Query 045528
Match_columns 195
No_of_seqs 147 out of 201
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 03:01:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3362 Predicted BBOX Zn-fing 100.0 1E-46 2.2E-51 305.7 3.4 152 26-193 3-156 (156)
2 PF04438 zf-HIT: HIT zinc fing 99.2 4.7E-12 1E-16 78.4 1.1 29 155-183 2-30 (30)
3 KOG4137 Uncharacterized conser 97.7 5.6E-05 1.2E-09 58.6 4.2 68 119-187 15-82 (102)
4 COG5195 Uncharacterized conser 97.2 0.00031 6.7E-09 55.4 3.5 69 117-187 30-98 (118)
5 PF01753 zf-MYND: MYND finger; 95.9 0.0054 1.2E-07 38.6 2.0 29 158-186 1-30 (37)
6 PF13824 zf-Mss51: Zinc-finger 94.0 0.032 7E-07 39.2 1.6 28 157-184 1-33 (55)
7 KOG1710 MYND Zn-finger and ank 93.7 0.016 3.5E-07 53.4 -0.3 33 155-187 319-353 (396)
8 cd00350 rubredoxin_like Rubred 92.8 0.054 1.2E-06 33.6 1.1 20 156-175 2-26 (33)
9 PF08265 YL1_C: YL1 nuclear pr 92.4 0.089 1.9E-06 32.7 1.7 29 156-184 1-29 (30)
10 PLN00206 DEAD-box ATP-dependen 90.3 0.14 3.1E-06 48.5 1.6 30 157-186 30-59 (518)
11 cd00729 rubredoxin_SM Rubredox 87.5 0.28 6.1E-06 30.8 1.0 20 156-175 3-27 (34)
12 PF00301 Rubredoxin: Rubredoxi 87.1 0.31 6.7E-06 33.0 1.1 11 165-175 33-43 (47)
13 PRK00420 hypothetical protein; 86.0 0.44 9.5E-06 37.8 1.6 21 156-176 24-50 (112)
14 cd00730 rubredoxin Rubredoxin; 85.4 0.47 1E-05 32.5 1.3 10 166-175 34-43 (50)
15 COG1592 Rubrerythrin [Energy p 82.1 0.7 1.5E-05 38.9 1.3 21 155-175 134-158 (166)
16 PRK14704 anaerobic ribonucleos 81.7 1.2 2.7E-05 44.0 3.1 28 140-174 551-580 (618)
17 TIGR02487 NrdD anaerobic ribon 81.5 1 2.2E-05 44.0 2.4 30 139-175 515-547 (579)
18 PF13240 zinc_ribbon_2: zinc-r 80.7 0.77 1.7E-05 26.6 0.8 19 157-175 1-22 (23)
19 PF09297 zf-NADH-PPase: NADH p 79.3 1.1 2.3E-05 27.4 1.1 20 156-175 4-30 (32)
20 PRK03824 hypA hydrogenase nick 78.1 0.92 2E-05 36.4 0.7 11 153-163 68-78 (135)
21 PRK07111 anaerobic ribonucleos 78.1 2 4.3E-05 43.4 3.2 22 153-174 678-701 (735)
22 PRK09263 anaerobic ribonucleos 77.2 1.5 3.3E-05 44.1 2.1 21 154-174 640-667 (711)
23 PRK00432 30S ribosomal protein 75.3 1.9 4.2E-05 29.3 1.6 36 140-177 7-48 (50)
24 PRK12495 hypothetical protein; 73.8 1.8 3.8E-05 38.3 1.4 22 155-176 42-68 (226)
25 PRK12380 hydrogenase nickel in 73.6 1.8 4E-05 33.7 1.3 24 152-175 67-95 (113)
26 PF13248 zf-ribbon_3: zinc-rib 73.6 1.6 3.5E-05 25.6 0.8 20 156-175 3-25 (26)
27 PRK01343 zinc-binding protein; 73.5 2.8 6.2E-05 29.7 2.1 25 156-184 10-34 (57)
28 TIGR02827 RNR_anaer_Bdell anae 72.4 2.4 5.2E-05 41.9 2.1 29 140-175 524-555 (586)
29 PF09862 DUF2089: Protein of u 71.9 1.8 4E-05 34.3 1.0 19 158-176 1-22 (113)
30 COG0675 Transposase and inacti 71.8 2 4.4E-05 36.4 1.3 20 156-175 310-331 (364)
31 smart00661 RPOL9 RNA polymeras 71.7 2.5 5.3E-05 27.7 1.4 19 156-174 1-28 (52)
32 PF07754 DUF1610: Domain of un 71.3 2.6 5.6E-05 25.0 1.3 11 164-174 14-24 (24)
33 PF01155 HypA: Hydrogenase exp 69.8 1.4 3.1E-05 34.1 -0.1 24 153-176 68-96 (113)
34 PRK08271 anaerobic ribonucleos 68.8 3.5 7.5E-05 41.1 2.3 23 153-175 564-589 (623)
35 PF14949 ARF7EP_C: ARF7 effect 68.7 2.6 5.7E-05 33.0 1.2 18 164-181 71-89 (103)
36 PRK08270 anaerobic ribonucleos 68.1 3.5 7.5E-05 41.2 2.2 23 153-175 624-648 (656)
37 PF07282 OrfB_Zn_ribbon: Putat 68.0 2.9 6.4E-05 29.0 1.2 20 156-175 29-55 (69)
38 PRK00762 hypA hydrogenase nick 66.9 2.7 5.8E-05 33.3 0.9 22 153-175 68-101 (124)
39 PF08271 TF_Zn_Ribbon: TFIIB z 66.5 3.8 8.2E-05 26.4 1.4 18 157-174 2-27 (43)
40 PRK00418 DNA gyrase inhibitor; 66.4 4.8 0.0001 29.0 2.0 30 155-184 6-35 (62)
41 PRK08579 anaerobic ribonucleos 65.8 3.8 8.2E-05 40.8 1.9 24 152-175 565-591 (625)
42 TIGR00100 hypA hydrogenase nic 65.4 2.9 6.4E-05 32.6 0.9 25 152-176 67-96 (115)
43 PRK14890 putative Zn-ribbon RN 65.3 2.6 5.6E-05 30.1 0.5 11 154-164 24-34 (59)
44 PRK00564 hypA hydrogenase nick 65.0 3.3 7.2E-05 32.4 1.1 23 153-175 69-97 (117)
45 PF12387 Peptidase_C74: Pestiv 64.8 3.1 6.7E-05 35.9 0.9 31 153-183 160-192 (200)
46 PF14446 Prok-RING_1: Prokaryo 64.8 4 8.7E-05 28.6 1.4 21 156-176 6-31 (54)
47 PHA00626 hypothetical protein 64.6 4 8.7E-05 29.1 1.3 20 157-176 13-33 (59)
48 PF13894 zf-C2H2_4: C2H2-type 64.0 3.5 7.6E-05 21.9 0.8 21 167-187 1-21 (24)
49 PRK13130 H/ACA RNA-protein com 63.6 3.6 7.8E-05 28.9 1.0 24 154-177 4-28 (56)
50 PHA02942 putative transposase; 63.5 3.9 8.4E-05 38.0 1.5 20 156-175 326-351 (383)
51 PF03884 DUF329: Domain of unk 62.8 3.3 7.2E-05 29.2 0.7 28 157-184 4-31 (57)
52 smart00290 ZnF_UBP Ubiquitin C 62.8 5.4 0.00012 25.9 1.7 23 157-179 1-24 (50)
53 TIGR01031 rpmF_bact ribosomal 62.3 5.4 0.00012 27.7 1.6 20 154-173 25-46 (55)
54 PRK12496 hypothetical protein; 62.2 4 8.6E-05 33.8 1.2 21 156-176 128-153 (164)
55 PF09538 FYDLN_acid: Protein o 62.0 3.5 7.5E-05 32.3 0.7 22 155-176 9-36 (108)
56 PRK11788 tetratricopeptide rep 61.7 5.3 0.00012 34.8 1.9 21 155-175 354-377 (389)
57 COG1571 Predicted DNA-binding 60.4 4.3 9.3E-05 38.8 1.2 23 157-179 352-380 (421)
58 COG2888 Predicted Zn-ribbon RN 59.9 5.5 0.00012 28.7 1.4 7 156-162 28-34 (61)
59 cd01675 RNR_III Class III ribo 59.8 4.6 9.9E-05 39.3 1.3 24 151-175 515-541 (555)
60 COG3024 Uncharacterized protei 59.7 5.1 0.00011 29.2 1.2 28 157-184 9-36 (65)
61 PF00641 zf-RanBP: Zn-finger i 59.5 4.6 0.0001 24.1 0.8 20 156-175 5-27 (30)
62 TIGR00269 conserved hypothetic 59.4 3.7 8.1E-05 31.2 0.5 19 155-173 80-99 (104)
63 PF13878 zf-C2H2_3: zinc-finge 59.2 4.7 0.0001 26.2 0.9 15 164-178 11-25 (41)
64 PF11781 RRN7: RNA polymerase 59.0 5.1 0.00011 25.5 1.0 18 157-174 10-33 (36)
65 smart00109 C1 Protein kinase C 59.0 5.9 0.00013 24.8 1.3 20 155-174 11-35 (49)
66 PRK05452 anaerobic nitric oxid 58.5 6.2 0.00013 37.6 1.9 25 151-175 421-467 (479)
67 PRK12286 rpmF 50S ribosomal pr 58.3 8 0.00017 27.1 2.0 18 156-173 28-47 (57)
68 smart00547 ZnF_RBZ Zinc finger 58.3 5.1 0.00011 22.9 0.8 19 157-175 4-25 (26)
69 smart00154 ZnF_AN1 AN1-like Zi 58.1 7.1 0.00015 25.2 1.6 22 158-179 1-25 (39)
70 PF14803 Nudix_N_2: Nudix N-te 57.8 5.6 0.00012 25.2 1.0 7 157-163 2-8 (34)
71 PRK04023 DNA polymerase II lar 57.7 6.5 0.00014 41.5 2.0 19 156-174 627-646 (1121)
72 PF04216 FdhE: Protein involve 57.4 3.4 7.4E-05 36.5 -0.0 9 156-164 173-181 (290)
73 PRK14714 DNA polymerase II lar 57.2 6.2 0.00014 42.5 1.8 20 156-175 680-701 (1337)
74 PF01783 Ribosomal_L32p: Ribos 57.1 6.5 0.00014 27.1 1.3 19 155-173 26-46 (56)
75 KOG3612 PHD Zn-finger protein 56.2 2.7 5.9E-05 41.5 -0.9 31 155-187 527-558 (588)
76 PF13597 NRDD: Anaerobic ribon 55.7 4.3 9.4E-05 39.5 0.3 30 140-176 483-514 (546)
77 COG4338 Uncharacterized protei 55.5 1.3 2.8E-05 30.9 -2.4 36 148-184 6-45 (54)
78 PRK14891 50S ribosomal protein 55.1 7.8 0.00017 31.7 1.7 42 153-194 2-53 (131)
79 PF00096 zf-C2H2: Zinc finger, 54.6 7.3 0.00016 21.2 1.0 21 167-187 1-21 (23)
80 PRK03681 hypA hydrogenase nick 54.6 6.8 0.00015 30.5 1.2 24 152-175 67-96 (114)
81 PF13696 zf-CCHC_2: Zinc knuck 54.4 9.6 0.00021 24.1 1.6 21 151-171 4-26 (32)
82 PF08792 A2L_zn_ribbon: A2L zi 54.2 8.1 0.00017 24.2 1.3 20 156-175 4-30 (33)
83 TIGR01384 TFS_arch transcripti 53.6 7.7 0.00017 29.0 1.3 20 157-176 2-26 (104)
84 PF13912 zf-C2H2_6: C2H2-type 53.3 8.5 0.00018 21.8 1.2 24 167-190 2-25 (27)
85 PRK14892 putative transcriptio 52.9 8.9 0.00019 29.7 1.6 24 153-176 19-52 (99)
86 smart00659 RPOLCX RNA polymera 52.7 9.4 0.0002 25.3 1.5 21 156-176 3-29 (44)
87 COG4068 Uncharacterized protei 51.7 7.3 0.00016 28.1 0.9 30 151-186 5-34 (64)
88 PRK00241 nudC NADH pyrophospha 51.7 8.1 0.00018 34.0 1.4 22 156-177 100-128 (256)
89 PF01428 zf-AN1: AN1-like Zinc 51.6 8.1 0.00018 25.0 1.0 22 158-179 1-26 (43)
90 PRK00398 rpoP DNA-directed RNA 51.2 8.6 0.00019 25.0 1.1 21 156-176 4-31 (46)
91 KOG2807 RNA polymerase II tran 50.0 29 0.00062 32.8 4.7 26 155-180 263-290 (378)
92 PHA00616 hypothetical protein 49.9 5.4 0.00012 26.9 -0.0 19 167-185 2-20 (44)
93 PF09889 DUF2116: Uncharacteri 49.9 8.3 0.00018 27.4 0.9 23 157-184 5-27 (59)
94 PF03833 PolC_DP2: DNA polymer 47.9 6 0.00013 41.0 0.0 34 157-190 669-704 (900)
95 PF12172 DUF35_N: Rubredoxin-l 47.9 9.1 0.0002 23.8 0.8 18 157-174 13-33 (37)
96 PF12773 DZR: Double zinc ribb 47.7 11 0.00024 24.5 1.2 22 153-174 10-37 (50)
97 cd07160 NR_DBD_LXR DNA-binding 47.2 11 0.00025 29.0 1.4 22 155-176 18-45 (101)
98 smart00064 FYVE Protein presen 47.0 11 0.00023 26.0 1.1 24 155-178 10-38 (68)
99 PF01363 FYVE: FYVE zinc finge 46.3 10 0.00023 26.1 1.0 24 155-178 9-37 (69)
100 PF13842 Tnp_zf-ribbon_2: DDE_ 45.6 14 0.00031 22.8 1.4 24 157-180 2-30 (32)
101 KOG0970 DNA polymerase alpha, 45.5 20 0.00044 38.6 3.3 22 48-73 49-70 (1429)
102 PRK05978 hypothetical protein; 45.2 10 0.00022 31.4 1.0 21 156-176 34-62 (148)
103 PF01780 Ribosomal_L37ae: Ribo 44.8 12 0.00027 28.7 1.3 23 155-177 35-64 (90)
104 PF14569 zf-UDP: Zinc-binding 44.8 10 0.00022 28.7 0.8 9 168-176 53-61 (80)
105 COG1645 Uncharacterized Zn-fin 44.4 13 0.00029 30.3 1.4 9 165-173 43-51 (131)
106 cd00029 C1 Protein kinase C co 43.5 16 0.00035 23.0 1.5 21 155-175 11-37 (50)
107 PF03833 PolC_DP2: DNA polymer 43.5 7.8 0.00017 40.2 0.0 36 156-191 656-696 (900)
108 KOG4850 Uncharacterized conser 43.3 9.6 0.00021 32.6 0.5 16 166-181 149-164 (190)
109 COG1997 RPL43A Ribosomal prote 42.6 17 0.00036 28.0 1.7 23 155-177 35-64 (89)
110 PLN02195 cellulose synthase A 42.0 12 0.00027 39.2 1.2 22 156-177 26-59 (977)
111 PF05129 Elf1: Transcription e 41.8 12 0.00026 27.8 0.7 26 151-176 18-56 (81)
112 PF10013 DUF2256: Uncharacteri 41.5 10 0.00023 25.4 0.4 32 151-183 5-40 (42)
113 TIGR01562 FdhE formate dehydro 41.2 13 0.00028 34.0 1.1 48 16-66 17-66 (305)
114 PF04640 PLATZ: PLATZ transcri 40.9 18 0.00038 26.7 1.5 23 155-182 49-71 (72)
115 PLN02189 cellulose synthase 40.4 14 0.0003 39.2 1.2 11 166-176 76-86 (1040)
116 TIGR02300 FYDLN_acid conserved 40.2 16 0.00035 29.8 1.3 22 155-176 9-36 (129)
117 PF05741 zf-nanos: Nanos RNA b 39.9 15 0.00032 25.8 1.0 14 161-174 28-41 (55)
118 PRK03564 formate dehydrogenase 39.7 14 0.00031 33.9 1.1 27 16-42 21-47 (309)
119 COG1198 PriA Primosomal protei 39.1 16 0.00034 37.3 1.3 19 157-175 464-484 (730)
120 PF02132 RecR: RecR protein; 38.7 4.9 0.00011 25.9 -1.5 18 155-172 17-35 (41)
121 PF02148 zf-UBP: Zn-finger in 38.7 17 0.00037 25.1 1.1 29 158-186 1-34 (63)
122 COG1998 RPS31 Ribosomal protei 38.7 19 0.0004 25.1 1.3 20 155-174 19-45 (51)
123 COG4888 Uncharacterized Zn rib 38.7 20 0.00043 28.3 1.6 26 151-176 18-56 (104)
124 TIGR00595 priA primosomal prot 38.2 16 0.00034 35.1 1.2 20 156-175 241-262 (505)
125 TIGR02098 MJ0042_CXXC MJ0042 f 38.2 16 0.00036 22.5 0.9 10 167-176 3-12 (38)
126 PF03604 DNA_RNApol_7kD: DNA d 38.1 22 0.00048 22.2 1.5 20 157-176 2-27 (32)
127 PLN02638 cellulose synthase A 38.0 15 0.00034 38.9 1.1 22 156-177 37-70 (1079)
128 PF14206 Cys_rich_CPCC: Cystei 37.5 16 0.00034 27.3 0.8 17 157-173 3-27 (78)
129 PLN02436 cellulose synthase A 36.9 17 0.00036 38.7 1.2 10 168-177 57-66 (1094)
130 PF10080 DUF2318: Predicted me 36.7 25 0.00054 27.3 1.9 37 140-176 20-62 (102)
131 cd00065 FYVE FYVE domain; Zinc 36.5 20 0.00044 23.5 1.2 26 157-183 4-34 (57)
132 PF08461 HTH_12: Ribonuclease 35.6 41 0.00089 23.7 2.7 31 39-71 19-49 (66)
133 PRK01110 rpmF 50S ribosomal pr 35.1 26 0.00055 24.7 1.5 6 157-163 42-47 (60)
134 PF14353 CpXC: CpXC protein 34.9 22 0.00049 27.4 1.4 15 162-176 34-48 (128)
135 TIGR00627 tfb4 transcription f 34.9 20 0.00043 32.3 1.2 20 157-176 257-279 (279)
136 PF14445 Prok-RING_2: Prokaryo 34.7 8.3 0.00018 27.2 -1.0 10 156-165 23-32 (57)
137 PF14392 zf-CCHC_4: Zinc knuck 34.5 18 0.00039 24.0 0.7 15 156-170 32-48 (49)
138 COG3364 Zn-ribbon containing p 34.4 19 0.0004 28.7 0.8 22 155-176 2-30 (112)
139 PF07649 C1_3: C1-like domain; 34.4 21 0.00046 21.2 0.9 18 157-174 2-23 (30)
140 smart00834 CxxC_CXXC_SSSS Puta 34.2 20 0.00044 22.0 0.9 11 166-176 5-15 (41)
141 TIGR00354 polC DNA polymerase, 34.1 19 0.00042 38.0 1.1 21 156-176 626-647 (1095)
142 PF13719 zinc_ribbon_5: zinc-r 33.8 21 0.00046 22.5 0.9 10 167-176 3-12 (37)
143 PLN02915 cellulose synthase A 33.6 20 0.00044 37.9 1.2 22 156-177 35-68 (1044)
144 cd07173 NR_DBD_AR DNA-binding 32.8 12 0.00026 27.6 -0.4 21 155-175 3-29 (82)
145 PF10571 UPF0547: Uncharacteri 32.7 25 0.00053 21.0 1.0 7 157-163 16-22 (26)
146 PRK04023 DNA polymerase II lar 32.5 27 0.00058 37.2 1.8 20 156-175 639-660 (1121)
147 PRK14873 primosome assembly pr 32.5 22 0.00048 35.6 1.2 19 157-175 412-431 (665)
148 PHA02768 hypothetical protein; 32.3 19 0.00041 25.3 0.5 22 166-187 5-26 (55)
149 smart00647 IBR In Between Ring 32.1 26 0.00057 23.1 1.2 15 167-182 41-55 (64)
150 PF13717 zinc_ribbon_4: zinc-r 32.0 24 0.00052 22.2 0.9 10 167-176 3-12 (36)
151 PF10083 DUF2321: Uncharacteri 32.0 9.2 0.0002 32.2 -1.3 23 153-175 26-48 (158)
152 COG4306 Uncharacterized protei 31.7 14 0.0003 30.7 -0.3 20 156-175 29-48 (160)
153 PRK14714 DNA polymerase II lar 31.5 26 0.00056 38.1 1.5 21 156-176 668-689 (1337)
154 KOG1356 Putative transcription 31.4 24 0.00052 36.7 1.2 34 151-185 225-261 (889)
155 COG1885 Uncharacterized protei 31.4 22 0.00048 28.4 0.8 9 139-147 40-48 (115)
156 cd06966 NR_DBD_CAR DNA-binding 31.0 20 0.00044 27.1 0.5 20 157-176 2-27 (94)
157 PF01412 ArfGap: Putative GTPa 31.0 30 0.00064 26.7 1.5 34 153-187 11-45 (116)
158 PF09855 DUF2082: Nucleic-acid 30.8 20 0.00044 25.7 0.5 10 167-176 1-10 (64)
159 PF00130 C1_1: Phorbol esters/ 30.7 35 0.00077 22.1 1.6 22 154-175 10-37 (53)
160 PF02150 RNA_POL_M_15KD: RNA p 30.5 20 0.00043 22.6 0.3 19 156-174 2-28 (35)
161 TIGR01206 lysW lysine biosynth 30.4 30 0.00064 24.1 1.2 20 157-176 4-32 (54)
162 PF08134 cIII: cIII protein fa 30.3 52 0.0011 22.1 2.3 21 38-65 21-41 (44)
163 PF06677 Auto_anti-p27: Sjogre 30.3 34 0.00074 22.5 1.5 9 165-173 33-41 (41)
164 TIGR00155 pqiA_fam integral me 30.3 27 0.00058 32.9 1.3 22 155-176 215-240 (403)
165 PRK14715 DNA polymerase II lar 30.2 25 0.00054 38.6 1.2 20 156-175 675-695 (1627)
166 KOG2462 C2H2-type Zn-finger pr 30.1 34 0.00074 31.2 1.9 38 151-188 126-183 (279)
167 smart00451 ZnF_U1 U1-like zinc 29.8 31 0.00066 20.4 1.1 24 165-188 2-25 (35)
168 PLN03119 putative ADP-ribosyla 29.4 31 0.00068 34.7 1.6 34 154-188 22-56 (648)
169 PLN02400 cellulose synthase 29.4 26 0.00055 37.4 1.1 7 157-163 38-44 (1085)
170 PRK05580 primosome assembly pr 29.3 26 0.00057 34.8 1.1 19 157-175 410-430 (679)
171 KOG4477 RING1 interactor RYBP 29.1 17 0.00037 31.8 -0.2 20 157-176 26-48 (228)
172 PF00643 zf-B_box: B-box zinc 29.1 28 0.0006 21.6 0.8 31 156-187 4-36 (42)
173 PF00628 PHD: PHD-finger; Int 28.9 43 0.00093 21.5 1.8 20 157-176 1-24 (51)
174 smart00355 ZnF_C2H2 zinc finge 28.8 32 0.00069 18.0 1.0 21 167-187 1-21 (26)
175 smart00531 TFIIE Transcription 28.7 27 0.00057 28.1 0.9 17 165-181 98-114 (147)
176 PF13413 HTH_25: Helix-turn-he 28.5 31 0.00066 24.1 1.0 23 51-73 17-39 (62)
177 cd06956 NR_DBD_RXR DNA-binding 28.3 14 0.00031 26.7 -0.7 19 156-174 1-25 (77)
178 PLN03165 chaperone protein dna 28.2 52 0.0011 26.0 2.4 36 138-173 24-59 (111)
179 PRK09521 exosome complex RNA-b 27.8 36 0.00078 28.3 1.5 22 155-176 149-176 (189)
180 PF11682 DUF3279: Protein of u 27.8 48 0.001 26.9 2.2 27 152-178 94-122 (128)
181 PRK13844 recombination protein 27.5 30 0.00066 30.0 1.1 20 155-174 57-77 (200)
182 COG1426 Predicted transcriptio 27.5 32 0.00069 30.9 1.2 27 49-75 21-47 (284)
183 PF03107 C1_2: C1 domain; Int 27.4 43 0.00093 20.0 1.4 17 157-173 2-22 (30)
184 PRK08332 ribonucleotide-diphos 27.4 34 0.00074 38.2 1.7 22 158-179 1707-1739(1740)
185 PF04828 GFA: Glutathione-depe 27.2 25 0.00054 24.5 0.4 15 150-164 43-57 (92)
186 COG2816 NPY1 NTP pyrophosphohy 27.2 36 0.00078 31.0 1.5 23 156-178 112-141 (279)
187 PF10263 SprT-like: SprT-like 27.2 32 0.00069 26.9 1.1 21 155-175 123-152 (157)
188 COG1545 Predicted nucleic-acid 26.9 34 0.00074 27.5 1.2 19 157-175 31-52 (140)
189 PF07975 C1_4: TFIIH C1-like d 26.6 28 0.0006 24.0 0.5 13 165-177 20-32 (51)
190 KOG2879 Predicted E3 ubiquitin 26.5 35 0.00075 31.4 1.3 22 156-177 240-263 (298)
191 TIGR00373 conserved hypothetic 26.2 31 0.00067 28.2 0.9 14 57-70 45-58 (158)
192 KOG2932 E3 ubiquitin ligase in 26.1 35 0.00077 32.1 1.3 37 151-188 86-124 (389)
193 TIGR00615 recR recombination p 25.8 34 0.00074 29.5 1.1 20 155-174 53-73 (195)
194 PRK06266 transcription initiat 25.6 32 0.0007 28.8 0.9 17 55-71 51-67 (178)
195 cd02345 ZZ_dah Zinc finger, ZZ 25.5 47 0.001 22.1 1.5 31 157-187 2-36 (49)
196 smart00249 PHD PHD zinc finger 25.3 51 0.0011 19.8 1.6 20 157-176 1-24 (47)
197 PF13465 zf-H2C2_2: Zinc-finge 25.2 32 0.00069 19.8 0.6 11 166-176 14-24 (26)
198 PF04032 Rpr2: RNAse P Rpr2/Rp 25.2 45 0.00097 23.6 1.4 10 154-163 45-54 (85)
199 cd00472 Ribosomal_L24e_L24 Rib 24.7 50 0.0011 22.9 1.5 39 156-194 4-52 (54)
200 COG3791 Uncharacterized conser 24.6 38 0.00083 26.8 1.1 23 137-164 56-78 (133)
201 TIGR00280 L37a ribosomal prote 24.6 39 0.00085 26.0 1.1 23 155-177 35-64 (91)
202 PTZ00255 60S ribosomal protein 24.1 45 0.00097 25.6 1.3 23 155-177 36-65 (90)
203 KOG1973 Chromatin remodeling p 24.0 39 0.00085 30.0 1.2 47 136-186 216-270 (274)
204 PF12855 Ecl1: Life-span regul 24.0 38 0.00083 22.5 0.8 30 156-187 7-36 (43)
205 smart00105 ArfGap Putative GTP 23.8 42 0.0009 25.7 1.1 31 156-187 4-35 (112)
206 KOG1802 RNA helicase nonsense 23.7 37 0.0008 35.1 1.0 26 155-180 60-88 (935)
207 TIGR02605 CxxC_CxxC_SSSS putat 23.0 41 0.0009 21.9 0.8 11 166-176 5-15 (52)
208 smart00653 eIF2B_5 domain pres 22.9 51 0.0011 25.8 1.4 20 156-175 81-110 (110)
209 PF06906 DUF1272: Protein of u 22.7 22 0.00048 25.3 -0.6 19 156-174 30-49 (57)
210 cd02334 ZZ_dystrophin Zinc fin 22.6 64 0.0014 21.8 1.7 30 157-186 2-35 (49)
211 KOG2462 C2H2-type Zn-finger pr 22.4 31 0.00067 31.5 0.2 26 167-192 244-269 (279)
212 smart00291 ZnF_ZZ Zinc-binding 22.3 73 0.0016 20.5 1.9 29 156-184 5-36 (44)
213 PHA02325 hypothetical protein 21.9 39 0.00085 24.9 0.6 15 175-190 31-45 (72)
214 KOG2907 RNA polymerase I trans 21.6 41 0.00089 27.1 0.7 22 155-176 74-112 (116)
215 cd00021 BBOX B-Box-type zinc f 21.5 55 0.0012 19.5 1.1 24 157-181 2-26 (39)
216 PF09723 Zn-ribbon_8: Zinc rib 21.2 48 0.001 21.3 0.8 11 166-176 5-15 (42)
217 PRK08351 DNA-directed RNA poly 21.2 54 0.0012 23.4 1.2 22 157-178 5-27 (61)
218 PRK03976 rpl37ae 50S ribosomal 21.1 50 0.0011 25.4 1.1 23 155-177 36-65 (90)
219 PF00105 zf-C4: Zinc finger, C 21.1 17 0.00037 25.3 -1.4 21 156-176 1-27 (70)
220 PF09401 NSP10: RNA synthesis 21.0 41 0.00089 27.3 0.6 15 156-170 107-121 (124)
221 cd02338 ZZ_PCMF_like Zinc fing 20.9 60 0.0013 21.6 1.3 29 157-185 2-34 (49)
222 KOG4602 Nanos and related prot 20.7 36 0.00077 31.2 0.2 18 164-181 266-291 (318)
223 PF02069 Metallothio_Pro: Prok 20.6 42 0.00091 23.4 0.5 15 173-187 27-41 (52)
224 PRK00076 recR recombination pr 20.5 50 0.0011 28.5 1.1 20 155-174 53-73 (196)
225 cd06955 NR_DBD_VDR DNA-binding 20.2 44 0.00095 26.0 0.6 21 156-176 7-33 (107)
226 PF05605 zf-Di19: Drought indu 20.2 58 0.0013 21.7 1.1 19 166-185 2-20 (54)
227 PF06524 NOA36: NOA36 protein; 20.1 37 0.00081 31.2 0.2 24 157-180 173-196 (314)
228 PHA00733 hypothetical protein 20.1 72 0.0016 25.3 1.8 32 156-187 74-120 (128)
229 PRK15103 paraquat-inducible me 20.0 76 0.0016 30.1 2.2 22 155-176 221-245 (419)
No 1
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1e-46 Score=305.70 Aligned_cols=152 Identities=32% Similarity=0.541 Sum_probs=125.5
Q ss_pred hhhhhhcccccchhhhhhhhhcCCHHHHHHHHHHHHHhhhCCCCCCCCccC-CCCc-ccCCCCCCCchhhhhhccCCCcc
Q 045528 26 MEDERRMSTRTRKVAPRMAAALASADNRTQAALARLEALENDNAGIETVEI-NDDD-GEASLDDDDDEGYMQKRHSKGTK 103 (195)
Q Consensus 26 ~~~~~R~S~R~r~~s~r~r~~vlDe~tR~rr~~~rLeaLE~DN~~~dp~~~-~dd~-~~~~~d~~d~~g~~~Kk~~k~~k 103 (195)
|..+.|.|.|+++.++++ |||+++|+++++++||+||+||||||||++ .+.. .+.++|+.++ +++
T Consensus 3 ~~~e~r~s~r~~~~~~rR---vlD~~ar~rr~~r~l~~Le~Dn~~ddpha~l~~~k~~p~f~d~l~~----------Gkr 69 (156)
T KOG3362|consen 3 HSFEERASQRIKDQEQRR---VLDLNARQRRDNRNLEALEQDNFHDDPHASLVKPKQLPKFDDDLMG----------GKR 69 (156)
T ss_pred cchHHHHHHHHhhhhhcc---ccchHHHHhhhhhhhHHHhhhccCCCcccccccccccccccHHHhc----------chh
Confidence 456779999999999995 889999999999999999999999999987 3332 2444443332 112
Q ss_pred chhhhHHHHHhhhcccccHHHHHHHhhhccCCCCCCCeEEEEeCCCCCCCCcccccccCCCCceeccCCCCcccChhhhh
Q 045528 104 RKTRQAKALEDARKAPRSFLELLHEANLESLPPHVPSYLRAAVGPPSKTSRRHFCTVCGFSANYTCVKCGMRFCCIRCQN 183 (195)
Q Consensus 104 rK~r~~~~l~~k~r~rknf~~lLeE~~l~~~~~~~p~Y~~a~a~ps~~~P~r~fC~VCG~~~~YtC~~Cg~ryCS~~C~~ 183 (195)
++.++....+++++|+|||++||||++++- ...|+|.++.|+|+.. |.|+||+||||||.|+|+.||++|||+.|+.
T Consensus 70 ~~~~~~~~~~~~~~~RKnf~~~Ldea~~~~--~k~~~Y~~~~a~p~~K-P~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 70 KKQKSYKSEKFKLRFRKNFQALLDEALLNL--MKNPNYHTAYAKPSFK-PLRKFCAVCGYDSKYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred hhccccccchhhhhHHHHHHHHHHccchhh--hhccchhhcccCCCCC-CcchhhhhcCCCchhHHHhcCCceeechhhh
Confidence 222233356778999999999999998752 4679999999999854 6779999999999999999999999999999
Q ss_pred hhcccccCcc
Q 045528 184 IHDDTRCLKF 193 (195)
Q Consensus 184 ~H~EtRC~K~ 193 (195)
+|+||||+||
T Consensus 147 ~HneTRC~kw 156 (156)
T KOG3362|consen 147 THNETRCMKW 156 (156)
T ss_pred hccccccccC
Confidence 9999999999
No 2
>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=99.19 E-value=4.7e-12 Score=78.39 Aligned_cols=29 Identities=45% Similarity=1.307 Sum_probs=23.9
Q ss_pred cccccccCCCCceeccCCCCcccChhhhh
Q 045528 155 RHFCTVCGFSANYTCVKCGMRFCCIRCQN 183 (195)
Q Consensus 155 r~fC~VCG~~~~YtC~~Cg~ryCS~~C~~ 183 (195)
+++|+|||++++|+|++||.+|||+.|++
T Consensus 2 ~~~C~vC~~~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 2 RKLCSVCGNPAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp -EEETSSSSEESEE-TTT--EESSHHHHH
T ss_pred cCCCccCcCCCEEECCCcCCceeCcEeEC
Confidence 57999999999999999999999999985
No 3
>KOG4137 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.67 E-value=5.6e-05 Score=58.58 Aligned_cols=68 Identities=18% Similarity=0.354 Sum_probs=53.5
Q ss_pred cccHHHHHHHhhhccCCCCCCCeEEEEeCCCCCCCCcccccccCCCCceeccCCCCcccChhhhhhhcc
Q 045528 119 PRSFLELLHEANLESLPPHVPSYLRAAVGPPSKTSRRHFCTVCGFSANYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 119 rknf~~lLeE~~l~~~~~~~p~Y~~a~a~ps~~~P~r~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
-||+-+++..+.++.+...-++|++..|+|| ..|+.+.|-|.|.++-|+||.=|.||-+..=|....|
T Consensus 15 ~kn~rq~~~~e~~q~l~~~k~tYfsi~appS-v~PakKycDvTGLpapYtdP~t~Lry~naeiY~~i~e 82 (102)
T KOG4137|consen 15 GKNMRQKILKELLQRLIEKKHTYFSIEAPPS-VKPAKKYCDVTGLPAPYTDPNTGLRYHNAEIYKLICE 82 (102)
T ss_pred CccHHHHHhhhhhhhcccccCceEEecCCCc-cccchhhccccCCcccccCCCccceeccHHHHHHHHH
Confidence 4555566666666555556689999999997 7777899999999999999999999988766665444
No 4
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=97.23 E-value=0.00031 Score=55.38 Aligned_cols=69 Identities=22% Similarity=0.466 Sum_probs=51.6
Q ss_pred cccccHHHHHHHhhhccCCCCCCCeEEEEeCCCCCCCCcccccccCCCCceeccCCCCcccChhhhhhhcc
Q 045528 117 KAPRSFLELLHEANLESLPPHVPSYLRAAVGPPSKTSRRHFCTVCGFSANYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 117 r~rknf~~lLeE~~l~~~~~~~p~Y~~a~a~ps~~~P~r~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
+.-|++-+||..+.++. -+.--+|+.+.|+|| ..|+.++|-|.|.++.||||.=|.||=...=|+...|
T Consensus 30 rr~ktlrQli~~~~i~n-e~sk~~Y~sieappS-v~P~~KyCDvTGL~a~Yt~P~t~lrYhn~eiY~lI~e 98 (118)
T COG5195 30 RRFKTLRQLIPRLTIEN-ESSKHRYLSIEAPPS-VKPRMKYCDVTGLPAPYTCPNTGLRYHNSEIYKLICE 98 (118)
T ss_pred cchhhHHHHcccccccc-ccccceeEeecCCCc-cccccccccccCCcccccCCCcCceeccHHHHHHhhc
Confidence 34567778886654432 111348999999987 7888899999999999999999999976665555443
No 5
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=95.93 E-value=0.0054 Score=38.60 Aligned_cols=29 Identities=34% Similarity=0.873 Sum_probs=25.1
Q ss_pred ccccCCCCceeccCC-CCcccChhhhhhhc
Q 045528 158 CTVCGFSANYTCVKC-GMRFCCIRCQNIHD 186 (195)
Q Consensus 158 C~VCG~~~~YtC~~C-g~ryCS~~C~~~H~ 186 (195)
|.+||..+.-.|.+| ...|||..|+..|.
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRADW 30 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHHHH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHHHH
Confidence 789999887799999 67999999999886
No 6
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=93.96 E-value=0.032 Score=39.22 Aligned_cols=28 Identities=29% Similarity=0.774 Sum_probs=23.3
Q ss_pred cccccCC----CCceeccCCCCc-ccChhhhhh
Q 045528 157 FCTVCGF----SANYTCVKCGMR-FCCIRCQNI 184 (195)
Q Consensus 157 fC~VCG~----~~~YtC~~Cg~r-yCS~~C~~~ 184 (195)
+|.||+. ...|.|+.||.+ |||..-+..
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~ 33 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEEHWED 33 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHHHHHH
Confidence 6999999 889999999996 588776543
No 7
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=93.74 E-value=0.016 Score=53.39 Aligned_cols=33 Identities=30% Similarity=0.848 Sum_probs=28.9
Q ss_pred cccccccCCCC-ceeccCCC-CcccChhhhhhhcc
Q 045528 155 RHFCTVCGFSA-NYTCVKCG-MRFCCIRCQNIHDD 187 (195)
Q Consensus 155 r~fC~VCG~~~-~YtC~~Cg-~ryCS~~C~~~H~E 187 (195)
-.||++||-+| +-+|..|- .-||+..|++.|+-
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf 353 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWF 353 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHhhhH
Confidence 35999999988 55999997 78999999999974
No 8
>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=92.76 E-value=0.054 Score=33.65 Aligned_cols=20 Identities=40% Similarity=1.072 Sum_probs=16.2
Q ss_pred ccccccCCC-----CceeccCCCCc
Q 045528 156 HFCTVCGFS-----ANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~-----~~YtC~~Cg~r 175 (195)
..|.||||. ....||.||..
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 479999994 36699999974
No 9
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=92.39 E-value=0.089 Score=32.69 Aligned_cols=29 Identities=24% Similarity=0.590 Sum_probs=26.4
Q ss_pred ccccccCCCCceeccCCCCcccChhhhhh
Q 045528 156 HFCTVCGFSANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 156 ~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
++|.|-|.+++|+.|.=|.+|.++..+++
T Consensus 1 k~C~iTglpA~Y~DP~T~l~Y~n~~ayk~ 29 (30)
T PF08265_consen 1 KYCDITGLPARYRDPKTGLPYANSEAYKI 29 (30)
T ss_pred CcccccCCCccccCCCCCCcccCHHHhhc
Confidence 58999999999999999999999887764
No 10
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=90.35 E-value=0.14 Score=48.54 Aligned_cols=30 Identities=27% Similarity=0.690 Sum_probs=28.5
Q ss_pred cccccCCCCceeccCCCCcccChhhhhhhc
Q 045528 157 FCTVCGFSANYTCVKCGMRFCCIRCQNIHD 186 (195)
Q Consensus 157 fC~VCG~~~~YtC~~Cg~ryCS~~C~~~H~ 186 (195)
.|-|||-+|-|-|-.=....||+.|...|-
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (518)
T PLN00206 30 KCVVCGRYGEYICDETDDDICSLECKQALL 59 (518)
T ss_pred eEEEecCccceeccCCCCccccHHHHHHHH
Confidence 599999999999999999999999999886
No 11
>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=87.52 E-value=0.28 Score=30.83 Aligned_cols=20 Identities=35% Similarity=0.946 Sum_probs=15.4
Q ss_pred ccccccCCC--C---ceeccCCCCc
Q 045528 156 HFCTVCGFS--A---NYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~--~---~YtC~~Cg~r 175 (195)
..|.||||. + -..||.||..
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCc
Confidence 479999984 3 3599999974
No 12
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=87.14 E-value=0.31 Score=33.00 Aligned_cols=11 Identities=27% Similarity=0.924 Sum_probs=6.4
Q ss_pred CceeccCCCCc
Q 045528 165 ANYTCVKCGMR 175 (195)
Q Consensus 165 ~~YtC~~Cg~r 175 (195)
..++||.||+.
T Consensus 33 ~~w~CP~C~a~ 43 (47)
T PF00301_consen 33 DDWVCPVCGAP 43 (47)
T ss_dssp TT-B-TTTSSB
T ss_pred CCCcCcCCCCc
Confidence 46688888864
No 13
>PRK00420 hypothetical protein; Validated
Probab=85.98 E-value=0.44 Score=37.76 Aligned_cols=21 Identities=29% Similarity=0.816 Sum_probs=16.9
Q ss_pred ccccccCC------CCceeccCCCCcc
Q 045528 156 HFCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~------~~~YtC~~Cg~ry 176 (195)
..|+|||+ .|.+-||.||..+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCee
Confidence 47999997 3577999999854
No 14
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=85.42 E-value=0.47 Score=32.46 Aligned_cols=10 Identities=30% Similarity=1.022 Sum_probs=7.1
Q ss_pred ceeccCCCCc
Q 045528 166 NYTCVKCGMR 175 (195)
Q Consensus 166 ~YtC~~Cg~r 175 (195)
.++||.||..
T Consensus 34 ~w~CP~C~a~ 43 (50)
T cd00730 34 DWVCPVCGAG 43 (50)
T ss_pred CCCCCCCCCc
Confidence 4588888763
No 15
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.10 E-value=0.7 Score=38.88 Aligned_cols=21 Identities=33% Similarity=0.899 Sum_probs=16.5
Q ss_pred cccccccCC--CC--ceeccCCCCc
Q 045528 155 RHFCTVCGF--SA--NYTCVKCGMR 175 (195)
Q Consensus 155 r~fC~VCG~--~~--~YtC~~Cg~r 175 (195)
...|.|||| .| .-.||-||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 469999999 33 4499999975
No 16
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=81.75 E-value=1.2 Score=44.00 Aligned_cols=28 Identities=21% Similarity=0.576 Sum_probs=21.4
Q ss_pred CeEEEEeCCCCCCCCcccccccCCCCc--eeccCCCC
Q 045528 140 SYLRAAVGPPSKTSRRHFCTVCGFSAN--YTCVKCGM 174 (195)
Q Consensus 140 ~Y~~a~a~ps~~~P~r~fC~VCG~~~~--YtC~~Cg~ 174 (195)
.|++. -|....|..|||.|. ++||.||.
T Consensus 551 ~Y~si-------n~~~~~C~~CGy~g~~~~~CP~CG~ 580 (618)
T PRK14704 551 GYGSI-------NHPVDRCKCCSYHGVIGNECPSCGN 580 (618)
T ss_pred ceEEe-------CCCCeecCCCCCCCCcCccCcCCCC
Confidence 47773 334569999999775 59999995
No 17
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=81.54 E-value=1 Score=44.01 Aligned_cols=30 Identities=27% Similarity=0.725 Sum_probs=22.5
Q ss_pred CCeEEEEeCCCCCCCCcccccccCCCCce---eccCCCCc
Q 045528 139 PSYLRAAVGPPSKTSRRHFCTVCGFSANY---TCVKCGMR 175 (195)
Q Consensus 139 p~Y~~a~a~ps~~~P~r~fC~VCG~~~~Y---tC~~Cg~r 175 (195)
-.|++. -|....|..|||.|.. .||.||..
T Consensus 515 i~Y~~~-------n~~~~~C~~CG~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 515 IGYFGI-------NPPVDVCEDCGYTGEGLNDKCPKCGSH 547 (579)
T ss_pred CceEEe-------ccCCccCCCCCCCCCCCCCcCcCCCCc
Confidence 348773 3334699999998865 79999965
No 18
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=80.73 E-value=0.77 Score=26.62 Aligned_cols=19 Identities=32% Similarity=0.929 Sum_probs=11.0
Q ss_pred cccccCC---CCceeccCCCCc
Q 045528 157 FCTVCGF---SANYTCVKCGMR 175 (195)
Q Consensus 157 fC~VCG~---~~~YtC~~Cg~r 175 (195)
||..||. .+.--|+.||.+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 4666775 223357777764
No 19
>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=79.32 E-value=1.1 Score=27.41 Aligned_cols=20 Identities=35% Similarity=0.957 Sum_probs=11.1
Q ss_pred ccccccCCCC-------ceeccCCCCc
Q 045528 156 HFCTVCGFSA-------NYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~-------~YtC~~Cg~r 175 (195)
.||+.||.+- .-.|+.||..
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 4999999742 2278998865
No 20
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.11 E-value=0.92 Score=36.42 Aligned_cols=11 Identities=27% Similarity=0.501 Sum_probs=8.9
Q ss_pred CCcccccccCC
Q 045528 153 SRRHFCTVCGF 163 (195)
Q Consensus 153 P~r~fC~VCG~ 163 (195)
|.+..|..||+
T Consensus 68 p~~~~C~~CG~ 78 (135)
T PRK03824 68 EAVLKCRNCGN 78 (135)
T ss_pred ceEEECCCCCC
Confidence 44579999997
No 21
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=78.07 E-value=2 Score=43.35 Aligned_cols=22 Identities=36% Similarity=0.886 Sum_probs=17.5
Q ss_pred CCcccccccCCCC--ceeccCCCC
Q 045528 153 SRRHFCTVCGFSA--NYTCVKCGM 174 (195)
Q Consensus 153 P~r~fC~VCG~~~--~YtC~~Cg~ 174 (195)
|...+|.+|||.+ .+.||.||.
T Consensus 678 ~~~~~C~~CG~~~~~~~~CP~CG~ 701 (735)
T PRK07111 678 HPVDRCPVCGYLGVIEDKCPKCGS 701 (735)
T ss_pred CCCeecCCCCCCCCcCccCcCCCC
Confidence 4456999999955 359999996
No 22
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=77.22 E-value=1.5 Score=44.05 Aligned_cols=21 Identities=43% Similarity=1.035 Sum_probs=17.0
Q ss_pred CcccccccCCCCc-------eeccCCCC
Q 045528 154 RRHFCTVCGFSAN-------YTCVKCGM 174 (195)
Q Consensus 154 ~r~fC~VCG~~~~-------YtC~~Cg~ 174 (195)
...+|.+|||.|. +.||.||.
T Consensus 640 ~~~~C~~CG~~Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 640 PIDECYECGFTGEFECTEKGFTCPKCGN 667 (711)
T ss_pred CCcccCCCCCCccccCCCCCCcCcCCCC
Confidence 3469999999654 48999996
No 23
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=75.33 E-value=1.9 Score=29.34 Aligned_cols=36 Identities=28% Similarity=0.661 Sum_probs=23.3
Q ss_pred CeEEEEeCCCCCCCCcccccccCC------CCceeccCCCCccc
Q 045528 140 SYLRAAVGPPSKTSRRHFCTVCGF------SANYTCVKCGMRFC 177 (195)
Q Consensus 140 ~Y~~a~a~ps~~~P~r~fC~VCG~------~~~YtC~~Cg~ryC 177 (195)
.|...... ...+...||..||. .+.+.|.+||--+-
T Consensus 7 ~~y~v~~~--~v~~~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 7 EYYEVDGG--KVKRKNKFCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred eeEEECCC--EEEEccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence 35555333 23344569999997 34779999997653
No 24
>PRK12495 hypothetical protein; Provisional
Probab=73.83 E-value=1.8 Score=38.26 Aligned_cols=22 Identities=23% Similarity=0.575 Sum_probs=17.4
Q ss_pred cccccccCC-----CCceeccCCCCcc
Q 045528 155 RHFCTVCGF-----SANYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~-----~~~YtC~~Cg~ry 176 (195)
..+|.+||. +|...|+.|+..+
T Consensus 42 a~hC~~CG~PIpa~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 42 NAHCDECGDPIFRHDGQEFCPTCQQPV 68 (226)
T ss_pred hhhcccccCcccCCCCeeECCCCCCcc
Confidence 369999996 4777899998765
No 25
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=73.58 E-value=1.8 Score=33.66 Aligned_cols=24 Identities=17% Similarity=0.475 Sum_probs=17.5
Q ss_pred CCCcccccccCC-C----CceeccCCCCc
Q 045528 152 TSRRHFCTVCGF-S----ANYTCVKCGMR 175 (195)
Q Consensus 152 ~P~r~fC~VCG~-~----~~YtC~~Cg~r 175 (195)
.|.+-.|..||. | ..+.||.||..
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 344679999997 2 23479999975
No 26
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.55 E-value=1.6 Score=25.64 Aligned_cols=20 Identities=35% Similarity=0.946 Sum_probs=13.7
Q ss_pred ccccccCCC---CceeccCCCCc
Q 045528 156 HFCTVCGFS---ANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~---~~YtC~~Cg~r 175 (195)
.+|.-||.. +.--|+.||.+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 478888872 23378888875
No 27
>PRK01343 zinc-binding protein; Provisional
Probab=73.55 E-value=2.8 Score=29.66 Aligned_cols=25 Identities=32% Similarity=0.808 Sum_probs=18.7
Q ss_pred ccccccCCCCceeccCCCCcccChhhhhh
Q 045528 156 HFCTVCGFSANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 156 ~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
+.|.+||.+.... ..+|||.+|..+
T Consensus 10 ~~CP~C~k~~~~~----~rPFCS~RC~~i 34 (57)
T PRK01343 10 RPCPECGKPSTRE----AYPFCSERCRDI 34 (57)
T ss_pred CcCCCCCCcCcCC----CCcccCHHHhhh
Confidence 5899999865431 348999999765
No 28
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=72.38 E-value=2.4 Score=41.91 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=21.2
Q ss_pred CeEEEEeCCCCCCCCcccccccCCC-Cc--eeccCCCCc
Q 045528 140 SYLRAAVGPPSKTSRRHFCTVCGFS-AN--YTCVKCGMR 175 (195)
Q Consensus 140 ~Y~~a~a~ps~~~P~r~fC~VCG~~-~~--YtC~~Cg~r 175 (195)
.|++. -|.-.+|.+|||. |. +.||.||..
T Consensus 524 ~Y~ti-------n~~~siC~~CGy~~g~~~~~CP~CGs~ 555 (586)
T TIGR02827 524 NYFCF-------NIKITICNDCHHIDKRTLHRCPVCGSA 555 (586)
T ss_pred ceEEe-------CCCCeecCCCCCcCCCcCCcCcCCCCc
Confidence 37773 3345699999994 52 699999953
No 29
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=71.86 E-value=1.8 Score=34.33 Aligned_cols=19 Identities=37% Similarity=0.992 Sum_probs=15.6
Q ss_pred ccccCC---CCceeccCCCCcc
Q 045528 158 CTVCGF---SANYTCVKCGMRF 176 (195)
Q Consensus 158 C~VCG~---~~~YtC~~Cg~ry 176 (195)
|.|||. ...+.|+.||+-+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 999997 4578999999854
No 30
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.83 E-value=2 Score=36.42 Aligned_cols=20 Identities=30% Similarity=0.959 Sum_probs=16.3
Q ss_pred ccccccCCC--CceeccCCCCc
Q 045528 156 HFCTVCGFS--ANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~--~~YtC~~Cg~r 175 (195)
+.|++||++ ..+.|+.||.-
T Consensus 310 ~~C~~cg~~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGHLSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCCccceeEECCCCCCe
Confidence 589999984 35799999973
No 31
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=71.75 E-value=2.5 Score=27.67 Aligned_cols=19 Identities=42% Similarity=1.200 Sum_probs=12.7
Q ss_pred ccccccCC---CC------ceeccCCCC
Q 045528 156 HFCTVCGF---SA------NYTCVKCGM 174 (195)
Q Consensus 156 ~fC~VCG~---~~------~YtC~~Cg~ 174 (195)
.||.-||. .. .|.|+.||-
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCC
Confidence 38888885 11 467888874
No 32
>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=71.33 E-value=2.6 Score=25.03 Aligned_cols=11 Identities=27% Similarity=1.081 Sum_probs=8.2
Q ss_pred CCceeccCCCC
Q 045528 164 SANYTCVKCGM 174 (195)
Q Consensus 164 ~~~YtC~~Cg~ 174 (195)
...|.||+||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 34789999984
No 33
>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=69.76 E-value=1.4 Score=34.11 Aligned_cols=24 Identities=29% Similarity=0.796 Sum_probs=14.9
Q ss_pred CCcccccccCCCC-----ceeccCCCCcc
Q 045528 153 SRRHFCTVCGFSA-----NYTCVKCGMRF 176 (195)
Q Consensus 153 P~r~fC~VCG~~~-----~YtC~~Cg~ry 176 (195)
|.+-.|..||+.. .+.||.||...
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp --EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred CCcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 4467999999822 35899999864
No 34
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=68.81 E-value=3.5 Score=41.05 Aligned_cols=23 Identities=22% Similarity=0.573 Sum_probs=17.9
Q ss_pred CCcccccccCCC--C-ceeccCCCCc
Q 045528 153 SRRHFCTVCGFS--A-NYTCVKCGMR 175 (195)
Q Consensus 153 P~r~fC~VCG~~--~-~YtC~~Cg~r 175 (195)
|....|.+|||. + .++||.||..
T Consensus 564 ~~~~iC~~CG~~~~g~~~~CP~CGs~ 589 (623)
T PRK08271 564 VKITICNDCHHIDKRTGKRCPICGSE 589 (623)
T ss_pred CCCccCCCCCCcCCCCCcCCcCCCCc
Confidence 345699999994 3 5599999964
No 35
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=68.67 E-value=2.6 Score=32.97 Aligned_cols=18 Identities=44% Similarity=1.106 Sum_probs=16.2
Q ss_pred CC-ceeccCCCCcccChhh
Q 045528 164 SA-NYTCVKCGMRFCCIRC 181 (195)
Q Consensus 164 ~~-~YtC~~Cg~ryCS~~C 181 (195)
+| .|-|++||.+-|+..|
T Consensus 71 ~GC~~PC~~C~S~KCG~~C 89 (103)
T PF14949_consen 71 PGCHYPCPKCGSRKCGPEC 89 (103)
T ss_pred CCccccCCCCCCCccChhh
Confidence 44 7889999999999999
No 36
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=68.15 E-value=3.5 Score=41.16 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=17.5
Q ss_pred CCcccccccCC-CC-ceeccCCCCc
Q 045528 153 SRRHFCTVCGF-SA-NYTCVKCGMR 175 (195)
Q Consensus 153 P~r~fC~VCG~-~~-~YtC~~Cg~r 175 (195)
|....|.+||| .| .+.||.||..
T Consensus 624 ~~~~~C~~CG~~~g~~~~CP~CG~~ 648 (656)
T PRK08270 624 PTFSICPKHGYLSGEHEFCPKCGEE 648 (656)
T ss_pred CCCcccCCCCCcCCCCCCCcCCcCc
Confidence 33469999999 44 3599999965
No 37
>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=67.98 E-value=2.9 Score=28.96 Aligned_cols=20 Identities=35% Similarity=1.034 Sum_probs=15.4
Q ss_pred ccccccCCCC-------ceeccCCCCc
Q 045528 156 HFCTVCGFSA-------NYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~-------~YtC~~Cg~r 175 (195)
..|++||... .+.|+.||..
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCE
Confidence 4899999733 3599999875
No 38
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=66.89 E-value=2.7 Score=33.25 Aligned_cols=22 Identities=27% Similarity=0.789 Sum_probs=15.9
Q ss_pred CCcccccccCCC-----Cc-------eeccCCCCc
Q 045528 153 SRRHFCTVCGFS-----AN-------YTCVKCGMR 175 (195)
Q Consensus 153 P~r~fC~VCG~~-----~~-------YtC~~Cg~r 175 (195)
|.+-.| -||.. .. +.||.||..
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 445799 99975 11 579999964
No 39
>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=66.45 E-value=3.8 Score=26.43 Aligned_cols=18 Identities=33% Similarity=0.999 Sum_probs=11.6
Q ss_pred cccccCC--------CCceeccCCCC
Q 045528 157 FCTVCGF--------SANYTCVKCGM 174 (195)
Q Consensus 157 fC~VCG~--------~~~YtC~~Cg~ 174 (195)
.|.+||. .|.+.|+.||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 4777775 25667888875
No 40
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=66.38 E-value=4.8 Score=28.97 Aligned_cols=30 Identities=30% Similarity=0.569 Sum_probs=20.2
Q ss_pred cccccccCCCCceeccCCCCcccChhhhhh
Q 045528 155 RHFCTVCGFSANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 155 r~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
..-|.+||....+.=..=..+|||.+|..+
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~I 35 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLI 35 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhh
Confidence 457899988655432223458999999764
No 41
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=65.82 E-value=3.8 Score=40.77 Aligned_cols=24 Identities=29% Similarity=0.735 Sum_probs=18.1
Q ss_pred CCCcccccccCC--CC-ceeccCCCCc
Q 045528 152 TSRRHFCTVCGF--SA-NYTCVKCGMR 175 (195)
Q Consensus 152 ~P~r~fC~VCG~--~~-~YtC~~Cg~r 175 (195)
-|...+|..||+ .+ ...||.||..
T Consensus 565 np~~~~C~~CG~~~~g~~~~CP~CGs~ 591 (625)
T PRK08579 565 TPAITVCNKCGRSTTGLYTRCPRCGSE 591 (625)
T ss_pred CCCCccCCCCCCccCCCCCcCcCCCCc
Confidence 345579999998 34 3499999964
No 42
>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=65.38 E-value=2.9 Score=32.59 Aligned_cols=25 Identities=24% Similarity=0.449 Sum_probs=17.9
Q ss_pred CCCcccccccCCCC-----ceeccCCCCcc
Q 045528 152 TSRRHFCTVCGFSA-----NYTCVKCGMRF 176 (195)
Q Consensus 152 ~P~r~fC~VCG~~~-----~YtC~~Cg~ry 176 (195)
.|.+-.|..||... .+.||.||.+-
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 34457999999722 33799999753
No 43
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=65.33 E-value=2.6 Score=30.13 Aligned_cols=11 Identities=27% Similarity=0.763 Sum_probs=7.6
Q ss_pred CcccccccCCC
Q 045528 154 RRHFCTVCGFS 164 (195)
Q Consensus 154 ~r~fC~VCG~~ 164 (195)
....|..||-.
T Consensus 24 ~~F~CPnCG~~ 34 (59)
T PRK14890 24 VKFLCPNCGEV 34 (59)
T ss_pred CEeeCCCCCCe
Confidence 34678888865
No 44
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.96 E-value=3.3 Score=32.42 Aligned_cols=23 Identities=26% Similarity=0.639 Sum_probs=16.7
Q ss_pred CCcccccccCCCC-----ce-eccCCCCc
Q 045528 153 SRRHFCTVCGFSA-----NY-TCVKCGMR 175 (195)
Q Consensus 153 P~r~fC~VCG~~~-----~Y-tC~~Cg~r 175 (195)
|.+-+|..||... .| .||.||.+
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 4457999999732 24 49999975
No 45
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=64.81 E-value=3.1 Score=35.86 Aligned_cols=31 Identities=32% Similarity=0.488 Sum_probs=23.9
Q ss_pred CCcccccccCC--CCceeccCCCCcccChhhhh
Q 045528 153 SRRHFCTVCGF--SANYTCVKCGMRFCCIRCQN 183 (195)
Q Consensus 153 P~r~fC~VCG~--~~~YtC~~Cg~ryCS~~C~~ 183 (195)
+.--+|.||-. |..-+||+||..-=++.|.-
T Consensus 160 ~hcilCtvCe~r~w~g~~CPKCGr~G~pi~CGm 192 (200)
T PF12387_consen 160 KHCILCTVCEGREWKGGNCPKCGRHGKPITCGM 192 (200)
T ss_pred CceEEEeeeecCccCCCCCCcccCCCCCeeccc
Confidence 33349999986 88889999998877777743
No 46
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=64.76 E-value=4 Score=28.61 Aligned_cols=21 Identities=33% Similarity=0.817 Sum_probs=16.9
Q ss_pred ccccccCC-C--C--ceeccCCCCcc
Q 045528 156 HFCTVCGF-S--A--NYTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~-~--~--~YtC~~Cg~ry 176 (195)
..|.+||. + + ...|+.||++|
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcc
Confidence 37999997 3 2 45999999988
No 47
>PHA00626 hypothetical protein
Probab=64.59 E-value=4 Score=29.14 Aligned_cols=20 Identities=20% Similarity=0.338 Sum_probs=14.6
Q ss_pred cccccCCCC-ceeccCCCCcc
Q 045528 157 FCTVCGFSA-NYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~~~-~YtC~~Cg~ry 176 (195)
-|.+|-.|+ .|.|+.||-.|
T Consensus 13 rcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 13 KEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred eeceecccCcceEcCCCCCee
Confidence 466666644 78999999776
No 48
>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=64.04 E-value=3.5 Score=21.94 Aligned_cols=21 Identities=24% Similarity=0.450 Sum_probs=15.0
Q ss_pred eeccCCCCcccChhhhhhhcc
Q 045528 167 YTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~~~H~E 187 (195)
|.|+-||..|=+..-+..|..
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 678888888888888887754
No 49
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=63.58 E-value=3.6 Score=28.93 Aligned_cols=24 Identities=25% Similarity=0.587 Sum_probs=18.2
Q ss_pred CcccccccCCCC-ceeccCCCCccc
Q 045528 154 RRHFCTVCGFSA-NYTCVKCGMRFC 177 (195)
Q Consensus 154 ~r~fC~VCG~~~-~YtC~~Cg~ryC 177 (195)
+...|..||... +..||.||..+-
T Consensus 4 ~mr~C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCCEEccccCcCCCCCCC
Confidence 345899999643 779999998653
No 50
>PHA02942 putative transposase; Provisional
Probab=63.54 E-value=3.9 Score=38.04 Aligned_cols=20 Identities=30% Similarity=0.901 Sum_probs=15.9
Q ss_pred ccccccCCC------CceeccCCCCc
Q 045528 156 HFCTVCGFS------ANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~------~~YtC~~Cg~r 175 (195)
..|++||.. ..|.|+.||..
T Consensus 326 q~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 326 VSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred ccCCCCCCccCcCCCCEEECCCCCCE
Confidence 589999974 24799999974
No 51
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=62.83 E-value=3.3 Score=29.21 Aligned_cols=28 Identities=29% Similarity=0.628 Sum_probs=13.6
Q ss_pred cccccCCCCceeccCCCCcccChhhhhh
Q 045528 157 FCTVCGFSANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 157 fC~VCG~~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
-|.+||....++=..=..+|||-+|..+
T Consensus 4 ~CP~C~k~~~~~~~n~~rPFCS~RCk~i 31 (57)
T PF03884_consen 4 KCPICGKPVEWSPENPFRPFCSERCKLI 31 (57)
T ss_dssp E-TTT--EEE-SSSSS--SSSSHHHHHH
T ss_pred cCCCCCCeecccCCCCcCCcccHhhccc
Confidence 4666665444432222347999999754
No 52
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=62.81 E-value=5.4 Score=25.87 Aligned_cols=23 Identities=35% Similarity=0.833 Sum_probs=18.9
Q ss_pred cccccCCCC-ceeccCCCCcccCh
Q 045528 157 FCTVCGFSA-NYTCVKCGMRFCCI 179 (195)
Q Consensus 157 fC~VCG~~~-~YtC~~Cg~ryCS~ 179 (195)
.|++||... .|.|..||.-+|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 499999744 78999999999854
No 53
>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=62.31 E-value=5.4 Score=27.66 Aligned_cols=20 Identities=30% Similarity=0.747 Sum_probs=13.4
Q ss_pred CcccccccCC--CCceeccCCC
Q 045528 154 RRHFCTVCGF--SANYTCVKCG 173 (195)
Q Consensus 154 ~r~fC~VCG~--~~~YtC~~Cg 173 (195)
....|..||. ....-|+.||
T Consensus 25 ~l~~C~~cG~~~~~H~vc~~cG 46 (55)
T TIGR01031 25 TLVVCPNCGEFKLPHRVCPSCG 46 (55)
T ss_pred cceECCCCCCcccCeeECCccC
Confidence 3456788886 3455787777
No 54
>PRK12496 hypothetical protein; Provisional
Probab=62.19 E-value=4 Score=33.77 Aligned_cols=21 Identities=29% Similarity=0.925 Sum_probs=15.3
Q ss_pred ccccccC--CCCce---eccCCCCcc
Q 045528 156 HFCTVCG--FSANY---TCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG--~~~~Y---tC~~Cg~ry 176 (195)
+.|.-|| |..+| .|+.||.+.
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChh
Confidence 4699999 44444 599999753
No 55
>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=61.97 E-value=3.5 Score=32.33 Aligned_cols=22 Identities=36% Similarity=0.931 Sum_probs=15.2
Q ss_pred cccccccCC--CC----ceeccCCCCcc
Q 045528 155 RHFCTVCGF--SA----NYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~--~~----~YtC~~Cg~ry 176 (195)
.++|..||. +. ...||+||+-|
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCcc
Confidence 458888884 43 34788888755
No 56
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=61.68 E-value=5.3 Score=34.75 Aligned_cols=21 Identities=38% Similarity=0.915 Sum_probs=16.8
Q ss_pred cccccccCCCC---ceeccCCCCc
Q 045528 155 RHFCTVCGFSA---NYTCVKCGMR 175 (195)
Q Consensus 155 r~fC~VCG~~~---~YtC~~Cg~r 175 (195)
...|+-||+.. .+.||+||+.
T Consensus 354 ~~~c~~cg~~~~~~~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFTARTLYWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCCCccceeECcCCCCc
Confidence 37899999955 3499999974
No 57
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.38 E-value=4.3 Score=38.82 Aligned_cols=23 Identities=35% Similarity=0.820 Sum_probs=18.4
Q ss_pred cccccCC----CC--ceeccCCCCcccCh
Q 045528 157 FCTVCGF----SA--NYTCVKCGMRFCCI 179 (195)
Q Consensus 157 fC~VCG~----~~--~YtC~~Cg~ryCS~ 179 (195)
.|..||. -| .|+|++||.++=+.
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCcc
Confidence 8999996 23 57999999988653
No 58
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=59.94 E-value=5.5 Score=28.68 Aligned_cols=7 Identities=43% Similarity=1.122 Sum_probs=4.0
Q ss_pred ccccccC
Q 045528 156 HFCTVCG 162 (195)
Q Consensus 156 ~fC~VCG 162 (195)
+.|.-||
T Consensus 28 F~CPnCG 34 (61)
T COG2888 28 FPCPNCG 34 (61)
T ss_pred eeCCCCC
Confidence 4566666
No 59
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=59.76 E-value=4.6 Score=39.34 Aligned_cols=24 Identities=33% Similarity=0.952 Sum_probs=18.4
Q ss_pred CCCCcccccccCCCC---ceeccCCCCc
Q 045528 151 KTSRRHFCTVCGFSA---NYTCVKCGMR 175 (195)
Q Consensus 151 ~~P~r~fC~VCG~~~---~YtC~~Cg~r 175 (195)
.-|.- +|..||+.+ .+.||.||..
T Consensus 515 ~~p~~-~C~~CG~~~~~~~~~CP~CGs~ 541 (555)
T cd01675 515 NTPID-ICNDCGYIGEGEGFKCPKCGSE 541 (555)
T ss_pred ecCCc-cCCCCCCCCcCCCCCCcCCCCc
Confidence 34544 999999965 4599999975
No 60
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.69 E-value=5.1 Score=29.15 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=17.8
Q ss_pred cccccCCCCceeccCCCCcccChhhhhh
Q 045528 157 FCTVCGFSANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 157 fC~VCG~~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
-|..||.+....-..=--+|||.+|..+
T Consensus 9 ~CP~Cgkpv~w~~~s~frPFCSkRCklI 36 (65)
T COG3024 9 PCPTCGKPVVWGEESPFRPFCSKRCKLI 36 (65)
T ss_pred cCCCCCCcccccccCCcCcchhHhhhhc
Confidence 5777776444433333458999999765
No 61
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=59.53 E-value=4.6 Score=24.09 Aligned_cols=20 Identities=35% Similarity=0.926 Sum_probs=12.5
Q ss_pred ccccccCC---CCceeccCCCCc
Q 045528 156 HFCTVCGF---SANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~---~~~YtC~~Cg~r 175 (195)
=.|.+|++ .....|..||+.
T Consensus 5 W~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 5 WKCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp EEETTTTEEEESSSSB-TTT--B
T ss_pred ccCCCCcCCchHHhhhhhCcCCC
Confidence 37899997 445689999864
No 62
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=59.38 E-value=3.7 Score=31.23 Aligned_cols=19 Identities=26% Similarity=0.630 Sum_probs=14.8
Q ss_pred cccccccCCCCce-eccCCC
Q 045528 155 RHFCTVCGFSANY-TCVKCG 173 (195)
Q Consensus 155 r~fC~VCG~~~~Y-tC~~Cg 173 (195)
.+.|.+||+++.- .|.-|-
T Consensus 80 ~~~C~~CG~pss~~iC~~C~ 99 (104)
T TIGR00269 80 LRRCERCGEPTSGRICKACK 99 (104)
T ss_pred CCcCCcCcCcCCccccHhhh
Confidence 4589999998865 787764
No 63
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=59.20 E-value=4.7 Score=26.23 Aligned_cols=15 Identities=33% Similarity=0.669 Sum_probs=10.7
Q ss_pred CCceeccCCCCcccC
Q 045528 164 SANYTCVKCGMRFCC 178 (195)
Q Consensus 164 ~~~YtC~~Cg~ryCS 178 (195)
++..+|+.||+-|-.
T Consensus 11 ~~~~~C~~CgM~Y~~ 25 (41)
T PF13878_consen 11 FGATTCPTCGMLYSP 25 (41)
T ss_pred cCCcCCCCCCCEECC
Confidence 445688888888754
No 64
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=58.98 E-value=5.1 Score=25.55 Aligned_cols=18 Identities=44% Similarity=1.080 Sum_probs=14.4
Q ss_pred cccccCC------CCceeccCCCC
Q 045528 157 FCTVCGF------SANYTCVKCGM 174 (195)
Q Consensus 157 fC~VCG~------~~~YtC~~Cg~ 174 (195)
-|.|||. -|.|.|.+||.
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCce
Confidence 5999995 46788998885
No 65
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=58.98 E-value=5.9 Score=24.77 Aligned_cols=20 Identities=25% Similarity=0.559 Sum_probs=15.0
Q ss_pred cccccccCC--CC---ceeccCCCC
Q 045528 155 RHFCTVCGF--SA---NYTCVKCGM 174 (195)
Q Consensus 155 r~fC~VCG~--~~---~YtC~~Cg~ 174 (195)
..+|.||+. |+ .|.|..|+.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~ 35 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKV 35 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCc
Confidence 458999986 54 678887754
No 66
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=58.46 E-value=6.2 Score=37.60 Aligned_cols=25 Identities=32% Similarity=0.866 Sum_probs=18.6
Q ss_pred CCCCcccccccCC---CC-------------------ceeccCCCCc
Q 045528 151 KTSRRHFCTVCGF---SA-------------------NYTCVKCGMR 175 (195)
Q Consensus 151 ~~P~r~fC~VCG~---~~-------------------~YtC~~Cg~r 175 (195)
....+..|.+||| +. .++||.||..
T Consensus 421 ~~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 3455568999998 22 5799999974
No 67
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=58.29 E-value=8 Score=27.05 Aligned_cols=18 Identities=33% Similarity=0.846 Sum_probs=10.0
Q ss_pred ccccccCCC--CceeccCCC
Q 045528 156 HFCTVCGFS--ANYTCVKCG 173 (195)
Q Consensus 156 ~fC~VCG~~--~~YtC~~Cg 173 (195)
..|..||.+ ...-|+.||
T Consensus 28 ~~C~~CG~~~~~H~vC~~CG 47 (57)
T PRK12286 28 VECPNCGEPKLPHRVCPSCG 47 (57)
T ss_pred eECCCCCCccCCeEECCCCC
Confidence 456666653 344666666
No 68
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=58.26 E-value=5.1 Score=22.89 Aligned_cols=19 Identities=32% Similarity=0.940 Sum_probs=14.1
Q ss_pred cccccCC---CCceeccCCCCc
Q 045528 157 FCTVCGF---SANYTCVKCGMR 175 (195)
Q Consensus 157 fC~VCG~---~~~YtC~~Cg~r 175 (195)
.|..|++ .....|..||.+
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhhhccccccCCc
Confidence 5888887 345689888874
No 69
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=58.11 E-value=7.1 Score=25.15 Aligned_cols=22 Identities=32% Similarity=0.927 Sum_probs=17.6
Q ss_pred ccccCC-CC--ceeccCCCCcccCh
Q 045528 158 CTVCGF-SA--NYTCVKCGMRFCCI 179 (195)
Q Consensus 158 C~VCG~-~~--~YtC~~Cg~ryCS~ 179 (195)
|.+|+. ++ .+.|..|+..||+.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 778886 33 67999999999985
No 70
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=57.77 E-value=5.6 Score=25.20 Aligned_cols=7 Identities=57% Similarity=1.426 Sum_probs=2.2
Q ss_pred cccccCC
Q 045528 157 FCTVCGF 163 (195)
Q Consensus 157 fC~VCG~ 163 (195)
||+.||.
T Consensus 2 fC~~CG~ 8 (34)
T PF14803_consen 2 FCPQCGG 8 (34)
T ss_dssp B-TTT--
T ss_pred ccccccC
Confidence 5555554
No 71
>PRK04023 DNA polymerase II large subunit; Validated
Probab=57.68 E-value=6.5 Score=41.55 Aligned_cols=19 Identities=37% Similarity=0.910 Sum_probs=12.1
Q ss_pred ccccccCCCCce-eccCCCC
Q 045528 156 HFCTVCGFSANY-TCVKCGM 174 (195)
Q Consensus 156 ~fC~VCG~~~~Y-tC~~Cg~ 174 (195)
.||.-||..+.+ .|+.||.
T Consensus 627 RfCpsCG~~t~~frCP~CG~ 646 (1121)
T PRK04023 627 RKCPSCGKETFYRRCPFCGT 646 (1121)
T ss_pred ccCCCCCCcCCcccCCCCCC
Confidence 477777765544 7777764
No 72
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=57.36 E-value=3.4 Score=36.50 Aligned_cols=9 Identities=44% Similarity=1.272 Sum_probs=2.5
Q ss_pred ccccccCCC
Q 045528 156 HFCTVCGFS 164 (195)
Q Consensus 156 ~fC~VCG~~ 164 (195)
.+|.|||.+
T Consensus 173 g~CPvCGs~ 181 (290)
T PF04216_consen 173 GYCPVCGSP 181 (290)
T ss_dssp SS-TTT---
T ss_pred CcCCCCCCc
Confidence 355555543
No 73
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=57.25 E-value=6.2 Score=42.47 Aligned_cols=20 Identities=35% Similarity=0.943 Sum_probs=16.4
Q ss_pred ccccccCCCC--ceeccCCCCc
Q 045528 156 HFCTVCGFSA--NYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~--~YtC~~Cg~r 175 (195)
.||..||..- .|.|+.||..
T Consensus 680 ~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 680 NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred ccCcccCCcCCCceeCccCCCc
Confidence 4999999864 7899999885
No 74
>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=57.10 E-value=6.5 Score=27.07 Aligned_cols=19 Identities=32% Similarity=0.730 Sum_probs=12.8
Q ss_pred cccccccCC--CCceeccCCC
Q 045528 155 RHFCTVCGF--SANYTCVKCG 173 (195)
Q Consensus 155 r~fC~VCG~--~~~YtC~~Cg 173 (195)
...|..||. ...+-|+.||
T Consensus 26 l~~c~~cg~~~~~H~vc~~cG 46 (56)
T PF01783_consen 26 LVKCPNCGEPKLPHRVCPSCG 46 (56)
T ss_dssp EEESSSSSSEESTTSBCTTTB
T ss_pred eeeeccCCCEecccEeeCCCC
Confidence 356777776 4466777776
No 75
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=56.18 E-value=2.7 Score=41.45 Aligned_cols=31 Identities=32% Similarity=0.839 Sum_probs=27.3
Q ss_pred cccccccCCCCceeccCC-CCcccChhhhhhhcc
Q 045528 155 RHFCTVCGFSANYTCVKC-GMRFCCIRCQNIHDD 187 (195)
Q Consensus 155 r~fC~VCG~~~~YtC~~C-g~ryCS~~C~~~H~E 187 (195)
...|.-|-..+.|-| | .+-|||+.|+..|.-
T Consensus 527 KQWC~nC~~EAiy~C--CWNTSYCsveCQQ~HW~ 558 (588)
T KOG3612|consen 527 KQWCYNCLDEAIYHC--CWNTSYCSVECQQGHWP 558 (588)
T ss_pred HHHHHhhhHHHHHHh--hccccccCcchhhccch
Confidence 359999999999966 5 899999999999976
No 76
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=55.66 E-value=4.3 Score=39.46 Aligned_cols=30 Identities=27% Similarity=0.705 Sum_probs=15.0
Q ss_pred CeEEEEeCCCCCCCCcccccccCCCC--ceeccCCCCcc
Q 045528 140 SYLRAAVGPPSKTSRRHFCTVCGFSA--NYTCVKCGMRF 176 (195)
Q Consensus 140 ~Y~~a~a~ps~~~P~r~fC~VCG~~~--~YtC~~Cg~ry 176 (195)
.|++. -|....|..|||.+ ...||.||..-
T Consensus 483 ~Y~~i-------n~~~~~C~~CG~~~~~~~~CP~CGs~~ 514 (546)
T PF13597_consen 483 PYFTI-------NPPIDICPDCGYIGGEGDKCPKCGSEN 514 (546)
T ss_dssp SEEEE-------E--EEEETTT---S--EEE-CCC----
T ss_pred CeEEE-------ecCcccccCCCcCCCCCCCCCCCCCcc
Confidence 38773 23356999999954 45999999863
No 77
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.55 E-value=1.3 Score=30.88 Aligned_cols=36 Identities=22% Similarity=0.793 Sum_probs=24.0
Q ss_pred CCCCCCCcccccccCCCCce--eccCC--CCcccChhhhhh
Q 045528 148 PPSKTSRRHFCTVCGFSANY--TCVKC--GMRFCCIRCQNI 184 (195)
Q Consensus 148 ps~~~P~r~fC~VCG~~~~Y--tC~~C--g~ryCS~~C~~~ 184 (195)
|-+..|. ++|.|||-+=.. .=.+| ...|||-.|...
T Consensus 6 ~Ka~lp~-KICpvCqRPFsWRkKW~~cWDeVKyCSeRCrr~ 45 (54)
T COG4338 6 PKATLPD-KICPVCQRPFSWRKKWARCWDEVKYCSERCRRL 45 (54)
T ss_pred cccccch-hhhhhhcCchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456676 699999974433 33445 457999999743
No 78
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=55.06 E-value=7.8 Score=31.69 Aligned_cols=42 Identities=21% Similarity=0.300 Sum_probs=25.2
Q ss_pred CCcccccccCC---CCcee-ccC-C--CCcccChhhhhhhcc---cccCccc
Q 045528 153 SRRHFCTVCGF---SANYT-CVK-C--GMRFCCIRCQNIHDD---TRCLKFV 194 (195)
Q Consensus 153 P~r~fC~VCG~---~~~Yt-C~~-C--g~ryCS~~C~~~H~E---tRC~K~~ 194 (195)
++...|++||+ ||.-+ =++ = -.+|||.+|...+.- -|=++||
T Consensus 2 m~~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~~kRnPRKlkWT 53 (131)
T PRK14891 2 VETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWT 53 (131)
T ss_pred CceeeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHHccCCCccchhH
Confidence 34568999997 55321 111 1 237899999866543 4556665
No 79
>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=54.58 E-value=7.3 Score=21.21 Aligned_cols=21 Identities=29% Similarity=0.550 Sum_probs=16.9
Q ss_pred eeccCCCCcccChhhhhhhcc
Q 045528 167 YTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~~~H~E 187 (195)
|.|+.||..|=+..=+..|..
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 789999999888777777754
No 80
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.57 E-value=6.8 Score=30.52 Aligned_cols=24 Identities=17% Similarity=0.502 Sum_probs=17.1
Q ss_pred CCCcccccccCCC-C----c-eeccCCCCc
Q 045528 152 TSRRHFCTVCGFS-A----N-YTCVKCGMR 175 (195)
Q Consensus 152 ~P~r~fC~VCG~~-~----~-YtC~~Cg~r 175 (195)
.|.+-+|.-||.. . . +.||.||..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 3446799999972 1 2 359999975
No 81
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=54.35 E-value=9.6 Score=24.09 Aligned_cols=21 Identities=24% Similarity=0.637 Sum_probs=16.4
Q ss_pred CCCCcccccccCCCCce--eccC
Q 045528 151 KTSRRHFCTVCGFSANY--TCVK 171 (195)
Q Consensus 151 ~~P~r~fC~VCG~~~~Y--tC~~ 171 (195)
.+|.-..|-+||..|.| -|+.
T Consensus 4 ~pP~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 4 KPPPGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCCCCEeecCCCCCccHhHCCC
Confidence 45556799999999988 6765
No 82
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=54.15 E-value=8.1 Score=24.25 Aligned_cols=20 Identities=30% Similarity=0.780 Sum_probs=15.2
Q ss_pred ccccccCCCCce-------eccCCCCc
Q 045528 156 HFCTVCGFSANY-------TCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~~Y-------tC~~Cg~r 175 (195)
..|.+||..+-+ .|+.||.-
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 479999976544 89999864
No 83
>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=53.57 E-value=7.7 Score=29.04 Aligned_cols=20 Identities=40% Similarity=1.057 Sum_probs=15.3
Q ss_pred cccccCC---C--CceeccCCCCcc
Q 045528 157 FCTVCGF---S--ANYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~---~--~~YtC~~Cg~ry 176 (195)
||..||. + +.+.|+.||..+
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCcc
Confidence 8999996 2 467999998653
No 84
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=53.26 E-value=8.5 Score=21.78 Aligned_cols=24 Identities=25% Similarity=0.797 Sum_probs=21.2
Q ss_pred eeccCCCCcccChhhhhhhccccc
Q 045528 167 YTCVKCGMRFCCIRCQNIHDDTRC 190 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~~~H~EtRC 190 (195)
|.|..|+..|-+..=+..|..+-|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 789999999999999999987655
No 85
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=52.93 E-value=8.9 Score=29.72 Aligned_cols=24 Identities=33% Similarity=0.647 Sum_probs=14.4
Q ss_pred CCcccccccCC--C--------CceeccCCCCcc
Q 045528 153 SRRHFCTVCGF--S--------ANYTCVKCGMRF 176 (195)
Q Consensus 153 P~r~fC~VCG~--~--------~~YtC~~Cg~ry 176 (195)
|....|..||. . +...|+.||..|
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 33456777773 1 355777777764
No 86
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.71 E-value=9.4 Score=25.33 Aligned_cols=21 Identities=33% Similarity=0.838 Sum_probs=14.8
Q ss_pred ccccccCC------CCceeccCCCCcc
Q 045528 156 HFCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~------~~~YtC~~Cg~ry 176 (195)
..|.-||. .+...|+.||.+.
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceE
Confidence 36888886 2356899888764
No 87
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=51.70 E-value=7.3 Score=28.14 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=21.0
Q ss_pred CCCCcccccccCCCCceeccCCCCcccChhhhhhhc
Q 045528 151 KTSRRHFCTVCGFSANYTCVKCGMRFCCIRCQNIHD 186 (195)
Q Consensus 151 ~~P~r~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~H~ 186 (195)
.+|.+ -|.|||..=. =+..+||-+|.++-+
T Consensus 5 v~PH~-HC~VCg~aIp-----~de~~CSe~C~eil~ 34 (64)
T COG4068 5 VVPHR-HCVVCGKAIP-----PDEQVCSEECGEILN 34 (64)
T ss_pred CCCCc-cccccCCcCC-----CccchHHHHHHHHHH
Confidence 45665 7999987321 167889999987644
No 88
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=51.67 E-value=8.1 Score=33.97 Aligned_cols=22 Identities=32% Similarity=0.901 Sum_probs=16.4
Q ss_pred ccccccCCCCce-------eccCCCCccc
Q 045528 156 HFCTVCGFSANY-------TCVKCGMRFC 177 (195)
Q Consensus 156 ~fC~VCG~~~~Y-------tC~~Cg~ryC 177 (195)
.||+.||.+-.. .|+.||..+-
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRERYY 128 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCEEC
Confidence 499999985332 6999987653
No 89
>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=51.64 E-value=8.1 Score=25.02 Aligned_cols=22 Identities=32% Similarity=0.987 Sum_probs=11.9
Q ss_pred ccc--cCCC--CceeccCCCCcccCh
Q 045528 158 CTV--CGFS--ANYTCVKCGMRFCCI 179 (195)
Q Consensus 158 C~V--CG~~--~~YtC~~Cg~ryCS~ 179 (195)
|++ |+.. -.+.|..||..||..
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLK 26 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TT
T ss_pred CccCcCcCccCCCeECCCCCcccCcc
Confidence 555 7662 357999999999974
No 90
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=51.15 E-value=8.6 Score=25.04 Aligned_cols=21 Identities=33% Similarity=0.759 Sum_probs=14.3
Q ss_pred ccccccCCC-----C--ceeccCCCCcc
Q 045528 156 HFCTVCGFS-----A--NYTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~~-----~--~YtC~~Cg~ry 176 (195)
.-|.-||.. . ..+||.||.++
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeE
Confidence 357888862 1 46888888765
No 91
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=50.02 E-value=29 Score=32.75 Aligned_cols=26 Identities=23% Similarity=0.735 Sum_probs=19.7
Q ss_pred cccccccCC--CCceeccCCCCcccChh
Q 045528 155 RHFCTVCGF--SANYTCVKCGMRFCCIR 180 (195)
Q Consensus 155 r~fC~VCG~--~~~YtC~~Cg~ryCS~~ 180 (195)
+.||+-=+- .|.|-||+|++++||+.
T Consensus 263 ps~C~CH~~~~~~Gy~CP~CkakvCsLP 290 (378)
T KOG2807|consen 263 PSFCACHSELSGGGYFCPQCKAKVCSLP 290 (378)
T ss_pred cchheeccccccCceeCCcccCeeecCC
Confidence 357764442 67899999999999963
No 92
>PHA00616 hypothetical protein
Probab=49.86 E-value=5.4 Score=26.85 Aligned_cols=19 Identities=32% Similarity=0.607 Sum_probs=15.0
Q ss_pred eeccCCCCcccChhhhhhh
Q 045528 167 YTCVKCGMRFCCIRCQNIH 185 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~~~H 185 (195)
|.|+.||..+.-..=+..|
T Consensus 2 YqC~~CG~~F~~~s~l~~H 20 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEH 20 (44)
T ss_pred CccchhhHHHhhHHHHHHH
Confidence 8999999999876655555
No 93
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=49.85 E-value=8.3 Score=27.36 Aligned_cols=23 Identities=30% Similarity=0.769 Sum_probs=16.1
Q ss_pred cccccCCCCceeccCCCCcccChhhhhh
Q 045528 157 FCTVCGFSANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 157 fC~VCG~~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
-|.|||.+=.- +..|||-.|.+.
T Consensus 5 HC~~CG~~Ip~-----~~~fCS~~C~~~ 27 (59)
T PF09889_consen 5 HCPVCGKPIPP-----DESFCSPKCREE 27 (59)
T ss_pred cCCcCCCcCCc-----chhhhCHHHHHH
Confidence 68888763321 478999999764
No 94
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=47.94 E-value=6 Score=40.99 Aligned_cols=34 Identities=26% Similarity=0.626 Sum_probs=0.0
Q ss_pred cccccCCC--CceeccCCCCcccChhhhhhhccccc
Q 045528 157 FCTVCGFS--ANYTCVKCGMRFCCIRCQNIHDDTRC 190 (195)
Q Consensus 157 fC~VCG~~--~~YtC~~Cg~ryCS~~C~~~H~EtRC 190 (195)
.|..||.+ -.|.|+.||..+=.-.|-+-..++.|
T Consensus 669 ~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~ 704 (900)
T PF03833_consen 669 RCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTS 704 (900)
T ss_dssp ------------------------------------
T ss_pred cCcccCCccccceeccccccccCccccccccccCcc
Confidence 45555543 24455555554433344433344333
No 95
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=47.91 E-value=9.1 Score=23.78 Aligned_cols=18 Identities=33% Similarity=0.833 Sum_probs=8.3
Q ss_pred cccccCC---CCceeccCCCC
Q 045528 157 FCTVCGF---SANYTCVKCGM 174 (195)
Q Consensus 157 fC~VCG~---~~~YtC~~Cg~ 174 (195)
-|.-||. +....|+.||.
T Consensus 13 rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 13 RCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp E-TTT--EEES--SEETTTT-
T ss_pred EcCCCCCEecCCCcCCCCcCc
Confidence 5777774 45667777764
No 96
>PF12773 DZR: Double zinc ribbon
Probab=47.69 E-value=11 Score=24.50 Aligned_cols=22 Identities=32% Similarity=0.851 Sum_probs=13.7
Q ss_pred CCcccccccCCCCc------eeccCCCC
Q 045528 153 SRRHFCTVCGFSAN------YTCVKCGM 174 (195)
Q Consensus 153 P~r~fC~VCG~~~~------YtC~~Cg~ 174 (195)
+.-.||.-||..-. +.|+.||.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcC
Confidence 33457888876322 46777776
No 97
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=47.17 E-value=11 Score=28.99 Aligned_cols=22 Identities=32% Similarity=0.714 Sum_probs=15.5
Q ss_pred cccccccCC------CCceeccCCCCcc
Q 045528 155 RHFCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~------~~~YtC~~Cg~ry 176 (195)
...|.|||. +|.++|-.|...|
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~aCk~FF 45 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEGCKGFF 45 (101)
T ss_pred CCCCeecCCcCcceEECcceehhhhhhh
Confidence 457999986 4455788886644
No 98
>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 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=46.25 E-value=10 Score=26.06 Aligned_cols=24 Identities=29% Similarity=0.773 Sum_probs=12.5
Q ss_pred cccccccCC-C----CceeccCCCCcccC
Q 045528 155 RHFCTVCGF-S----ANYTCVKCGMRFCC 178 (195)
Q Consensus 155 r~fC~VCG~-~----~~YtC~~Cg~ryCS 178 (195)
...|.+|+. + .++.|-.||.-+|+
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCS 37 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEEC
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECC
Confidence 357888985 3 36799999999986
No 100
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=45.56 E-value=14 Score=22.83 Aligned_cols=24 Identities=33% Similarity=0.895 Sum_probs=18.1
Q ss_pred cccccCCC-----CceeccCCCCcccChh
Q 045528 157 FCTVCGFS-----ANYTCVKCGMRFCCIR 180 (195)
Q Consensus 157 fC~VCG~~-----~~YtC~~Cg~ryCS~~ 180 (195)
-|.||..- ..|.|..|+...|-..
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 37777764 6799999998877654
No 101
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=45.50 E-value=20 Score=38.63 Aligned_cols=22 Identities=14% Similarity=0.291 Sum_probs=13.4
Q ss_pred CCHHHHHHHHHHHHHhhhCCCCCCCC
Q 045528 48 ASADNRTQAALARLEALENDNAGIET 73 (195)
Q Consensus 48 lDe~tR~rr~~~rLeaLE~DN~~~dp 73 (195)
+||+.=..+++++++ |+|..|.
T Consensus 49 VDeeEY~k~v~~r~~----DdfvVdD 70 (1429)
T KOG0970|consen 49 VDEEEYRKIVRQRLD----DDFVVDD 70 (1429)
T ss_pred cCHHHHHHHHHHHhc----CCeEEeC
Confidence 377665566666665 6676544
No 102
>PRK05978 hypothetical protein; Provisional
Probab=45.23 E-value=10 Score=31.35 Aligned_cols=21 Identities=33% Similarity=0.895 Sum_probs=14.4
Q ss_pred ccccccCC---CCce-----eccCCCCcc
Q 045528 156 HFCTVCGF---SANY-----TCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~---~~~Y-----tC~~Cg~ry 176 (195)
.-|..||. +..| +|+.||..|
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCcc
Confidence 46888885 3333 788888876
No 103
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=44.82 E-value=12 Score=28.65 Aligned_cols=23 Identities=35% Similarity=0.986 Sum_probs=16.9
Q ss_pred cccccccCCC-------CceeccCCCCccc
Q 045528 155 RHFCTVCGFS-------ANYTCVKCGMRFC 177 (195)
Q Consensus 155 r~fC~VCG~~-------~~YtC~~Cg~ryC 177 (195)
.++|++||.. |...|.+||..+.
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 4799999974 4468999987654
No 104
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=44.81 E-value=10 Score=28.67 Aligned_cols=9 Identities=33% Similarity=1.139 Sum_probs=2.4
Q ss_pred eccCCCCcc
Q 045528 168 TCVKCGMRF 176 (195)
Q Consensus 168 tC~~Cg~ry 176 (195)
.|++|+++|
T Consensus 53 ~CpqCkt~y 61 (80)
T PF14569_consen 53 VCPQCKTRY 61 (80)
T ss_dssp B-TTT--B-
T ss_pred cccccCCCc
Confidence 444444444
No 105
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.38 E-value=13 Score=30.33 Aligned_cols=9 Identities=33% Similarity=0.896 Sum_probs=4.4
Q ss_pred CceeccCCC
Q 045528 165 ANYTCVKCG 173 (195)
Q Consensus 165 ~~YtC~~Cg 173 (195)
|..-||.||
T Consensus 43 G~v~CPvC~ 51 (131)
T COG1645 43 GEVFCPVCG 51 (131)
T ss_pred CeEECCCCC
Confidence 444555555
No 106
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=43.48 E-value=16 Score=23.04 Aligned_cols=21 Identities=29% Similarity=0.735 Sum_probs=15.3
Q ss_pred cccccccCC--C----CceeccCCCCc
Q 045528 155 RHFCTVCGF--S----ANYTCVKCGMR 175 (195)
Q Consensus 155 r~fC~VCG~--~----~~YtC~~Cg~r 175 (195)
..+|.||+. | ..|.|..|+..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCc
Confidence 358999985 5 46788888653
No 107
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=43.48 E-value=7.8 Score=40.22 Aligned_cols=36 Identities=28% Similarity=0.808 Sum_probs=0.0
Q ss_pred ccccccCCCCce-eccCCCCc----ccChhhhhhhcccccC
Q 045528 156 HFCTVCGFSANY-TCVKCGMR----FCCIRCQNIHDDTRCL 191 (195)
Q Consensus 156 ~fC~VCG~~~~Y-tC~~Cg~r----yCS~~C~~~H~EtRC~ 191 (195)
..|.-||..+-+ +|+.||.+ |=+..|.....+..|.
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~ 696 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEEDECP 696 (900)
T ss_dssp -----------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCccccceeccccccccCccccc
Confidence 389999999877 99999996 3334576666555554
No 108
>KOG4850 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.31 E-value=9.6 Score=32.58 Aligned_cols=16 Identities=44% Similarity=1.198 Sum_probs=15.3
Q ss_pred ceeccCCCCcccChhh
Q 045528 166 NYTCVKCGMRFCCIRC 181 (195)
Q Consensus 166 ~YtC~~Cg~ryCS~~C 181 (195)
-|.|+.||.--|...|
T Consensus 149 ~Y~C~~CGSTkCG~~C 164 (190)
T KOG4850|consen 149 HYPCKQCGSTKCGIGC 164 (190)
T ss_pred eecccccccccccccc
Confidence 6899999999999999
No 109
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.58 E-value=17 Score=28.02 Aligned_cols=23 Identities=39% Similarity=1.145 Sum_probs=17.3
Q ss_pred cccccccCCC-------CceeccCCCCccc
Q 045528 155 RHFCTVCGFS-------ANYTCVKCGMRFC 177 (195)
Q Consensus 155 r~fC~VCG~~-------~~YtC~~Cg~ryC 177 (195)
.|.|.+||.. |...|.+||..|-
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeec
Confidence 4789999974 4558999987654
No 110
>PLN02195 cellulose synthase A
Probab=41.98 E-value=12 Score=39.23 Aligned_cols=22 Identities=23% Similarity=0.798 Sum_probs=17.3
Q ss_pred ccccccCCC------------CceeccCCCCccc
Q 045528 156 HFCTVCGFS------------ANYTCVKCGMRFC 177 (195)
Q Consensus 156 ~fC~VCG~~------------~~YtC~~Cg~ryC 177 (195)
.-|.+|||+ |+-.||.|++||=
T Consensus 26 vaC~eC~~pvCrpCyeyer~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 26 VACHECSYPLCKACLEYEIKEGRKVCLRCGGPYD 59 (977)
T ss_pred EEeccCCCccccchhhhhhhcCCccCCccCCccc
Confidence 468888875 6668999999884
No 111
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=41.75 E-value=12 Score=27.79 Aligned_cols=26 Identities=27% Similarity=0.576 Sum_probs=11.0
Q ss_pred CCCCcccccccC-------------CCCceeccCCCCcc
Q 045528 151 KTSRRHFCTVCG-------------FSANYTCVKCGMRF 176 (195)
Q Consensus 151 ~~P~r~fC~VCG-------------~~~~YtC~~Cg~ry 176 (195)
.+|...-|.+|| ..|..+|-.||..|
T Consensus 18 ~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 18 KLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp --SS----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred CCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 344555677777 24556788887766
No 112
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=41.51 E-value=10 Score=25.38 Aligned_cols=32 Identities=25% Similarity=0.851 Sum_probs=19.7
Q ss_pred CCCCcccccccCCCCce--eccCC--CCcccChhhhh
Q 045528 151 KTSRRHFCTVCGFSANY--TCVKC--GMRFCCIRCQN 183 (195)
Q Consensus 151 ~~P~r~fC~VCG~~~~Y--tC~~C--g~ryCS~~C~~ 183 (195)
.+|. ++|.|||-+=.. .=-+| ...|||-.|..
T Consensus 5 ~lp~-K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR~ 40 (42)
T PF10013_consen 5 NLPS-KICPVCGRPFTWRKKWARCWDEVKYCSDRCRR 40 (42)
T ss_pred cCCC-CcCcccCCcchHHHHHHHhchhhccHHHHhcc
Confidence 3455 699999863221 22234 45899998853
No 113
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=41.17 E-value=13 Score=34.00 Aligned_cols=48 Identities=15% Similarity=0.002 Sum_probs=24.7
Q ss_pred CCchhhhhcchhhhhhcccccchhhhhhhhhcCCHHHH--HHHHHHHHHhhhC
Q 045528 16 SPSPLRKKKNMEDERRMSTRTRKVAPRMAAALASADNR--TQAALARLEALEN 66 (195)
Q Consensus 16 ~~~~~~~~~~~~~~~R~S~R~r~~s~r~r~~vlDe~tR--~rr~~~rLeaLE~ 66 (195)
...|+.-----.-=.|...|.+.++..- .+.+=-+ .+.+++|+++|++
T Consensus 17 ~~p~l~~p~~~~lf~~RA~RL~~LA~~~---pl~dyL~f~A~la~aQ~~~l~~ 66 (305)
T TIGR01562 17 KIPPHLHPPLRDLFNRRAERLLQLAEGH---PLGDYLRFVAGICRLQQALLDN 66 (305)
T ss_pred CCCCeecCChhhHHHHHHHHHHHHhccC---CHHHHHHHHHHHHHHHHHHHhh
Confidence 4444543332333346677777777653 3322222 2556667777776
No 114
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=40.86 E-value=18 Score=26.67 Aligned_cols=23 Identities=30% Similarity=0.804 Sum_probs=14.0
Q ss_pred cccccccCCCCceeccCCCCcccChhhh
Q 045528 155 RHFCTVCGFSANYTCVKCGMRFCCIRCQ 182 (195)
Q Consensus 155 r~fC~VCG~~~~YtC~~Cg~ryCS~~C~ 182 (195)
-+.|.+|+-+=.- ..+|||+.|-
T Consensus 49 ~~~C~~C~R~L~d-----~~~fCSl~CK 71 (72)
T PF04640_consen 49 GNICETCHRSLQD-----PYRFCSLSCK 71 (72)
T ss_pred CCccCCCCCCCCC-----CCeEEeeeEE
Confidence 3467776653221 2589999983
No 115
>PLN02189 cellulose synthase
Probab=40.44 E-value=14 Score=39.17 Aligned_cols=11 Identities=27% Similarity=0.911 Sum_probs=5.3
Q ss_pred ceeccCCCCcc
Q 045528 166 NYTCVKCGMRF 176 (195)
Q Consensus 166 ~YtC~~Cg~ry 176 (195)
+-.||+|+++|
T Consensus 76 ~q~CpqCkt~Y 86 (1040)
T PLN02189 76 TQNCPQCKTRY 86 (1040)
T ss_pred CccCcccCCch
Confidence 33455555554
No 116
>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=40.23 E-value=16 Score=29.85 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=16.1
Q ss_pred cccccccCC------CCceeccCCCCcc
Q 045528 155 RHFCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~------~~~YtC~~Cg~ry 176 (195)
.+.|..||. .....||+||.-|
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCcc
Confidence 458999984 2345899999866
No 117
>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=39.89 E-value=15 Score=25.81 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=5.9
Q ss_pred cCCCCceeccCCCC
Q 045528 161 CGFSANYTCVKCGM 174 (195)
Q Consensus 161 CG~~~~YtC~~Cg~ 174 (195)
|-..-.|+|+-||+
T Consensus 28 CPvLr~y~Cp~CgA 41 (55)
T PF05741_consen 28 CPVLRKYVCPICGA 41 (55)
T ss_dssp -TTGGG---TTT--
T ss_pred CHHHhcCcCCCCcC
Confidence 33477899999987
No 118
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=39.75 E-value=14 Score=33.89 Aligned_cols=27 Identities=22% Similarity=0.133 Sum_probs=14.0
Q ss_pred CCchhhhhcchhhhhhcccccchhhhh
Q 045528 16 SPSPLRKKKNMEDERRMSTRTRKVAPR 42 (195)
Q Consensus 16 ~~~~~~~~~~~~~~~R~S~R~r~~s~r 42 (195)
+..|++-----.-=.|...|.+.++..
T Consensus 21 ~~p~ll~p~~~~lf~~RA~Rl~~LA~~ 47 (309)
T PRK03564 21 MIPPLLFANLKNLYNRRAERLRQLAEN 47 (309)
T ss_pred CCCceecCCcccHHHHHHHHHHHHHhc
Confidence 344444332223334667777777765
No 119
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=39.06 E-value=16 Score=37.28 Aligned_cols=19 Identities=32% Similarity=1.020 Sum_probs=10.9
Q ss_pred cccccCCCCce--eccCCCCc
Q 045528 157 FCTVCGFSANY--TCVKCGMR 175 (195)
Q Consensus 157 fC~VCG~~~~Y--tC~~Cg~r 175 (195)
+|.-||+.... .||.||..
T Consensus 464 ~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 464 RCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred EeCCCCCCCCCCCCCCCCCCC
Confidence 66666665433 66666653
No 120
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=38.73 E-value=4.9 Score=25.95 Aligned_cols=18 Identities=33% Similarity=0.973 Sum_probs=8.8
Q ss_pred cccccccCCCCce-eccCC
Q 045528 155 RHFCTVCGFSANY-TCVKC 172 (195)
Q Consensus 155 r~fC~VCG~~~~Y-tC~~C 172 (195)
.++|.+||+++.- .|.-|
T Consensus 17 i~~C~~C~nlse~~~C~IC 35 (41)
T PF02132_consen 17 IKFCSICGNLSEEDPCEIC 35 (41)
T ss_dssp -EE-SSS--EESSSS-HHH
T ss_pred CCccCCCCCcCCCCcCcCC
Confidence 4699999997743 56544
No 121
>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=38.71 E-value=17 Score=25.06 Aligned_cols=29 Identities=31% Similarity=0.684 Sum_probs=19.7
Q ss_pred ccccCCC--CceeccCCCCcccCh---hhhhhhc
Q 045528 158 CTVCGFS--ANYTCVKCGMRFCCI---RCQNIHD 186 (195)
Q Consensus 158 C~VCG~~--~~YtC~~Cg~ryCS~---~C~~~H~ 186 (195)
|++|+.. ..|.|..||.-.|.. .....|-
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~ 34 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHY 34 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHH
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhh
Confidence 7888854 577999999999985 4444443
No 122
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=38.69 E-value=19 Score=25.13 Aligned_cols=20 Identities=40% Similarity=1.097 Sum_probs=15.0
Q ss_pred cccccccCC-------CCceeccCCCC
Q 045528 155 RHFCTVCGF-------SANYTCVKCGM 174 (195)
Q Consensus 155 r~fC~VCG~-------~~~YtC~~Cg~ 174 (195)
..||+-||- -..|.|-+||-
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccc
Confidence 459999992 23789999984
No 123
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=38.65 E-value=20 Score=28.31 Aligned_cols=26 Identities=27% Similarity=0.769 Sum_probs=16.1
Q ss_pred CCCCcccccccCCCC-------------ceeccCCCCcc
Q 045528 151 KTSRRHFCTVCGFSA-------------NYTCVKCGMRF 176 (195)
Q Consensus 151 ~~P~r~fC~VCG~~~-------------~YtC~~Cg~ry 176 (195)
.+|.+.-|.+||-.. ...|-.||.+|
T Consensus 18 ~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 18 VLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred cCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 455566677777532 33677777765
No 124
>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=38.24 E-value=16 Score=35.10 Aligned_cols=20 Identities=35% Similarity=0.936 Sum_probs=12.5
Q ss_pred ccccccCCCCc--eeccCCCCc
Q 045528 156 HFCTVCGFSAN--YTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~~--YtC~~Cg~r 175 (195)
-.|.-||+... ..||.||..
T Consensus 241 l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred EEcCCCcCcCCCCCCCCCCCCC
Confidence 36777777443 377777663
No 125
>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=38.18 E-value=16 Score=22.50 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=7.9
Q ss_pred eeccCCCCcc
Q 045528 167 YTCVKCGMRF 176 (195)
Q Consensus 167 YtC~~Cg~ry 176 (195)
++||.||+.|
T Consensus 3 ~~CP~C~~~~ 12 (38)
T TIGR02098 3 IQCPNCKTSF 12 (38)
T ss_pred EECCCCCCEE
Confidence 6788888865
No 126
>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=38.12 E-value=22 Score=22.19 Aligned_cols=20 Identities=35% Similarity=0.946 Sum_probs=11.4
Q ss_pred cccccCCC------CceeccCCCCcc
Q 045528 157 FCTVCGFS------ANYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~~------~~YtC~~Cg~ry 176 (195)
.|.-||.. ...+|+.||-|.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeE
Confidence 46666651 234788887653
No 127
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=38.00 E-value=15 Score=38.93 Aligned_cols=22 Identities=32% Similarity=0.910 Sum_probs=18.3
Q ss_pred ccccccCCC------------CceeccCCCCccc
Q 045528 156 HFCTVCGFS------------ANYTCVKCGMRFC 177 (195)
Q Consensus 156 ~fC~VCG~~------------~~YtC~~Cg~ryC 177 (195)
.-|.+|||+ |+-.||+|++||=
T Consensus 37 VAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk 70 (1079)
T PLN02638 37 VACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK 70 (1079)
T ss_pred EEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 578899885 6778999999995
No 128
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=37.45 E-value=16 Score=27.27 Aligned_cols=17 Identities=35% Similarity=1.013 Sum_probs=10.5
Q ss_pred cccccCCCC-------ce-eccCCC
Q 045528 157 FCTVCGFSA-------NY-TCVKCG 173 (195)
Q Consensus 157 fC~VCG~~~-------~Y-tC~~Cg 173 (195)
.|.+|||.- .| .|+-|+
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCC
Confidence 577777732 25 777774
No 129
>PLN02436 cellulose synthase A
Probab=36.93 E-value=17 Score=38.72 Aligned_cols=10 Identities=30% Similarity=1.178 Sum_probs=4.9
Q ss_pred eccCCCCccc
Q 045528 168 TCVKCGMRFC 177 (195)
Q Consensus 168 tC~~Cg~ryC 177 (195)
-|--||-+.|
T Consensus 57 ACn~C~fpvC 66 (1094)
T PLN02436 57 ACNECAFPVC 66 (1094)
T ss_pred eeccCCCccc
Confidence 4555555444
No 130
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=36.74 E-value=25 Score=27.33 Aligned_cols=37 Identities=24% Similarity=0.584 Sum_probs=24.7
Q ss_pred CeEEEEeCCCCCCCCcccccccCCCC------ceeccCCCCcc
Q 045528 140 SYLRAAVGPPSKTSRRHFCTVCGFSA------NYTCVKCGMRF 176 (195)
Q Consensus 140 ~Y~~a~a~ps~~~P~r~fC~VCG~~~------~YtC~~Cg~ry 176 (195)
.|+....+..+....--.|.|||-.| ...|..||.++
T Consensus 20 rff~i~~~dg~~~va~daCeiC~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 20 RFFAIKKPDGSYRVAFDACEICGPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred EEEEEECCCCCEEEEEEeccccCCCceEEECCEEEEecCCCEE
Confidence 35555455544445556899998644 34899999986
No 131
>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=36.54 E-value=20 Score=23.52 Aligned_cols=26 Identities=35% Similarity=0.958 Sum_probs=18.9
Q ss_pred cccccCC-----CCceeccCCCCcccChhhhh
Q 045528 157 FCTVCGF-----SANYTCVKCGMRFCCIRCQN 183 (195)
Q Consensus 157 fC~VCG~-----~~~YtC~~Cg~ryCS~~C~~ 183 (195)
.|.+|+. ..++.|..||..+|+ .|..
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~-~C~~ 34 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRIFCS-KCSS 34 (57)
T ss_pred cCcccCccccCCccccccCcCcCCcCh-HHcC
Confidence 6778874 236789999999987 4443
No 132
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=35.60 E-value=41 Score=23.69 Aligned_cols=31 Identities=26% Similarity=0.321 Sum_probs=22.7
Q ss_pred hhhhhhhhcCCHHHHHHHHHHHHHhhhCCCCCC
Q 045528 39 VAPRMAAALASADNRTQAALARLEALENDNAGI 71 (195)
Q Consensus 39 ~s~r~r~~vlDe~tR~rr~~~rLeaLE~DN~~~ 71 (195)
++..+. .-+.+--.+.++++|.+||.|.|..
T Consensus 19 l~~~L~--~~g~~~se~avRrrLr~me~~Glt~ 49 (66)
T PF08461_consen 19 LAEELK--LRGEELSEEAVRRRLRAMERDGLTR 49 (66)
T ss_pred HHHHHH--hcChhhhHHHHHHHHHHHHHCCCcc
Confidence 444543 2266666788999999999999775
No 133
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=35.06 E-value=26 Score=24.72 Aligned_cols=6 Identities=17% Similarity=0.512 Sum_probs=3.6
Q ss_pred cccccCC
Q 045528 157 FCTVCGF 163 (195)
Q Consensus 157 fC~VCG~ 163 (195)
.|. |||
T Consensus 42 vc~-cG~ 47 (60)
T PRK01110 42 VSP-KGY 47 (60)
T ss_pred ecC-Ccc
Confidence 566 664
No 134
>PF14353 CpXC: CpXC protein
Probab=34.91 E-value=22 Score=27.43 Aligned_cols=15 Identities=40% Similarity=0.981 Sum_probs=10.2
Q ss_pred CCCCceeccCCCCcc
Q 045528 162 GFSANYTCVKCGMRF 176 (195)
Q Consensus 162 G~~~~YtC~~Cg~ry 176 (195)
|-.-.|+||.||..+
T Consensus 34 g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKF 48 (128)
T ss_pred CCcCEEECCCCCCce
Confidence 445677888888753
No 135
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.88 E-value=20 Score=32.34 Aligned_cols=20 Identities=35% Similarity=0.886 Sum_probs=0.0
Q ss_pred cccccCC-CCce--eccCCCCcc
Q 045528 157 FCTVCGF-SANY--TCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~-~~~Y--tC~~Cg~ry 176 (195)
+|+||.- +..+ .|+.||++|
T Consensus 257 vCs~Clsi~C~~p~~C~~Cgt~f 279 (279)
T TIGR00627 257 VCSVCLSVLCQYTPICKTCKTAF 279 (279)
T ss_pred ECCCccCCcCCCCCCCCCCCCCC
No 136
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=34.72 E-value=8.3 Score=27.16 Aligned_cols=10 Identities=40% Similarity=0.843 Sum_probs=8.3
Q ss_pred ccccccCCCC
Q 045528 156 HFCTVCGFSA 165 (195)
Q Consensus 156 ~fC~VCG~~~ 165 (195)
..|.+||-|+
T Consensus 23 RQCvlCGRWa 32 (57)
T PF14445_consen 23 RQCVLCGRWA 32 (57)
T ss_pred HHHhhhchhh
Confidence 3899999887
No 137
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=34.55 E-value=18 Score=23.99 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=11.5
Q ss_pred ccccccCCCCce--ecc
Q 045528 156 HFCTVCGFSANY--TCV 170 (195)
Q Consensus 156 ~fC~VCG~~~~Y--tC~ 170 (195)
.||..||..|.. .|+
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 599999998854 454
No 138
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=34.44 E-value=19 Score=28.69 Aligned_cols=22 Identities=41% Similarity=0.786 Sum_probs=15.9
Q ss_pred cccccccCC-CCc------eeccCCCCcc
Q 045528 155 RHFCTVCGF-SAN------YTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~-~~~------YtC~~Cg~ry 176 (195)
.|.|.-||- +.. -.||+||-++
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~nk 30 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGCNK 30 (112)
T ss_pred CceecccccccccccHHHHccCccccchh
Confidence 378999996 443 2799998754
No 139
>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=34.43 E-value=21 Score=21.22 Aligned_cols=18 Identities=33% Similarity=0.966 Sum_probs=8.8
Q ss_pred cccccCCCC----ceeccCCCC
Q 045528 157 FCTVCGFSA----NYTCVKCGM 174 (195)
Q Consensus 157 fC~VCG~~~----~YtC~~Cg~ 174 (195)
.|.+||..+ .|.|..|.-
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 689999843 689998853
No 140
>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=34.21 E-value=20 Score=22.02 Aligned_cols=11 Identities=45% Similarity=1.277 Sum_probs=8.3
Q ss_pred ceeccCCCCcc
Q 045528 166 NYTCVKCGMRF 176 (195)
Q Consensus 166 ~YtC~~Cg~ry 176 (195)
.|.|+.||..|
T Consensus 5 ~y~C~~Cg~~f 15 (41)
T smart00834 5 EYRCEDCGHTF 15 (41)
T ss_pred EEEcCCCCCEE
Confidence 36888888855
No 141
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=34.13 E-value=19 Score=38.05 Aligned_cols=21 Identities=29% Similarity=0.703 Sum_probs=17.6
Q ss_pred ccccccCCCCce-eccCCCCcc
Q 045528 156 HFCTVCGFSANY-TCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~~~~Y-tC~~Cg~ry 176 (195)
..|.-||..+-+ +|+.||.+.
T Consensus 626 RKCPkCG~yTlk~rCP~CG~~T 647 (1095)
T TIGR00354 626 RKCPQCGKESFWLKCPVCGELT 647 (1095)
T ss_pred EECCCCCcccccccCCCCCCcc
Confidence 389999998855 999999873
No 142
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=33.80 E-value=21 Score=22.46 Aligned_cols=10 Identities=50% Similarity=1.128 Sum_probs=7.7
Q ss_pred eeccCCCCcc
Q 045528 167 YTCVKCGMRF 176 (195)
Q Consensus 167 YtC~~Cg~ry 176 (195)
.+||.|++.|
T Consensus 3 i~CP~C~~~f 12 (37)
T PF13719_consen 3 ITCPNCQTRF 12 (37)
T ss_pred EECCCCCceE
Confidence 5788888876
No 143
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=33.62 E-value=20 Score=37.95 Aligned_cols=22 Identities=41% Similarity=1.020 Sum_probs=17.8
Q ss_pred ccccccCCC------------CceeccCCCCccc
Q 045528 156 HFCTVCGFS------------ANYTCVKCGMRFC 177 (195)
Q Consensus 156 ~fC~VCG~~------------~~YtC~~Cg~ryC 177 (195)
.-|.+|||+ |+-.||+|+++|=
T Consensus 35 VAC~eC~fpvCr~cyeye~~~g~~~cp~c~t~y~ 68 (1044)
T PLN02915 35 VACHVCGFPVCKPCYEYERSEGNQCCPQCNTRYK 68 (1044)
T ss_pred EEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence 478888875 6668999999995
No 144
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=32.84 E-value=12 Score=27.65 Aligned_cols=21 Identities=29% Similarity=0.710 Sum_probs=14.0
Q ss_pred cccccccCC------CCceeccCCCCc
Q 045528 155 RHFCTVCGF------SANYTCVKCGMR 175 (195)
Q Consensus 155 r~fC~VCG~------~~~YtC~~Cg~r 175 (195)
+..|.|||. +|.++|-.|...
T Consensus 3 ~~~C~VCg~~a~g~hyGv~sC~aCk~F 29 (82)
T cd07173 3 QKTCLICGDEASGCHYGALTCGSCKVF 29 (82)
T ss_pred CCCCeecCCcCcceEECcchhhhHHHH
Confidence 358999987 334477777553
No 145
>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=32.73 E-value=25 Score=20.96 Aligned_cols=7 Identities=57% Similarity=1.891 Sum_probs=3.1
Q ss_pred cccccCC
Q 045528 157 FCTVCGF 163 (195)
Q Consensus 157 fC~VCG~ 163 (195)
+|..|||
T Consensus 16 ~Cp~CG~ 22 (26)
T PF10571_consen 16 FCPHCGY 22 (26)
T ss_pred cCCCCCC
Confidence 4444444
No 146
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.54 E-value=27 Score=37.24 Aligned_cols=20 Identities=35% Similarity=1.064 Sum_probs=13.7
Q ss_pred ccccccCCC--CceeccCCCCc
Q 045528 156 HFCTVCGFS--ANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~--~~YtC~~Cg~r 175 (195)
.+|..||.. ..|.|+.||..
T Consensus 639 frCP~CG~~Te~i~fCP~CG~~ 660 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGIE 660 (1121)
T ss_pred ccCCCCCCCCCcceeCccccCc
Confidence 478888764 56677777663
No 147
>PRK14873 primosome assembly protein PriA; Provisional
Probab=32.49 E-value=22 Score=35.59 Aligned_cols=19 Identities=37% Similarity=1.031 Sum_probs=10.4
Q ss_pred cccccCCCC-ceeccCCCCc
Q 045528 157 FCTVCGFSA-NYTCVKCGMR 175 (195)
Q Consensus 157 fC~VCG~~~-~YtC~~Cg~r 175 (195)
.|.-||+.. ...|+.||..
T Consensus 412 ~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 412 RCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred ECCCCcCCCcCccCCCCcCC
Confidence 466666632 3366666653
No 148
>PHA02768 hypothetical protein; Provisional
Probab=32.29 E-value=19 Score=25.30 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=17.4
Q ss_pred ceeccCCCCcccChhhhhhhcc
Q 045528 166 NYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 166 ~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
.|.|+.||.+|=...-+..|.-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r 26 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLR 26 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHH
Confidence 4799999999988777776654
No 149
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=32.06 E-value=26 Score=23.08 Aligned_cols=15 Identities=60% Similarity=1.575 Sum_probs=8.6
Q ss_pred eeccCCCCcccChhhh
Q 045528 167 YTCVKCGMRFCCIRCQ 182 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~ 182 (195)
.+|+.||..|| ..|.
T Consensus 41 v~C~~C~~~fC-~~C~ 55 (64)
T smart00647 41 VTCPKCGFSFC-FRCK 55 (64)
T ss_pred eECCCCCCeEC-CCCC
Confidence 36666666666 3443
No 150
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.00 E-value=24 Score=22.25 Aligned_cols=10 Identities=30% Similarity=0.996 Sum_probs=7.8
Q ss_pred eeccCCCCcc
Q 045528 167 YTCVKCGMRF 176 (195)
Q Consensus 167 YtC~~Cg~ry 176 (195)
.+|++|++.|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 5788888876
No 151
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.97 E-value=9.2 Score=32.19 Aligned_cols=23 Identities=30% Similarity=0.813 Sum_probs=19.3
Q ss_pred CCcccccccCCCCceeccCCCCc
Q 045528 153 SRRHFCTVCGFSANYTCVKCGMR 175 (195)
Q Consensus 153 P~r~fC~VCG~~~~YtC~~Cg~r 175 (195)
++..||.-||-.-.-.||.|+..
T Consensus 26 ~~~~fC~kCG~~tI~~Cp~C~~~ 48 (158)
T PF10083_consen 26 LREKFCSKCGAKTITSCPNCSTP 48 (158)
T ss_pred HHHHHHHHhhHHHHHHCcCCCCC
Confidence 44569999999988999999764
No 152
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.73 E-value=14 Score=30.67 Aligned_cols=20 Identities=30% Similarity=0.788 Sum_probs=17.1
Q ss_pred ccccccCCCCceeccCCCCc
Q 045528 156 HFCTVCGFSANYTCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~~YtC~~Cg~r 175 (195)
-||+-||-.-...||.|.+.
T Consensus 29 afcskcgeati~qcp~csas 48 (160)
T COG4306 29 AFCSKCGEATITQCPICSAS 48 (160)
T ss_pred HHHhhhchHHHhcCCccCCc
Confidence 49999999888899999764
No 153
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.48 E-value=26 Score=38.08 Aligned_cols=21 Identities=29% Similarity=0.759 Sum_probs=15.8
Q ss_pred ccccccCCCCc-eeccCCCCcc
Q 045528 156 HFCTVCGFSAN-YTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~~~~-YtC~~Cg~ry 176 (195)
..|.-||.... ..|+.||.+.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EECCCCCCccccccCcccCCcC
Confidence 48999997543 3999999774
No 154
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=31.44 E-value=24 Score=36.73 Aligned_cols=34 Identities=26% Similarity=0.706 Sum_probs=25.1
Q ss_pred CCCCcccccccCC-CCce--eccCCCCcccChhhhhhh
Q 045528 151 KTSRRHFCTVCGF-SANY--TCVKCGMRFCCIRCQNIH 185 (195)
Q Consensus 151 ~~P~r~fC~VCG~-~~~Y--tC~~Cg~ryCS~~C~~~H 185 (195)
.+..+-.|.+|-. ..+| +|++||.+|| +.|+..-
T Consensus 225 ~~g~~~mC~~C~~tlfn~hw~C~~C~~~~C-l~C~r~~ 261 (889)
T KOG1356|consen 225 VKGIREMCDRCETTLFNIHWRCPRCGFGVC-LDCYRKW 261 (889)
T ss_pred ccCcchhhhhhcccccceeEEccccCCeee-ecchhhc
Confidence 3444569999986 4444 9999999977 6777654
No 155
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.39 E-value=22 Score=28.37 Aligned_cols=9 Identities=33% Similarity=0.645 Sum_probs=5.9
Q ss_pred CCeEEEEeC
Q 045528 139 PSYLRAAVG 147 (195)
Q Consensus 139 p~Y~~a~a~ 147 (195)
-+|....++
T Consensus 40 LdyV~ie~G 48 (115)
T COG1885 40 LDYVEIEVG 48 (115)
T ss_pred CCeEEEecc
Confidence 468887654
No 156
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=30.98 E-value=20 Score=27.06 Aligned_cols=20 Identities=40% Similarity=0.833 Sum_probs=14.0
Q ss_pred cccccCC------CCceeccCCCCcc
Q 045528 157 FCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~------~~~YtC~~Cg~ry 176 (195)
.|.|||. +|.++|-.|.+.|
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~aC~~FF 27 (94)
T cd06966 2 ICGVCGDKALGYNFNAITCESCKAFF 27 (94)
T ss_pred CCeeCCCcCcceEECcceeeeehhee
Confidence 5899986 3445788887644
No 157
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=30.95 E-value=30 Score=26.67 Aligned_cols=34 Identities=24% Similarity=0.759 Sum_probs=22.8
Q ss_pred CCcccccccCCCC-ceeccCCCCcccChhhhhhhcc
Q 045528 153 SRRHFCTVCGFSA-NYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 153 P~r~fC~VCG~~~-~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
|.-+.|.-||-.. .|.|+.=|...| +.|-.+|+.
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC-~~Cag~HR~ 45 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLC-LECAGIHRS 45 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE--HHHHHHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhh-HHHHHHHHH
Confidence 3346999999844 888888777666 679999987
No 158
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=30.83 E-value=20 Score=25.68 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=7.8
Q ss_pred eeccCCCCcc
Q 045528 167 YTCVKCGMRF 176 (195)
Q Consensus 167 YtC~~Cg~ry 176 (195)
|.|++||..-
T Consensus 1 y~C~KCg~~~ 10 (64)
T PF09855_consen 1 YKCPKCGNEE 10 (64)
T ss_pred CCCCCCCCcc
Confidence 7899998753
No 159
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=30.72 E-value=35 Score=22.13 Aligned_cols=22 Identities=36% Similarity=1.020 Sum_probs=14.9
Q ss_pred CcccccccCC--CC----ceeccCCCCc
Q 045528 154 RRHFCTVCGF--SA----NYTCVKCGMR 175 (195)
Q Consensus 154 ~r~fC~VCG~--~~----~YtC~~Cg~r 175 (195)
...+|.||+. || .|.|..|+..
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 3469999997 33 6799988864
No 160
>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=30.51 E-value=20 Score=22.58 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=10.5
Q ss_pred ccccccCCC--------CceeccCCCC
Q 045528 156 HFCTVCGFS--------ANYTCVKCGM 174 (195)
Q Consensus 156 ~fC~VCG~~--------~~YtC~~Cg~ 174 (195)
+||.-||.. ..+.|..||-
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 478888751 2224777764
No 161
>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=30.39 E-value=30 Score=24.08 Aligned_cols=20 Identities=30% Similarity=0.770 Sum_probs=13.3
Q ss_pred cccccCCC--------C-ceeccCCCCcc
Q 045528 157 FCTVCGFS--------A-NYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~~--------~-~YtC~~Cg~ry 176 (195)
-|.+||.. | .+.|+.||+.|
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 57888751 2 34888888754
No 162
>PF08134 cIII: cIII protein family; InterPro: IPR012995 This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon [].
Probab=30.34 E-value=52 Score=22.08 Aligned_cols=21 Identities=33% Similarity=0.381 Sum_probs=13.6
Q ss_pred hhhhhhhhhcCCHHHHHHHHHHHHHhhh
Q 045528 38 KVAPRMAAALASADNRTQAALARLEALE 65 (195)
Q Consensus 38 ~~s~r~r~~vlDe~tR~rr~~~rLeaLE 65 (195)
++++|.|+. -|.+..|||+|=
T Consensus 21 ELskr~rrL-------IRaa~k~lealc 41 (44)
T PF08134_consen 21 ELSKRIRRL-------IRAARKQLEALC 41 (44)
T ss_pred HHHHHHHHH-------HHHHHHHHHHHh
Confidence 355565543 266788999984
No 163
>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=30.32 E-value=34 Score=22.47 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=4.5
Q ss_pred CceeccCCC
Q 045528 165 ANYTCVKCG 173 (195)
Q Consensus 165 ~~YtC~~Cg 173 (195)
+.+.|+.|+
T Consensus 33 g~~~Cv~C~ 41 (41)
T PF06677_consen 33 GKIYCVSCG 41 (41)
T ss_pred CCEECCCCC
Confidence 344555553
No 164
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=30.30 E-value=27 Score=32.86 Aligned_cols=22 Identities=18% Similarity=0.608 Sum_probs=16.3
Q ss_pred cccccccCC----CCceeccCCCCcc
Q 045528 155 RHFCTVCGF----SANYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~----~~~YtC~~Cg~ry 176 (195)
...|..||. .....|++||...
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcc
Confidence 346999997 2245899999864
No 165
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=30.16 E-value=25 Score=38.59 Aligned_cols=20 Identities=40% Similarity=0.903 Sum_probs=17.8
Q ss_pred ccccccCCCCce-eccCCCCc
Q 045528 156 HFCTVCGFSANY-TCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~~Y-tC~~Cg~r 175 (195)
..|.-||..+-| .|+.||++
T Consensus 675 ~~Cp~Cg~~~~~~~Cp~CG~~ 695 (1627)
T PRK14715 675 FKCPKCGKVGLYHVCPFCGTR 695 (1627)
T ss_pred eeCCCCCCccccccCcccCCc
Confidence 379999999988 99999987
No 166
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=30.06 E-value=34 Score=31.23 Aligned_cols=38 Identities=24% Similarity=0.504 Sum_probs=30.0
Q ss_pred CCCCcccccccCC-CCce-------------------eccCCCCcccChhhhhhhccc
Q 045528 151 KTSRRHFCTVCGF-SANY-------------------TCVKCGMRFCCIRCQNIHDDT 188 (195)
Q Consensus 151 ~~P~r~fC~VCG~-~~~Y-------------------tC~~Cg~ryCS~~C~~~H~Et 188 (195)
..+.|..|.-||. .+.+ .|.-||..|=|+--+..|--|
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT 183 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT 183 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhc
Confidence 4556789999997 5544 499999999999988887653
No 167
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=29.84 E-value=31 Score=20.39 Aligned_cols=24 Identities=17% Similarity=0.326 Sum_probs=16.9
Q ss_pred CceeccCCCCcccChhhhhhhccc
Q 045528 165 ANYTCVKCGMRFCCIRCQNIHDDT 188 (195)
Q Consensus 165 ~~YtC~~Cg~ryCS~~C~~~H~Et 188 (195)
+.|.|.-|+..+=+..-+..|..+
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 456777777777777777777654
No 168
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=29.42 E-value=31 Score=34.66 Aligned_cols=34 Identities=24% Similarity=0.592 Sum_probs=27.9
Q ss_pred CcccccccCCCC-ceeccCCCCcccChhhhhhhccc
Q 045528 154 RRHFCTVCGFSA-NYTCVKCGMRFCCIRCQNIHDDT 188 (195)
Q Consensus 154 ~r~fC~VCG~~~-~YtC~~Cg~ryCS~~C~~~H~Et 188 (195)
.-..|.-||-.+ .|.|...|...| +.|-.+|++.
T Consensus 22 gNk~CADCgs~~P~WASiNlGIFIC-i~CSGIHRsL 56 (648)
T PLN03119 22 PNRRCINCNSLGPQYVCTTFWTFVC-MACSGIHREF 56 (648)
T ss_pred CCCccccCCCCCCCceeeccceEEe-ccchhhhccC
Confidence 346999999855 789999999988 5899999873
No 169
>PLN02400 cellulose synthase
Probab=29.40 E-value=26 Score=37.40 Aligned_cols=7 Identities=43% Similarity=1.388 Sum_probs=3.8
Q ss_pred cccccCC
Q 045528 157 FCTVCGF 163 (195)
Q Consensus 157 fC~VCG~ 163 (195)
+|.|||-
T Consensus 38 iCqICGD 44 (1085)
T PLN02400 38 ICQICGD 44 (1085)
T ss_pred eeeeccc
Confidence 5555554
No 170
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.32 E-value=26 Score=34.84 Aligned_cols=19 Identities=32% Similarity=0.954 Sum_probs=12.4
Q ss_pred cccccCCCCc--eeccCCCCc
Q 045528 157 FCTVCGFSAN--YTCVKCGMR 175 (195)
Q Consensus 157 fC~VCG~~~~--YtC~~Cg~r 175 (195)
.|.-||+... .+|+.||..
T Consensus 410 ~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 410 RCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred ECCCCcCCCCCCCCCCCCcCC
Confidence 5777777543 377777664
No 171
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=29.11 E-value=17 Score=31.79 Aligned_cols=20 Identities=35% Similarity=0.974 Sum_probs=15.9
Q ss_pred cccccCCC---CceeccCCCCcc
Q 045528 157 FCTVCGFS---ANYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~~---~~YtC~~Cg~ry 176 (195)
-|+||-|. .-|.|.-||.|-
T Consensus 26 dCsvCTFrNsAeAfkC~vCdvRK 48 (228)
T KOG4477|consen 26 DCSVCTFRNSAEAFKCFVCDVRK 48 (228)
T ss_pred eeeeeeecchhhhhheeeecccc
Confidence 79999983 378999998763
No 172
>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=29.06 E-value=28 Score=21.63 Aligned_cols=31 Identities=19% Similarity=0.434 Sum_probs=23.2
Q ss_pred ccccccCCC-CceeccCCCCcccChhhhhh-hcc
Q 045528 156 HFCTVCGFS-ANYTCVKCGMRFCCIRCQNI-HDD 187 (195)
Q Consensus 156 ~fC~VCG~~-~~YtC~~Cg~ryCS~~C~~~-H~E 187 (195)
.+|..|+.. ..|-|..|+..+|.. |... |+.
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~~C~~-C~~~~H~~ 36 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEPLCSE-CTVSGHKG 36 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEEEEHH-HHHTSTTT
T ss_pred ccCccCCccceEEEecCCCCccCcc-CCCCCCCC
Confidence 489999987 899999999999864 4433 543
No 173
>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=28.86 E-value=43 Score=21.48 Aligned_cols=20 Identities=35% Similarity=0.949 Sum_probs=11.5
Q ss_pred cccccCCCC----ceeccCCCCcc
Q 045528 157 FCTVCGFSA----NYTCVKCGMRF 176 (195)
Q Consensus 157 fC~VCG~~~----~YtC~~Cg~ry 176 (195)
+|.|||... -..|-.|+..|
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEE
T ss_pred eCcCCCCcCCCCCeEEcCCCChhh
Confidence 577777622 22677776543
No 174
>smart00355 ZnF_C2H2 zinc finger.
Probab=28.84 E-value=32 Score=18.01 Aligned_cols=21 Identities=29% Similarity=0.554 Sum_probs=15.0
Q ss_pred eeccCCCCcccChhhhhhhcc
Q 045528 167 YTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~~~H~E 187 (195)
|.|..|+..+-+..=+..|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 567888888777766666653
No 175
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.66 E-value=27 Score=28.06 Aligned_cols=17 Identities=24% Similarity=0.759 Sum_probs=11.2
Q ss_pred CceeccCCCCcccChhh
Q 045528 165 ANYTCVKCGMRFCCIRC 181 (195)
Q Consensus 165 ~~YtC~~Cg~ryCS~~C 181 (195)
..|.||.||.+|=...-
T Consensus 98 ~~Y~Cp~C~~~y~~~ea 114 (147)
T smart00531 98 AYYKCPNCQSKYTFLEA 114 (147)
T ss_pred cEEECcCCCCEeeHHHH
Confidence 35788888877754443
No 176
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=28.47 E-value=31 Score=24.05 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHhhhCCCCCCCC
Q 045528 51 DNRTQAALARLEALENDNAGIET 73 (195)
Q Consensus 51 ~tR~rr~~~rLeaLE~DN~~~dp 73 (195)
+...+.....|++||++||..-|
T Consensus 17 a~~t~I~~~~l~aiE~~~~~~lp 39 (62)
T PF13413_consen 17 AEETKISVSYLEAIENGDFDSLP 39 (62)
T ss_dssp HHHCS--HHHHHHHHCT-GCCSS
T ss_pred HHHhCCCHHHHHHHHCcChhhCC
Confidence 33445678899999999998755
No 177
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=28.28 E-value=14 Score=26.73 Aligned_cols=19 Identities=37% Similarity=0.997 Sum_probs=12.7
Q ss_pred ccccccCC------CCceeccCCCC
Q 045528 156 HFCTVCGF------SANYTCVKCGM 174 (195)
Q Consensus 156 ~fC~VCG~------~~~YtC~~Cg~ 174 (195)
|.|.|||. +|.++|-.|..
T Consensus 1 ~~C~VC~~~~~g~hygv~sC~aC~~ 25 (77)
T cd06956 1 HICAICGDRASGKHYGVYSCEGCKG 25 (77)
T ss_pred CCCcccCCcCcceEECceeehhHHH
Confidence 57999986 33446776655
No 178
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=28.20 E-value=52 Score=26.00 Aligned_cols=36 Identities=17% Similarity=0.451 Sum_probs=22.3
Q ss_pred CCCeEEEEeCCCCCCCCcccccccCCCCceeccCCC
Q 045528 138 VPSYLRAAVGPPSKTSRRHFCTVCGFSANYTCVKCG 173 (195)
Q Consensus 138 ~p~Y~~a~a~ps~~~P~r~fC~VCG~~~~YtC~~Cg 173 (195)
.|-|+..+..-....-...+|..|...|.++|+.|+
T Consensus 24 ~~~~~~~q~~~~~~~~~~v~C~~C~GsG~~~C~~C~ 59 (111)
T PLN03165 24 IPVFYETQIDNAAKRENTQPCFPCSGTGAQVCRFCV 59 (111)
T ss_pred CcEEEEEeeehhhhhccCCCCCCCCCCCCcCCCCCc
Confidence 355555554332233334588888888878888884
No 179
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=27.78 E-value=36 Score=28.27 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=17.5
Q ss_pred cccccccCC------CCceeccCCCCcc
Q 045528 155 RHFCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~------~~~YtC~~Cg~ry 176 (195)
.-+|+.||- |....|+.||.++
T Consensus 149 ~a~~~~~g~~~~~~~~~~~~c~~~~~~e 176 (189)
T PRK09521 149 YAMCSRCRTPLVKKGENELKCPNCGNIE 176 (189)
T ss_pred EEEccccCCceEECCCCEEECCCCCCEE
Confidence 347999997 5667999999865
No 180
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=27.75 E-value=48 Score=26.90 Aligned_cols=27 Identities=26% Similarity=0.765 Sum_probs=21.0
Q ss_pred CCCcccccccC--CCCceeccCCCCcccC
Q 045528 152 TSRRHFCTVCG--FSANYTCVKCGMRFCC 178 (195)
Q Consensus 152 ~P~r~fC~VCG--~~~~YtC~~Cg~ryCS 178 (195)
.+..-+|.-|| |.|.--|+.|++-.=|
T Consensus 94 ~~~~W~Cv~C~~~Y~GeK~C~~C~tGiYS 122 (128)
T PF11682_consen 94 RKTDWHCVMCGNHYHGEKYCPKCGTGIYS 122 (128)
T ss_pred cCceEEEecCCCccCcCEecCCCCCcccc
Confidence 45556999999 4888899999886544
No 181
>PRK13844 recombination protein RecR; Provisional
Probab=27.52 E-value=30 Score=29.96 Aligned_cols=20 Identities=20% Similarity=0.451 Sum_probs=15.5
Q ss_pred cccccccCCCCce-eccCCCC
Q 045528 155 RHFCTVCGFSANY-TCVKCGM 174 (195)
Q Consensus 155 r~fC~VCG~~~~Y-tC~~Cg~ 174 (195)
.++|++||+++.- -|.-|..
T Consensus 57 i~~C~~C~~lte~~~C~IC~d 77 (200)
T PRK13844 57 IKKCVYCQALTEDDVCNICSN 77 (200)
T ss_pred CCcCCCCCCCCCCCCCCCCCC
Confidence 5799999997744 7887754
No 182
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=27.52 E-value=32 Score=30.90 Aligned_cols=27 Identities=26% Similarity=0.161 Sum_probs=22.6
Q ss_pred CHHHHHHHHHHHHHhhhCCCCCCCCcc
Q 045528 49 SADNRTQAALARLEALENDNAGIETVE 75 (195)
Q Consensus 49 De~tR~rr~~~rLeaLE~DN~~~dp~~ 75 (195)
|-+++.+...+-|.+||.|||...|..
T Consensus 21 dva~~t~I~~~~L~aiEeg~~~~lp~~ 47 (284)
T COG1426 21 DVAARTKIRKSYLRALEEGNFDKLPGP 47 (284)
T ss_pred HHHHHhCccHHHHHHHhcCccccccch
Confidence 556677888999999999999997764
No 183
>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=27.43 E-value=43 Score=20.04 Aligned_cols=17 Identities=35% Similarity=0.970 Sum_probs=12.5
Q ss_pred cccccCC---CC-ceeccCCC
Q 045528 157 FCTVCGF---SA-NYTCVKCG 173 (195)
Q Consensus 157 fC~VCG~---~~-~YtC~~Cg 173 (195)
.|.||+. +. -|+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 5889986 33 57888876
No 184
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=27.41 E-value=34 Score=38.20 Aligned_cols=22 Identities=41% Similarity=0.830 Sum_probs=19.5
Q ss_pred ccccCCC-----------CceeccCCCCcccCh
Q 045528 158 CTVCGFS-----------ANYTCVKCGMRFCCI 179 (195)
Q Consensus 158 C~VCG~~-----------~~YtC~~Cg~ryCS~ 179 (195)
|.+||.. |-.+|+.||---|++
T Consensus 1707 cp~c~~~~~~~~~~~~~~gc~~c~~cg~s~c~~ 1739 (1740)
T PRK08332 1707 CPVCYEKEGKLVELRMESGCATCPVCGWSKCVI 1739 (1740)
T ss_pred CCCCCCCCCcceeeEecCCceeCCCCCCccccC
Confidence 9999987 677999999988875
No 185
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=27.25 E-value=25 Score=24.52 Aligned_cols=15 Identities=40% Similarity=0.860 Sum_probs=9.2
Q ss_pred CCCCCcccccccCCC
Q 045528 150 SKTSRRHFCTVCGFS 164 (195)
Q Consensus 150 ~~~P~r~fC~VCG~~ 164 (195)
+..-.+.||..||-+
T Consensus 43 ~~~~~r~FC~~CGs~ 57 (92)
T PF04828_consen 43 GKGVERYFCPTCGSP 57 (92)
T ss_dssp TSSCEEEEETTT--E
T ss_pred CCcCcCcccCCCCCe
Confidence 345567899999863
No 186
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.19 E-value=36 Score=30.99 Aligned_cols=23 Identities=35% Similarity=0.818 Sum_probs=17.3
Q ss_pred ccccccCCC-----C--ceeccCCCCcccC
Q 045528 156 HFCTVCGFS-----A--NYTCVKCGMRFCC 178 (195)
Q Consensus 156 ~fC~VCG~~-----~--~YtC~~Cg~ryCS 178 (195)
.||+-||.. + .+-|+.||..+=+
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHEHFP 141 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCccCC
Confidence 399999973 2 4489999987644
No 187
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=27.18 E-value=32 Score=26.93 Aligned_cols=21 Identities=33% Similarity=0.793 Sum_probs=14.0
Q ss_pred cccccccCC---------CCceeccCCCCc
Q 045528 155 RHFCTVCGF---------SANYTCVKCGMR 175 (195)
Q Consensus 155 r~fC~VCG~---------~~~YtC~~Cg~r 175 (195)
..-|..||. +..|.|..||..
T Consensus 123 ~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~ 152 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRSKRKRYRCGRCGGP 152 (157)
T ss_pred EEEcCCCCCEeeeecccchhhEECCCCCCE
Confidence 346777772 446788888754
No 188
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.93 E-value=34 Score=27.54 Aligned_cols=19 Identities=37% Similarity=0.849 Sum_probs=9.7
Q ss_pred cccccCC---CCceeccCCCCc
Q 045528 157 FCTVCGF---SANYTCVKCGMR 175 (195)
Q Consensus 157 fC~VCG~---~~~YtC~~Cg~r 175 (195)
-|..||. +..--|+.||.+
T Consensus 31 kC~~CG~v~~PPr~~Cp~C~~~ 52 (140)
T COG1545 31 KCKKCGRVYFPPRAYCPKCGSE 52 (140)
T ss_pred EcCCCCeEEcCCcccCCCCCCC
Confidence 4555553 444455555544
No 189
>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=26.56 E-value=28 Score=24.03 Aligned_cols=13 Identities=46% Similarity=1.260 Sum_probs=7.1
Q ss_pred CceeccCCCCccc
Q 045528 165 ANYTCVKCGMRFC 177 (195)
Q Consensus 165 ~~YtC~~Cg~ryC 177 (195)
+.|.|++|+.-||
T Consensus 20 ~~y~C~~C~~~FC 32 (51)
T PF07975_consen 20 SRYRCPKCKNHFC 32 (51)
T ss_dssp EEE--TTTT--B-
T ss_pred CeEECCCCCCccc
Confidence 5799999999998
No 190
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.47 E-value=35 Score=31.39 Aligned_cols=22 Identities=36% Similarity=0.794 Sum_probs=15.3
Q ss_pred ccccccCCCC--ceeccCCCCccc
Q 045528 156 HFCTVCGFSA--NYTCVKCGMRFC 177 (195)
Q Consensus 156 ~fC~VCG~~~--~YtC~~Cg~ryC 177 (195)
.-|.|||.|. .+.=-.||..||
T Consensus 240 ~~C~~Cg~~PtiP~~~~~C~HiyC 263 (298)
T KOG2879|consen 240 TECPVCGEPPTIPHVIGKCGHIYC 263 (298)
T ss_pred ceeeccCCCCCCCeeeccccceee
Confidence 4788888866 335555777776
No 191
>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=26.19 E-value=31 Score=28.24 Aligned_cols=14 Identities=21% Similarity=0.086 Sum_probs=6.9
Q ss_pred HHHHHHhhhCCCCC
Q 045528 57 ALARLEALENDNAG 70 (195)
Q Consensus 57 ~~~rLeaLE~DN~~ 70 (195)
+++.|-.|..+++.
T Consensus 45 VRk~L~~L~e~~Lv 58 (158)
T TIGR00373 45 VRKALYALYDAGLA 58 (158)
T ss_pred HHHHHHHHHHCCCc
Confidence 44445555555444
No 192
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=26.12 E-value=35 Score=32.07 Aligned_cols=37 Identities=35% Similarity=0.831 Sum_probs=26.5
Q ss_pred CCCCcccccccCC-CCce-eccCCCCcccChhhhhhhccc
Q 045528 151 KTSRRHFCTVCGF-SANY-TCVKCGMRFCCIRCQNIHDDT 188 (195)
Q Consensus 151 ~~P~r~fC~VCG~-~~~Y-tC~~Cg~ryCS~~C~~~H~Et 188 (195)
.-|+.|||--||+ ...| +=+-|---|| ++|-..|.+-
T Consensus 86 l~p~VHfCd~Cd~PI~IYGRmIPCkHvFC-l~CAr~~~dK 124 (389)
T KOG2932|consen 86 LGPRVHFCDRCDFPIAIYGRMIPCKHVFC-LECARSDSDK 124 (389)
T ss_pred cCcceEeecccCCcceeeecccccchhhh-hhhhhcCccc
Confidence 4577899999999 5567 6666666666 6676666653
No 193
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.81 E-value=34 Score=29.51 Aligned_cols=20 Identities=30% Similarity=0.738 Sum_probs=15.6
Q ss_pred cccccccCCCCce-eccCCCC
Q 045528 155 RHFCTVCGFSANY-TCVKCGM 174 (195)
Q Consensus 155 r~fC~VCG~~~~Y-tC~~Cg~ 174 (195)
.++|++||+++.- -|.-|..
T Consensus 53 i~~C~~C~~lse~~~C~IC~d 73 (195)
T TIGR00615 53 LRTCSVCGAISDQEVCNICSD 73 (195)
T ss_pred CCcCCCCCCCCCCCcCCCCCC
Confidence 5799999997744 7888854
No 194
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.56 E-value=32 Score=28.82 Aligned_cols=17 Identities=12% Similarity=-0.070 Sum_probs=12.6
Q ss_pred HHHHHHHHhhhCCCCCC
Q 045528 55 QAALARLEALENDNAGI 71 (195)
Q Consensus 55 rr~~~rLeaLE~DN~~~ 71 (195)
..++++|..|+.|+...
T Consensus 51 ~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 51 NTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHHHHHCCCeE
Confidence 55777888888887765
No 195
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=25.51 E-value=47 Score=22.15 Aligned_cols=31 Identities=23% Similarity=0.623 Sum_probs=23.7
Q ss_pred cccccCC---CC-ceeccCCCCcccChhhhhhhcc
Q 045528 157 FCTVCGF---SA-NYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 157 fC~VCG~---~~-~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
.|.+|+. .| .|.|..|....-.+.|+....+
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~ 36 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRE 36 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCc
Confidence 4778876 33 6899999988888899876654
No 196
>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 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=25.23 E-value=32 Score=19.83 Aligned_cols=11 Identities=45% Similarity=1.153 Sum_probs=6.5
Q ss_pred ceeccCCCCcc
Q 045528 166 NYTCVKCGMRF 176 (195)
Q Consensus 166 ~YtC~~Cg~ry 176 (195)
.|.|+.||..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 36666666543
No 198
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=25.16 E-value=45 Score=23.62 Aligned_cols=10 Identities=40% Similarity=1.109 Sum_probs=5.7
Q ss_pred CcccccccCC
Q 045528 154 RRHFCTVCGF 163 (195)
Q Consensus 154 ~r~fC~VCG~ 163 (195)
.+.||.-||.
T Consensus 45 kr~~Ck~C~~ 54 (85)
T PF04032_consen 45 KRTICKKCGS 54 (85)
T ss_dssp CCTB-TTT--
T ss_pred hcccccCCCC
Confidence 4679999987
No 199
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=24.71 E-value=50 Score=22.94 Aligned_cols=39 Identities=26% Similarity=0.576 Sum_probs=22.1
Q ss_pred ccccccCC---CCce--eccCC--CCcccChhhhhhhcc---cccCccc
Q 045528 156 HFCTVCGF---SANY--TCVKC--GMRFCCIRCQNIHDD---TRCLKFV 194 (195)
Q Consensus 156 ~fC~VCG~---~~~Y--tC~~C--g~ryCS~~C~~~H~E---tRC~K~~ 194 (195)
..|+.||+ +|.- --.+= -.+|||.+|...+.- -|=++||
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~~~krnPRkv~WT 52 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWT 52 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHHHCcCCCCcceee
Confidence 57999987 4421 01111 126799999876543 4445554
No 200
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=24.63 E-value=38 Score=26.79 Aligned_cols=23 Identities=35% Similarity=0.804 Sum_probs=15.6
Q ss_pred CCCCeEEEEeCCCCCCCCcccccccCCC
Q 045528 137 HVPSYLRAAVGPPSKTSRRHFCTVCGFS 164 (195)
Q Consensus 137 ~~p~Y~~a~a~ps~~~P~r~fC~VCG~~ 164 (195)
+.|.|... +....+.||..||-+
T Consensus 56 g~~~~~~~-----s~~~~r~FC~~CGs~ 78 (133)
T COG3791 56 GLPTYYFS-----SGSAGRGFCPTCGSP 78 (133)
T ss_pred CCceEEee-----cCCCCCeecccCCCc
Confidence 45667653 344567799999974
No 201
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=24.60 E-value=39 Score=26.02 Aligned_cols=23 Identities=39% Similarity=1.039 Sum_probs=16.6
Q ss_pred cccccccCCC-------CceeccCCCCccc
Q 045528 155 RHFCTVCGFS-------ANYTCVKCGMRFC 177 (195)
Q Consensus 155 r~fC~VCG~~-------~~YtC~~Cg~ryC 177 (195)
.+.|+.||.. |...|-.||.-+-
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 4799999864 3458999987553
No 202
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=24.14 E-value=45 Score=25.62 Aligned_cols=23 Identities=26% Similarity=0.775 Sum_probs=16.4
Q ss_pred cccccccCCC-------CceeccCCCCccc
Q 045528 155 RHFCTVCGFS-------ANYTCVKCGMRFC 177 (195)
Q Consensus 155 r~fC~VCG~~-------~~YtC~~Cg~ryC 177 (195)
.+.|+.||.. |...|-.||.-+-
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCCEEe
Confidence 3789999864 3458888877553
No 203
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=24.04 E-value=39 Score=30.02 Aligned_cols=47 Identities=26% Similarity=0.525 Sum_probs=30.6
Q ss_pred CCCCCeEEEEeCCCCCCCCcccccc--cCC-CCceeccCC-----CCcccChhhhhhhc
Q 045528 136 PHVPSYLRAAVGPPSKTSRRHFCTV--CGF-SANYTCVKC-----GMRFCCIRCQNIHD 186 (195)
Q Consensus 136 ~~~p~Y~~a~a~ps~~~P~r~fC~V--CG~-~~~YtC~~C-----g~ryCS~~C~~~H~ 186 (195)
.+.|.|..-. -.+ +-.- .-|-- |.+ |=.|.|+.= |.+||. .|-..+.
T Consensus 216 ~~e~~yC~Cn-qvs-yg~M-i~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~-~C~~~~~ 270 (274)
T KOG1973|consen 216 PDEPTYCICN-QVS-YGKM-IGCDNPGCPIEWFHFTCVGLKTKPKGKWYCP-RCKAENK 270 (274)
T ss_pred CCCCEEEEec-ccc-cccc-cccCCCCCCcceEEEeccccccCCCCcccch-hhhhhhh
Confidence 4456777654 221 2232 36666 995 999999965 668999 8876553
No 204
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=23.96 E-value=38 Score=22.52 Aligned_cols=30 Identities=20% Similarity=0.572 Sum_probs=20.4
Q ss_pred ccccccCCCCceeccCCCCcccChhhhhhhcc
Q 045528 156 HFCTVCGFSANYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 156 ~fC~VCG~~~~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
.||.||+..-.- +.=|.-|||-.|...-.+
T Consensus 7 ~yC~~Cdk~~~~--~~~~~lYCSe~Cr~~D~~ 36 (43)
T PF12855_consen 7 DYCIVCDKQIDP--PDDGSLYCSEECRLKDQE 36 (43)
T ss_pred hHHHHhhccccC--CCCCccccCHHHHhHhhh
Confidence 489999873211 334889999999765443
No 205
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=23.78 E-value=42 Score=25.74 Aligned_cols=31 Identities=32% Similarity=0.783 Sum_probs=24.7
Q ss_pred ccccccCCCC-ceeccCCCCcccChhhhhhhcc
Q 045528 156 HFCTVCGFSA-NYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 156 ~fC~VCG~~~-~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
.+|.-||... .|.++.-|...| +.|-.+|+.
T Consensus 4 ~~CaDC~~~~p~w~s~~~GifvC-~~CsgiHR~ 35 (112)
T smart00105 4 KKCFDCGAPNPTWASVNLGVFLC-IECSGIHRS 35 (112)
T ss_pred CcccCCCCCCCCcEEeccceeEh-HHhHHHHHh
Confidence 5899999855 678888888777 578888887
No 206
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=23.66 E-value=37 Score=35.14 Aligned_cols=26 Identities=42% Similarity=0.995 Sum_probs=21.5
Q ss_pred cccccccCCCC---ceeccCCCCcccChh
Q 045528 155 RHFCTVCGFSA---NYTCVKCGMRFCCIR 180 (195)
Q Consensus 155 r~fC~VCG~~~---~YtC~~Cg~ryCS~~ 180 (195)
+|.|.-||... ...|+.||.+||..+
T Consensus 60 ~~~c~Ycgi~~p~~v~kc~~c~Kwfcn~r 88 (935)
T KOG1802|consen 60 EHACAYCGISEPACVIKCNTCGKWFCNSR 88 (935)
T ss_pred hhhhhhccCCCchheeeccccCceeecCC
Confidence 58999999833 559999999999754
No 207
>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=22.95 E-value=41 Score=21.95 Aligned_cols=11 Identities=55% Similarity=1.455 Sum_probs=7.9
Q ss_pred ceeccCCCCcc
Q 045528 166 NYTCVKCGMRF 176 (195)
Q Consensus 166 ~YtC~~Cg~ry 176 (195)
.|.|..||..|
T Consensus 5 ey~C~~Cg~~f 15 (52)
T TIGR02605 5 EYRCTACGHRF 15 (52)
T ss_pred EEEeCCCCCEe
Confidence 46888888744
No 208
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=22.88 E-value=51 Score=25.81 Aligned_cols=20 Identities=35% Similarity=1.034 Sum_probs=14.2
Q ss_pred ccccccCCCCc--------e--eccCCCCc
Q 045528 156 HFCTVCGFSAN--------Y--TCVKCGMR 175 (195)
Q Consensus 156 ~fC~VCG~~~~--------Y--tC~~Cg~r 175 (195)
.+|..||.+.- | .|-.||++
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 58999998652 1 58888864
No 209
>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=22.72 E-value=22 Score=25.31 Aligned_cols=19 Identities=37% Similarity=0.871 Sum_probs=14.2
Q ss_pred ccccccCCCC-ceeccCCCC
Q 045528 156 HFCTVCGFSA-NYTCVKCGM 174 (195)
Q Consensus 156 ~fC~VCG~~~-~YtC~~Cg~ 174 (195)
.||.-|-..- ...||.||-
T Consensus 30 TFC~~C~e~~l~~~CPNCgG 49 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGG 49 (57)
T ss_pred cccHHHHHHHhcCcCcCCCC
Confidence 4777777644 779999985
No 210
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=22.62 E-value=64 Score=21.80 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=22.1
Q ss_pred cccccCC---CC-ceeccCCCCcccChhhhhhhc
Q 045528 157 FCTVCGF---SA-NYTCVKCGMRFCCIRCQNIHD 186 (195)
Q Consensus 157 fC~VCG~---~~-~YtC~~Cg~ryCS~~C~~~H~ 186 (195)
.|.+|+. .| .|+|..|-..--...|+..-.
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~ 35 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGR 35 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCC
Confidence 4788884 33 889999988777788876443
No 211
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=22.40 E-value=31 Score=31.49 Aligned_cols=26 Identities=35% Similarity=0.754 Sum_probs=14.4
Q ss_pred eeccCCCCcccChhhhhhhcccccCc
Q 045528 167 YTCVKCGMRFCCIRCQNIHDDTRCLK 192 (195)
Q Consensus 167 YtC~~Cg~ryCS~~C~~~H~EtRC~K 192 (195)
|.|.+||..|-=..=+.-|.|+-|++
T Consensus 244 ~qC~~C~KsFsl~SyLnKH~ES~C~~ 269 (279)
T KOG2462|consen 244 HQCPRCGKSFALKSYLNKHSESACLK 269 (279)
T ss_pred ccCcchhhHHHHHHHHHHhhhhcccc
Confidence 45555555555455555566666654
No 212
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=22.31 E-value=73 Score=20.52 Aligned_cols=29 Identities=28% Similarity=0.646 Sum_probs=22.4
Q ss_pred ccccccCC---CCceeccCCCCcccChhhhhh
Q 045528 156 HFCTVCGF---SANYTCVKCGMRFCCIRCQNI 184 (195)
Q Consensus 156 ~fC~VCG~---~~~YtC~~Cg~ryCS~~C~~~ 184 (195)
..|.+||. ...|+|..|....-...|+..
T Consensus 5 ~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 5 YSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred cCCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 36899986 337899999887777788765
No 213
>PHA02325 hypothetical protein
Probab=21.87 E-value=39 Score=24.86 Aligned_cols=15 Identities=27% Similarity=0.802 Sum_probs=10.6
Q ss_pred cccChhhhhhhccccc
Q 045528 175 RFCCIRCQNIHDDTRC 190 (195)
Q Consensus 175 ryCS~~C~~~H~EtRC 190 (195)
-...+-|++.|.+ .|
T Consensus 31 DLAGLVCN~lg~~-~C 45 (72)
T PHA02325 31 DLAGLVCNKLGDD-TC 45 (72)
T ss_pred hhhhhhhcccCCc-cc
Confidence 3466788888887 45
No 214
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=21.65 E-value=41 Score=27.06 Aligned_cols=22 Identities=45% Similarity=1.112 Sum_probs=16.3
Q ss_pred cccccccCCCC-----------------ceeccCCCCcc
Q 045528 155 RHFCTVCGFSA-----------------NYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~~~-----------------~YtC~~Cg~ry 176 (195)
-|.|.-||-.. -|||++|+-++
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEcCccceee
Confidence 45888888642 48999998764
No 215
>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=21.46 E-value=55 Score=19.54 Aligned_cols=24 Identities=21% Similarity=0.574 Sum_probs=19.8
Q ss_pred cccccCC-CCceeccCCCCcccChhh
Q 045528 157 FCTVCGF-SANYTCVKCGMRFCCIRC 181 (195)
Q Consensus 157 fC~VCG~-~~~YtC~~Cg~ryCS~~C 181 (195)
+|..++. +..|-|..|+...| ..|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC-~~C 26 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLC-VDC 26 (39)
T ss_pred CCCccCCcceEEEeCccChhhh-hhc
Confidence 5888887 77899999999998 445
No 216
>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=21.23 E-value=48 Score=21.34 Aligned_cols=11 Identities=45% Similarity=1.316 Sum_probs=8.2
Q ss_pred ceeccCCCCcc
Q 045528 166 NYTCVKCGMRF 176 (195)
Q Consensus 166 ~YtC~~Cg~ry 176 (195)
.|.|..||..|
T Consensus 5 ey~C~~Cg~~f 15 (42)
T PF09723_consen 5 EYRCEECGHEF 15 (42)
T ss_pred EEEeCCCCCEE
Confidence 47899998654
No 217
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=21.18 E-value=54 Score=23.45 Aligned_cols=22 Identities=27% Similarity=0.692 Sum_probs=15.9
Q ss_pred cccccCC-CCceeccCCCCcccC
Q 045528 157 FCTVCGF-SANYTCVKCGMRFCC 178 (195)
Q Consensus 157 fC~VCG~-~~~YtC~~Cg~ryCS 178 (195)
-|-.|.+ ...-+||.||..-++
T Consensus 5 AC~~C~~i~~~~~CP~Cgs~~~T 27 (61)
T PRK08351 5 ACRHCHYITTEDRCPVCGSRDLS 27 (61)
T ss_pred hhhhCCcccCCCcCCCCcCCccc
Confidence 6888888 333389999986654
No 218
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.14 E-value=50 Score=25.37 Aligned_cols=23 Identities=43% Similarity=1.174 Sum_probs=16.6
Q ss_pred cccccccCCC-------CceeccCCCCccc
Q 045528 155 RHFCTVCGFS-------ANYTCVKCGMRFC 177 (195)
Q Consensus 155 r~fC~VCG~~-------~~YtC~~Cg~ryC 177 (195)
.+.|+.||.. |...|.+||.-+.
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 3789999763 3468999987653
No 219
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. 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 two C4-type zinc finger modules involved in DNA-binding. 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, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=21.10 E-value=17 Score=25.35 Aligned_cols=21 Identities=43% Similarity=0.879 Sum_probs=14.0
Q ss_pred ccccccCCCC------ceeccCCCCcc
Q 045528 156 HFCTVCGFSA------NYTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~~~------~YtC~~Cg~ry 176 (195)
+.|.|||..+ .++|-.|...|
T Consensus 1 ~~C~VCg~~~~~~~ygv~sC~~C~~FF 27 (70)
T PF00105_consen 1 KKCKVCGDPASGYHYGVLSCNACKMFF 27 (70)
T ss_dssp -BSTTTSSBESEEETTEEEEHHHHHHH
T ss_pred CCCeECCCccCcccccccccccceeee
Confidence 3699999853 35787776543
No 220
>PF09401 NSP10: RNA synthesis protein NSP10; InterPro: IPR018995 Non-structural protein 10 (NSP10) is involved in RNA synthesis. It is synthesised as part of a replicase polyprotein, whose cleavage generates many non-structural proteins []. NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet []. A cluster of basic residues on the protein surface suggests a nucleic acid-binding function. ; GO: 0003723 RNA binding, 0008270 zinc ion binding, 0019079 viral genome replication, 0048471 perinuclear region of cytoplasm; PDB: 2XYQ_B 2XYR_B 2XYV_B 3R24_B 2GA6_I 2G9T_V 2FYG_A.
Probab=20.95 E-value=41 Score=27.32 Aligned_cols=15 Identities=47% Similarity=0.966 Sum_probs=10.3
Q ss_pred ccccccCCCCceecc
Q 045528 156 HFCTVCGFSANYTCV 170 (195)
Q Consensus 156 ~fC~VCG~~~~YtC~ 170 (195)
..|.|||.|-+|-|.
T Consensus 107 ~vC~vCg~W~~~gC~ 121 (124)
T PF09401_consen 107 EVCTVCGCWLNNGCT 121 (124)
T ss_dssp -B-TTTSSBTTTC--
T ss_pred ceeeeeceEecCCcc
Confidence 379999999999875
No 221
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=20.93 E-value=60 Score=21.59 Aligned_cols=29 Identities=31% Similarity=0.779 Sum_probs=20.6
Q ss_pred cccccC---CCC-ceeccCCCCcccChhhhhhh
Q 045528 157 FCTVCG---FSA-NYTCVKCGMRFCCIRCQNIH 185 (195)
Q Consensus 157 fC~VCG---~~~-~YtC~~Cg~ryCS~~C~~~H 185 (195)
.|.+|+ .+| .|+|..|....=...|+..-
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~ 34 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSG 34 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCC
Confidence 478888 244 68999998776667776543
No 222
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=20.68 E-value=36 Score=31.25 Aligned_cols=18 Identities=28% Similarity=0.899 Sum_probs=13.7
Q ss_pred CCceeccCCCC--------cccChhh
Q 045528 164 SANYTCVKCGM--------RFCCIRC 181 (195)
Q Consensus 164 ~~~YtC~~Cg~--------ryCS~~C 181 (195)
.-.|.|+-||+ +||.+.=
T Consensus 266 LR~YVCPiCGATgDnAHTiKyCPl~~ 291 (318)
T KOG4602|consen 266 LRSYVCPICGATGDNAHTIKYCPLAF 291 (318)
T ss_pred HhhhcCccccccCCcccceecccccC
Confidence 34689999997 7887653
No 223
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=20.56 E-value=42 Score=23.36 Aligned_cols=15 Identities=33% Similarity=0.775 Sum_probs=12.2
Q ss_pred CCcccChhhhhhhcc
Q 045528 173 GMRFCCIRCQNIHDD 187 (195)
Q Consensus 173 g~ryCS~~C~~~H~E 187 (195)
|..|||..|-+.|..
T Consensus 27 Gk~YCS~aCA~gH~~ 41 (52)
T PF02069_consen 27 GKYYCSEACANGHPN 41 (52)
T ss_dssp S-EESSHHHHHTSSS
T ss_pred CEeeecHHHhccCCC
Confidence 678999999999943
No 224
>PRK00076 recR recombination protein RecR; Reviewed
Probab=20.54 E-value=50 Score=28.50 Aligned_cols=20 Identities=30% Similarity=0.728 Sum_probs=15.6
Q ss_pred cccccccCCCCce-eccCCCC
Q 045528 155 RHFCTVCGFSANY-TCVKCGM 174 (195)
Q Consensus 155 r~fC~VCG~~~~Y-tC~~Cg~ 174 (195)
.++|.+||+.+.- -|.-|..
T Consensus 53 i~~C~~C~~lse~~~C~IC~d 73 (196)
T PRK00076 53 IKHCSVCGNLTEQDPCEICSD 73 (196)
T ss_pred CCcCCCCCCcCCCCcCCCCCC
Confidence 5799999997744 7888854
No 225
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=20.21 E-value=44 Score=26.04 Aligned_cols=21 Identities=38% Similarity=0.747 Sum_probs=14.5
Q ss_pred ccccccCC------CCceeccCCCCcc
Q 045528 156 HFCTVCGF------SANYTCVKCGMRF 176 (195)
Q Consensus 156 ~fC~VCG~------~~~YtC~~Cg~ry 176 (195)
..|.|||. +|.++|-.|...|
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~aCk~FF 33 (107)
T cd06955 7 RICGVCGDRATGFHFNAMTCEGCKGFF 33 (107)
T ss_pred CCCeecCCcCcccEECcceeeeeccee
Confidence 46999986 3445788886643
No 226
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=20.18 E-value=58 Score=21.67 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=13.9
Q ss_pred ceeccCCCCcccChhhhhhh
Q 045528 166 NYTCVKCGMRFCCIRCQNIH 185 (195)
Q Consensus 166 ~YtC~~Cg~ryCS~~C~~~H 185 (195)
.|+||=||. +.+..=+..|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H 20 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEH 20 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHH
Confidence 578888888 7776655555
No 227
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=20.11 E-value=37 Score=31.18 Aligned_cols=24 Identities=29% Similarity=0.876 Sum_probs=19.3
Q ss_pred cccccCCCCceeccCCCCcccChh
Q 045528 157 FCTVCGFSANYTCVKCGMRFCCIR 180 (195)
Q Consensus 157 fC~VCG~~~~YtC~~Cg~ryCS~~ 180 (195)
-|..|.-.|.|+|.+|-+-||--.
T Consensus 173 KC~SCNrlGq~sCLRCK~cfCddH 196 (314)
T PF06524_consen 173 KCQSCNRLGQYSCLRCKICFCDDH 196 (314)
T ss_pred cccccccccchhhhheeeeehhhh
Confidence 477788889999999988888643
No 228
>PHA00733 hypothetical protein
Probab=20.09 E-value=72 Score=25.27 Aligned_cols=32 Identities=22% Similarity=0.405 Sum_probs=24.0
Q ss_pred ccccccCCC---------------CceeccCCCCcccChhhhhhhcc
Q 045528 156 HFCTVCGFS---------------ANYTCVKCGMRFCCIRCQNIHDD 187 (195)
Q Consensus 156 ~fC~VCG~~---------------~~YtC~~Cg~ryCS~~C~~~H~E 187 (195)
..|..||.. ..|.|..||..|....-+..|..
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~ 120 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVC 120 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHH
Confidence 578888852 35799999999988777776643
No 229
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=20.05 E-value=76 Score=30.07 Aligned_cols=22 Identities=23% Similarity=0.520 Sum_probs=16.0
Q ss_pred cccccccCCC--C-ceeccCCCCcc
Q 045528 155 RHFCTVCGFS--A-NYTCVKCGMRF 176 (195)
Q Consensus 155 r~fC~VCG~~--~-~YtC~~Cg~ry 176 (195)
...|..||.. + .-.|++||...
T Consensus 221 l~~C~~Cd~l~~~~~a~CpRC~~~L 245 (419)
T PRK15103 221 LRSCSCCTAILPADQPVCPRCHTKG 245 (419)
T ss_pred CCcCCCCCCCCCCCCCCCCCCCCcC
Confidence 3469999973 2 33799999853
Done!