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA 67 (151)
Q Consensus 12 ~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 67 (151)
....|..|-+.+.. ++....++|.|.|-..|+..++... .+-+|| .|.+
T Consensus 364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n-----~~rsCP--~Crk 413 (518)
T KOG1941|consen 364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN-----GTRSCP--NCRK 413 (518)
T ss_pred HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC-----CCCCCc--cHHH
Confidence 34679999887764 3445667999999999999998443 245888 5663
No 135
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=71.25 E-value=5.8 Score=21.82 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=27.1
Q ss_pred CeeecccccccCC-CCCceecCCCCCccchHHHHH
Q 043988 12 PSFVCEICVESRS-LYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 12 ~~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
....|++|-+.+. ..+.+....|+-.+-++|+..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 3457999998885 566777788999999999865
No 136
>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=70.94 E-value=3.5 Score=21.24 Aligned_cols=27 Identities=19% Similarity=0.485 Sum_probs=18.4
Q ss_pred eecCcccCCcccccc--ccccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDE--GEAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~--~~~~~~~~C~~C~~ 129 (151)
+.|+ +|+..+... ..+.....||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCE--ECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeC--CCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4587 898766655 22356788988876
No 137
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=70.59 E-value=2.1 Score=23.15 Aligned_cols=26 Identities=23% Similarity=0.750 Sum_probs=17.7
Q ss_pred eecCcccCCc-cccccccccCcccCcccchhh
Q 043988 101 FYCPYKDCSS-MLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~-~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.+|| .|+. ++... ...+.|..|++..
T Consensus 21 ~fCP--~Cg~~~m~~~---~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCP--RCGSGFMAEH---LDRWHCGKCGYTE 47 (50)
T ss_pred CcCc--CCCcchhecc---CCcEECCCcCCEE
Confidence 4899 7887 44432 3578899898753
No 138
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=68.57 E-value=2.9 Score=30.55 Aligned_cols=17 Identities=24% Similarity=0.745 Sum_probs=11.2
Q ss_pred CCCCeeecccccccCCC
Q 043988 9 DGTPSFVCEICVESRSL 25 (151)
Q Consensus 9 ~~~~~~~C~iC~~~~~~ 25 (151)
.+.+.++|-+|...++.
T Consensus 61 ~~~p~v~CrVCq~~I~i 77 (256)
T PF09788_consen 61 GGAPVVTCRVCQSLIDI 77 (256)
T ss_pred CCCceEEeecCCceecc
Confidence 34567788888765543
No 139
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=68.56 E-value=3 Score=21.70 Aligned_cols=41 Identities=24% Similarity=0.543 Sum_probs=17.8
Q ss_pred cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988 16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP 61 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP 61 (151)
|.+|-+-......-...+|+-++-..|+..|+...- ..+||
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~-----~~~CP 41 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS-----NPKCP 41 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S-----S-B-T
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC-----CCCCc
Confidence 455654332222222235888899999999987652 22677
No 140
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=68.29 E-value=4.9 Score=27.85 Aligned_cols=31 Identities=19% Similarity=0.509 Sum_probs=22.2
Q ss_pred CCeeecCcccCCccccccccccCcccCcccchh
Q 043988 98 HKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 98 ~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
+..+.|| .|...+..+......+.||.||..
T Consensus 111 ~~~y~C~--~~~~r~sfdeA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 111 NNYYVCP--NCHVKYSFDEAMELGFTCPKCGED 141 (176)
T ss_pred CCceeCC--CCCCcccHHHHHHhCCCCCCCCch
Confidence 4456897 787777776555566899988753
No 141
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=67.45 E-value=10 Score=24.99 Aligned_cols=14 Identities=14% Similarity=0.394 Sum_probs=10.3
Q ss_pred eeecCcccCCcccccc
Q 043988 100 KFYCPYKDCSSMLIDE 115 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~ 115 (151)
..+|+ +|+..+...
T Consensus 70 ~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCR--NCGNEWSLK 83 (135)
T ss_pred EEECC--CCCCEEecc
Confidence 45899 999777654
No 142
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=67.21 E-value=2.8 Score=36.47 Aligned_cols=52 Identities=21% Similarity=0.417 Sum_probs=36.2
Q ss_pred CeeecccccccCC--CCCce--ecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988 12 PSFVCEICVESRS--LYDSF--DVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE 70 (151)
Q Consensus 12 ~~~~C~iC~~~~~--~~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~ 70 (151)
...+|+||+.-.+ ....+ ....|.|.|-..|+-+|+++.. .-+|| -|...++
T Consensus 1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~-----~s~CP--lCRseit 1523 (1525)
T COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA-----RSNCP--LCRSEIT 1523 (1525)
T ss_pred CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC-----CCCCC--ccccccc
Confidence 4468999987554 11111 2346899999999999998863 24788 5776554
No 143
>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=67.07 E-value=3.9 Score=22.61 Aligned_cols=46 Identities=22% Similarity=0.397 Sum_probs=29.0
Q ss_pred eecccccccCCCCCceecCCC--CCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988 14 FVCEICVESRSLYDSFDVKGC--SHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF 71 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~ 71 (151)
-.|..|-.+++....-. .-| ..+||.+|....+. =.|| .|+..|..
T Consensus 6 pnCE~C~~dLp~~s~~A-~ICSfECTFC~~C~e~~l~---------~~CP--NCgGelv~ 53 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEA-YICSFECTFCADCAETMLN---------GVCP--NCGGELVR 53 (57)
T ss_pred CCccccCCCCCCCCCcc-eEEeEeCcccHHHHHHHhc---------CcCc--CCCCcccc
Confidence 46888877776543111 124 36799999877642 3688 58766543
No 144
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=67.06 E-value=1.9 Score=23.78 Aligned_cols=47 Identities=28% Similarity=0.579 Sum_probs=27.6
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFED 73 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~ 73 (151)
...|-.|.... ..- .+++|+|..|..|+-.. .. =-|| =|...+...+
T Consensus 7 ~~~~~~~~~~~--~~~-~~~pCgH~I~~~~f~~~--------rY-ngCP--fC~~~~~~~~ 53 (55)
T PF14447_consen 7 EQPCVFCGFVG--TKG-TVLPCGHLICDNCFPGE--------RY-NGCP--FCGTPFEFDD 53 (55)
T ss_pred ceeEEEccccc--ccc-ccccccceeeccccChh--------hc-cCCC--CCCCcccCCC
Confidence 34555554322 222 34589999999996531 11 2677 5777766543
No 145
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=66.88 E-value=2.2 Score=27.12 Aligned_cols=88 Identities=17% Similarity=0.367 Sum_probs=43.4
Q ss_pred ccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCC--HHHHHHHHHHH---HhhhhcC-CCe--eecCcccC
Q 043988 37 FNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILP--DDVFARWGLAL---CESALVG-HKK--FYCPYKDC 108 (151)
Q Consensus 37 ~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~--~~~~~~~~~~~---~~~~~~~-~~~--~~Cp~~~C 108 (151)
.||.+|-.-.-.- .....+.|+ .|+..++........- ...+..+-..+ .+..... ... ..|| .|
T Consensus 8 ~FC~~CG~ll~~~---~~~~~~~C~--~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~ve~~~~~~ga~I~~kCp--kC 80 (116)
T KOG2907|consen 8 DFCSDCGSLLEEP---SAQSTVLCI--RCKIEYPVSQFSGLVVETKSLFDEFTSALAEKVENESSADGAVIKHKCP--KC 80 (116)
T ss_pred chhhhhhhhcccc---cccCceEec--cccccCCHHHhCCeeEEEEEeecccchhhhhhhcccccccccchhccCc--cc
Confidence 4777774332211 123345588 6888777776643321 11222221111 2221222 122 2699 89
Q ss_pred Ccccc-c--------cccccCcccCcccchhh
Q 043988 109 SSMLI-D--------EGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 109 ~~~~~-~--------~~~~~~~~~C~~C~~~~ 131 (151)
++--- . +++.-..++|++|++.|
T Consensus 81 ghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 81 GHEEMSYHTLQLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred CCchhhhhhhhcccccCCceEEEEcCccceee
Confidence 86221 1 13345678999998765
No 146
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=66.87 E-value=3.1 Score=26.26 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=18.5
Q ss_pred ecCcccCCccccccccccCcccCcccchhhh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLFC 132 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C 132 (151)
.|| .|+.-...+++ ..+.||.|+++|=
T Consensus 4 ~CP--~C~seytY~dg--~~~iCpeC~~EW~ 30 (109)
T TIGR00686 4 PCP--KCNSEYTYHDG--TQLICPSCLYEWN 30 (109)
T ss_pred cCC--cCCCcceEecC--CeeECcccccccc
Confidence 366 88876666543 4588888888763
No 147
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=66.53 E-value=3.3 Score=26.36 Aligned_cols=10 Identities=40% Similarity=1.045 Sum_probs=6.6
Q ss_pred hhhcCCCCCC
Q 043988 131 FCVQCKVPWH 140 (151)
Q Consensus 131 ~C~~C~~~~H 140 (151)
.|..|+++-+
T Consensus 87 ~CM~C~~pLT 96 (114)
T PF11023_consen 87 ACMHCKEPLT 96 (114)
T ss_pred ccCcCCCcCc
Confidence 4777777654
No 148
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=66.52 E-value=3.9 Score=17.01 Aligned_cols=16 Identities=38% Similarity=0.806 Sum_probs=13.1
Q ss_pred hhhcCCCCCCCCCCch
Q 043988 131 FCVQCKVPWHSEFDCS 146 (151)
Q Consensus 131 ~C~~C~~~~H~~~~C~ 146 (151)
.|+.|++.-|.-..|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4889999889887775
No 149
>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=66.10 E-value=0.96 Score=21.64 Aligned_cols=21 Identities=14% Similarity=0.474 Sum_probs=11.6
Q ss_pred ccCCCCCCCCCccChhHHhhc
Q 043988 57 NISCPQLGCEARLEFEDCRLI 77 (151)
Q Consensus 57 ~i~CP~~~C~~~~~~~~i~~~ 77 (151)
.++||..+|.+.+........
T Consensus 2 ~vrCPvkdC~EEv~lgKY~~H 22 (30)
T PF10426_consen 2 VVRCPVKDCDEEVSLGKYSHH 22 (30)
T ss_dssp EEE--STT---EEEHHHHHHH
T ss_pred ccccccccCcchhhhhhhccc
Confidence 478999999998887765443
No 150
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=65.85 E-value=1.8 Score=20.79 Aligned_cols=25 Identities=32% Similarity=0.640 Sum_probs=11.8
Q ss_pred cCcccCCccccccccccCcccCcccchhh
Q 043988 103 CPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 103 Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
|| .|+.-.... +...+.||.|+++|
T Consensus 5 Cp--~C~se~~y~--D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 5 CP--LCGSEYTYE--DGELLVCPECGHEW 29 (30)
T ss_dssp -T--TT-----EE---SSSEEETTTTEEE
T ss_pred CC--CCCCcceec--cCCEEeCCcccccC
Confidence 55 666554443 34557888887754
No 151
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=64.50 E-value=1.1 Score=24.17 Aligned_cols=34 Identities=21% Similarity=0.638 Sum_probs=28.7
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
..++|..|-+..+..+..+..-||-.-|.+||+.
T Consensus 6 sry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~d 39 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISELRQCVLCGRWACNSCWQD 39 (57)
T ss_pred hhHhHHhhcccCcHHHHHHHhhhchhhhhhhhhh
Confidence 3578999998888877777667999999999986
No 152
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=64.43 E-value=3.2 Score=22.17 Aligned_cols=29 Identities=17% Similarity=0.445 Sum_probs=17.5
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
+..||++.|+..+.... -.....|.+|+.
T Consensus 18 rk~CP~~~CG~GvFMA~-H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAE-HKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE--SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeee-cCCCccCCCccc
Confidence 35799999998554332 234567777764
No 153
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=63.93 E-value=6.2 Score=24.64 Aligned_cols=33 Identities=27% Similarity=0.535 Sum_probs=20.9
Q ss_pred CCCeeecCcccCCccccc-c-ccccCcccCcccchhh
Q 043988 97 GHKKFYCPYKDCSSMLID-E-GEAIRKSNCPHCRRLF 131 (151)
Q Consensus 97 ~~~~~~Cp~~~C~~~~~~-~-~~~~~~~~C~~C~~~~ 131 (151)
....+.|| .|+..... . +....++.|+.||+.+
T Consensus 18 lpt~f~CP--~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 18 LPKIFECP--RCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CCcEeECC--CCCCeEeeeecCCCcceEECCCCCCcc
Confidence 34567899 88843221 1 2245688899888764
No 154
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=63.67 E-value=3.7 Score=25.57 Aligned_cols=24 Identities=29% Similarity=0.870 Sum_probs=14.6
Q ss_pred ecCcccCCccccccccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
+|| .|+.++...+ ..+.|+.|++.
T Consensus 2 fC~--~Cg~~l~~~~---~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCP--KCGSLMTPKN---GVYVCPSCGYE 25 (104)
T ss_pred CCc--ccCcccccCC---CeEECcCCCCc
Confidence 566 7777775432 34667766655
No 155
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=62.50 E-value=4.2 Score=22.38 Aligned_cols=29 Identities=28% Similarity=0.550 Sum_probs=19.2
Q ss_pred eecCcccCCcccccccc-ccCcccCcccchhh
Q 043988 101 FYCPYKDCSSMLIDEGE-AIRKSNCPHCRRLF 131 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~-~~~~~~C~~C~~~~ 131 (151)
+.|| .|+..+...+. ..-.+.||.||..+
T Consensus 3 ~~CP--~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECP--DCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCC--CCCCEEecCCCccCCEEeCCCCCCEE
Confidence 3577 88887766532 23467888887754
No 156
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=62.31 E-value=5.7 Score=17.97 Aligned_cols=10 Identities=30% Similarity=0.790 Sum_probs=6.9
Q ss_pred cCcccCcccc
Q 043988 119 IRKSNCPHCR 128 (151)
Q Consensus 119 ~~~~~C~~C~ 128 (151)
...+.||.||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 5567777776
No 157
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=62.24 E-value=3.8 Score=22.64 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=19.0
Q ss_pred eecCcccCCccccccccccCcccCcccchhhhh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCV 133 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~ 133 (151)
+.|| +|...-..-+.....+.|..|+...|.
T Consensus 8 VkCp--~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCP--GCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-T--TT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECC--CCCCeeEEEecCCeEEEcccCCCEecC
Confidence 4688 998766655556778899888887664
No 158
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=62.04 E-value=13 Score=27.56 Aligned_cols=103 Identities=22% Similarity=0.543 Sum_probs=55.4
Q ss_pred CCeeecccccccCCCCCce--------ecCCCCCccchHHHHHHHHH-----HHhCCccccCCCCCCCCCccChhHHhhc
Q 043988 11 TPSFVCEICVESRSLYDSF--------DVKGCSHFNCTSCIVRYIAS-----KLEGNITNISCPQLGCEARLEFEDCRLI 77 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~--------~~~~C~H~fC~~Cl~~~~~~-----~i~~~~~~i~CP~~~C~~~~~~~~i~~~ 77 (151)
...+.|+-|...+....-. .+..=.=.-|..|=+.|+.. .|....++..|+ -|++.|...=
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~--iCGKaFSRPW---- 201 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECG--ICGKAFSRPW---- 201 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccc--cccccccchH----
Confidence 4567888887665422100 00000112455565555443 233344556666 5777665443
Q ss_pred CCHHHHHHHHHHHHhhhhcC---CCeeecCcccCCcccccc---------ccccCcccCcccchhhhh
Q 043988 78 LPDDVFARWGLALCESALVG---HKKFYCPYKDCSSMLIDE---------GEAIRKSNCPHCRRLFCV 133 (151)
Q Consensus 78 l~~~~~~~~~~~~~~~~~~~---~~~~~Cp~~~C~~~~~~~---------~~~~~~~~C~~C~~~~C~ 133 (151)
+++..|.. ..-+.|| .|+..|--. ..+..+++|+.|++.|=+
T Consensus 202 ------------LLQGHiRTHTGEKPF~C~--hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 202 ------------LLQGHIRTHTGEKPFSCP--HCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred ------------HhhcccccccCCCCccCC--cccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 22333332 2347898 898766433 234568999999998854
No 159
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.50 E-value=2.4 Score=35.14 Aligned_cols=35 Identities=20% Similarity=0.586 Sum_probs=25.4
Q ss_pred eeecccccccCCCC--CceecCCCCCccchHHHHHHHH
Q 043988 13 SFVCEICVESRSLY--DSFDVKGCSHFNCTSCIVRYIA 48 (151)
Q Consensus 13 ~~~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~ 48 (151)
...|+||+..+... .++. +.|||+.|+-|+.....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvs-l~cghtic~~c~~~lyn 47 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVS-LQCGHTICGHCVQLLYN 47 (861)
T ss_pred HhhchHHHHHHHHHhcCccc-ccccchHHHHHHHhHhh
Confidence 45799998766543 3344 58999999999886543
No 160
>PRK10220 hypothetical protein; Provisional
Probab=61.18 E-value=4.7 Score=25.53 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=18.2
Q ss_pred ecCcccCCccccccccccCcccCcccchhhh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLFC 132 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C 132 (151)
.|| .|+.-..++++ ..+.||.|+++|=
T Consensus 5 ~CP--~C~seytY~d~--~~~vCpeC~hEW~ 31 (111)
T PRK10220 5 HCP--KCNSEYTYEDN--GMYICPECAHEWN 31 (111)
T ss_pred cCC--CCCCcceEcCC--CeEECCcccCcCC
Confidence 366 88776666543 4578888887763
No 161
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=60.89 E-value=9.2 Score=20.69 Aligned_cols=30 Identities=23% Similarity=0.745 Sum_probs=21.9
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHHH
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRY 46 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 46 (151)
.|.||-........+.+ .=| ..|.+|+...
T Consensus 1 ~C~iCg~kigl~~~~k~-~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI-KDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec-cCc-cchHHHHHHh
Confidence 48999888765444444 456 8999999775
No 162
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=60.82 E-value=19 Score=23.02 Aligned_cols=26 Identities=23% Similarity=0.681 Sum_probs=17.2
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..+|+ +|+..+.... ...+.||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~--~~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCE--TCQQYVTLLT--QRVRRCPQCHG 95 (114)
T ss_pred EEEcc--cCCCeeecCC--ccCCcCcCcCC
Confidence 45899 9997665432 23367998874
No 163
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=60.53 E-value=3.1 Score=32.43 Aligned_cols=43 Identities=19% Similarity=0.336 Sum_probs=30.1
Q ss_pred CCcccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHH
Q 043988 3 SNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRY 46 (151)
Q Consensus 3 s~a~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 46 (151)
|....+.+....+|||||-.++...-+.. -|.-.+|.+|+..+
T Consensus 64 s~Hlls~~rr~~ecpicflyyps~~n~~r-cC~~~Ic~ecf~~~ 106 (482)
T KOG2789|consen 64 SSHLLSTSRRKTECPICFLYYPSAKNLVR-CCSETICGECFAPF 106 (482)
T ss_pred ccchhhhccccccCceeeeecccccchhh-hhccchhhhheecc
Confidence 33444445567899999977765333433 59999999998864
No 164
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.00 E-value=9 Score=23.42 Aligned_cols=17 Identities=18% Similarity=0.452 Sum_probs=14.4
Q ss_pred ccchHHHHHHHHHHHhC
Q 043988 37 FNCTSCIVRYIASKLEG 53 (151)
Q Consensus 37 ~fC~~Cl~~~~~~~i~~ 53 (151)
-||++||..|.....+.
T Consensus 42 gFCRNCLs~Wy~eaae~ 58 (104)
T COG3492 42 GFCRNCLSNWYREAAEA 58 (104)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 49999999999887654
No 165
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.44 E-value=10 Score=27.80 Aligned_cols=35 Identities=14% Similarity=0.170 Sum_probs=25.9
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHH
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL 51 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 51 (151)
--|..|+.+. .+++.. .=||.|+++++.+||..+-
T Consensus 44 dcCsLtLqPc--~dPvit-~~GylfdrEaILe~ilaqK 78 (303)
T KOG3039|consen 44 DCCSLTLQPC--RDPVIT-PDGYLFDREAILEYILAQK 78 (303)
T ss_pred ceeeeecccc--cCCccC-CCCeeeeHHHHHHHHHHHH
Confidence 3578888665 444443 5799999999999998653
No 167
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=59.38 E-value=5.9 Score=33.15 Aligned_cols=32 Identities=25% Similarity=0.831 Sum_probs=22.6
Q ss_pred CCeeecCcccCCccccccccccCcccCcccchh------hhhcCCCC
Q 043988 98 HKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL------FCVQCKVP 138 (151)
Q Consensus 98 ~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~------~C~~C~~~ 138 (151)
.+.++|+ .|+..+. ...||.||+. ||..|+..
T Consensus 13 ~~akFC~--~CG~~l~-------~~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 13 NNNRFCQ--KCGTSLT-------HKPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCCcccc--ccCCCCC-------CCcCCCCCCCCCcccccccccCCc
Confidence 3456788 7876552 2368889877 99999874
No 168
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=58.98 E-value=3.6 Score=18.64 Aligned_cols=10 Identities=50% Similarity=1.168 Sum_probs=7.2
Q ss_pred ccCcccchhh
Q 043988 122 SNCPHCRRLF 131 (151)
Q Consensus 122 ~~C~~C~~~~ 131 (151)
+.||.||..|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5677777766
No 169
>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 COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=58.41 E-value=18 Score=26.96 Aligned_cols=49 Identities=16% Similarity=0.283 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccccccccccCcccCcccchh
Q 043988 78 LPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 78 l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
++...+..+-+...-... .....+|+ .|+....... ......|+.|++.
T Consensus 90 ~~~~~~~~~~~a~~l~~w-~~~~RFCg--~CG~~~~~~~-~g~~~~C~~cg~~ 138 (279)
T COG2816 90 LDEGLFGLAARAVQLLEW-YRSHRFCG--RCGTKTYPRE-GGWARVCPKCGHE 138 (279)
T ss_pred CCHHHHHHHHHHHHHHHH-HhhCcCCC--CCCCcCcccc-CceeeeCCCCCCc
Confidence 455666555433211100 23456899 9999888764 3677899988764
No 171
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=58.32 E-value=8 Score=21.66 Aligned_cols=36 Identities=22% Similarity=0.563 Sum_probs=25.7
Q ss_pred ecCcccCCcccccc-ccccCcccCcccchhhhhcCCCCC
Q 043988 102 YCPYKDCSSMLIDE-GEAIRKSNCPHCRRLFCVQCKVPW 139 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~ 139 (151)
.|| -|....... .+..+.-+|..|+...|-.|+=..
T Consensus 4 ~CP--lCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP 40 (61)
T PF05715_consen 4 LCP--LCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNP 40 (61)
T ss_pred cCC--cccchhhcCCCCCCCccHHHHHhhhhhcccCCCC
Confidence 466 666544332 235678899999999999998744
No 172
>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=58.11 E-value=18 Score=19.33 Aligned_cols=47 Identities=19% Similarity=0.504 Sum_probs=23.4
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA 67 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 67 (151)
..||+-+..+. -+.....|.|.-|.+ +..|+......+. ..|| -|.+
T Consensus 3 L~CPls~~~i~--~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~--W~CP--iC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIR--IPVRGKNCKHLQCFD-LESFLESNQRTPK--WKCP--ICNK 49 (50)
T ss_dssp SB-TTTSSB-S--SEEEETT--SS--EE-HHHHHHHHHHS-----B-T--TT--
T ss_pred eeCCCCCCEEE--eCccCCcCcccceEC-HHHHHHHhhccCC--eECc--CCcC
Confidence 46788776553 355566899997765 6677777665554 6898 4653
No 173
>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=58.11 E-value=3.1 Score=23.72 Aligned_cols=34 Identities=26% Similarity=0.641 Sum_probs=16.9
Q ss_pred CeeecccccccCCCC-CceecCCCCCccchHHHHH
Q 043988 12 PSFVCEICVESRSLY-DSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~ 45 (151)
....|.+|...+... .-..--.||+.||.+|...
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence 345899998888642 2233457999999999754
No 174
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=58.03 E-value=8.2 Score=20.58 Aligned_cols=27 Identities=19% Similarity=0.506 Sum_probs=16.5
Q ss_pred eecCcccCCccccccc--cccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDEG--EAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~--~~~~~~~C~~C~~ 129 (151)
+.|+ +|+..+.... .+.....||.||.
T Consensus 6 y~C~--~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCT--ACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeC--CCCCEeEEEEecCCCCCCCCCCCCC
Confidence 3577 8887555431 1234567888876
No 175
>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=58.01 E-value=14 Score=20.67 Aligned_cols=32 Identities=13% Similarity=0.376 Sum_probs=20.9
Q ss_pred cccccccCCCCCceecCCCCCccchH----HHHHHHHH
Q 043988 16 CEICVESRSLYDSFDVKGCSHFNCTS----CIVRYIAS 49 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~H~fC~~----Cl~~~~~~ 49 (151)
|..|... ..+++.-+.|++.+|.. -+..+.+.
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~ 36 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYKE 36 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHHH
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhcc
Confidence 5566543 34667777899999986 77777664
No 176
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=57.78 E-value=22 Score=22.61 Aligned_cols=25 Identities=32% Similarity=0.838 Sum_probs=16.7
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..+|+ +|+..+... ...+.||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~---~~~~~CP~Cgs 94 (113)
T PRK12380 70 QAWCW--DCSQVVEIH---QHDAQCPHCHG 94 (113)
T ss_pred EEEcc--cCCCEEecC---CcCccCcCCCC
Confidence 45798 898666553 24456888874
No 177
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=57.49 E-value=12 Score=22.24 Aligned_cols=50 Identities=22% Similarity=0.532 Sum_probs=20.3
Q ss_pred CeeecccccccCCC---CCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988 12 PSFVCEICVESRSL---YDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL 69 (151)
Q Consensus 12 ~~~~C~iC~~~~~~---~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~ 69 (151)
....|.||-++... .++ +....|+...|+.|+.--. ++|. -.|| .|+...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYEr----keg~--q~Cp--qCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYER----KEGN--QVCP--QCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHH----HTS---SB-T--TT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHh----hcCc--cccc--ccCCCc
Confidence 45689999988663 233 3345789999999987643 3342 4788 577443
No 178
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=57.48 E-value=8.5 Score=21.40 Aligned_cols=27 Identities=22% Similarity=0.620 Sum_probs=17.4
Q ss_pred cCCCeeecCcccCCccccccccccCcccCcccchh
Q 043988 96 VGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 96 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.......|| .|+.+ ...+..|+.||++
T Consensus 23 ~~~~l~~C~--~CG~~------~~~H~vC~~CG~Y 49 (57)
T PRK12286 23 KAPGLVECP--NCGEP------KLPHRVCPSCGYY 49 (57)
T ss_pred cCCcceECC--CCCCc------cCCeEECCCCCcC
Confidence 345566888 88743 3456778777753
No 179
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=57.37 E-value=23 Score=22.62 Aligned_cols=25 Identities=32% Similarity=0.674 Sum_probs=17.1
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..+|+ +|+..+.... ..+.||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~---~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECE--DCSEEVSPEI---DLYRCPKCHG 94 (115)
T ss_pred EEEcc--cCCCEEecCC---cCccCcCCcC
Confidence 45799 8987666532 3567888875
No 180
>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=56.90 E-value=8.3 Score=20.85 Aligned_cols=36 Identities=19% Similarity=0.438 Sum_probs=24.1
Q ss_pred eecccccccCCCC-CceecCCCCCccchHHHHHHHHH
Q 043988 14 FVCEICVESRSLY-DSFDVKGCSHFNCTSCIVRYIAS 49 (151)
Q Consensus 14 ~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~ 49 (151)
..|.+|-..+... .-.....||+.||.+|.......
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~ 39 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPL 39 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeec
Confidence 3688887665532 12334579999999998876543
No 181
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=56.75 E-value=7.6 Score=24.38 Aligned_cols=23 Identities=30% Similarity=0.719 Sum_probs=19.9
Q ss_pred CCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988 33 GCSHFNCTSCIVRYIASKLEGNITNISCPQ 62 (151)
Q Consensus 33 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~ 62 (151)
.|.|.|-.-|+.+++++. -.||-
T Consensus 80 ~CNHaFH~hCisrWlktr-------~vCPL 102 (114)
T KOG2930|consen 80 VCNHAFHFHCISRWLKTR-------NVCPL 102 (114)
T ss_pred ecchHHHHHHHHHHHhhc-------CcCCC
Confidence 599999999999999985 47884
No 182
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=56.07 E-value=10 Score=32.36 Aligned_cols=47 Identities=30% Similarity=0.668 Sum_probs=33.8
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
...+.|.+|--.......+- ..|+|..-.+|++.|++..- .||. +|+
T Consensus 1026 ~~~~~C~~C~l~V~gss~~C-g~C~Hv~H~sc~~eWf~~gd-------~Cps-GCG 1072 (1081)
T KOG0309|consen 1026 GFTFQCAICHLAVRGSSNFC-GTCGHVGHTSCMMEWFRTGD-------VCPS-GCG 1072 (1081)
T ss_pred cceeeeeeEeeEeeccchhh-ccccccccHHHHHHHHhcCC-------cCCC-CCC
Confidence 45677888865554444444 47999999999999997752 7775 454
No 183
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=55.70 E-value=7.9 Score=25.28 Aligned_cols=29 Identities=28% Similarity=0.408 Sum_probs=18.9
Q ss_pred CeeecCcccCCccccccccccCcccCcccchhh
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.++.|| .|+..|.--+ ..-+.||+||..|
T Consensus 8 tKr~Cp--~cg~kFYDLn--k~p~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICP--NTGSKFYDLN--RRPAVSPYTGEQF 36 (129)
T ss_pred ccccCC--CcCccccccC--CCCccCCCcCCcc
Confidence 345788 7877665432 2447888888765
No 184
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.69 E-value=10 Score=19.83 Aligned_cols=25 Identities=16% Similarity=0.363 Sum_probs=14.2
Q ss_pred ecCcccCCccccccccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.|. +|+..+... ....+.||.||+.
T Consensus 4 ~C~--~Cg~~~~~~--~~~~irC~~CG~r 28 (44)
T smart00659 4 ICG--ECGRENEIK--SKDVVRCRECGYR 28 (44)
T ss_pred ECC--CCCCEeecC--CCCceECCCCCce
Confidence 355 666655544 2345677777653
No 185
>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=55.58 E-value=8.1 Score=19.94 Aligned_cols=23 Identities=35% Similarity=0.806 Sum_probs=15.3
Q ss_pred ecCcccCCccccccccccCcccCcccc
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCR 128 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~ 128 (151)
+|| .|+.++.... ...+.|+.|+
T Consensus 19 ~Cp--~C~~PL~~~k--~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCP--DCGTPLMRDK--DGKIYCVSCG 41 (41)
T ss_pred ccC--CCCCeeEEec--CCCEECCCCC
Confidence 688 8988777632 3356777663
No 186
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=55.53 E-value=8.7 Score=20.09 Aligned_cols=29 Identities=28% Similarity=0.641 Sum_probs=18.4
Q ss_pred CeeecCcccCCccccccccccCcccCcccch
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
+.+.|| .|+..-...........|..|++
T Consensus 17 ~g~~CP--~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 17 DGFVCP--HCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCC--CCCCeeeEEeCCCCeEECCCCCC
Confidence 446799 88875333333356778877765
No 187
>PLN03086 PRLI-interacting factor K; Provisional
Probab=55.18 E-value=12 Score=30.88 Aligned_cols=58 Identities=21% Similarity=0.480 Sum_probs=35.4
Q ss_pred cccCCCCCCCCCccChhHHhhcCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccccccccccCcccCcccchhh
Q 043988 56 TNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 56 ~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
..+.||+ |...++...+...+.. =....+.||..+|+..+.... ...+..|+.|+..|
T Consensus 406 ~~V~C~N--C~~~i~l~~l~lHe~~---------------C~r~~V~Cp~~~Cg~v~~r~e-l~~H~~C~~Cgk~f 463 (567)
T PLN03086 406 DTVECRN--CKHYIPSRSIALHEAY---------------CSRHNVVCPHDGCGIVLRVEE-AKNHVHCEKCGQAF 463 (567)
T ss_pred CeEECCC--CCCccchhHHHHHHhh---------------CCCcceeCCcccccceeeccc-cccCccCCCCCCcc
Confidence 3568884 8887777765432211 112345688666887775543 35667788776654
No 188
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=55.07 E-value=2.2 Score=25.19 Aligned_cols=49 Identities=24% Similarity=0.436 Sum_probs=30.6
Q ss_pred eecccccccCCC---------CCceec-CCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 14 FVCEICVESRSL---------YDSFDV-KGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 14 ~~C~iC~~~~~~---------~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
.+|.||.-+++. .+-+.+ -.|.|.|-.-|+.+++...-.+ -.||+ |...
T Consensus 21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq----~~CPm--cRq~ 79 (84)
T KOG1493|consen 21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQ----GQCPM--CRQT 79 (84)
T ss_pred CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCcccc----ccCCc--chhe
Confidence 378888766652 222222 2478999999999887665433 46785 5543
No 189
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=55.07 E-value=8.8 Score=20.24 Aligned_cols=34 Identities=18% Similarity=0.410 Sum_probs=25.1
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA 48 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 48 (151)
.|.||.......+++.-..|+-.|-..|+.....
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~ 34 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEK 34 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChh
Confidence 3778877666677777778888888888766544
No 190
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.01 E-value=18 Score=26.70 Aligned_cols=56 Identities=27% Similarity=0.622 Sum_probs=38.0
Q ss_pred CCCCCeeecccccccCCCCCc--eecCCCC-----CccchHHHHHHHHHHHhC-CccccCCCCCCCC
Q 043988 8 DDGTPSFVCEICVESRSLYDS--FDVKGCS-----HFNCTSCIVRYIASKLEG-NITNISCPQLGCE 66 (151)
Q Consensus 8 ~~~~~~~~C~iC~~~~~~~~~--~~~~~C~-----H~fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~ 66 (151)
++.+....|-|||..-..... +. -+|. |-.-.+|+..||..+-.. ..-.+.|| .|+
T Consensus 15 ~~~e~eR~CWiCF~TdeDn~~a~WV-~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~--QCq 78 (293)
T KOG3053|consen 15 DNQELERCCWICFATDEDNRLAAWV-HPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCP--QCQ 78 (293)
T ss_pred CccccceeEEEEeccCcccchhhhc-ccccccCccHHHHHHHHHHHHhHHhcCCCCceeech--hhc
Confidence 345566789999986543221 22 2564 558899999999887653 34578999 576
No 191
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=53.98 E-value=7.1 Score=19.81 Aligned_cols=19 Identities=37% Similarity=0.907 Sum_probs=15.5
Q ss_pred cccCcccchhhhhcCCCCC
Q 043988 121 KSNCPHCRRLFCVQCKVPW 139 (151)
Q Consensus 121 ~~~C~~C~~~~C~~C~~~~ 139 (151)
-+.|..|+..||..-..+.
T Consensus 12 ~f~C~~C~~~FC~~HR~~e 30 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLPE 30 (39)
T ss_pred CeECCccCCccccccCCcc
Confidence 5789899999999877653
No 192
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=53.82 E-value=14 Score=27.21 Aligned_cols=46 Identities=26% Similarity=0.437 Sum_probs=32.4
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE 66 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~ 66 (151)
..||+=+.++. .++.-..|||.|=++=+..++-. ...+.||..+|.
T Consensus 177 ~rdPis~~~I~--nPviSkkC~HvydrDsI~~~l~~-----~~~i~CPv~gC~ 222 (262)
T KOG2979|consen 177 NRDPISKKPIV--NPVISKKCGHVYDRDSIMQILCD-----EITIRCPVLGCE 222 (262)
T ss_pred ccCchhhhhhh--chhhhcCcCcchhhhhHHHHhcc-----CceeecccccCC
Confidence 35777665543 33333479999999987776544 336899999998
No 193
>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=52.68 E-value=8.7 Score=18.65 Aligned_cols=22 Identities=18% Similarity=0.454 Sum_probs=13.1
Q ss_pred cCCccccccccccCcccCcccchh
Q 043988 107 DCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 107 ~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
+|+..+.... ...+.|+.||+.
T Consensus 5 ~Cg~~~~~~~--~~~irC~~CG~R 26 (32)
T PF03604_consen 5 ECGAEVELKP--GDPIRCPECGHR 26 (32)
T ss_dssp SSSSSE-BST--SSTSSBSSSS-S
T ss_pred cCCCeeEcCC--CCcEECCcCCCe
Confidence 7777666543 344788888764
No 194
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=52.52 E-value=16 Score=23.19 Aligned_cols=25 Identities=24% Similarity=0.651 Sum_probs=15.9
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..+|. +|+..+..... .+.||.||.
T Consensus 70 ~~~C~--~Cg~~~~~~~~---~~~CP~Cgs 94 (113)
T PF01155_consen 70 RARCR--DCGHEFEPDEF---DFSCPRCGS 94 (113)
T ss_dssp EEEET--TTS-EEECHHC---CHH-SSSSS
T ss_pred cEECC--CCCCEEecCCC---CCCCcCCcC
Confidence 45798 99987776532 367888875
No 195
>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=52.26 E-value=8.4 Score=17.63 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=15.2
Q ss_pred cCCCCCCCCCccChhHHhhcCC
Q 043988 58 ISCPQLGCEARLEFEDCRLILP 79 (151)
Q Consensus 58 i~CP~~~C~~~~~~~~i~~~l~ 79 (151)
+.|| -|...+....+...||
T Consensus 2 v~CP--iC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCP--VCFREVPENLINSHLD 21 (26)
T ss_pred CcCC--CCcCcccHHHHHHHHH
Confidence 5788 6888887777777666
No 196
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=52.11 E-value=7.5 Score=25.56 Aligned_cols=24 Identities=29% Similarity=0.736 Sum_probs=17.4
Q ss_pred eecCcccCCccccccccccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.+|| .|+.+++..+ -.+.||.|++
T Consensus 29 ~hCp--~Cg~PLF~Kd---G~v~CPvC~~ 52 (131)
T COG1645 29 KHCP--KCGTPLFRKD---GEVFCPVCGY 52 (131)
T ss_pred hhCc--ccCCcceeeC---CeEECCCCCc
Confidence 4799 8998877743 3478888875
No 197
>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=51.81 E-value=5.4 Score=23.19 Aligned_cols=9 Identities=22% Similarity=0.305 Sum_probs=4.0
Q ss_pred cCCcccccc
Q 043988 107 DCSSMLIDE 115 (151)
Q Consensus 107 ~C~~~~~~~ 115 (151)
.|...+...
T Consensus 6 ~C~~~L~~~ 14 (70)
T PF07191_consen 6 KCQQELEWQ 14 (70)
T ss_dssp SS-SBEEEE
T ss_pred CCCCccEEe
Confidence 555554443
No 198
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=51.23 E-value=19 Score=18.95 Aligned_cols=34 Identities=26% Similarity=0.641 Sum_probs=22.3
Q ss_pred cccccccCCCCCceecCCCC--C---ccchHHHHHHHHHH
Q 043988 16 CEICVESRSLYDSFDVKGCS--H---FNCTSCIVRYIASK 50 (151)
Q Consensus 16 C~iC~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~ 50 (151)
|-||+++....+.+.. +|+ - ..-.+||..|+..+
T Consensus 1 CrIC~~~~~~~~~li~-pC~C~Gs~~~vH~~CL~~W~~~~ 39 (47)
T PF12906_consen 1 CRICLEGEEEDEPLIS-PCRCKGSMKYVHRSCLERWIRES 39 (47)
T ss_dssp ETTTTEE-SSSS-EE--SSS-SSCCGSEECCHHHHHHHHH
T ss_pred CeEeCCcCCCCCceec-ccccCCCcchhHHHHHHHHHHhc
Confidence 5689887765553332 554 3 57889999999884
No 199
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.12 E-value=18 Score=25.19 Aligned_cols=61 Identities=20% Similarity=0.395 Sum_probs=37.1
Q ss_pred CCCCeeecccccccCC---CCC-ceecCCCCCccchHHHHHHHHHHHhCC----ccccCCCCCCCCCccCh
Q 043988 9 DGTPSFVCEICVESRS---LYD-SFDVKGCSHFNCTSCIVRYIASKLEGN----ITNISCPQLGCEARLEF 71 (151)
Q Consensus 9 ~~~~~~~C~iC~~~~~---~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~----~~~i~CP~~~C~~~~~~ 71 (151)
..+....|.||+.-.. .++ .-...+||..|-.-|+..|++..+-.. +..=.|| -|+.++..
T Consensus 161 kdd~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCP--YCS~Pial 229 (234)
T KOG3268|consen 161 KDDELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECP--YCSDPIAL 229 (234)
T ss_pred cchhhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCC--CCCCccee
Confidence 3444567888875322 111 122236899999999999998876532 2233677 57766543
No 200
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.35 E-value=33 Score=21.97 Aligned_cols=26 Identities=23% Similarity=0.691 Sum_probs=16.4
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..+|. +|+..+.... .....||.||.
T Consensus 71 ~~~C~--~Cg~~~~~~~--~~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECK--DCSHVFKPNA--LDYGVCEKCHS 96 (117)
T ss_pred EEEhh--hCCCccccCC--ccCCcCcCCCC
Confidence 45798 8986665532 23345888875
No 201
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=49.07 E-value=13 Score=28.12 Aligned_cols=32 Identities=19% Similarity=0.403 Sum_probs=20.7
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRY 46 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 46 (151)
..-|.-|--.+.+ .=.+..|.|.||.+|.+..
T Consensus 90 VHfCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~~ 121 (389)
T KOG2932|consen 90 VHFCDRCDFPIAI--YGRMIPCKHVFCLECARSD 121 (389)
T ss_pred eEeecccCCccee--eecccccchhhhhhhhhcC
Confidence 4568878433322 2234589999999997653
No 202
>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=48.91 E-value=42 Score=21.12 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=21.6
Q ss_pred CCccchHHHHHHHHHHHhCC--ccccCCCCCCCCC
Q 043988 35 SHFNCTSCIVRYIASKLEGN--ITNISCPQLGCEA 67 (151)
Q Consensus 35 ~H~fC~~Cl~~~~~~~i~~~--~~~i~CP~~~C~~ 67 (151)
.-.||..||.......+.+- ...-.|| .|..
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP--~Crg 69 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCP--KCRG 69 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECC--CCCC
Confidence 77899999998777666442 2346898 4544
No 203
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=47.99 E-value=9.1 Score=19.64 Aligned_cols=25 Identities=28% Similarity=0.615 Sum_probs=11.9
Q ss_pred eecccccccCCCCCceecCC----CCCccchHH
Q 043988 14 FVCEICVESRSLYDSFDVKG----CSHFNCTSC 42 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~----C~H~fC~~C 42 (151)
.-||+|-. .+-+.+.. =++.+|++|
T Consensus 4 ~pCP~CGG----~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGG----KDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-----TTTEEEETT----S-EEETTT
T ss_pred CCCCCCcC----ccccccCcCcccCCCEECCCC
Confidence 46889843 22233112 388899888
No 204
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=47.35 E-value=6.3 Score=29.51 Aligned_cols=28 Identities=25% Similarity=0.635 Sum_probs=21.2
Q ss_pred eecCcccCCccccccccccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
..|| .|+..+..++-..+...||+|++.
T Consensus 27 ~~c~--~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 27 TKCP--KCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred eECC--CCcchhhHHHHHhhCCCCCCCCCc
Confidence 3588 999888877544566899999873
No 205
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=47.22 E-value=10 Score=27.17 Aligned_cols=34 Identities=21% Similarity=0.612 Sum_probs=21.8
Q ss_pred CCeeecCcccCCccccccc-----------cccCcccCcccchhh
Q 043988 98 HKKFYCPYKDCSSMLIDEG-----------EAIRKSNCPHCRRLF 131 (151)
Q Consensus 98 ~~~~~Cp~~~C~~~~~~~~-----------~~~~~~~C~~C~~~~ 131 (151)
+.++-||+|.|..++.... ...-.+.|.+|+..|
T Consensus 136 SqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 136 SQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred cceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 4567899999998876651 112356666676543
No 206
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.00 E-value=11 Score=32.04 Aligned_cols=60 Identities=20% Similarity=0.336 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHhhh-----hcCC---CeeecCc-------ccCCccccccccccCcccCcccchh-----hhhcCCC
Q 043988 78 LPDDVFARWGLALCESA-----LVGH---KKFYCPY-------KDCSSMLIDEGEAIRKSNCPHCRRL-----FCVQCKV 137 (151)
Q Consensus 78 l~~~~~~~~~~~~~~~~-----~~~~---~~~~Cp~-------~~C~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~ 137 (151)
|++.+++..++.+.... ++.. ..+.|.. |+|+.++..- ...+.+.|..||+. .|..|+.
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H-~~~~~L~CH~Cg~~~~~p~~Cp~Cgs 483 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLH-KATGQLRCHYCGYQEPIPQSCPECGS 483 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEe-cCCCeeEeCCCCCCCCCCCCCCCCCC
Confidence 66777777766655421 1111 1223430 0565555543 34578888888887 6888887
Q ss_pred C
Q 043988 138 P 138 (151)
Q Consensus 138 ~ 138 (151)
.
T Consensus 484 ~ 484 (730)
T COG1198 484 E 484 (730)
T ss_pred C
Confidence 5
No 207
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.24 E-value=15 Score=21.49 Aligned_cols=48 Identities=23% Similarity=0.496 Sum_probs=28.6
Q ss_pred ecccccccCCCCCceecCCC--CCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988 15 VCEICVESRSLYDSFDVKGC--SHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC 74 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i 74 (151)
.|..|-.+++.... ...-| .|+||.+|...-+ .=.|| .|+..+...-+
T Consensus 7 nCECCDrDLpp~s~-dA~ICtfEcTFCadCae~~l---------~g~CP--nCGGelv~RP~ 56 (84)
T COG3813 7 NCECCDRDLPPDST-DARICTFECTFCADCAENRL---------HGLCP--NCGGELVARPI 56 (84)
T ss_pred CCcccCCCCCCCCC-ceeEEEEeeehhHhHHHHhh---------cCcCC--CCCchhhcCcC
Confidence 57778666664321 11234 5899999976533 22688 68876654433
No 208
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=45.97 E-value=9 Score=21.75 Aligned_cols=27 Identities=26% Similarity=0.527 Sum_probs=19.3
Q ss_pred eecCcccCCccccccccccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
..|| .|+...... .....+.|+.||..
T Consensus 29 q~C~--~CG~~~~~~-~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCP--RCGHRNKKR-RSGRVFTCPNCGFE 55 (69)
T ss_pred cCcc--Ccccccccc-cccceEEcCCCCCE
Confidence 4688 898877762 34667888887764
No 209
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=45.65 E-value=14 Score=18.02 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=16.3
Q ss_pred eecCcccCCccccccccccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
..|+ .|++..+.. .......|+.|+..
T Consensus 4 ~~C~--~C~~~~i~~-~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCS--KCGGNGIVN-KEDDYEVCIFCGSS 30 (33)
T ss_pred eEcC--CCCCCeEEE-ecCCeEEcccCCcE
Confidence 4577 688766663 22345677777654
No 210
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=45.61 E-value=7.9 Score=20.99 Aligned_cols=27 Identities=22% Similarity=0.689 Sum_probs=13.1
Q ss_pred ecCcccCCcccccc-ccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDE-GEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~~ 130 (151)
.|+ .|+..+-.. +-....+.||.|+..
T Consensus 6 RC~--~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 6 RCG--HCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred ecc--chhHHHhhhcCccEEEEECCCCCcc
Confidence 455 555544442 223345566655543
No 211
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=45.04 E-value=15 Score=20.19 Aligned_cols=26 Identities=23% Similarity=0.682 Sum_probs=16.4
Q ss_pred cCCCeeecCcccCCccccccccccCcccCcccch
Q 043988 96 VGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 96 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.......|| .|+. ....+..|+.||+
T Consensus 22 ~~p~l~~C~--~cG~------~~~~H~vc~~cG~ 47 (55)
T TIGR01031 22 TAPTLVVCP--NCGE------FKLPHRVCPSCGY 47 (55)
T ss_pred cCCcceECC--CCCC------cccCeeECCccCe
Confidence 344566788 7874 2345667777775
No 212
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=45.02 E-value=7 Score=29.38 Aligned_cols=28 Identities=25% Similarity=0.695 Sum_probs=20.8
Q ss_pred ecCcccCCccccccccccCcccCcccchhh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.|| .|+..+....-..+...||+|++.+
T Consensus 29 ~c~--~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 29 KCP--SCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred ECC--CccchhhHHHHHhcCCCCCCCCCCe
Confidence 588 9998887775445567899888743
No 213
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.72 E-value=6.5 Score=29.58 Aligned_cols=26 Identities=15% Similarity=0.416 Sum_probs=20.5
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|| .|+..+..+.-..+...||+|++
T Consensus 40 kc~--~C~~~~~~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 40 QCE--NCYGLNYKKFLKSKMNICEQCGY 65 (296)
T ss_pred ECC--CccchhhHHHHHHcCCCCCCCCC
Confidence 588 89988887755566788998887
No 214
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=43.99 E-value=9.5 Score=20.76 Aligned_cols=31 Identities=23% Similarity=0.470 Sum_probs=16.5
Q ss_pred eeecCcccCCccc-cc-------cccccCcccCcccchh
Q 043988 100 KFYCPYKDCSSML-ID-------EGEAIRKSNCPHCRRL 130 (151)
Q Consensus 100 ~~~Cp~~~C~~~~-~~-------~~~~~~~~~C~~C~~~ 130 (151)
.+.||+|+|-.-. .. ...+...+.|..|++.
T Consensus 6 vl~C~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~ 44 (52)
T PF02748_consen 6 VLKCPNPNCITNSNEPVESRFYVIDKEPIKLRCHYCERI 44 (52)
T ss_dssp SSE-SSTTBTTT-TSSS--EEEEEETTTCEEEETTT--E
T ss_pred EEEcCCCCcccCCCCCCCceEEEEeCCCCEEEeeCCCCE
Confidence 4689999996551 11 1234566777766653
No 215
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=43.69 E-value=22 Score=19.57 Aligned_cols=24 Identities=25% Similarity=0.748 Sum_probs=15.9
Q ss_pred CCeeecCcccCCccccccccccCcccCcccch
Q 043988 98 HKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 98 ~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.+...|| .|+.+ ...+..|+.||+
T Consensus 24 ~~l~~c~--~cg~~------~~~H~vc~~cG~ 47 (56)
T PF01783_consen 24 PNLVKCP--NCGEP------KLPHRVCPSCGY 47 (56)
T ss_dssp TSEEESS--SSSSE------ESTTSBCTTTBB
T ss_pred cceeeec--cCCCE------ecccEeeCCCCe
Confidence 4567899 88743 345567877764
No 216
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=43.49 E-value=55 Score=20.75 Aligned_cols=49 Identities=20% Similarity=0.404 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHHHhhhhc-CCCeeecCcccCCccccccccccCcccCcccchhhhhcCCC
Q 043988 78 LPDDVFARWGLALCESALV-GHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKV 137 (151)
Q Consensus 78 l~~~~~~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 137 (151)
|++...+.++.++.=.... ......|+ +|+....... .|+..+|..|+.
T Consensus 19 l~~~~~k~~~~il~Crt~~~G~~~~~C~--~Cg~~~~~~~---------SCk~R~CP~C~~ 68 (111)
T PF14319_consen 19 LSPYQRKAVEAILACRTEALGFHRYRCE--DCGHEKIVYN---------SCKNRHCPSCQA 68 (111)
T ss_pred CCHHHHHHHHHHHhcCCccCCcceeecC--CCCceEEecC---------cccCcCCCCCCC
Confidence 3344444444444332222 22345788 7876544432 455566666654
No 217
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.97 E-value=34 Score=24.78 Aligned_cols=58 Identities=17% Similarity=0.319 Sum_probs=40.0
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCC-ccccCCCCCCCC-CccChhH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGN-ITNISCPQLGCE-ARLEFED 73 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~-~~~~~~~ 73 (151)
.-.|..|-.++...+.+.+ .|-|.|--.|+.+.....-.+. -.-..|| .|. ++|+...
T Consensus 50 ~pNC~LC~t~La~gdt~RL-vCyhlfHW~ClneraA~lPanTAPaGyqCP--~Cs~eiFPp~N 109 (299)
T KOG3970|consen 50 NPNCRLCNTPLASGDTTRL-VCYHLFHWKCLNERAANLPANTAPAGYQCP--CCSQEIFPPIN 109 (299)
T ss_pred CCCCceeCCccccCcceee-hhhhhHHHHHhhHHHhhCCCcCCCCcccCC--CCCCccCCCcc
Confidence 3479999888877787775 7999999999998765433222 2246888 576 4555443
No 218
>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=42.80 E-value=22 Score=19.06 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=22.5
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHH
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRY 46 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~ 46 (151)
+.|..|-..+.....+.. =+..||..|..+.
T Consensus 27 f~C~~C~~~l~~~~~~~~--~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 27 FKCSKCGKPLNDGDFYEK--DGKPYCKDCYQKR 57 (58)
T ss_dssp SBETTTTCBTTTSSEEEE--TTEEEEHHHHHHH
T ss_pred cccCCCCCccCCCeeEeE--CCEEECHHHHhhh
Confidence 578889887776664444 4688999997653
No 219
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.62 E-value=11 Score=28.33 Aligned_cols=29 Identities=31% Similarity=0.747 Sum_probs=20.4
Q ss_pred eeecccccccCCCCCceecCCCCCc-cchHHHH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIV 44 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~ 44 (151)
...|.||++.- .+-+. ++|||. .|..|-+
T Consensus 300 ~~LC~ICmDaP--~DCvf-LeCGHmVtCt~CGk 329 (350)
T KOG4275|consen 300 RRLCAICMDAP--RDCVF-LECGHMVTCTKCGK 329 (350)
T ss_pred HHHHHHHhcCC--cceEE-eecCcEEeehhhcc
Confidence 56799999633 45454 589997 6888743
No 220
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=42.50 E-value=9.8 Score=30.79 Aligned_cols=48 Identities=19% Similarity=0.311 Sum_probs=32.6
Q ss_pred CCCCcccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988 1 RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA 48 (151)
Q Consensus 1 ~~s~a~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~ 48 (151)
|++++........++|.||-...+.-..+....|.-.|-..||..-+.
T Consensus 532 ~st~~~s~~~a~~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLT 579 (707)
T KOG0957|consen 532 RSTPAISAPKAMNYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLT 579 (707)
T ss_pred cCCcccccccccceeeeeeccchhhHHHhhcchhhceeeccccCCccc
Confidence 677777778888999999976554333344445666677777665443
No 221
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=42.40 E-value=17 Score=27.80 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=24.6
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHH
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
.|-.|.++......+....|.+.||.+|=.-
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~ 362 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDCDVF 362 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccchHH
Confidence 4888977776667778788999999999443
No 222
>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=42.38 E-value=31 Score=22.02 Aligned_cols=35 Identities=23% Similarity=0.430 Sum_probs=23.6
Q ss_pred eeecCcccCCccccccccccCcccCcccchhhhhcCCCC
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVP 138 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~ 138 (151)
...|. .|+..+..-. .....|..|++.+|..|+..
T Consensus 54 ~~~C~--~C~~~fg~l~--~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCA--RCGKPFGFLF--NRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-T--TTS-BCSCTS--TTCEEETTTTEEEETTSEEE
T ss_pred Ccchh--hhCCcccccC--CCCCcCCcCCccccCccCCc
Confidence 34788 7876554332 23479999999999999874
No 223
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=42.20 E-value=19 Score=20.19 Aligned_cols=28 Identities=25% Similarity=0.616 Sum_probs=20.2
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|.+.+|.+++..+-.....-.||.|+.
T Consensus 20 ~Ct~e~C~gWmR~nFs~~~~p~CPlC~s 47 (59)
T PF14169_consen 20 ECTSEDCNGWMRDNFSFEEEPVCPLCKS 47 (59)
T ss_pred EeCCCCCCcccccccccCCCccCCCcCC
Confidence 5999999999988744344457776654
No 224
>PRK12495 hypothetical protein; Provisional
Probab=41.96 E-value=35 Score=24.57 Aligned_cols=26 Identities=19% Similarity=0.653 Sum_probs=15.7
Q ss_pred CeeecCcccCCccccccccccCcccCcccch
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..++|+ .|+..++.- .-...|+.|+.
T Consensus 41 sa~hC~--~CG~PIpa~---pG~~~Cp~CQ~ 66 (226)
T PRK12495 41 TNAHCD--ECGDPIFRH---DGQEFCPTCQQ 66 (226)
T ss_pred chhhcc--cccCcccCC---CCeeECCCCCC
Confidence 356899 999887732 22344555543
No 225
>PRK02935 hypothetical protein; Provisional
Probab=41.91 E-value=15 Score=23.19 Aligned_cols=10 Identities=30% Similarity=0.979 Sum_probs=6.5
Q ss_pred hhhcCCCCCC
Q 043988 131 FCVQCKVPWH 140 (151)
Q Consensus 131 ~C~~C~~~~H 140 (151)
.|..|++|-+
T Consensus 88 ~CM~C~~PLT 97 (110)
T PRK02935 88 ACMHCNQPLT 97 (110)
T ss_pred ecCcCCCcCC
Confidence 5777777553
No 226
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=41.86 E-value=23 Score=16.49 Aligned_cols=28 Identities=14% Similarity=0.260 Sum_probs=7.7
Q ss_pred ecccccccCCCCCceecCCCCCccchHH
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSC 42 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~C 42 (151)
.|.+|-.+....-.+.-..|.-.+..+|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 4667765554423444455655555444
No 227
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=41.35 E-value=17 Score=20.02 Aligned_cols=28 Identities=21% Similarity=0.516 Sum_probs=13.6
Q ss_pred eecCcccCCcccccc---cc--ccCcccCcccchh
Q 043988 101 FYCPYKDCSSMLIDE---GE--AIRKSNCPHCRRL 130 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~---~~--~~~~~~C~~C~~~ 130 (151)
+.|| .|++.-... +. ...-+.||+|.++
T Consensus 5 i~CP--~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 5 ILCP--ICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EECC--CCCCccceeeecCceeccccccCCCCCce
Confidence 3577 777533222 11 2334566666554
No 228
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.94 E-value=52 Score=21.63 Aligned_cols=56 Identities=16% Similarity=0.210 Sum_probs=31.3
Q ss_pred HhhcCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccccccccccCcccCcccchhhhh
Q 043988 74 CRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCV 133 (151)
Q Consensus 74 i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~ 133 (151)
+...-+.+.|.+|...+... +.-.+.+.=| -=.+.++..+.+.+...| .||+.||-
T Consensus 26 msa~kdhdrf~kylavlqdr-v~~~dpillp--vg~hlfi~qs~~~rv~rc-ecghsf~d 81 (165)
T COG4647 26 MSAYKDHDRFFKYLAVLQDR-VDWDDPILLP--VGDHLFICQSAQKRVIRC-ECGHSFGD 81 (165)
T ss_pred HhccccHHHHHHHHHHHHhh-cccCCCeeee--cCCcEEEEecccccEEEE-eccccccC
Confidence 34445567788887765543 3322222212 223344444555667888 79999984
No 229
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=40.82 E-value=23 Score=21.06 Aligned_cols=33 Identities=21% Similarity=0.514 Sum_probs=21.7
Q ss_pred eecCcccCCccccccccccCcccCcccchhhhhcC
Q 043988 101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQC 135 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C 135 (151)
+.|| +|-.+--.-......+.|+.|+...|..=
T Consensus 35 VkC~--gc~~iT~vfSHaqtvVvc~~c~~il~~~t 67 (84)
T KOG1779|consen 35 VKCP--GCFKITTVFSHAQTVVVCEGCSTILCQPT 67 (84)
T ss_pred EEcC--CceEEEEEeecCceEEEcCCCceEEEEec
Confidence 3588 77664444344567788888888777543
No 230
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.61 E-value=37 Score=22.24 Aligned_cols=32 Identities=28% Similarity=0.690 Sum_probs=20.9
Q ss_pred CeeecCcccCCcccccc-c---cccCcccCcccchhhh
Q 043988 99 KKFYCPYKDCSSMLIDE-G---EAIRKSNCPHCRRLFC 132 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~-~---~~~~~~~C~~C~~~~C 132 (151)
....|| .|+...... + .......|+.|++.|=
T Consensus 29 ~~~~cP--~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 29 TKVNCP--RCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred ccCcCC--CCCccceeeECCccccccccccCCcCccee
Confidence 346899 787666222 1 2356789999988763
No 231
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=39.60 E-value=36 Score=23.77 Aligned_cols=10 Identities=30% Similarity=0.760 Sum_probs=6.9
Q ss_pred ecCcccCCcc
Q 043988 102 YCPYKDCSSM 111 (151)
Q Consensus 102 ~Cp~~~C~~~ 111 (151)
.||+..|++.
T Consensus 101 ~CPRv~C~~~ 110 (184)
T PF01214_consen 101 RCPRVYCNGQ 110 (184)
T ss_dssp B-SBGGGTT-
T ss_pred cCCcccCCCC
Confidence 6999999863
No 232
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=39.46 E-value=12 Score=19.92 Aligned_cols=17 Identities=35% Similarity=0.815 Sum_probs=13.9
Q ss_pred hhhhcCCCCCCCCCCch
Q 043988 130 LFCVQCKVPWHSEFDCS 146 (151)
Q Consensus 130 ~~C~~C~~~~H~~~~C~ 146 (151)
.||..|+..-|....|+
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 58999999889887775
No 233
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.07 E-value=21 Score=31.58 Aligned_cols=33 Identities=24% Similarity=0.682 Sum_probs=22.9
Q ss_pred CeeecCcccCCccccccccccCcccCcccch-----hhhhcCCCCCC
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR-----LFCVQCKVPWH 140 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~-----~~C~~C~~~~H 140 (151)
...+|| .|+... ....||.||. .||..|+....
T Consensus 625 g~RfCp--sCG~~t-------~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 625 GRRKCP--SCGKET-------FYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cCccCC--CCCCcC-------CcccCCCCCCCCCcceeCccccCcCC
Confidence 346899 888642 4578888875 37888877654
No 234
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.68 E-value=23 Score=30.63 Aligned_cols=40 Identities=23% Similarity=0.450 Sum_probs=29.0
Q ss_pred eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988 14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA 67 (151)
Q Consensus 14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~ 67 (151)
-.|..|--+...+- +. ..|||.|-+.|+. ++ .-.|| .|.-
T Consensus 841 skCs~C~~~LdlP~-Vh-F~CgHsyHqhC~e--------~~--~~~CP--~C~~ 880 (933)
T KOG2114|consen 841 SKCSACEGTLDLPF-VH-FLCGHSYHQHCLE--------DK--EDKCP--KCLP 880 (933)
T ss_pred eeecccCCccccce-ee-eecccHHHHHhhc--------cC--cccCC--ccch
Confidence 47999987776543 33 3699999999988 22 35898 6874
No 235
>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=37.54 E-value=6.5 Score=16.82 Aligned_cols=8 Identities=38% Similarity=1.198 Sum_probs=3.8
Q ss_pred cCcccchh
Q 043988 123 NCPHCRRL 130 (151)
Q Consensus 123 ~C~~C~~~ 130 (151)
.|+.|++.
T Consensus 2 ~C~~C~~~ 9 (23)
T PF00096_consen 2 KCPICGKS 9 (23)
T ss_dssp EETTTTEE
T ss_pred CCCCCCCc
Confidence 35555543
No 236
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=36.80 E-value=13 Score=18.84 Aligned_cols=6 Identities=33% Similarity=0.839 Sum_probs=2.9
Q ss_pred cCCccc
Q 043988 107 DCSSML 112 (151)
Q Consensus 107 ~C~~~~ 112 (151)
.|+..+
T Consensus 4 ~C~~~l 9 (41)
T PF13453_consen 4 RCGTEL 9 (41)
T ss_pred CCCccc
Confidence 555533
No 237
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=36.24 E-value=12 Score=27.93 Aligned_cols=27 Identities=30% Similarity=0.712 Sum_probs=22.0
Q ss_pred ecCcccCCccccccccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.|| .|+..+...+-..+...||+|++.
T Consensus 30 KCp--~c~~~~y~~eL~~n~~vcp~c~~h 56 (294)
T COG0777 30 KCP--SCGEMLYRKELESNLKVCPKCGHH 56 (294)
T ss_pred ECC--CccceeeHHHHHhhhhcccccCcc
Confidence 588 999988887666778889988874
No 238
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=35.65 E-value=29 Score=31.49 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=7.7
Q ss_pred eeecCcccCCccc
Q 043988 100 KFYCPYKDCSSML 112 (151)
Q Consensus 100 ~~~Cp~~~C~~~~ 112 (151)
.+.|| +|+...
T Consensus 667 ~rkCP--kCG~~t 677 (1337)
T PRK14714 667 RRRCP--SCGTET 677 (1337)
T ss_pred EEECC--CCCCcc
Confidence 35799 888643
No 239
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=34.22 E-value=9.7 Score=31.95 Aligned_cols=58 Identities=22% Similarity=0.402 Sum_probs=39.1
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL 76 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~ 76 (151)
..+..+|+||+..+..+ +.+.|.|.||..|+...+...-. ...|| -|...+.....+.
T Consensus 18 ~~k~lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~----~~~~~--lc~~~~eK~s~~E 75 (684)
T KOG4362|consen 18 MQKILECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKG----PKQCA--LCKSDIEKRSLRE 75 (684)
T ss_pred HhhhccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCc----cccch--hhhhhhhhhhccc
Confidence 34567999999887543 44589999999999886654321 34566 3665555555544
No 240
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=33.71 E-value=22 Score=24.02 Aligned_cols=33 Identities=21% Similarity=0.422 Sum_probs=20.5
Q ss_pred CeeecCcccCCcccc--------ccccccCcccCcccchhh
Q 043988 99 KKFYCPYKDCSSMLI--------DEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~--------~~~~~~~~~~C~~C~~~~ 131 (151)
..+.||+|+|-.-.. ..+.....+.|..|++.+
T Consensus 104 gi~kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~ 144 (152)
T PRK00893 104 GVLKCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKEF 144 (152)
T ss_pred ceEECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCEe
Confidence 346799999965421 112345577887777654
No 241
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=32.96 E-value=12 Score=16.85 Aligned_cols=9 Identities=33% Similarity=0.995 Sum_probs=4.6
Q ss_pred ccCcccchh
Q 043988 122 SNCPHCRRL 130 (151)
Q Consensus 122 ~~C~~C~~~ 130 (151)
+.|+.|++.
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 455555543
No 242
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=32.94 E-value=21 Score=22.94 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=17.0
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
..||. +|+..+..+. ..+.||.|+.
T Consensus 70 ~~~C~--~C~~~~~~e~---~~~~CP~C~s 94 (115)
T COG0375 70 ECWCL--DCGQEVELEE---LDYRCPKCGS 94 (115)
T ss_pred EEEec--cCCCeecchh---heeECCCCCC
Confidence 45898 8988777653 2344888873
No 243
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=32.90 E-value=65 Score=23.75 Aligned_cols=28 Identities=25% Similarity=0.542 Sum_probs=16.1
Q ss_pred ecCcccCCcccccc-------ccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDE-------GEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~-------~~~~~~~~C~~C~~ 129 (151)
.||+..|.+.-... +....++.||.|+-
T Consensus 122 ~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~D 156 (251)
T PTZ00396 122 HCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQE 156 (251)
T ss_pred CCCCccCCCCcccccccCCCcCcCceeEeCCCchh
Confidence 69999998643332 12344556665543
No 244
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=32.90 E-value=25 Score=18.95 Aligned_cols=27 Identities=19% Similarity=0.574 Sum_probs=16.0
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
...|| .|+..++..+. .....|..||+
T Consensus 19 ~~~CP--rCG~gvfmA~H-~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCP--RCGPGVFMADH-KDRWACGKCGY 45 (51)
T ss_pred cccCC--CCCCcchhhhc-CceeEeccccc
Confidence 34799 78853333322 23677877775
No 245
>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=32.37 E-value=12 Score=15.63 Aligned_cols=8 Identities=38% Similarity=1.194 Sum_probs=3.0
Q ss_pred cCcccchh
Q 043988 123 NCPHCRRL 130 (151)
Q Consensus 123 ~C~~C~~~ 130 (151)
.|+.|+..
T Consensus 2 ~C~~C~~~ 9 (24)
T PF13894_consen 2 QCPICGKS 9 (24)
T ss_dssp E-SSTS-E
T ss_pred CCcCCCCc
Confidence 35555543
No 246
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=32.26 E-value=30 Score=17.40 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=11.9
Q ss_pred ecCcccCCcccccc-ccccCcccC
Q 043988 102 YCPYKDCSSMLIDE-GEAIRKSNC 124 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~-~~~~~~~~C 124 (151)
.|| .|+..++.. +.....+.|
T Consensus 3 ~CP--~Cg~~lv~r~~k~g~F~~C 24 (39)
T PF01396_consen 3 KCP--KCGGPLVLRRGKKGKFLGC 24 (39)
T ss_pred CCC--CCCceeEEEECCCCCEEEC
Confidence 477 777766655 222355566
No 247
>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=31.78 E-value=29 Score=28.19 Aligned_cols=31 Identities=26% Similarity=0.492 Sum_probs=21.5
Q ss_pred cCCccccccccccCcccCcccchh-----hhhcCCCC
Q 043988 107 DCSSMLIDEGEAIRKSNCPHCRRL-----FCVQCKVP 138 (151)
Q Consensus 107 ~C~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 138 (151)
.|+..+... ...+.+.|..||+. .|..|+..
T Consensus 227 ~C~~~l~~h-~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 227 NCDVSLTYH-KKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCceEEe-cCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 566555543 24567899999887 58888774
No 248
>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=31.78 E-value=36 Score=16.58 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=14.3
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|+ .|++++..+. .--.||.|++
T Consensus 4 ~C~--~CG~i~~g~~---~p~~CP~Cg~ 26 (34)
T cd00729 4 VCP--VCGYIHEGEE---APEKCPICGA 26 (34)
T ss_pred ECC--CCCCEeECCc---CCCcCcCCCC
Confidence 477 8887765432 2237887765
No 249
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.07 E-value=22 Score=23.48 Aligned_cols=28 Identities=39% Similarity=1.033 Sum_probs=18.2
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHHHHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
...-+|.||.... |. .+||| .|..|-..
T Consensus 63 ~ddatC~IC~KTK-----FA-DG~GH-~C~YCq~r 90 (169)
T KOG3799|consen 63 GDDATCGICHKTK-----FA-DGCGH-NCSYCQTR 90 (169)
T ss_pred CcCcchhhhhhcc-----cc-cccCc-ccchhhhh
Confidence 4456899998655 22 47999 46666433
No 250
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=30.37 E-value=27 Score=19.94 Aligned_cols=31 Identities=19% Similarity=0.521 Sum_probs=15.8
Q ss_pred eeecCcccCCccccccccccCcccCcccchh
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
+.-||..+|....+........+.|..|+..
T Consensus 6 lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 4578844443333333333445667666664
No 251
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=30.03 E-value=88 Score=26.97 Aligned_cols=30 Identities=27% Similarity=0.768 Sum_probs=20.8
Q ss_pred eeecCcccCCcccccc---------ccccCcccCcccchhh
Q 043988 100 KFYCPYKDCSSMLIDE---------GEAIRKSNCPHCRRLF 131 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~---------~~~~~~~~C~~C~~~~ 131 (151)
.|.|+ .|+..|-.. ..+..-+.|+.|++.|
T Consensus 281 KFKCt--ECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRF 319 (1007)
T KOG3623|consen 281 KFKCT--ECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRF 319 (1007)
T ss_pred ccccc--ccchhhhhHHHHHhhheeecCCCCcCCccccccc
Confidence 46788 888877665 2234457888888766
No 252
>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=29.99 E-value=19 Score=29.13 Aligned_cols=35 Identities=23% Similarity=0.557 Sum_probs=18.2
Q ss_pred CccchHHHHHHHHHHHh--CCc---cccCCCCCCCCCccChh
Q 043988 36 HFNCTSCIVRYIASKLE--GNI---TNISCPQLGCEARLEFE 72 (151)
Q Consensus 36 H~fC~~Cl~~~~~~~i~--~~~---~~i~CP~~~C~~~~~~~ 72 (151)
-.||.+||..+-...+. .+. .=+.|| .|...|...
T Consensus 26 ~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP--~C~~~L~~~ 65 (483)
T PF05502_consen 26 SYYCPNCLFEVPSSEARSEKNRCSRNCFDCP--ICFSPLSVR 65 (483)
T ss_pred eeECccccccCChhhheeccceeccccccCC--CCCCcceeE
Confidence 34777777666555542 111 225666 466555443
No 253
>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=29.81 E-value=40 Score=16.15 Aligned_cols=23 Identities=30% Similarity=0.654 Sum_probs=13.9
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|+ .|+++.... .....||.|+.
T Consensus 3 ~C~--~CGy~y~~~---~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCP--VCGYIYDGE---EAPWVCPVCGA 25 (33)
T ss_pred ECC--CCCCEECCC---cCCCcCcCCCC
Confidence 466 788765543 23457887765
No 254
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=29.50 E-value=23 Score=20.70 Aligned_cols=14 Identities=29% Similarity=0.624 Sum_probs=8.6
Q ss_pred ecCcccCCcccccc
Q 043988 102 YCPYKDCSSMLIDE 115 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~ 115 (151)
.|.+++|+..|...
T Consensus 29 qC~N~eCg~tF~t~ 42 (72)
T PRK09678 29 QCQNVNCSATFITY 42 (72)
T ss_pred ecCCCCCCCEEEEE
Confidence 56767777655443
No 255
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=29.42 E-value=28 Score=20.82 Aligned_cols=18 Identities=33% Similarity=0.715 Sum_probs=16.3
Q ss_pred CCCCccchHHHHHHHHHH
Q 043988 33 GCSHFNCTSCIVRYIASK 50 (151)
Q Consensus 33 ~C~H~fC~~Cl~~~~~~~ 50 (151)
-|.|.|-..|+.+++.++
T Consensus 53 ~CnHaFH~HCI~rWL~Tk 70 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTK 70 (88)
T ss_pred ecchHHHHHHHHHHHhhC
Confidence 599999999999999883
No 256
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=29.17 E-value=15 Score=18.54 Aligned_cols=13 Identities=15% Similarity=0.306 Sum_probs=7.6
Q ss_pred cCcccCcccchhh
Q 043988 119 IRKSNCPHCRRLF 131 (151)
Q Consensus 119 ~~~~~C~~C~~~~ 131 (151)
-..+.|..|++.|
T Consensus 26 T~fy~C~~C~~~w 38 (39)
T PF01096_consen 26 TLFYVCCNCGHRW 38 (39)
T ss_dssp EEEEEESSSTEEE
T ss_pred eEEEEeCCCCCee
Confidence 4456666666543
No 257
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=28.98 E-value=30 Score=24.22 Aligned_cols=29 Identities=21% Similarity=0.497 Sum_probs=21.6
Q ss_pred ecCcccCCccccccccccCcccCcccchhhhhcC
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQC 135 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C 135 (151)
.|+ .|+..+... .+.+.||.|++.==+++
T Consensus 151 ~Cs--rC~~~L~~~---~~~l~Cp~Cg~tEkRKi 179 (188)
T COG1096 151 RCS--RCRAPLVKK---GNMLKCPNCGNTEKRKI 179 (188)
T ss_pred Ecc--CCCcceEEc---CcEEECCCCCCEEeeee
Confidence 588 999999883 46689999987544433
No 258
>PHA00616 hypothetical protein
Probab=28.96 E-value=23 Score=18.59 Aligned_cols=12 Identities=25% Similarity=0.667 Sum_probs=8.9
Q ss_pred ccCcccchhhhh
Q 043988 122 SNCPHCRRLFCV 133 (151)
Q Consensus 122 ~~C~~C~~~~C~ 133 (151)
.+|+.||..|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 468888888764
No 259
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=28.90 E-value=31 Score=19.04 Aligned_cols=11 Identities=45% Similarity=1.011 Sum_probs=3.1
Q ss_pred cCcccCcccch
Q 043988 119 IRKSNCPHCRR 129 (151)
Q Consensus 119 ~~~~~C~~C~~ 129 (151)
.+.+.||.||+
T Consensus 31 Lr~y~Cp~CgA 41 (55)
T PF05741_consen 31 LRKYVCPICGA 41 (55)
T ss_dssp GGG---TTT--
T ss_pred HhcCcCCCCcC
Confidence 34456665554
No 260
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=28.72 E-value=81 Score=21.56 Aligned_cols=53 Identities=19% Similarity=0.435 Sum_probs=33.0
Q ss_pred CCCeeecccccccCCCCCceecCCCCC---ccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSH---FNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF 71 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H---~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~ 71 (151)
......|=||+++... . ..--.|.. ..-++|+..|+..+ ....|+ -|......
T Consensus 5 s~~~~~CRIC~~~~~~-~-~~PC~CkGs~k~VH~sCL~rWi~~s-----~~~~Ce--iC~~~Y~i 60 (162)
T PHA02825 5 SLMDKCCWICKDEYDV-V-TNYCNCKNENKIVHKECLEEWINTS-----KNKSCK--ICNGPYNI 60 (162)
T ss_pred CCCCCeeEecCCCCCC-c-cCCcccCCCchHHHHHHHHHHHhcC-----CCCccc--ccCCeEEE
Confidence 3456699999987642 2 21113433 45899999999854 246788 56654433
No 261
>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=28.34 E-value=37 Score=15.88 Aligned_cols=24 Identities=13% Similarity=0.404 Sum_probs=12.4
Q ss_pred ecccccccCCCCCceecCCCCCcc
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFN 38 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~f 38 (151)
.|.+|....+....+.-..|...+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~l 25 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTL 25 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeE
Confidence 577886655543244444454333
No 262
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=28.16 E-value=51 Score=16.32 Aligned_cols=27 Identities=22% Similarity=0.550 Sum_probs=14.1
Q ss_pred eecCcccCCcccccc-ccccCcccCcccch
Q 043988 101 FYCPYKDCSSMLIDE-GEAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~ 129 (151)
+.|| .|+.+.... ........|..||.
T Consensus 2 r~C~--~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICP--KCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEET--TTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcC--CCCCccccccCCCCCCCccCCCCC
Confidence 3566 777665554 22234456666654
No 263
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.13 E-value=1.7e+02 Score=21.73 Aligned_cols=70 Identities=11% Similarity=0.211 Sum_probs=45.0
Q ss_pred CCeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCC-HHHHHHHHH
Q 043988 11 TPSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILP-DDVFARWGL 88 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~-~~~~~~~~~ 88 (151)
...|.|||=--+++. ..++.+-.|||.|=..=+++. + .-.|+ .|+..+...++--|-+ +++++.|..
T Consensus 109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei-----k----as~C~--~C~a~y~~~dvIvlNg~~E~~dllk~ 177 (293)
T KOG3113|consen 109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI-----K----ASVCH--VCGAAYQEDDVIVLNGTEEDVDLLKT 177 (293)
T ss_pred cceeecccccceecceEEEEEEeccceeccHHHHHHh-----h----hcccc--ccCCcccccCeEeeCCCHHHHHHHHH
Confidence 457899998655554 345556689999876655542 2 13677 6998888887765544 455555544
Q ss_pred HHH
Q 043988 89 ALC 91 (151)
Q Consensus 89 ~~~ 91 (151)
++.
T Consensus 178 rme 180 (293)
T KOG3113|consen 178 RME 180 (293)
T ss_pred HHH
Confidence 433
No 264
>PRK05978 hypothetical protein; Provisional
Probab=28.09 E-value=36 Score=22.93 Aligned_cols=27 Identities=19% Similarity=0.402 Sum_probs=14.7
Q ss_pred ecCcccCCccccccccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.|| .|+.--...+--..+-.|+.||..
T Consensus 35 rCP--~CG~G~LF~g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 35 RCP--ACGEGKLFRAFLKPVDHCAACGED 61 (148)
T ss_pred cCC--CCCCCcccccccccCCCccccCCc
Confidence 588 777543333323445567766654
No 265
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=27.51 E-value=18 Score=17.89 Aligned_cols=30 Identities=27% Similarity=0.652 Sum_probs=13.2
Q ss_pred cchHHHHHHHHHHHhC-CccccCCCCCCCCCcc
Q 043988 38 NCTSCIVRYIASKLEG-NITNISCPQLGCEARL 69 (151)
Q Consensus 38 fC~~Cl~~~~~~~i~~-~~~~i~CP~~~C~~~~ 69 (151)
+|.+|+++|....-.. ..-.+.|+ .|+-.+
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~--~CGPr~ 31 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCT--NCGPRY 31 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BT--TCC-SC
T ss_pred CCHHHHHHHcCCCCCcccCcCccCC--CCCCCE
Confidence 4788888775432111 22357887 576443
No 266
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=27.42 E-value=31 Score=21.53 Aligned_cols=31 Identities=16% Similarity=0.351 Sum_probs=18.0
Q ss_pred CCeeecccccccCCCCCceecCCCCCccchHH
Q 043988 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSC 42 (151)
Q Consensus 11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~C 42 (151)
...|+|.-||=....++.-. ..=|+.+|++|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~-~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAR-EKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhcc-ccCCCEecccc
Confidence 44577888875554444332 23467777776
No 267
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=27.15 E-value=19 Score=22.63 Aligned_cols=32 Identities=22% Similarity=0.540 Sum_probs=19.5
Q ss_pred ccCcccCcccchhhhhcCCCCCCCCCCchhhhhC
Q 043988 118 AIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151 (151)
Q Consensus 118 ~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~ 151 (151)
+.....||.|++ =|..|+.. -=|..|...++|
T Consensus 64 DCL~~~C~GC~~-PC~~C~S~-KCG~~CR~nRkw 95 (103)
T PF14949_consen 64 DCLDEDCPGCHY-PCPKCGSR-KCGPECRCNRKW 95 (103)
T ss_pred cccCCCCCCccc-cCCCCCCC-ccChhhCcCCce
Confidence 455566666654 46666552 336788888877
No 268
>PRK12496 hypothetical protein; Provisional
Probab=27.01 E-value=27 Score=23.87 Aligned_cols=24 Identities=17% Similarity=0.469 Sum_probs=11.9
Q ss_pred ecCcccCCccccccccccCcccCcccchh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL 130 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~ 130 (151)
.|+ +|+..+..+. ..-.||.||..
T Consensus 129 ~C~--gC~~~~~~~~---~~~~C~~CG~~ 152 (164)
T PRK12496 129 VCK--GCKKKYPEDY---PDDVCEICGSP 152 (164)
T ss_pred ECC--CCCccccCCC---CCCcCCCCCCh
Confidence 377 7775554321 11256666543
No 269
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=26.88 E-value=39 Score=16.28 Aligned_cols=11 Identities=36% Similarity=1.235 Sum_probs=6.7
Q ss_pred cCCCCCCCCCc
Q 043988 58 ISCPQLGCEAR 68 (151)
Q Consensus 58 i~CP~~~C~~~ 68 (151)
++||.++|...
T Consensus 2 ~~CPtpGCdg~ 12 (31)
T PF01530_consen 2 LKCPTPGCDGS 12 (31)
T ss_dssp TSSSSTT--SC
T ss_pred CcCCCCCCCcc
Confidence 57998888753
No 270
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.44 E-value=60 Score=25.14 Aligned_cols=31 Identities=19% Similarity=0.528 Sum_probs=21.0
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHH
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
...+-.|.||.++... ..+.+|||.-| |...
T Consensus 302 ~~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~c 332 (355)
T KOG1571|consen 302 LPQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLC 332 (355)
T ss_pred cCCCCceEEecCCccc---eeeecCCcEEE--chHH
Confidence 3456689999976643 44458999966 6433
No 271
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=26.39 E-value=1.1e+02 Score=17.18 Aligned_cols=13 Identities=15% Similarity=0.470 Sum_probs=9.1
Q ss_pred cccCCCCCCCCCccC
Q 043988 56 TNISCPQLGCEARLE 70 (151)
Q Consensus 56 ~~i~CP~~~C~~~~~ 70 (151)
.++.|+ .|+..+.
T Consensus 3 iPVRCF--TCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCF--TCGKVIG 15 (60)
T ss_dssp -SSS-S--TTTSBTC
T ss_pred CceecC--CCCCChh
Confidence 478998 7998775
No 272
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.82 E-value=37 Score=26.96 Aligned_cols=26 Identities=23% Similarity=0.640 Sum_probs=20.3
Q ss_pred ecCcccCCccccccccccCcccCcccchhh
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.|| .|+..+...+.. -+.|++||+.+
T Consensus 352 ~Cp--~Cg~~m~S~G~~--g~rC~kCg~~~ 377 (421)
T COG1571 352 VCP--RCGGRMKSAGRN--GFRCKKCGTRA 377 (421)
T ss_pred CCC--ccCCchhhcCCC--CcccccccccC
Confidence 488 999988876543 78999998753
No 273
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=25.75 E-value=37 Score=26.49 Aligned_cols=34 Identities=18% Similarity=0.601 Sum_probs=24.1
Q ss_pred CCCeeecccccccCCCCCceecCCCCCccchHHHHH
Q 043988 10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR 45 (151)
Q Consensus 10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~ 45 (151)
+...+-|.=|-... .+.+..++|+..||++|+.-
T Consensus 36 ~~gk~~C~RC~~~~--~~~~~~lp~~~~YCr~Cl~m 69 (441)
T COG4098 36 ENGKYRCNRCGNTH--IELFAKLPCGCLYCRNCLMM 69 (441)
T ss_pred ccCcEEehhcCCcc--hhhhcccccceEeehhhhhc
Confidence 34568899997543 23344458999999999753
No 274
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=25.62 E-value=50 Score=15.82 Aligned_cols=25 Identities=20% Similarity=0.644 Sum_probs=17.2
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|. .|+..+.... ....+.|..|+.
T Consensus 3 ~C~--~C~t~L~yP~-gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCG--GCRTLLMYPR-GASSVRCALCQT 27 (31)
T ss_pred CcC--CCCcEeecCC-CCCeEECCCCCe
Confidence 466 7887777654 367788887764
No 275
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=25.39 E-value=36 Score=21.53 Aligned_cols=23 Identities=26% Similarity=0.580 Sum_probs=12.8
Q ss_pred cCCccccccccccCcccCcccchhh
Q 043988 107 DCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 107 ~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
.|+.-...++. ..+.||.|.+.|
T Consensus 8 ~c~sEytYed~--~~~~cpec~~ew 30 (112)
T COG2824 8 KCNSEYTYEDG--GQLICPECAHEW 30 (112)
T ss_pred ccCCceEEecC--ceEeCchhcccc
Confidence 67655554433 256777666544
No 276
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=25.09 E-value=53 Score=24.01 Aligned_cols=59 Identities=19% Similarity=0.241 Sum_probs=33.3
Q ss_pred HhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCcccccc
Q 043988 51 LEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDE 115 (151)
Q Consensus 51 i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~ 115 (151)
|.++.+..+||. .|. ..+..+|+..--..|+.-++++.++.....-||...|+......
T Consensus 183 I~~~~~~nrCpi-tl~-----p~~~pils~kcnh~~e~D~I~~~lq~~~trvcp~~~Csq~~~~~ 241 (275)
T COG5627 183 IHQELLSNRCPI-TLN-----PDFYPILSSKCNHKPEMDLINKKLQVECTRVCPRLICSQKEVVD 241 (275)
T ss_pred hhhhhhcccCCc-ccC-----cchhHHHHhhhcccccHHHHHHHhcCCceeecchhhcchheecc
Confidence 334555567763 222 12233444433344555556666666677789999997766554
No 277
>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=24.91 E-value=59 Score=17.41 Aligned_cols=46 Identities=20% Similarity=0.538 Sum_probs=20.9
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF 71 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~ 71 (151)
.+.|..|+-.. ...+.. =.|..|..|+..++..+ -.|| -|+..++.
T Consensus 2 r~nCKsCWf~~--k~Li~C--~dHYLCl~CLt~ml~~s-------~~C~--iC~~~LPt 47 (50)
T PF03854_consen 2 RYNCKSCWFAN--KGLIKC--SDHYLCLNCLTLMLSRS-------DRCP--ICGKPLPT 47 (50)
T ss_dssp -----SS-S----SSEEE---SS-EEEHHHHHHT-SSS-------SEET--TTTEE---
T ss_pred CccChhhhhcC--CCeeee--cchhHHHHHHHHHhccc-------cCCC--cccCcCcc
Confidence 46788887443 333332 36999999998876442 2677 47766653
No 278
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=24.89 E-value=1.4e+02 Score=21.96 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=19.9
Q ss_pred CeeecCcccCCccccccccccCcccCcccch
Q 043988 99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
...+|| .|+..+.... ......|+.|+.
T Consensus 98 ~~~fC~--~CG~~~~~~~-~~~~~~C~~c~~ 125 (256)
T PRK00241 98 SHRFCG--YCGHPMHPSK-TEWAMLCPHCRE 125 (256)
T ss_pred cCcccc--ccCCCCeecC-CceeEECCCCCC
Confidence 456999 8998776643 345678888775
No 279
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=24.59 E-value=73 Score=21.13 Aligned_cols=33 Identities=21% Similarity=0.143 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHhhhhcC--CC-eeecCcccCCcccccc
Q 043988 81 DVFARWGLALCESALVG--HK-KFYCPYKDCSSMLIDE 115 (151)
Q Consensus 81 ~~~~~~~~~~~~~~~~~--~~-~~~Cp~~~C~~~~~~~ 115 (151)
+..+++.+.+....+.. .+ ..-|+ .|+..+..-
T Consensus 69 ~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v 104 (147)
T PF01927_consen 69 DPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPV 104 (147)
T ss_pred CHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeec
Confidence 44555555544443332 23 24799 888766443
No 280
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=24.34 E-value=32 Score=17.45 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=5.4
Q ss_pred CcccCcccch
Q 043988 120 RKSNCPHCRR 129 (151)
Q Consensus 120 ~~~~C~~C~~ 129 (151)
..+.|..|++
T Consensus 27 ~fy~C~~C~~ 36 (40)
T smart00440 27 VFYVCTKCGH 36 (40)
T ss_pred EEEEeCCCCC
Confidence 4555655554
No 281
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=23.86 E-value=38 Score=17.87 Aligned_cols=35 Identities=17% Similarity=0.602 Sum_probs=23.7
Q ss_pred ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhC
Q 043988 15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEG 53 (151)
Q Consensus 15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~ 53 (151)
.|.||-.... +-+.+ -+..+|.+|-+..+.....+
T Consensus 1 ~CiiC~~~~~--~GI~I--~~~fIC~~CE~~iv~~~~~d 35 (46)
T PF10764_consen 1 KCIICGKEKE--EGIHI--YGKFICSDCEKEIVNTETDD 35 (46)
T ss_pred CeEeCCCcCC--CCEEE--ECeEehHHHHHHhccCCCCC
Confidence 3778876553 33443 48899999998887765543
No 282
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.81 E-value=36 Score=14.18 Aligned_cols=9 Identities=44% Similarity=1.545 Sum_probs=4.9
Q ss_pred cCcccchhh
Q 043988 123 NCPHCRRLF 131 (151)
Q Consensus 123 ~C~~C~~~~ 131 (151)
.|+.|+..|
T Consensus 2 ~C~~C~~~f 10 (26)
T smart00355 2 RCPECGKVF 10 (26)
T ss_pred CCCCCcchh
Confidence 455565554
No 283
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.61 E-value=1.3e+02 Score=20.66 Aligned_cols=24 Identities=29% Similarity=0.697 Sum_probs=17.0
Q ss_pred eeecCcccCCccccccccccCcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
...|| -||+++..+. --.||.||+
T Consensus 134 ~~vC~--vCGy~~~ge~----P~~CPiCga 157 (166)
T COG1592 134 VWVCP--VCGYTHEGEA----PEVCPICGA 157 (166)
T ss_pred EEEcC--CCCCcccCCC----CCcCCCCCC
Confidence 44699 9999887632 247888874
No 284
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.54 E-value=1.9e+02 Score=17.82 Aligned_cols=61 Identities=16% Similarity=0.334 Sum_probs=29.0
Q ss_pred CccChhHHhhcCCHH----HHHHHHHHHHhhhhcCC-Cee----ecCcccCCccccccccccCcccCcccchhh
Q 043988 67 ARLEFEDCRLILPDD----VFARWGLALCESALVGH-KKF----YCPYKDCSSMLIDEGEAIRKSNCPHCRRLF 131 (151)
Q Consensus 67 ~~~~~~~i~~~l~~~----~~~~~~~~~~~~~~~~~-~~~----~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~ 131 (151)
+.++...|..+++.+ .++.++....-. -... ..+ .|- +||+.+..+. -..--.||.|+.++
T Consensus 17 eplt~~ei~~~~~~~~~~~v~~~L~hiak~l-kr~g~~Llv~Pa~Ck--kCGfef~~~~-ik~pSRCP~CKSE~ 86 (97)
T COG3357 17 EPLTVAEIFELLNGEKEKEVYDHLEHIAKSL-KRKGKRLLVRPARCK--KCGFEFRDDK-IKKPSRCPKCKSEW 86 (97)
T ss_pred CcchHHHHHHHHcCCchHHHHHHHHHHHHHH-HhCCceEEecChhhc--ccCccccccc-cCCcccCCcchhhc
Confidence 456777776666542 333333221111 1111 111 355 8887776531 12235677666543
No 285
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=23.52 E-value=41 Score=18.09 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=13.2
Q ss_pred ecCcccCCccccccccccCcccCcccch
Q 043988 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~ 129 (151)
.|. .|+..+... .....+.||.||+
T Consensus 8 ~C~--~Cg~~~~~~-~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCA--RCGREVELD-QETRGIRCPYCGS 32 (49)
T ss_pred Ehh--hcCCeeehh-hccCceeCCCCCc
Confidence 355 666655322 2344566766665
No 286
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=23.35 E-value=34 Score=31.07 Aligned_cols=38 Identities=29% Similarity=0.649 Sum_probs=30.6
Q ss_pred CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHH
Q 043988 12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL 51 (151)
Q Consensus 12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i 51 (151)
..+.|+||.+..-...++. .|||.+|..|...+...+.
T Consensus 1152 ~~~~c~ic~dil~~~~~I~--~cgh~~c~~c~~~~l~~~s 1189 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIA--GCGHEPCCRCDELWLYASS 1189 (1394)
T ss_pred cccchHHHHHHHHhcCCee--eechhHhhhHHHHHHHHhc
Confidence 4468999998876555554 5999999999999988774
No 287
>PLN02189 cellulose synthase
Probab=22.76 E-value=79 Score=28.27 Aligned_cols=49 Identities=31% Similarity=0.669 Sum_probs=31.3
Q ss_pred CeeecccccccCCC---CCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988 12 PSFVCEICVESRSL---YDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR 68 (151)
Q Consensus 12 ~~~~C~iC~~~~~~---~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~ 68 (151)
....|.||.++... .++ +..-.|+-..|+.|. +|- .++| .-.|| .|+..
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eye---r~eg--~q~Cp--qCkt~ 85 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYE---RREG--TQNCP--QCKTR 85 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchh-hhh---hhcC--CccCc--ccCCc
Confidence 34589999998652 233 444469999999998 442 2233 24788 46543
No 288
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=22.75 E-value=1.2e+02 Score=19.02 Aligned_cols=39 Identities=18% Similarity=0.174 Sum_probs=30.3
Q ss_pred eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHh
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLE 52 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~ 52 (151)
.+.|-||-+++...+.|++. =+-..-.+|++.-+...+.
T Consensus 2 kWkC~iCg~~I~~gqlFTF~-~kG~VH~~C~~~~~~~k~~ 40 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQLFTFT-KKGPVHYECFREKASKKLY 40 (101)
T ss_pred ceEEEecCCeeeecceEEEe-cCCcEeHHHHHHHHhhhcc
Confidence 57899999999888888874 4467788999887665543
No 289
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=22.31 E-value=1.4e+02 Score=17.41 Aligned_cols=16 Identities=19% Similarity=0.557 Sum_probs=12.5
Q ss_pred eeecCcccCCcccccc
Q 043988 100 KFYCPYKDCSSMLIDE 115 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~ 115 (151)
.+.||..+|.......
T Consensus 37 ~i~CPC~~C~N~~~~~ 52 (77)
T PF13963_consen 37 MIRCPCRKCKNEKRQS 52 (77)
T ss_pred ceECCchhhccCccCC
Confidence 6799999998766544
No 290
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.73 E-value=1.7e+02 Score=18.88 Aligned_cols=27 Identities=19% Similarity=0.551 Sum_probs=13.9
Q ss_pred eeecCcccCCccccccccc--c--CcccCcccch
Q 043988 100 KFYCPYKDCSSMLIDEGEA--I--RKSNCPHCRR 129 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~~~~--~--~~~~C~~C~~ 129 (151)
..+| +|+..+...... . +.+.||.||.
T Consensus 70 ~~~C---~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 70 EIEC---ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred eEEe---eCcCcccccccchhccccCCcCcCCCC
Confidence 3467 577655443111 1 2356887763
No 291
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=20.95 E-value=1.1e+02 Score=15.75 Aligned_cols=33 Identities=15% Similarity=0.484 Sum_probs=19.3
Q ss_pred eeecccccccCCCCCceecCCCCC-ccchHHHHH
Q 043988 13 SFVCEICVESRSLYDSFDVKGCSH-FNCTSCIVR 45 (151)
Q Consensus 13 ~~~C~iC~~~~~~~~~~~~~~C~H-~fC~~Cl~~ 45 (151)
.+.|..|..+.....-+.-+.|.. .+|.+|...
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 467888876322233455556764 489999876
No 292
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=20.94 E-value=27 Score=16.55 Aligned_cols=14 Identities=36% Similarity=1.008 Sum_probs=7.2
Q ss_pred cCcccCcccchhhh
Q 043988 119 IRKSNCPHCRRLFC 132 (151)
Q Consensus 119 ~~~~~C~~C~~~~C 132 (151)
..+..||.|+..+|
T Consensus 11 ~~kY~Cp~C~~~~C 24 (30)
T PF04438_consen 11 PAKYRCPRCGARYC 24 (30)
T ss_dssp EESEE-TTT--EES
T ss_pred CCEEECCCcCCcee
Confidence 34567888877766
No 293
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=20.81 E-value=1.1e+02 Score=16.68 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=16.4
Q ss_pred eecCcccCCc---cccccccccCcccCcccch
Q 043988 101 FYCPYKDCSS---MLIDEGEAIRKSNCPHCRR 129 (151)
Q Consensus 101 ~~Cp~~~C~~---~~~~~~~~~~~~~C~~C~~ 129 (151)
+.|+ .|.. .....+.....+.|+.|++
T Consensus 23 LIC~--~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 23 LICS--KCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred EECc--ccchhhcccccccCCceEEEcCCCCC
Confidence 5688 6653 2222334456888988875
No 294
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=20.70 E-value=42 Score=15.55 Aligned_cols=24 Identities=33% Similarity=0.876 Sum_probs=10.0
Q ss_pred cCcccCCccccccc-cccCcccCcccc
Q 043988 103 CPYKDCSSMLIDEG-EAIRKSNCPHCR 128 (151)
Q Consensus 103 Cp~~~C~~~~~~~~-~~~~~~~C~~C~ 128 (151)
|| .|+..+.... .......|+.|.
T Consensus 4 C~--rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 4 CP--RCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp -T--TT--BBEEEEETTEEEEE-TTTC
T ss_pred Cc--cCCCcceEeEecCCCCeECcCCc
Confidence 55 6776655442 234455666553
No 295
>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=20.59 E-value=30 Score=18.16 Aligned_cols=12 Identities=17% Similarity=0.744 Sum_probs=6.1
Q ss_pred ecCcccCCcccc
Q 043988 102 YCPYKDCSSMLI 113 (151)
Q Consensus 102 ~Cp~~~C~~~~~ 113 (151)
.|.++.|+..+.
T Consensus 27 qC~N~~Cg~tfv 38 (47)
T PF04606_consen 27 QCTNPECGHTFV 38 (47)
T ss_pred EECCCcCCCEEE
Confidence 455555555443
No 296
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=20.57 E-value=78 Score=15.71 Aligned_cols=26 Identities=27% Similarity=0.807 Sum_probs=14.1
Q ss_pred eeecCcccCCccc-ccc-c---cccCcccCccc
Q 043988 100 KFYCPYKDCSSML-IDE-G---EAIRKSNCPHC 127 (151)
Q Consensus 100 ~~~Cp~~~C~~~~-~~~-~---~~~~~~~C~~C 127 (151)
.+.|| .|+..- +.. + .....+.|..|
T Consensus 5 ~v~CP--~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCP--RCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCC--CCCCCCcceeCCCCCCCCEeEecCcC
Confidence 36788 777655 332 2 23445666554
No 297
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=20.57 E-value=87 Score=19.78 Aligned_cols=29 Identities=17% Similarity=0.487 Sum_probs=19.6
Q ss_pred eeecCcccCCcccccc-------ccccCcccCcccchh
Q 043988 100 KFYCPYKDCSSMLIDE-------GEAIRKSNCPHCRRL 130 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~-------~~~~~~~~C~~C~~~ 130 (151)
..+|+ +|..++... ......++|..||..
T Consensus 56 R~~Ck--kC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~ 91 (105)
T COG2023 56 RTICK--KCYTPLVPGKNARVRLRKGRVVVTCLECGTI 91 (105)
T ss_pred HHhcc--ccCcccccCcceEEEEcCCeEEEEecCCCcE
Confidence 35899 999876665 123467788877754
No 298
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=20.41 E-value=32 Score=25.18 Aligned_cols=30 Identities=27% Similarity=0.900 Sum_probs=10.1
Q ss_pred eeecCcccCCcccccc---ccccCcccCcccchhh
Q 043988 100 KFYCPYKDCSSMLIDE---GEAIRKSNCPHCRRLF 131 (151)
Q Consensus 100 ~~~Cp~~~C~~~~~~~---~~~~~~~~C~~C~~~~ 131 (151)
..+|| .|+..-... +...-.+.|+.|+.+|
T Consensus 31 n~yCP--~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 31 NMYCP--NCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp H---T--TT--SS-EE--------EEE-TTT--EE
T ss_pred CCcCC--CCCChhHhhccCCCccceeECCCCchHH
Confidence 45899 787652222 2234567888887654
No 299
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.34 E-value=62 Score=27.43 Aligned_cols=31 Identities=26% Similarity=0.600 Sum_probs=21.0
Q ss_pred cCCccccccccccCcccCcccchh-----hhhcCCCC
Q 043988 107 DCSSMLIDEGEAIRKSNCPHCRRL-----FCVQCKVP 138 (151)
Q Consensus 107 ~C~~~~~~~~~~~~~~~C~~C~~~-----~C~~C~~~ 138 (151)
.|+..+... ...+.+.|..||+. .|..|+..
T Consensus 395 ~C~~~l~~h-~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 395 HCDASLTLH-RFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCceeEE-CCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 566655443 23567889999886 58888764
No 300
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.26 E-value=1.1e+02 Score=16.51 Aligned_cols=12 Identities=25% Similarity=1.115 Sum_probs=7.6
Q ss_pred CCeeecCcccCCcc
Q 043988 98 HKKFYCPYKDCSSM 111 (151)
Q Consensus 98 ~~~~~Cp~~~C~~~ 111 (151)
...++|| .|+.+
T Consensus 44 ~~i~~Cp--~CgRi 55 (56)
T PF02591_consen 44 DEIVFCP--NCGRI 55 (56)
T ss_pred CCeEECc--CCCcc
Confidence 3456777 67654
Done!