Query 027127
Match_columns 228
No_of_seqs 163 out of 410
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 05:20:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027127hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 7.8E-44 1.7E-48 321.1 -0.2 154 60-223 22-175 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 2.9E-25 6.4E-30 164.0 4.1 70 73-156 1-71 (71)
3 COG4357 Zinc finger domain con 99.4 2.8E-14 6E-19 112.8 1.8 73 70-146 12-92 (105)
4 PRK14890 putative Zn-ribbon RN 95.3 0.014 3.1E-07 42.7 2.5 46 119-171 5-56 (59)
5 PF12773 DZR: Double zinc ribb 92.5 0.12 2.7E-06 34.8 2.7 22 124-145 1-23 (50)
6 COG2888 Predicted Zn-ribbon RN 91.3 0.14 2.9E-06 37.9 1.8 45 121-171 9-58 (61)
7 PRK04023 DNA polymerase II lar 88.9 0.36 7.7E-06 51.7 3.3 31 136-170 628-658 (1121)
8 PF09538 FYDLN_acid: Protein o 88.5 0.27 5.9E-06 39.5 1.8 26 134-171 9-34 (108)
9 PF13248 zf-ribbon_3: zinc-rib 86.7 0.3 6.5E-06 29.6 0.8 24 121-144 2-26 (26)
10 PF07191 zinc-ribbons_6: zinc- 86.2 0.47 1E-05 35.9 1.8 36 120-155 16-59 (70)
11 PRK14559 putative protein seri 85.7 0.54 1.2E-05 47.9 2.5 32 122-153 2-34 (645)
12 PHA00626 hypothetical protein 85.5 0.73 1.6E-05 33.8 2.4 30 136-171 2-31 (59)
13 TIGR00595 priA primosomal prot 84.3 0.95 2.1E-05 44.4 3.4 49 82-143 214-262 (505)
14 PF13240 zinc_ribbon_2: zinc-r 83.2 0.61 1.3E-05 27.9 1.0 21 124-144 2-23 (23)
15 PRK14714 DNA polymerase II lar 83.2 1.2 2.5E-05 48.9 3.7 48 121-170 667-716 (1337)
16 PF10571 UPF0547: Uncharacteri 79.7 1.3 2.8E-05 27.4 1.5 23 123-145 2-25 (26)
17 COG1198 PriA Primosomal protei 77.9 2.4 5.2E-05 44.0 3.8 53 82-147 436-488 (730)
18 PRK05580 primosome assembly pr 77.4 2.1 4.6E-05 43.4 3.2 49 82-143 382-430 (679)
19 PF07282 OrfB_Zn_ribbon: Putat 75.7 2.3 4.9E-05 30.3 2.1 27 134-171 28-54 (69)
20 PRK04023 DNA polymerase II lar 75.1 2.4 5.3E-05 45.7 3.0 48 120-173 625-673 (1121)
21 PRK14873 primosome assembly pr 74.9 2.8 6.1E-05 42.8 3.4 48 82-143 384-431 (665)
22 PRK14714 DNA polymerase II lar 74.8 2.6 5.5E-05 46.4 3.1 33 135-171 668-700 (1337)
23 TIGR02300 FYDLN_acid conserved 74.8 1.9 4.1E-05 36.1 1.7 27 134-172 9-35 (129)
24 KOG2272 Focal adhesion protein 74.3 1.5 3.2E-05 41.1 1.1 51 91-159 100-151 (332)
25 KOG1940 Zn-finger protein [Gen 73.0 1.6 3.5E-05 40.5 1.0 31 67-98 174-204 (276)
26 PF12773 DZR: Double zinc ribb 72.3 3.2 6.9E-05 27.8 2.1 23 121-143 12-38 (50)
27 PF03107 C1_2: C1 domain; Int 66.3 4.5 9.6E-05 25.2 1.7 20 168-187 2-22 (30)
28 PF07191 zinc-ribbons_6: zinc- 64.6 5.2 0.00011 30.3 2.0 42 145-191 16-61 (70)
29 PF06524 NOA36: NOA36 protein; 62.6 3.3 7E-05 38.9 0.8 68 88-171 140-217 (314)
30 PF04216 FdhE: Protein involve 61.1 6.4 0.00014 35.6 2.4 48 119-170 195-245 (290)
31 PRK14892 putative transcriptio 60.5 5.3 0.00011 31.9 1.5 35 178-218 19-54 (99)
32 PRK00398 rpoP DNA-directed RNA 60.4 8.6 0.00019 25.7 2.4 8 163-170 21-28 (46)
33 PRK14559 putative protein seri 59.3 5.6 0.00012 40.7 1.9 32 121-153 15-48 (645)
34 PHA00626 hypothetical protein 59.0 6.4 0.00014 29.0 1.6 34 122-157 1-34 (59)
35 COG1198 PriA Primosomal protei 58.3 10 0.00023 39.5 3.6 49 114-170 427-482 (730)
36 PF08271 TF_Zn_Ribbon: TFIIB z 57.4 9.6 0.00021 25.2 2.1 7 137-143 3-9 (43)
37 PF13453 zf-TFIIB: Transcripti 56.4 9.7 0.00021 25.0 2.0 26 136-170 1-26 (41)
38 PRK14890 putative Zn-ribbon RN 56.2 9.2 0.0002 28.2 2.1 33 120-154 24-56 (59)
39 PF05191 ADK_lid: Adenylate ki 55.1 2.8 6.1E-05 27.5 -0.7 27 136-171 3-29 (36)
40 PF01529 zf-DHHC: DHHC palmito 53.4 8.1 0.00018 31.3 1.6 48 139-192 41-88 (174)
41 PF01096 TFIIS_C: Transcriptio 52.0 12 0.00025 24.7 1.8 34 136-170 2-35 (39)
42 KOG1312 DHHC-type Zn-finger pr 51.2 4.5 9.7E-05 38.4 -0.3 33 166-201 148-180 (341)
43 KOG1311 DHHC-type Zn-finger pr 51.0 10 0.00022 34.2 1.9 45 141-191 108-152 (299)
44 PF01599 Ribosomal_S27: Riboso 50.4 12 0.00026 26.3 1.8 22 133-154 17-46 (47)
45 COG1996 RPC10 DNA-directed RNA 49.2 12 0.00027 26.5 1.7 28 144-171 4-32 (49)
46 cd00350 rubredoxin_like Rubred 49.2 13 0.00029 23.5 1.8 25 146-171 1-25 (33)
47 PRK00432 30S ribosomal protein 49.2 12 0.00026 26.2 1.7 9 162-170 36-44 (50)
48 PF01529 zf-DHHC: DHHC palmito 49.1 15 0.00032 29.8 2.4 16 176-191 58-73 (174)
49 KOG4399 C2HC-type Zn-finger pr 47.7 3.6 7.7E-05 38.6 -1.5 76 140-218 198-273 (325)
50 cd02249 ZZ Zinc finger, ZZ typ 47.6 16 0.00035 24.5 2.0 19 179-198 13-37 (46)
51 PF03833 PolC_DP2: DNA polymer 47.4 6.2 0.00013 42.0 0.0 45 135-188 656-700 (900)
52 PF14353 CpXC: CpXC protein 46.8 20 0.00044 28.4 2.9 11 136-146 3-13 (128)
53 KOG3362 Predicted BBOX Zn-fing 46.1 6.8 0.00015 33.7 0.0 25 145-175 117-143 (156)
54 cd02341 ZZ_ZZZ3 Zinc finger, Z 45.5 17 0.00036 25.3 1.9 7 187-193 30-36 (48)
55 PF03604 DNA_RNApol_7kD: DNA d 44.1 16 0.00034 23.6 1.5 24 147-170 1-24 (32)
56 PF05502 Dynactin_p62: Dynacti 43.9 12 0.00026 37.0 1.3 10 89-98 4-13 (483)
57 PF07649 C1_3: C1-like domain; 43.8 13 0.00029 22.8 1.1 20 169-188 3-23 (30)
58 smart00451 ZnF_U1 U1-like zinc 43.7 12 0.00025 22.9 0.8 14 144-157 1-14 (35)
59 PF00643 zf-B_box: B-box zinc 43.2 20 0.00044 22.9 1.9 21 135-155 4-24 (42)
60 smart00064 FYVE Protein presen 43.1 16 0.00036 25.7 1.6 24 134-170 10-33 (68)
61 PF03833 PolC_DP2: DNA polymer 42.8 8.1 0.00018 41.1 0.0 47 119-171 653-700 (900)
62 PRK00415 rps27e 30S ribosomal 42.3 16 0.00036 26.8 1.5 35 121-155 11-51 (59)
63 smart00661 RPOL9 RNA polymeras 42.2 22 0.00047 23.7 2.1 9 162-170 19-27 (52)
64 TIGR00595 priA primosomal prot 41.4 31 0.00066 34.0 3.7 24 119-146 211-234 (505)
65 PF04438 zf-HIT: HIT zinc fing 41.2 13 0.00028 23.5 0.7 16 137-153 5-20 (30)
66 PF15616 TerY-C: TerY-C metal 40.0 31 0.00067 28.9 3.0 33 135-170 78-112 (131)
67 COG1998 RPS31 Ribosomal protei 40.0 20 0.00043 25.8 1.6 19 135-153 20-44 (51)
68 PRK06266 transcription initiat 39.6 18 0.00039 31.2 1.6 9 162-170 116-124 (178)
69 TIGR00373 conserved hypothetic 38.8 17 0.00036 30.6 1.3 10 161-170 107-116 (158)
70 cd02337 ZZ_CBP Zinc finger, ZZ 38.6 22 0.00048 23.8 1.6 20 164-187 1-20 (41)
71 COG1675 TFA1 Transcription ini 38.4 14 0.00031 32.2 0.8 37 178-221 111-149 (176)
72 PF13717 zinc_ribbon_4: zinc-r 38.4 23 0.00051 23.0 1.7 9 121-129 25-33 (36)
73 COG5273 Uncharacterized protei 38.0 16 0.00036 34.0 1.2 22 135-156 98-119 (309)
74 KOG4317 Predicted Zn-finger pr 37.8 15 0.00032 35.5 0.9 20 136-155 9-28 (383)
75 PF05502 Dynactin_p62: Dynacti 36.7 29 0.00062 34.4 2.7 50 137-196 16-68 (483)
76 PRK00464 nrdR transcriptional 36.3 21 0.00045 30.4 1.5 12 136-147 30-41 (154)
77 PF09723 Zn-ribbon_8: Zinc rib 36.0 27 0.00058 23.2 1.7 8 163-170 26-33 (42)
78 PF12760 Zn_Tnp_IS1595: Transp 35.8 48 0.0011 22.2 3.0 9 135-143 19-27 (46)
79 COG2888 Predicted Zn-ribbon RN 35.5 25 0.00055 26.1 1.6 33 120-154 26-58 (61)
80 PRK03564 formate dehydrogenase 35.2 45 0.00098 31.5 3.6 25 119-143 210-235 (309)
81 PRK14892 putative transcriptio 34.2 38 0.00083 27.0 2.6 9 180-188 42-50 (99)
82 PF08274 PhnA_Zn_Ribbon: PhnA 34.1 23 0.00049 22.7 1.0 23 136-170 4-26 (30)
83 TIGR02098 MJ0042_CXXC MJ0042 f 33.2 32 0.0007 21.8 1.7 9 121-129 25-33 (38)
84 PF13639 zf-RING_2: Ring finge 32.8 11 0.00025 24.4 -0.5 14 208-221 2-15 (44)
85 KOG0269 WD40 repeat-containing 32.2 22 0.00048 37.6 1.1 50 135-193 754-806 (839)
86 PF06220 zf-U1: U1 zinc finger 31.9 18 0.00039 23.9 0.3 13 144-156 1-13 (38)
87 PRK00564 hypA hydrogenase nick 31.8 31 0.00068 27.7 1.8 13 132-144 69-81 (117)
88 PF01363 FYVE: FYVE zinc finge 31.8 33 0.00071 24.2 1.7 24 134-170 9-32 (69)
89 COG2051 RPS27A Ribosomal prote 31.1 27 0.00058 26.4 1.2 27 121-147 19-51 (67)
90 PF12675 DUF3795: Protein of u 30.9 26 0.00057 26.0 1.1 35 135-169 35-69 (78)
91 cd00065 FYVE FYVE domain; Zinc 30.9 29 0.00063 23.4 1.3 23 135-170 3-25 (57)
92 PF15227 zf-C3HC4_4: zinc fing 30.8 18 0.0004 24.0 0.2 11 209-219 1-11 (42)
93 PRK04136 rpl40e 50S ribosomal 30.1 30 0.00065 24.6 1.2 23 120-142 13-36 (48)
94 KOG1315 Predicted DHHC-type Zn 29.9 30 0.00065 32.6 1.5 18 140-157 103-120 (307)
95 KOG2462 C2H2-type Zn-finger pr 29.8 53 0.0012 30.8 3.1 69 119-192 159-255 (279)
96 PRK07219 DNA topoisomerase I; 29.6 1.3E+02 0.0029 31.6 6.3 65 149-217 672-744 (822)
97 PRK00420 hypothetical protein; 29.3 39 0.00083 27.6 1.9 20 135-154 24-48 (112)
98 PF10058 DUF2296: Predicted in 29.0 43 0.00093 23.8 1.9 9 121-129 22-30 (54)
99 PF00130 C1_1: Phorbol esters/ 28.8 48 0.001 22.1 2.0 11 160-170 25-35 (53)
100 COG0143 MetG Methionyl-tRNA sy 28.7 41 0.00088 34.1 2.3 50 146-200 126-175 (558)
101 PF13719 zinc_ribbon_5: zinc-r 28.7 43 0.00092 21.7 1.7 9 121-129 25-33 (37)
102 KOG1311 DHHC-type Zn-finger pr 28.6 33 0.00072 30.9 1.6 34 162-201 112-145 (299)
103 COG5273 Uncharacterized protei 28.2 35 0.00076 31.8 1.7 31 168-201 111-141 (309)
104 PF01422 zf-NF-X1: NF-X1 type 28.1 47 0.001 19.7 1.6 19 196-214 2-20 (20)
105 cd07973 Spt4 Transcription elo 27.7 33 0.00071 27.3 1.2 19 123-141 5-27 (98)
106 PRK14873 primosome assembly pr 27.6 62 0.0013 33.4 3.5 29 114-146 375-404 (665)
107 PF11331 DUF3133: Protein of u 27.2 70 0.0015 22.4 2.6 37 91-133 7-43 (46)
108 PRK03681 hypA hydrogenase nick 27.1 42 0.00091 26.8 1.7 14 131-144 67-80 (114)
109 TIGR00100 hypA hydrogenase nic 26.9 49 0.0011 26.4 2.1 14 131-144 67-80 (115)
110 smart00440 ZnF_C2C2 C2C2 Zinc 26.3 73 0.0016 21.1 2.5 33 136-170 2-35 (40)
111 PLN03086 PRLI-interacting fact 26.2 45 0.00097 34.1 2.1 85 117-216 403-514 (567)
112 PRK08351 DNA-directed RNA poly 26.2 40 0.00086 24.9 1.3 20 123-143 5-24 (61)
113 PRK12380 hydrogenase nickel in 25.8 33 0.00072 27.4 0.9 9 121-129 70-78 (113)
114 smart00659 RPOLCX RNA polymera 25.5 67 0.0015 21.9 2.3 12 160-171 16-27 (44)
115 COG1645 Uncharacterized Zn-fin 25.4 42 0.00091 28.2 1.5 19 135-153 29-51 (131)
116 smart00401 ZnF_GATA zinc finge 25.2 54 0.0012 22.8 1.8 29 136-171 5-33 (52)
117 TIGR01384 TFS_arch transcripti 24.8 62 0.0013 24.7 2.3 8 180-187 90-97 (104)
118 PF14445 Prok-RING_2: Prokaryo 24.7 4.4 9.5E-05 29.4 -3.8 46 142-192 3-53 (57)
119 PF01667 Ribosomal_S27e: Ribos 24.7 54 0.0012 23.7 1.8 34 121-154 7-46 (55)
120 TIGR00244 transcriptional regu 24.6 47 0.001 28.5 1.7 13 135-147 29-41 (147)
121 cd00202 ZnF_GATA Zinc finger D 24.0 30 0.00066 24.4 0.4 18 154-171 12-29 (54)
122 PF09297 zf-NADH-PPase: NADH p 23.9 31 0.00068 21.4 0.4 21 123-143 5-30 (32)
123 PF11023 DUF2614: Protein of u 23.9 52 0.0011 27.2 1.7 27 118-144 66-95 (114)
124 PF00569 ZZ: Zinc finger, ZZ t 23.8 62 0.0014 21.7 1.9 24 162-187 3-26 (46)
125 PF03966 Trm112p: Trm112p-like 23.7 38 0.00083 24.4 0.8 12 81-92 53-64 (68)
126 PF12172 DUF35_N: Rubredoxin-l 23.6 40 0.00087 21.4 0.8 22 121-142 11-33 (37)
127 smart00154 ZnF_AN1 AN1-like Zi 23.5 77 0.0017 20.9 2.2 23 180-202 12-36 (39)
128 PF06677 Auto_anti-p27: Sjogre 23.2 58 0.0013 22.1 1.6 11 135-145 18-28 (41)
129 KOG4399 C2HC-type Zn-finger pr 23.2 20 0.00042 33.9 -0.9 53 135-191 250-302 (325)
130 TIGR03655 anti_R_Lar restricti 23.2 90 0.002 21.5 2.6 7 136-142 3-9 (53)
131 PLN00209 ribosomal protein S27 23.1 56 0.0012 25.8 1.7 36 121-156 36-77 (86)
132 TIGR01562 FdhE formate dehydro 23.1 1E+02 0.0022 29.1 3.7 26 119-144 208-234 (305)
133 PRK11788 tetratricopeptide rep 22.7 51 0.0011 29.3 1.6 23 134-156 354-378 (389)
134 COG0675 Transposase and inacti 22.6 59 0.0013 28.1 2.0 24 134-157 309-333 (364)
135 smart00531 TFIIE Transcription 22.6 61 0.0013 26.7 1.9 8 209-216 126-133 (147)
136 COG4888 Uncharacterized Zn rib 22.2 67 0.0015 26.2 2.0 27 162-188 21-54 (104)
137 PRK05580 primosome assembly pr 22.1 93 0.002 31.8 3.5 23 119-145 379-401 (679)
138 PF13445 zf-RING_UBOX: RING-ty 21.8 33 0.00071 23.2 0.2 9 209-219 1-9 (43)
139 COG1144 Pyruvate:ferredoxin ox 21.7 41 0.00089 26.7 0.7 15 178-192 63-77 (91)
140 KOG1701 Focal adhesion adaptor 21.4 54 0.0012 32.8 1.6 13 181-193 428-440 (468)
141 KOG2593 Transcription initiati 21.3 47 0.001 33.0 1.2 9 162-170 152-160 (436)
142 PF02318 FYVE_2: FYVE-type zin 21.2 27 0.00058 27.8 -0.4 40 122-167 55-98 (118)
143 KOG4275 Predicted E3 ubiquitin 21.2 28 0.0006 33.4 -0.4 20 135-156 322-341 (350)
144 PF13913 zf-C2HC_2: zinc-finge 21.0 46 0.001 19.9 0.7 12 135-146 3-14 (25)
145 PRK03824 hypA hydrogenase nick 20.8 63 0.0014 26.5 1.7 8 163-170 107-114 (135)
146 PRK12496 hypothetical protein; 20.8 45 0.00097 28.3 0.8 24 122-145 128-154 (164)
147 PF13824 zf-Mss51: Zinc-finger 20.6 69 0.0015 23.2 1.7 12 160-171 11-22 (55)
148 smart00291 ZnF_ZZ Zinc-binding 20.5 89 0.0019 20.7 2.1 21 163-186 4-24 (44)
149 PF00301 Rubredoxin: Rubredoxi 20.5 75 0.0016 22.1 1.7 10 146-155 1-10 (47)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=7.8e-44 Score=321.06 Aligned_cols=154 Identities=50% Similarity=1.070 Sum_probs=148.6
Q ss_pred CchhhccCCCccCccccccCcceecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCC
Q 027127 60 STELLRKGFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVN 139 (228)
Q Consensus 60 ~~~~~d~~~~~~GC~HY~R~ckIr~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~n 139 (228)
+.++.|++.+++||+||+|++++++|||++||+||+||+++. +|.++|+.+.+|+|+.|.++|++++.|.+
T Consensus 22 ~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~---------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~ 92 (276)
T KOG1940|consen 22 HSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE---------DHDLDRKTVYELLCMKCRKIQPVGQICSN 92 (276)
T ss_pred ccccccccccccCCchhhhccccccccccceeeeEEecChhh---------hcccchhhhhhhhhhhHHhhhhhhhcccc
Confidence 347889999999999999999999999999999999999975 89999999999999999999999999999
Q ss_pred CCCccceEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCccccccccCCccccCCCCCCCCccccCccccC
Q 027127 140 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEVIHYN 219 (228)
Q Consensus 140 Cg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~~l~~~HkCiE~~~~~nCPIC~E~lFtS 219 (228)
|+..+|+|||.+|+||||+++ .||||+.|||||+|++++||||++|+.|++..+.++|+|+|++++.|||||.|+||+|
T Consensus 93 c~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~~~fhc~~c~~c~~~~~~~~H~c~e~~~~~ncPic~e~l~~s 171 (276)
T KOG1940|consen 93 CHVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGLDFFHCKKCKACLSAYLSNWHKCVERSSEFNCPICKEYLFLS 171 (276)
T ss_pred chhhhhhhcCccccccccccc-ceeccccccccccccccchhHHhhhHhHHhhhcccccchhhhcccCCCchhHHHhccc
Confidence 999999999999999999999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhh
Q 027127 220 FPVA 223 (228)
Q Consensus 220 ~~~~ 223 (228)
.+++
T Consensus 172 ~~~~ 175 (276)
T KOG1940|consen 172 FEDA 175 (276)
T ss_pred cccC
Confidence 8665
No 2
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.91 E-value=2.9e-25 Score=164.01 Aligned_cols=70 Identities=46% Similarity=1.129 Sum_probs=53.5
Q ss_pred ccccccC-cceecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCccceEecCc
Q 027127 73 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCES 151 (228)
Q Consensus 73 C~HY~R~-ckIr~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~Fa~YfC~i 151 (228)
|+||+|+ ++|+||||++|||||+||||+. +|+++|+.+++|+||.|+++|++++. +|+ |+|+|++
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~---------~H~~~~~~~~~v~Cg~C~~~~~~~~~--~c~---~~~~C~~ 66 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELE---------DHPFDRWPVKRVICGKCRTEQPIDEY--SCG---ADYFCPI 66 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCS---------SS---TTT--EEEETTT--EEES-SB--TT-----SEEETT
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhc---------cCccccccccCeECCCCCCccChhhh--hcC---CCccCcC
Confidence 8999999 9999999999999999999975 89999999999999999999999887 777 9999999
Q ss_pred ccccc
Q 027127 152 CKLFD 156 (228)
Q Consensus 152 Ckl~D 156 (228)
|++||
T Consensus 67 C~~~~ 71 (71)
T PF05495_consen 67 CGLYF 71 (71)
T ss_dssp TTEEE
T ss_pred cCCCC
Confidence 99986
No 3
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.44 E-value=2.8e-14 Score=112.80 Aligned_cols=73 Identities=22% Similarity=0.572 Sum_probs=59.0
Q ss_pred ccCccccccC---cceecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccc-----cccCCCCC
Q 027127 70 EYGCQHYRRR---CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKV-----QQVCVNCG 141 (228)
Q Consensus 70 ~~GC~HY~R~---ckIr~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v-----~~~C~nCg 141 (228)
+.||.||+.. ++|||.||+|||+|++||||+++++- +.++++.+..+.||||.|.++..+ ...||+|.
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf----~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPF----EPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCC----ccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 4699999996 78999999999999999999985443 233344556788999999987554 36799999
Q ss_pred Cccce
Q 027127 142 VCMGE 146 (228)
Q Consensus 142 ~~Fa~ 146 (228)
.+||.
T Consensus 88 spFNp 92 (105)
T COG4357 88 SPFNP 92 (105)
T ss_pred CCCCc
Confidence 99984
No 4
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=95.30 E-value=0.014 Score=42.74 Aligned_cols=46 Identities=37% Similarity=0.949 Sum_probs=33.6
Q ss_pred CCeeEcCCCCcccc-----ccccCCCCCCc-cceEecCccccccCCCCCCeeecCCCCc
Q 027127 119 VNQVICSLCGTEQK-----VQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 119 vk~VlCg~C~teQ~-----v~~~C~nCg~~-Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
.+...|..|+.+-. +.-.|||||.. . |-|.+|+-+. .+|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I--~RC~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPNCGEVII--YRCEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCCCCCeeE--eechhHHhcC-----CceECCCCCC
Confidence 34567889986533 24579999985 4 4499998774 4799999986
No 5
>PF12773 DZR: Double zinc ribbon
Probab=92.50 E-value=0.12 Score=34.79 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=14.9
Q ss_pred cCCCCccccc-cccCCCCCCccc
Q 027127 124 CSLCGTEQKV-QQVCVNCGVCMG 145 (228)
Q Consensus 124 Cg~C~teQ~v-~~~C~nCg~~Fa 145 (228)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 5567766554 567888887776
No 6
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.26 E-value=0.14 Score=37.89 Aligned_cols=45 Identities=33% Similarity=0.886 Sum_probs=34.1
Q ss_pred eeEcCCCCccccc-----cccCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 121 QVICSLCGTEQKV-----QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 121 ~VlCg~C~teQ~v-----~~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
...|..|+.+-.+ .-.|||||... =|-|.+|+.+. .+|-|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~-I~Rc~~CRk~g-----~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVE-IYRCAKCRKLG-----NPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCcee-eehhhhHHHcC-----CceECCCcCc
Confidence 4689999987533 35799999544 36689998774 4799999986
No 7
>PRK04023 DNA polymerase II large subunit; Validated
Probab=88.85 E-value=0.36 Score=51.72 Aligned_cols=31 Identities=29% Similarity=0.676 Sum_probs=14.2
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
.|+.||......+|+.|.=. .+.+|.|+.||
T Consensus 628 fCpsCG~~t~~frCP~CG~~----Te~i~fCP~CG 658 (1121)
T PRK04023 628 KCPSCGKETFYRRCPFCGTH----TEPVYRCPRCG 658 (1121)
T ss_pred cCCCCCCcCCcccCCCCCCC----CCcceeCcccc
Confidence 44444444444444444322 34455555553
No 8
>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=88.53 E-value=0.27 Score=39.52 Aligned_cols=26 Identities=31% Similarity=0.871 Sum_probs=20.3
Q ss_pred cccCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 134 ~~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
..+|++||++| | +.+|.|-.|++||.
T Consensus 9 KR~Cp~CG~kF----------Y--DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 9 KRTCPSCGAKF----------Y--DLNKDPIVCPKCGT 34 (108)
T ss_pred cccCCCCcchh----------c--cCCCCCccCCCCCC
Confidence 35799999865 5 45789999999984
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=86.66 E-value=0.3 Score=29.64 Aligned_cols=24 Identities=33% Similarity=0.908 Sum_probs=17.7
Q ss_pred eeEcCCCCccccc-cccCCCCCCcc
Q 027127 121 QVICSLCGTEQKV-QQVCVNCGVCM 144 (228)
Q Consensus 121 ~VlCg~C~teQ~v-~~~C~nCg~~F 144 (228)
.+.|..|+++-+. +..|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 3678889886444 56899999864
No 10
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=86.19 E-value=0.47 Score=35.86 Aligned_cols=36 Identities=28% Similarity=0.813 Sum_probs=22.1
Q ss_pred CeeEcCCCCccccccccCCCCCCcc--------ceEecCccccc
Q 027127 120 NQVICSLCGTEQKVQQVCVNCGVCM--------GEYFCESCKLF 155 (228)
Q Consensus 120 k~VlCg~C~teQ~v~~~C~nCg~~F--------a~YfC~iCkl~ 155 (228)
....|..|+..-.....||.||..+ +.|||..|+=.
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gL 59 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGL 59 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-E
T ss_pred CEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCce
Confidence 4778888887766667788887763 68999988743
No 11
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.72 E-value=0.54 Score=47.91 Aligned_cols=32 Identities=28% Similarity=0.781 Sum_probs=19.9
Q ss_pred eEcCCCCccccc-cccCCCCCCccceEecCccc
Q 027127 122 VICSLCGTEQKV-QQVCVNCGVCMGEYFCESCK 153 (228)
Q Consensus 122 VlCg~C~teQ~v-~~~C~nCg~~Fa~YfC~iCk 153 (228)
++|..|+++.+. +..|++||..+..-.|..|.
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG 34 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCG 34 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCC
Confidence 357777776554 45677777777644555554
No 12
>PHA00626 hypothetical protein
Probab=85.48 E-value=0.73 Score=33.83 Aligned_cols=30 Identities=23% Similarity=0.534 Sum_probs=17.0
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
.||+||..- -+-|.+|+.| .+.|-|++||.
T Consensus 2 ~CP~CGS~~-Ivrcg~cr~~-----snrYkCkdCGY 31 (59)
T PHA00626 2 SCPKCGSGN-IAKEKTMRGW-----SDDYVCCDCGY 31 (59)
T ss_pred CCCCCCCce-eeeeceeccc-----CcceEcCCCCC
Confidence 467777631 1256666665 33566666664
No 13
>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=84.31 E-value=0.95 Score=44.36 Aligned_cols=49 Identities=22% Similarity=0.658 Sum_probs=41.6
Q ss_pred eecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCc
Q 027127 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (228)
Q Consensus 82 Ir~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~ 143 (228)
+.|.-||....|..|.-.+. -|. ....+.|-.|+..+++...||+||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLT---------YHK----KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceE---------Eec----CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 79999999999999987665 342 23589999999999999999999875
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.21 E-value=0.61 Score=27.87 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=15.1
Q ss_pred cCCCCccccc-cccCCCCCCcc
Q 027127 124 CSLCGTEQKV-QQVCVNCGVCM 144 (228)
Q Consensus 124 Cg~C~teQ~v-~~~C~nCg~~F 144 (228)
|..|+++-+. +..|++||+.+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6778877444 66899998764
No 15
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=83.17 E-value=1.2 Score=48.87 Aligned_cols=48 Identities=31% Similarity=0.715 Sum_probs=24.6
Q ss_pred eeEcCCCCccccccccCCCCCCcc-ceEecCcccccc-CCCCCCeeecCCCC
Q 027127 121 QVICSLCGTEQKVQQVCVNCGVCM-GEYFCESCKLFD-DDTSKKQYHCDGCG 170 (228)
Q Consensus 121 ~VlCg~C~teQ~v~~~C~nCg~~F-a~YfC~iCkl~D-dd~~K~~yHC~~CG 170 (228)
...|..|+++-+ ...|+.||... ..|+|+.|..-- .+++. ...|+.||
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CG 716 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCD 716 (1337)
T ss_pred EEECCCCCCccc-cccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCC
Confidence 356777776533 24677777665 345566665421 11122 34555555
No 16
>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=79.71 E-value=1.3 Score=27.37 Aligned_cols=23 Identities=30% Similarity=0.778 Sum_probs=17.9
Q ss_pred EcCCCCccccc-cccCCCCCCccc
Q 027127 123 ICSLCGTEQKV-QQVCVNCGVCMG 145 (228)
Q Consensus 123 lCg~C~teQ~v-~~~C~nCg~~Fa 145 (228)
.|..|+.+-+. +..|++||..|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 37778877665 568999999986
No 17
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=77.87 E-value=2.4 Score=44.05 Aligned_cols=53 Identities=25% Similarity=0.578 Sum_probs=43.0
Q ss_pred eecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCccceE
Q 027127 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEY 147 (228)
Q Consensus 82 Ir~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~Fa~Y 147 (228)
+.|.-||..+.|++|=.-.. -|. .+..+.|-.|+..+++...|++||...=+|
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt---------~H~----~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~ 488 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLT---------LHK----ATGQLRCHYCGYQEPIPQSCPECGSEHLRA 488 (730)
T ss_pred eecccCCCcccCCCCCcceE---------Eec----CCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence 89999999999999965443 121 136999999999999999999999884444
No 18
>PRK05580 primosome assembly protein PriA; Validated
Probab=77.38 E-value=2.1 Score=43.43 Aligned_cols=49 Identities=22% Similarity=0.641 Sum_probs=41.5
Q ss_pred eecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCc
Q 027127 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (228)
Q Consensus 82 Ir~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~ 143 (228)
+.|.-||....|..|.-.+. -|. ....+.|-.|+..++....|++||..
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~---------~h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLT---------LHR----FQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred eEhhhCcCccCCCCCCCcee---------EEC----CCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 89999999999999987654 232 23589999999999999999999876
No 19
>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=75.70 E-value=2.3 Score=30.28 Aligned_cols=27 Identities=30% Similarity=0.760 Sum_probs=17.9
Q ss_pred cccCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 134 ~~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
++.|+.||..... ......|.|+.||.
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCC
Confidence 5788888887766 23445666666664
No 20
>PRK04023 DNA polymerase II large subunit; Validated
Probab=75.14 E-value=2.4 Score=45.70 Aligned_cols=48 Identities=27% Similarity=0.656 Sum_probs=36.4
Q ss_pred CeeEcCCCCccccccccCCCCCC-ccceEecCccccccCCCCCCeeecCCCCcce
Q 027127 120 NQVICSLCGTEQKVQQVCVNCGV-CMGEYFCESCKLFDDDTSKKQYHCDGCGICR 173 (228)
Q Consensus 120 k~VlCg~C~teQ~v~~~C~nCg~-~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICR 173 (228)
..-.|..|+++. +...|++||. .-.-|||+.|.-- -..|.|+.||.=.
T Consensus 625 g~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~El 673 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGREP 673 (1121)
T ss_pred cCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCCCC
Confidence 345899999986 5679999997 4678999999432 2358899998643
No 21
>PRK14873 primosome assembly protein PriA; Provisional
Probab=74.95 E-value=2.8 Score=42.83 Aligned_cols=48 Identities=23% Similarity=0.505 Sum_probs=39.3
Q ss_pred eecCCCCCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCc
Q 027127 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (228)
Q Consensus 82 Ir~pCC~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~ 143 (228)
+.|.-||....|.+|.--+. -|. ....+.|-.|+..+ ....|++||..
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~---------~h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLG---------LPS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCeeECCCCCCcee---------Eec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 89999999999999987665 232 23589999999976 57899999876
No 22
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=74.85 E-value=2.6 Score=46.39 Aligned_cols=33 Identities=30% Similarity=0.754 Sum_probs=25.5
Q ss_pred ccCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
..|++||..-...||+.|.-. .+.+|+|+.||.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~----te~vy~CPsCGa 700 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTH----TEPVYVCPDCGA 700 (1337)
T ss_pred EECCCCCCccccccCcccCCc----CCCceeCccCCC
Confidence 589999987666799999654 345788888876
No 23
>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=74.80 E-value=1.9 Score=36.13 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=20.5
Q ss_pred cccCCCCCCccceEecCccccccCCCCCCeeecCCCCcc
Q 027127 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 172 (228)
Q Consensus 134 ~~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGIC 172 (228)
...|++||++| | +.+|.+-.|++||.=
T Consensus 9 Kr~Cp~cg~kF----------Y--DLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSKF----------Y--DLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCccc----------c--ccCCCCccCCCcCCc
Confidence 35788888865 5 457899999999853
No 24
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=74.34 E-value=1.5 Score=41.07 Aligned_cols=51 Identities=24% Similarity=0.713 Sum_probs=31.4
Q ss_pred ecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCccceEecCcccc-ccCCC
Q 027127 91 FDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL-FDDDT 159 (228)
Q Consensus 91 YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~Fa~YfC~iCkl-~Ddd~ 159 (228)
|.|.+|-..+. +--+.|.+ -+.+|-.|+....+ .--|+|-|.+|+- .|+++
T Consensus 100 F~Cd~Cn~~La---------d~gf~rnq-gr~LC~~Cn~k~Ka--------~~~g~YvC~KCh~~iD~~~ 151 (332)
T KOG2272|consen 100 FRCDLCNKHLA---------DQGFYRNQ-GRALCRECNQKEKA--------KGRGRYVCQKCHAHIDEQP 151 (332)
T ss_pred chhHHHHHHHh---------hhhhHhhc-chHHhhhhhhhhcc--------cccceeehhhhhhhccccc
Confidence 56777766654 22334443 46777777765333 2368999999974 45544
No 25
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=72.96 E-value=1.6 Score=40.51 Aligned_cols=31 Identities=19% Similarity=0.485 Sum_probs=26.9
Q ss_pred CCCccCccccccCcceecCCCCCeecCcchhh
Q 027127 67 GFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHN 98 (228)
Q Consensus 67 ~~~~~GC~HY~R~ckIr~pCC~k~YpCR~CHD 98 (228)
....+.|.||...=.++.++|.. |+|..||+
T Consensus 174 ~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 174 DAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred cCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 34557899999966699999999 99999999
No 26
>PF12773 DZR: Double zinc ribbon
Probab=72.35 E-value=3.2 Score=27.85 Aligned_cols=23 Identities=35% Similarity=0.853 Sum_probs=13.7
Q ss_pred eeEcCCCCcccc--c--cccCCCCCCc
Q 027127 121 QVICSLCGTEQK--V--QQVCVNCGVC 143 (228)
Q Consensus 121 ~VlCg~C~teQ~--v--~~~C~nCg~~ 143 (228)
.-.|..|++..+ . ...|++||..
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCC
Confidence 456777776654 1 2457777664
No 27
>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=66.33 E-value=4.5 Score=25.16 Aligned_cols=20 Identities=35% Similarity=0.894 Sum_probs=13.7
Q ss_pred CCCcceecCCCc-eeeccccC
Q 027127 168 GCGICRIGGCDN-FFHCNKCR 187 (228)
Q Consensus 168 ~CGICRvG~~~~-ffHC~~C~ 187 (228)
.|++||.-.... +++|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 467776655444 88888887
No 28
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=64.60 E-value=5.2 Score=30.30 Aligned_cols=42 Identities=38% Similarity=0.921 Sum_probs=20.9
Q ss_pred ceEecCccccccCCCCCCeeecCCCC----cceecCCCceeeccccCcccc
Q 027127 145 GEYFCESCKLFDDDTSKKQYHCDGCG----ICRIGGCDNFFHCNKCRCCYS 191 (228)
Q Consensus 145 a~YfC~iCkl~Ddd~~K~~yHC~~CG----ICRvG~~~~ffHC~~C~~C~s 191 (228)
+.|+|..|.-- =+..-.||+|| +-+.=|..||| |..|+-=+|
T Consensus 16 ~~~~C~~C~~~----~~~~a~CPdC~~~Le~LkACGAvdYF-C~~c~gLiS 61 (70)
T PF07191_consen 16 GHYHCEACQKD----YKKEAFCPDCGQPLEVLKACGAVDYF-CNHCHGLIS 61 (70)
T ss_dssp TEEEETTT--E----EEEEEE-TTT-SB-EEEEETTEEEEE--TTTT-EE-
T ss_pred CEEECcccccc----ceecccCCCcccHHHHHHHhccccee-eccCCceee
Confidence 57777777431 14566788888 44444556676 555554343
No 29
>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=62.60 E-value=3.3 Score=38.87 Aligned_cols=68 Identities=31% Similarity=0.738 Sum_probs=38.1
Q ss_pred CCeecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccccccCCCCCCccceEecCcccc-c-cCCC------
Q 027127 88 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL-F-DDDT------ 159 (228)
Q Consensus 88 ~k~YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v~~~C~nCg~~Fa~YfC~iCkl-~-Ddd~------ 159 (228)
|++|.|-+|++-+..+. .-.|.. .|+....-+-.|.+|+ .+|.|.|..||. | ||-.
T Consensus 140 Grif~CsfC~~flCEDD----QFEHQA-----------sCQvLe~E~~KC~SCN-rlGq~sCLRCK~cfCddHvrrKg~k 203 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCEDD----QFEHQA-----------SCQVLESETFKCQSCN-RLGQYSCLRCKICFCDDHVRRKGFK 203 (314)
T ss_pred CeEEEeecCCCeeeccc----hhhhhh-----------hhhhhhcccccccccc-cccchhhhheeeeehhhhhhhcccc
Confidence 56788888887665211 012221 2444444455777776 478888888874 2 3321
Q ss_pred --CCCeeecCCCCc
Q 027127 160 --SKKQYHCDGCGI 171 (228)
Q Consensus 160 --~K~~yHC~~CGI 171 (228)
...++-|++||.
T Consensus 204 y~k~k~~PCPKCg~ 217 (314)
T PF06524_consen 204 YEKGKPIPCPKCGY 217 (314)
T ss_pred cccCCCCCCCCCCC
Confidence 124566666663
No 30
>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=61.13 E-value=6.4 Score=35.64 Aligned_cols=48 Identities=31% Similarity=0.703 Sum_probs=24.5
Q ss_pred CCeeEcCCCCccccc-cccCCCCCCccceEecCccccc--cCCCCCCeeecCCCC
Q 027127 119 VNQVICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKLF--DDDTSKKQYHCDGCG 170 (228)
Q Consensus 119 vk~VlCg~C~teQ~v-~~~C~nCg~~Fa~YfC~iCkl~--Ddd~~K~~yHC~~CG 170 (228)
.+.+.|+.|+++=.+ -..|++||..-..-+ .+| ++++.-.++-|+.||
T Consensus 195 ~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l----~~~~~e~~~~~rve~C~~C~ 245 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFVRIKCPYCGNTDHEKL----EYFTVEGEPAYRVEVCESCG 245 (290)
T ss_dssp EEEEEETTT--EEE--TTS-TTT---SS-EE----E--------SEEEEEETTTT
T ss_pred cEEEEcCCCCCeeeecCCCCcCCCCCCCcce----eeEecCCCCcEEEEECCccc
Confidence 368999999999766 468999998765543 233 444455677777775
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=60.54 E-value=5.3 Score=31.85 Aligned_cols=35 Identities=20% Similarity=0.503 Sum_probs=23.9
Q ss_pred CceeeccccC-ccccccccCCccccCCCCCCCCccccCcccc
Q 027127 178 DNFFHCNKCR-CCYSMLLKNSHPCVEGAMHHDCPVCCEVIHY 218 (228)
Q Consensus 178 ~~ffHC~~C~-~C~s~~l~~~HkCiE~~~~~nCPIC~E~lFt 218 (228)
..+|+|..|| .-+++.+. + +..+..||+|+.|-=.
T Consensus 19 pt~f~CP~Cge~~v~v~~~--k----~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIK--K----NIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeecC--C----CcceEECCCCCCccCE
Confidence 4688888888 44443432 2 5778899999987533
No 32
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.41 E-value=8.6 Score=25.74 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=4.6
Q ss_pred eeecCCCC
Q 027127 163 QYHCDGCG 170 (228)
Q Consensus 163 ~yHC~~CG 170 (228)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 45666665
No 33
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=59.30 E-value=5.6 Score=40.74 Aligned_cols=32 Identities=31% Similarity=0.803 Sum_probs=16.3
Q ss_pred eeEcCCCCccccccccCCCCCCc--cceEecCccc
Q 027127 121 QVICSLCGTEQKVQQVCVNCGVC--MGEYFCESCK 153 (228)
Q Consensus 121 ~VlCg~C~teQ~v~~~C~nCg~~--Fa~YfC~iCk 153 (228)
.-.|..|++.... ..|++||.. .+.-||+.|-
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~~~fC~~CG 48 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVDEAHCPNCG 48 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcccccccccC
Confidence 3356666555432 356666543 4445555554
No 34
>PHA00626 hypothetical protein
Probab=58.95 E-value=6.4 Score=28.99 Aligned_cols=34 Identities=21% Similarity=0.450 Sum_probs=25.2
Q ss_pred eEcCCCCccccccccCCCCCCccceEecCccccccC
Q 027127 122 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFDD 157 (228)
Q Consensus 122 VlCg~C~teQ~v~~~C~nCg~~Fa~YfC~iCkl~Dd 157 (228)
|.|..|+..+-+ .|.-|...-++|-|..|.+++.
T Consensus 1 m~CP~CGS~~Iv--rcg~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKTMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCCceee--eeceecccCcceEcCCCCCeec
Confidence 467778776665 6666777778888999987754
No 35
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=58.26 E-value=10 Score=39.48 Aligned_cols=49 Identities=24% Similarity=0.611 Sum_probs=32.1
Q ss_pred CCCCC-CCeeEcCCCCccccccccCCCCCCccc------eEecCccccccCCCCCCeeecCCCC
Q 027127 114 IPRHE-VNQVICSLCGTEQKVQQVCVNCGVCMG------EYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 114 ldR~~-vk~VlCg~C~teQ~v~~~C~nCg~~Fa------~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
++|+. .+.++|..|+.. ..|+||...+. ...|--|..= .+.+.+|+.||
T Consensus 427 lnRRGys~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cg 482 (730)
T COG1198 427 LNRRGYAPLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECG 482 (730)
T ss_pred EccCCccceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCC
Confidence 34543 458999999875 35999987764 4455555432 45666677776
No 36
>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=57.36 E-value=9.6 Score=25.22 Aligned_cols=7 Identities=57% Similarity=1.322 Sum_probs=3.6
Q ss_pred CCCCCCc
Q 027127 137 CVNCGVC 143 (228)
Q Consensus 137 C~nCg~~ 143 (228)
||+||..
T Consensus 3 Cp~Cg~~ 9 (43)
T PF08271_consen 3 CPNCGSK 9 (43)
T ss_dssp BTTTSSS
T ss_pred CcCCcCC
Confidence 5555553
No 37
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=56.42 E-value=9.7 Score=25.01 Aligned_cols=26 Identities=27% Similarity=0.591 Sum_probs=16.0
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
.||.|+..|..+. + .+-.+++|+.||
T Consensus 1 ~CP~C~~~l~~~~-----~----~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVR-----L----GDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEE-----E----CCEEEEECCCCC
Confidence 3777777776553 1 224677777775
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=56.25 E-value=9.2 Score=28.16 Aligned_cols=33 Identities=24% Similarity=0.646 Sum_probs=24.5
Q ss_pred CeeEcCCCCccccccccCCCCCCccceEecCcccc
Q 027127 120 NQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (228)
Q Consensus 120 k~VlCg~C~teQ~v~~~C~nCg~~Fa~YfC~iCkl 154 (228)
.+..|..|+.+.- ..|..|....+.|.|++|.|
T Consensus 24 ~~F~CPnCG~~~I--~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVII--YRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeE--eechhHHhcCCceECCCCCC
Confidence 4777888876422 25888888888888888876
No 39
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=55.05 E-value=2.8 Score=27.55 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=13.7
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
.|++||..++.+| ++.|..--|+.||-
T Consensus 3 ~C~~Cg~~Yh~~~---------~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEF---------NPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTT---------B--SSTTBCTTTTE
T ss_pred CcCCCCCcccccc---------CCCCCCCccCCCCC
Confidence 3556666655443 34455555666653
No 40
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=53.44 E-value=8.1 Score=31.30 Aligned_cols=48 Identities=21% Similarity=0.451 Sum_probs=36.2
Q ss_pred CCCCccceEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCccccc
Q 027127 139 NCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSM 192 (228)
Q Consensus 139 nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~ 192 (228)
..+......+|.+|+.+-- ...+||..||.|-.+- -.||.==|.|+..
T Consensus 41 ~~~~~~~~~~C~~C~~~kp---~Rs~HC~~C~~CV~~~---DHHC~w~~~cIG~ 88 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKP---PRSHHCRVCNRCVLRF---DHHCPWLGNCIGR 88 (174)
T ss_pred ccccCCCCEECcccCCcCC---Ccceeccccccccccc---cccchhhcccccc
Confidence 3457778889999999833 2578999999998873 3588888888764
No 41
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=51.97 E-value=12 Score=24.75 Aligned_cols=34 Identities=26% Similarity=0.571 Sum_probs=16.3
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
.|++||..-+.|| .+=--=-|.+....|.|-+||
T Consensus 2 ~Cp~Cg~~~a~~~-~~Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-QIQTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE-EESSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE-EeeccCCCCCCeEEEEeCCCC
Confidence 4888888777665 100000233455566666665
No 42
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=51.21 E-value=4.5 Score=38.44 Aligned_cols=33 Identities=27% Similarity=0.644 Sum_probs=27.7
Q ss_pred cCCCCcceecCCCceeeccccCccccccccCCcccc
Q 027127 166 CDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (228)
Q Consensus 166 C~~CGICRvG~~~~ffHC~~C~~C~s~~l~~~HkCi 201 (228)
=.+|..|++.+.-...||..||.|+.. -.|.|+
T Consensus 148 ~~kCSTCki~KPARSKHCsiCNrCV~r---fDHHCi 180 (341)
T KOG1312|consen 148 NVKCSTCKIRKPARSKHCSICNRCVHR---FDHHCI 180 (341)
T ss_pred CCccccccCCCccccccchHHHHHHHH---hccceE
Confidence 367899999988889999999999864 478886
No 43
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=50.97 E-value=10 Score=34.21 Aligned_cols=45 Identities=24% Similarity=0.671 Sum_probs=27.3
Q ss_pred CCccceEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCcccc
Q 027127 141 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS 191 (228)
Q Consensus 141 g~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s 191 (228)
|......||..|+++-- +.-.||.-||.|-.+- =-||.==|.|+.
T Consensus 108 ~~~~~~~~C~~C~~~rP---pRs~HCsvC~~CV~rf---DHHC~WvnnCVG 152 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYRP---PRSSHCSVCNNCVLRF---DHHCPWLNNCIG 152 (299)
T ss_pred CcccceEEcCcCcccCC---CCcccchhhccccccc---CCCCCCccceEC
Confidence 45556788999999833 3455776666665552 135555555543
No 44
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=50.41 E-value=12 Score=26.30 Aligned_cols=22 Identities=23% Similarity=0.792 Sum_probs=14.4
Q ss_pred ccccCC--CCCCc------cceEecCcccc
Q 027127 133 VQQVCV--NCGVC------MGEYFCESCKL 154 (228)
Q Consensus 133 v~~~C~--nCg~~------Fa~YfC~iCkl 154 (228)
....|| .||.- +.|+||++|.+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 345788 78763 57788888764
No 45
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=49.25 E-value=12 Score=26.50 Aligned_cols=28 Identities=32% Similarity=0.716 Sum_probs=17.0
Q ss_pred cceEecCcc-ccccCCCCCCeeecCCCCc
Q 027127 144 MGEYFCESC-KLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 144 Fa~YfC~iC-kl~Ddd~~K~~yHC~~CGI 171 (228)
+..|-|..| +.++.+....-..|+.||.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 345666666 3445455666777777775
No 46
>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=49.21 E-value=13 Score=23.45 Aligned_cols=25 Identities=28% Similarity=0.787 Sum_probs=16.4
Q ss_pred eEecCccccccCCCCCCeeecCCCCc
Q 027127 146 EYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 146 ~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
+|-|.+|-+.-+ +.+.++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 367788865533 2457888888875
No 47
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=49.16 E-value=12 Score=26.16 Aligned_cols=9 Identities=44% Similarity=1.505 Sum_probs=5.1
Q ss_pred CeeecCCCC
Q 027127 162 KQYHCDGCG 170 (228)
Q Consensus 162 ~~yHC~~CG 170 (228)
..|+|..||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 455565555
No 48
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=49.05 E-value=15 Score=29.79 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=8.1
Q ss_pred CCCceeeccccCcccc
Q 027127 176 GCDNFFHCNKCRCCYS 191 (228)
Q Consensus 176 ~~~~ffHC~~C~~C~s 191 (228)
....-.||..||.|+-
T Consensus 58 kp~Rs~HC~~C~~CV~ 73 (174)
T PF01529_consen 58 KPPRSHHCRVCNRCVL 73 (174)
T ss_pred CCCcceeccccccccc
Confidence 3344555555555543
No 49
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=47.74 E-value=3.6 Score=38.65 Aligned_cols=76 Identities=26% Similarity=0.581 Sum_probs=54.1
Q ss_pred CCCccceEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCccccccccCCccccCCCCCCCCccccCcccc
Q 027127 140 CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEVIHY 218 (228)
Q Consensus 140 Cg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~~l~~~HkCiE~~~~~nCPIC~E~lFt 218 (228)
=|..=+-.||..|-.|- .+-.-||+.|+.|..-.++-+-||..|-.|+-.++-.--.|---+...-|-||+|+...
T Consensus 198 ~~~EE~~~~~~~~~~Yv---~~~~~H~~~~~S~~~~~~~~~~H~~~~~~~~~~~~i~C~~~~~~A~~~~C~iC~~~~~~ 273 (325)
T KOG4399|consen 198 LPTEEGYRFCSPCQRYV---SLENQHCEHCNSCTSKDGRKWNHCFLCKKCVKPSWIHCSICNHCAVKHGCFICGELDHK 273 (325)
T ss_pred cccccceEEEeehHHHH---HHHhhhchhhcccccchhHHHhHhHHhhhhcccceeeeecccchhhhcceeeccccccc
Confidence 45666777899998883 46677999999998777677888988888888777333333333445667788877643
No 50
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=47.57 E-value=16 Score=24.48 Aligned_cols=19 Identities=32% Similarity=0.765 Sum_probs=9.6
Q ss_pred ceeecccc------CccccccccCCc
Q 027127 179 NFFHCNKC------RCCYSMLLKNSH 198 (228)
Q Consensus 179 ~ffHC~~C------~~C~s~~l~~~H 198 (228)
..|||.+| ..|++... ..|
T Consensus 13 ~r~~C~~C~d~dLC~~Cf~~~~-~~H 37 (46)
T cd02249 13 VRYHCLVCEDFDLCSSCYAKGK-KGH 37 (46)
T ss_pred CEEECCCCCCCcCHHHHHCcCc-CCC
Confidence 35555544 45666553 344
No 51
>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=47.43 E-value=6.2 Score=41.95 Aligned_cols=45 Identities=29% Similarity=0.659 Sum_probs=0.0
Q ss_pred ccCCCCCCccceEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCc
Q 027127 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRC 188 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~ 188 (228)
-.|++||..--.-.|+.|.-. ....|.|+.||+ ++.. .+|.+||.
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~-~~~~----~~C~~C~~ 700 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI-EVEE----DECPKCGR 700 (900)
T ss_dssp ------------------------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc----cccceecccccc-ccCc----cccccccc
Confidence 367888877666677777654 446788888876 2221 16777765
No 52
>PF14353 CpXC: CpXC protein
Probab=46.85 E-value=20 Score=28.39 Aligned_cols=11 Identities=27% Similarity=0.634 Sum_probs=5.8
Q ss_pred cCCCCCCccce
Q 027127 136 VCVNCGVCMGE 146 (228)
Q Consensus 136 ~C~nCg~~Fa~ 146 (228)
+||+||+.|..
T Consensus 3 tCP~C~~~~~~ 13 (128)
T PF14353_consen 3 TCPHCGHEFEF 13 (128)
T ss_pred CCCCCCCeeEE
Confidence 45566555533
No 53
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=46.08 E-value=6.8 Score=33.75 Aligned_cols=25 Identities=32% Similarity=0.883 Sum_probs=18.6
Q ss_pred ceEecCccccccCCCCCCeeecCCCC--cceec
Q 027127 145 GEYFCESCKLFDDDTSKKQYHCDGCG--ICRIG 175 (228)
Q Consensus 145 a~YfC~iCkl~Ddd~~K~~yHC~~CG--ICRvG 175 (228)
.+-||++|-+| ++|-|-.|| +|-|+
T Consensus 117 ~r~fCaVCG~~------S~ysC~~CG~kyCsv~ 143 (156)
T KOG3362|consen 117 LRKFCAVCGYD------SKYSCVNCGTKYCSVR 143 (156)
T ss_pred cchhhhhcCCC------chhHHHhcCCceeech
Confidence 45678888855 578888888 67776
No 54
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=45.46 E-value=17 Score=25.31 Aligned_cols=7 Identities=14% Similarity=0.092 Sum_probs=3.6
Q ss_pred Ccccccc
Q 027127 187 RCCYSML 193 (228)
Q Consensus 187 ~~C~s~~ 193 (228)
..|+...
T Consensus 30 ~~C~~~~ 36 (48)
T cd02341 30 QDCVVKG 36 (48)
T ss_pred HHHHhCc
Confidence 3565544
No 55
>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=44.06 E-value=16 Score=23.62 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=11.1
Q ss_pred EecCccccccCCCCCCeeecCCCC
Q 027127 147 YFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 147 YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
|.|..|..--+....++-.|+.||
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCCcCCCeeEcCCCCcEECCcCC
Confidence 344444332223344555666666
No 56
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=43.94 E-value=12 Score=37.01 Aligned_cols=10 Identities=50% Similarity=1.437 Sum_probs=7.1
Q ss_pred CeecCcchhh
Q 027127 89 EIFDCRHCHN 98 (228)
Q Consensus 89 k~YpCR~CHD 98 (228)
+.|-|+.||.
T Consensus 4 ~L~fC~~C~~ 13 (483)
T PF05502_consen 4 ELYFCEHCHK 13 (483)
T ss_pred cceecccccc
Confidence 4577888874
No 57
>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=43.79 E-value=13 Score=22.76 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=6.2
Q ss_pred CCcceecCCC-ceeeccccCc
Q 027127 169 CGICRIGGCD-NFFHCNKCRC 188 (228)
Q Consensus 169 CGICRvG~~~-~ffHC~~C~~ 188 (228)
|++|+..+.. .+++|..|+.
T Consensus 3 C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 3 CDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp -TTTS----S--EEE-TTT--
T ss_pred CCcCCCcCCCCceEECccCCC
Confidence 4444444332 5666666654
No 58
>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=43.66 E-value=12 Score=22.91 Aligned_cols=14 Identities=21% Similarity=0.795 Sum_probs=9.6
Q ss_pred cceEecCccccccC
Q 027127 144 MGEYFCESCKLFDD 157 (228)
Q Consensus 144 Fa~YfC~iCkl~Dd 157 (228)
++.|||++|+.|=.
T Consensus 1 ~~~~~C~~C~~~~~ 14 (35)
T smart00451 1 TGGFYCKLCNVTFT 14 (35)
T ss_pred CcCeEccccCCccC
Confidence 35788888876533
No 59
>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=43.20 E-value=20 Score=22.93 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=15.5
Q ss_pred ccCCCCCCccceEecCccccc
Q 027127 135 QVCVNCGVCMGEYFCESCKLF 155 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~ 155 (228)
..|..++...+.|||..|+.+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~ 24 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEP 24 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEE
T ss_pred ccCccCCccceEEEecCCCCc
Confidence 467888887788888888754
No 60
>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 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=42.82 E-value=8.1 Score=41.14 Aligned_cols=47 Identities=28% Similarity=0.761 Sum_probs=0.0
Q ss_pred CCeeEcCCCCccccccccCCCCCCc-cceEecCccccccCCCCCCeeecCCCCc
Q 027127 119 VNQVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 119 vk~VlCg~C~teQ~v~~~C~nCg~~-Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
+-.-.|..|+++ .+...|+.||.. .-.|+|+.|+.--++. +|+.||.
T Consensus 653 i~~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 653 IGRRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp ------------------------------------------------------
T ss_pred eecccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 335579999887 445789999975 5678899997643321 8999884
No 62
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=42.25 E-value=16 Score=26.80 Aligned_cols=35 Identities=34% Similarity=0.585 Sum_probs=26.0
Q ss_pred eeEcCCCCccccc------cccCCCCCCccceEecCccccc
Q 027127 121 QVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKLF 155 (228)
Q Consensus 121 ~VlCg~C~teQ~v------~~~C~nCg~~Fa~YfC~iCkl~ 155 (228)
.|.|..|+.+|.+ .-.|..||..+++-.=++-+|.
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~ 51 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIK 51 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeee
Confidence 7899999999865 2479999998877655555443
No 63
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=42.18 E-value=22 Score=23.69 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=5.3
Q ss_pred CeeecCCCC
Q 027127 162 KQYHCDGCG 170 (228)
Q Consensus 162 ~~yHC~~CG 170 (228)
..|-|+.||
T Consensus 19 ~~~vC~~Cg 27 (52)
T smart00661 19 RRFVCRKCG 27 (52)
T ss_pred CEEECCcCC
Confidence 356666666
No 64
>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=41.45 E-value=31 Score=34.02 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=17.9
Q ss_pred CCeeEcCCCCccccccccCCCCCCccce
Q 027127 119 VNQVICSLCGTEQKVQQVCVNCGVCMGE 146 (228)
Q Consensus 119 vk~VlCg~C~teQ~v~~~C~nCg~~Fa~ 146 (228)
.+.++|..|+.. ..|++|+..+.-
T Consensus 211 a~~~~C~~Cg~~----~~C~~C~~~l~~ 234 (505)
T TIGR00595 211 SKNLLCRSCGYI----LCCPNCDVSLTY 234 (505)
T ss_pred CCeeEhhhCcCc----cCCCCCCCceEE
Confidence 467889999875 368999877743
No 65
>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=41.17 E-value=13 Score=23.51 Aligned_cols=16 Identities=38% Similarity=1.026 Sum_probs=7.3
Q ss_pred CCCCCCccceEecCccc
Q 027127 137 CVNCGVCMGEYFCESCK 153 (228)
Q Consensus 137 C~nCg~~Fa~YfC~iCk 153 (228)
|.-||. .++|-|+.|.
T Consensus 5 C~vC~~-~~kY~Cp~C~ 20 (30)
T PF04438_consen 5 CSVCGN-PAKYRCPRCG 20 (30)
T ss_dssp ETSSSS-EESEE-TTT-
T ss_pred CccCcC-CCEEECCCcC
Confidence 444555 5555555554
No 66
>PF15616 TerY-C: TerY-C metal binding domain
Probab=40.02 E-value=31 Score=28.90 Aligned_cols=33 Identities=36% Similarity=0.792 Sum_probs=22.8
Q ss_pred ccCCCCCCccceEecCcc-cccc-CCCCCCeeecCCCC
Q 027127 135 QVCVNCGVCMGEYFCESC-KLFD-DDTSKKQYHCDGCG 170 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iC-kl~D-dd~~K~~yHC~~CG 170 (228)
..||.||..+|---| .| ||+- +.+ ....|+-||
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~Ci~g~--~~~~CPwCg 112 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFCIDGE--GEVTCPWCG 112 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEEeCCC--CCEECCCCC
Confidence 689999999999999 58 5553 221 255666665
No 67
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=40.02 E-value=20 Score=25.80 Aligned_cols=19 Identities=32% Similarity=0.962 Sum_probs=11.3
Q ss_pred ccCCCCCC--cc----ceEecCccc
Q 027127 135 QVCVNCGV--CM----GEYFCESCK 153 (228)
Q Consensus 135 ~~C~nCg~--~F----a~YfC~iCk 153 (228)
..||+||. -| .||+|++|.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCg 44 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCG 44 (51)
T ss_pred ccCCCCCCcchhhhcCceeEecccc
Confidence 57888883 33 355555554
No 68
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.58 E-value=18 Score=31.16 Aligned_cols=9 Identities=22% Similarity=0.825 Sum_probs=4.0
Q ss_pred CeeecCCCC
Q 027127 162 KQYHCDGCG 170 (228)
Q Consensus 162 ~~yHC~~CG 170 (228)
.-|+|+.||
T Consensus 116 ~~Y~Cp~C~ 124 (178)
T PRK06266 116 MFFFCPNCH 124 (178)
T ss_pred CEEECCCCC
Confidence 344444443
No 69
>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=38.76 E-value=17 Score=30.63 Aligned_cols=10 Identities=10% Similarity=0.268 Sum_probs=4.6
Q ss_pred CCeeecCCCC
Q 027127 161 KKQYHCDGCG 170 (228)
Q Consensus 161 K~~yHC~~CG 170 (228)
..-|+|+.||
T Consensus 107 ~~~Y~Cp~c~ 116 (158)
T TIGR00373 107 NMFFICPNMC 116 (158)
T ss_pred CCeEECCCCC
Confidence 3444444444
No 70
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=38.56 E-value=22 Score=23.80 Aligned_cols=20 Identities=30% Similarity=0.856 Sum_probs=11.2
Q ss_pred eecCCCCcceecCCCceeeccccC
Q 027127 164 YHCDGCGICRIGGCDNFFHCNKCR 187 (228)
Q Consensus 164 yHC~~CGICRvG~~~~ffHC~~C~ 187 (228)
|+|+.|+. +++ ..|||..|.
T Consensus 1 y~C~~C~~--~~~--~r~~C~~C~ 20 (41)
T cd02337 1 YTCNECKH--HVE--TRWHCTVCE 20 (41)
T ss_pred CcCCCCCC--cCC--CceECCCCc
Confidence 55666654 332 567776663
No 71
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=38.43 E-value=14 Score=32.22 Aligned_cols=37 Identities=24% Similarity=0.554 Sum_probs=25.0
Q ss_pred CceeeccccCccccccccCCccccCCCCCCCCccccCcc--ccChh
Q 027127 178 DNFFHCNKCRCCYSMLLKNSHPCVEGAMHHDCPVCCEVI--HYNFP 221 (228)
Q Consensus 178 ~~ffHC~~C~~C~s~~l~~~HkCiE~~~~~nCPIC~E~l--FtS~~ 221 (228)
.+||||..|..=+|..-.- -+..+||.|++.| ++|.+
T Consensus 111 ~~~y~C~~~~~r~sfdeA~-------~~~F~Cp~Cg~~L~~~d~s~ 149 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAM-------ELGFTCPKCGEDLEEYDSSE 149 (176)
T ss_pred CCceeCCCCCCcccHHHHH-------HhCCCCCCCCchhhhccchH
Confidence 5799997777666553221 2237899999998 55554
No 72
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=38.39 E-value=23 Score=22.96 Aligned_cols=9 Identities=56% Similarity=1.180 Sum_probs=4.7
Q ss_pred eeEcCCCCc
Q 027127 121 QVICSLCGT 129 (228)
Q Consensus 121 ~VlCg~C~t 129 (228)
.|.|+.|++
T Consensus 25 ~v~C~~C~~ 33 (36)
T PF13717_consen 25 KVRCSKCGH 33 (36)
T ss_pred EEECCCCCC
Confidence 555555544
No 73
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=37.97 E-value=16 Score=33.95 Aligned_cols=22 Identities=23% Similarity=0.608 Sum_probs=17.0
Q ss_pred ccCCCCCCccceEecCcccccc
Q 027127 135 QVCVNCGVCMGEYFCESCKLFD 156 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~D 156 (228)
..+...|.-..+-||.+|+.|-
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~K 119 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYK 119 (309)
T ss_pred hhhhhcCccccceecccccccc
Confidence 4566677778888999999983
No 74
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=37.75 E-value=15 Score=35.47 Aligned_cols=20 Identities=45% Similarity=1.007 Sum_probs=17.0
Q ss_pred cCCCCCCccceEecCccccc
Q 027127 136 VCVNCGVCMGEYFCESCKLF 155 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~ 155 (228)
.|+-||+.+++|.|+-|+|.
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eccccccccccccCCCCCcc
Confidence 57788999999999999875
No 75
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=36.67 E-value=29 Score=34.38 Aligned_cols=50 Identities=22% Similarity=0.609 Sum_probs=28.1
Q ss_pred CCCC-CCccceEecCccccccCCCC--CCeeecCCCCcceecCCCceeeccccCccccccccC
Q 027127 137 CVNC-GVCMGEYFCESCKLFDDDTS--KKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKN 196 (228)
Q Consensus 137 C~nC-g~~Fa~YfC~iCkl~Ddd~~--K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~~l~~ 196 (228)
|+.| ...+-.|||+.|-+---..+ -....|. .+-|-|..|..-+++...+
T Consensus 16 c~~c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC~----------r~Cf~CP~C~~~L~~~~~~ 68 (483)
T PF05502_consen 16 CPRCVSEEIDSYYCPNCLFEVPSSEARSEKNRCS----------RNCFDCPICFSPLSVRASD 68 (483)
T ss_pred ChhhcccccceeECccccccCChhhheeccceec----------cccccCCCCCCcceeEecc
Confidence 5555 45677888888854321111 1223442 2457788888877776544
No 76
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=36.32 E-value=21 Score=30.39 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=7.6
Q ss_pred cCCCCCCccceE
Q 027127 136 VCVNCGVCMGEY 147 (228)
Q Consensus 136 ~C~nCg~~Fa~Y 147 (228)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 466666666665
No 77
>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=35.98 E-value=27 Score=23.22 Aligned_cols=8 Identities=38% Similarity=1.070 Sum_probs=3.7
Q ss_pred eeecCCCC
Q 027127 163 QYHCDGCG 170 (228)
Q Consensus 163 ~yHC~~CG 170 (228)
.-.|+.||
T Consensus 26 ~~~CP~Cg 33 (42)
T PF09723_consen 26 PVPCPECG 33 (42)
T ss_pred CCcCCCCC
Confidence 33455444
No 78
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=35.81 E-value=48 Score=22.17 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=5.2
Q ss_pred ccCCCCCCc
Q 027127 135 QVCVNCGVC 143 (228)
Q Consensus 135 ~~C~nCg~~ 143 (228)
.+||.||..
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 356666655
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=35.49 E-value=25 Score=26.11 Aligned_cols=33 Identities=24% Similarity=0.632 Sum_probs=20.6
Q ss_pred CeeEcCCCCccccccccCCCCCCccceEecCcccc
Q 027127 120 NQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL 154 (228)
Q Consensus 120 k~VlCg~C~teQ~v~~~C~nCg~~Fa~YfC~iCkl 154 (228)
....|..|+.++-+ .|..|...-+.|-|++|-|
T Consensus 26 v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeee--hhhhHHHcCCceECCCcCc
Confidence 45666666655443 5666666666677776655
No 80
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.23 E-value=45 Score=31.47 Aligned_cols=25 Identities=32% Similarity=0.739 Sum_probs=20.9
Q ss_pred CCeeEcCCCCccccc-cccCCCCCCc
Q 027127 119 VNQVICSLCGTEQKV-QQVCVNCGVC 143 (228)
Q Consensus 119 vk~VlCg~C~teQ~v-~~~C~nCg~~ 143 (228)
.+...|+.|+++=.+ -..|++||..
T Consensus 210 ~RyL~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 210 LRYLHCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCC
Confidence 468999999999766 5689999974
No 81
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=34.22 E-value=38 Score=26.97 Aligned_cols=9 Identities=22% Similarity=0.866 Sum_probs=4.3
Q ss_pred eeeccccCc
Q 027127 180 FFHCNKCRC 188 (228)
Q Consensus 180 ffHC~~C~~ 188 (228)
...|.+||.
T Consensus 42 h~~C~~CG~ 50 (99)
T PRK14892 42 IITCGNCGL 50 (99)
T ss_pred eEECCCCCC
Confidence 444555544
No 82
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=34.13 E-value=23 Score=22.65 Aligned_cols=23 Identities=26% Similarity=0.582 Sum_probs=10.2
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
.|+.|+..++- .+..+|-|+.||
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECG 26 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTT
T ss_pred CCCCCCCccee------------ccCCEEeCCccc
Confidence 57777766653 234678888876
No 83
>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=33.21 E-value=32 Score=21.78 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.4
Q ss_pred eeEcCCCCc
Q 027127 121 QVICSLCGT 129 (228)
Q Consensus 121 ~VlCg~C~t 129 (228)
.+.|+.|++
T Consensus 25 ~v~C~~C~~ 33 (38)
T TIGR02098 25 KVRCGKCGH 33 (38)
T ss_pred EEECCCCCC
Confidence 455555544
No 84
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=32.80 E-value=11 Score=24.42 Aligned_cols=14 Identities=29% Similarity=0.740 Sum_probs=10.7
Q ss_pred CCccccCccccChh
Q 027127 208 DCPVCCEVIHYNFP 221 (228)
Q Consensus 208 nCPIC~E~lFtS~~ 221 (228)
+||||++.+-++..
T Consensus 2 ~C~IC~~~~~~~~~ 15 (44)
T PF13639_consen 2 ECPICLEEFEDGEK 15 (44)
T ss_dssp CETTTTCBHHTTSC
T ss_pred CCcCCChhhcCCCe
Confidence 69999999876443
No 85
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=32.19 E-value=22 Score=37.64 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=39.8
Q ss_pred ccCCCCCCccceE---ecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCcccccc
Q 027127 135 QVCVNCGVCMGEY---FCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSML 193 (228)
Q Consensus 135 ~~C~nCg~~Fa~Y---fC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~~ 193 (228)
-.|++|++.++.- +|+.|.--.. .+|-+|+.+-+.-++||..|+-+.-.+
T Consensus 754 ~~~~nc~a~~~~~~~~~c~rc~s~a~---------~~CtVC~~vi~G~~~~c~~C~H~gH~s 806 (839)
T KOG0269|consen 754 YACPNCDAPMVLTKLWQCDRCESRAS---------AKCTVCDLVIRGVDVWCQVCGHGGHDS 806 (839)
T ss_pred ccccccCCccccccceeechHHHHhh---------cCceeecceeeeeEeecccccccccHH
Confidence 4799999988765 8888875533 268889999888899999999986653
No 86
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=31.86 E-value=18 Score=23.91 Aligned_cols=13 Identities=38% Similarity=1.076 Sum_probs=5.6
Q ss_pred cceEecCcccccc
Q 027127 144 MGEYFCESCKLFD 156 (228)
Q Consensus 144 Fa~YfC~iCkl~D 156 (228)
|-+|||+-|+.|-
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 4589999998875
No 87
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.84 E-value=31 Score=27.67 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=6.2
Q ss_pred cccccCCCCCCcc
Q 027127 132 KVQQVCVNCGVCM 144 (228)
Q Consensus 132 ~v~~~C~nCg~~F 144 (228)
|+...|..||..|
T Consensus 69 p~~~~C~~Cg~~~ 81 (117)
T PRK00564 69 KVELECKDCSHVF 81 (117)
T ss_pred CCEEEhhhCCCcc
Confidence 3344555555433
No 88
>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=31.84 E-value=33 Score=24.20 Aligned_cols=24 Identities=29% Similarity=0.812 Sum_probs=11.0
Q ss_pred cccCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 027127 134 QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 134 ~~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
+..|..|+..|+- -+..+||-.||
T Consensus 9 ~~~C~~C~~~F~~-------------~~rrhhCr~CG 32 (69)
T PF01363_consen 9 ASNCMICGKKFSL-------------FRRRHHCRNCG 32 (69)
T ss_dssp -SB-TTT--B-BS-------------SS-EEE-TTT-
T ss_pred CCcCcCcCCcCCC-------------ceeeEccCCCC
Confidence 4577788888852 25678888887
No 89
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=31.06 E-value=27 Score=26.39 Aligned_cols=27 Identities=41% Similarity=0.817 Sum_probs=20.8
Q ss_pred eeEcCCCCccccc------cccCCCCCCccceE
Q 027127 121 QVICSLCGTEQKV------QQVCVNCGVCMGEY 147 (228)
Q Consensus 121 ~VlCg~C~teQ~v------~~~C~nCg~~Fa~Y 147 (228)
.|.|.-|+.+|-+ ...|..||..+++-
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 7889999998876 14688888877654
No 90
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=30.90 E-value=26 Score=25.99 Aligned_cols=35 Identities=29% Similarity=0.606 Sum_probs=24.8
Q ss_pred ccCCCCCCccceEecCccccccCCCCCCeeecCCC
Q 027127 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGC 169 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~C 169 (228)
..|+.|...=....+..|.+.+=-.+|.+-||-.|
T Consensus 35 ~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC 69 (78)
T PF12675_consen 35 IRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGEC 69 (78)
T ss_pred CcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecC
Confidence 46888866555577888887766667777777766
No 91
>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=30.87 E-value=29 Score=23.39 Aligned_cols=23 Identities=30% Similarity=0.950 Sum_probs=14.4
Q ss_pred ccCCCCCCccceEecCccccccCCCCCCeeecCCCC
Q 027127 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CG 170 (228)
+.|..|+..|+. .+..+||..||
T Consensus 3 ~~C~~C~~~F~~-------------~~rk~~Cr~Cg 25 (57)
T cd00065 3 SSCMGCGKPFTL-------------TRRRHHCRNCG 25 (57)
T ss_pred CcCcccCccccC-------------CccccccCcCc
Confidence 457777777763 13456777766
No 92
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=30.76 E-value=18 Score=23.95 Aligned_cols=11 Identities=27% Similarity=1.047 Sum_probs=8.1
Q ss_pred CccccCccccC
Q 027127 209 CPVCCEVIHYN 219 (228)
Q Consensus 209 CPIC~E~lFtS 219 (228)
||||+++|.+-
T Consensus 1 CpiC~~~~~~P 11 (42)
T PF15227_consen 1 CPICLDLFKDP 11 (42)
T ss_dssp ETTTTSB-SSE
T ss_pred CCccchhhCCc
Confidence 89999988654
No 93
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=30.11 E-value=30 Score=24.58 Aligned_cols=23 Identities=30% Similarity=0.743 Sum_probs=19.4
Q ss_pred CeeEcCCCCccccc-cccCCCCCC
Q 027127 120 NQVICSLCGTEQKV-QQVCVNCGV 142 (228)
Q Consensus 120 k~VlCg~C~teQ~v-~~~C~nCg~ 142 (228)
..+||+.|+...++ +..|..||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 57899999999887 568998886
No 94
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=29.89 E-value=30 Score=32.63 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=13.4
Q ss_pred CCCccceEecCccccccC
Q 027127 140 CGVCMGEYFCESCKLFDD 157 (228)
Q Consensus 140 Cg~~Fa~YfC~iCkl~Dd 157 (228)
|+..=+--||.+|+.|--
T Consensus 103 ~~~~g~~R~C~kC~~iKP 120 (307)
T KOG1315|consen 103 RTSDGAVRYCDKCKCIKP 120 (307)
T ss_pred ecCCCCceeecccccccC
Confidence 455556789999999944
No 95
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=29.79 E-value=53 Score=30.84 Aligned_cols=69 Identities=22% Similarity=0.543 Sum_probs=40.7
Q ss_pred CCeeEcCCCCccccc-------------cccCCCCCCccceEecCccccccC----CCCCCeeecCCCCcc-------ee
Q 027127 119 VNQVICSLCGTEQKV-------------QQVCVNCGVCMGEYFCESCKLFDD----DTSKKQYHCDGCGIC-------RI 174 (228)
Q Consensus 119 vk~VlCg~C~teQ~v-------------~~~C~nCg~~Fa~YfC~iCkl~Dd----d~~K~~yHC~~CGIC-------Rv 174 (228)
.+.-.|-.|++++-- .-.|.-||+.|.|-- |+-. -...+||-|+.||== |.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPW-----LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRA 233 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPW-----LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRA 233 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchH-----HhhcccccccCCCCccCCcccchhcchHHHHH
Confidence 567889999886322 236888998887531 2222 235577877766511 00
Q ss_pred ----cCCCceeeccccCccccc
Q 027127 175 ----GGCDNFFHCNKCRCCYSM 192 (228)
Q Consensus 175 ----G~~~~ffHC~~C~~C~s~ 192 (228)
-....-|-|.+|+-=.+.
T Consensus 234 HmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 234 HMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred HHHhhcCCccccCcchhhHHHH
Confidence 012346778888765554
No 96
>PRK07219 DNA topoisomerase I; Validated
Probab=29.64 E-value=1.3e+02 Score=31.59 Aligned_cols=65 Identities=17% Similarity=0.451 Sum_probs=35.2
Q ss_pred cCccccccCCC--CCCeeecCCCCcc---eecCCCceeeccc---cCccccccccCCccccCCCCCCCCccccCccc
Q 027127 149 CESCKLFDDDT--SKKQYHCDGCGIC---RIGGCDNFFHCNK---CRCCYSMLLKNSHPCVEGAMHHDCPVCCEVIH 217 (228)
Q Consensus 149 C~iCkl~Ddd~--~K~~yHC~~CGIC---RvG~~~~ffHC~~---C~~C~s~~l~~~HkCiE~~~~~nCPIC~E~lF 217 (228)
|+.|+...... ......|+.||-= |.|....|+-|.. |+.=+++.- ..+. ..+...||-|+..|+
T Consensus 672 CP~C~~~~~~~~~~~~~~~CP~Cg~~l~~k~gr~G~F~~Cs~yp~C~~~~~l~~-~~~~---~~~~~~CpkCg~~l~ 744 (822)
T PRK07219 672 CPDCEAEKEEEDPDEVIGPCPKCGGELAIKQLKYGSFLGCTNYPKCKYTLPLPR-RGKI---TVTDEKCPECGLPLL 744 (822)
T ss_pred CCCCCCCccccccccccccCCCCCCeeEEEcCCCCCeeeCCCCCCCCceeeccc-cccc---ccccCCCCCCCCeEE
Confidence 88887664321 2346799999721 3333234888865 764333221 1000 124467888877654
No 97
>PRK00420 hypothetical protein; Validated
Probab=29.31 E-value=39 Score=27.59 Aligned_cols=20 Identities=25% Similarity=0.492 Sum_probs=12.1
Q ss_pred ccCCCCCCccc-----eEecCcccc
Q 027127 135 QVCVNCGVCMG-----EYFCESCKL 154 (228)
Q Consensus 135 ~~C~nCg~~Fa-----~YfC~iCkl 154 (228)
..||.||.+|- ..||+.|.-
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 57777877543 355666543
No 98
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=28.99 E-value=43 Score=23.79 Aligned_cols=9 Identities=44% Similarity=0.925 Sum_probs=5.4
Q ss_pred eeEcCCCCc
Q 027127 121 QVICSLCGT 129 (228)
Q Consensus 121 ~VlCg~C~t 129 (228)
.+||..|..
T Consensus 22 aLIC~~C~~ 30 (54)
T PF10058_consen 22 ALICSKCFS 30 (54)
T ss_pred eEECcccch
Confidence 566666654
No 99
>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=28.79 E-value=48 Score=22.11 Aligned_cols=11 Identities=45% Similarity=1.168 Sum_probs=5.3
Q ss_pred CCCeeecCCCC
Q 027127 160 SKKQYHCDGCG 170 (228)
Q Consensus 160 ~K~~yHC~~CG 170 (228)
.+.-|+|..|+
T Consensus 25 ~~~g~~C~~C~ 35 (53)
T PF00130_consen 25 GKQGYRCSWCG 35 (53)
T ss_dssp SSCEEEETTTT
T ss_pred CCCeEEECCCC
Confidence 34445555444
No 100
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.70 E-value=41 Score=34.14 Aligned_cols=50 Identities=24% Similarity=0.464 Sum_probs=32.7
Q ss_pred eEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCccccccccCCccc
Q 027127 146 EYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPC 200 (228)
Q Consensus 146 ~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~~l~~~HkC 200 (228)
-+||..|..|--| ..-.=.|+.||..+.||- ||+.||..++.....+-+|
T Consensus 126 ~~Yc~~~e~fl~d-r~v~g~cp~cg~~~arGD----~Ce~Cg~~~~P~~l~~p~~ 175 (558)
T COG0143 126 GLYCVSCERFLPD-RYVEGTCPKCGGEDARGD----QCENCGRTLDPTELINPVC 175 (558)
T ss_pred eeEcccccccccc-hheeccCCCcCccccCcc----hhhhccCcCCchhcCCCee
Confidence 3566666544221 234458999999998863 7999999998864333333
No 101
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=28.69 E-value=43 Score=21.73 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=4.3
Q ss_pred eeEcCCCCc
Q 027127 121 QVICSLCGT 129 (228)
Q Consensus 121 ~VlCg~C~t 129 (228)
.|.|+.|++
T Consensus 25 ~vrC~~C~~ 33 (37)
T PF13719_consen 25 KVRCPKCGH 33 (37)
T ss_pred EEECCCCCc
Confidence 455554443
No 102
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=28.58 E-value=33 Score=30.88 Aligned_cols=34 Identities=29% Similarity=0.618 Sum_probs=24.4
Q ss_pred CeeecCCCCcceecCCCceeeccccCccccccccCCcccc
Q 027127 162 KQYHCDGCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (228)
Q Consensus 162 ~~yHC~~CGICRvG~~~~ffHC~~C~~C~s~~l~~~HkCi 201 (228)
....|+.|.+-| ..-.-||..||.|+.. -+|.|.
T Consensus 112 ~~~~C~~C~~~r---PpRs~HCsvC~~CV~r---fDHHC~ 145 (299)
T KOG1311|consen 112 EWKYCDTCQLYR---PPRSSHCSVCNNCVLR---FDHHCP 145 (299)
T ss_pred ceEEcCcCcccC---CCCcccchhhcccccc---cCCCCC
Confidence 467777776654 4568899999999864 466664
No 103
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=28.25 E-value=35 Score=31.80 Aligned_cols=31 Identities=29% Similarity=0.594 Sum_probs=23.9
Q ss_pred CCCcceecCCCceeeccccCccccccccCCcccc
Q 027127 168 GCGICRIGGCDNFFHCNKCRCCYSMLLKNSHPCV 201 (228)
Q Consensus 168 ~CGICRvG~~~~ffHC~~C~~C~s~~l~~~HkCi 201 (228)
.|.-|+.-+.+-.-||..||.|+-. =+|.|+
T Consensus 111 ~C~~C~~~KP~RS~HC~~Cn~CV~k---~DHHC~ 141 (309)
T COG5273 111 FCSTCNIYKPPRSHHCSICNRCVLK---FDHHCP 141 (309)
T ss_pred eccccccccCCCCccchhhcchhhc---cCccCc
Confidence 4777888887888899999999754 467665
No 104
>PF01422 zf-NF-X1: NF-X1 type zinc finger; InterPro: IPR000967 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 domain presumed to be a zinc binding domain. The following pattern describes the zinc finger: C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C where X can be any amino acid, and numbers in brackets indicate the number of residues. The two position can be either His or Cys. This domain is found in the human transcriptional repressor NK-X1, a repressor of HLA-DRA transcription; the Drosophila shuttle craft protein, which plays an essential role during the late stages of embryonic neurogenesis; and a yeast hypothetical protein YNL023C. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=28.08 E-value=47 Score=19.66 Aligned_cols=19 Identities=26% Similarity=0.669 Sum_probs=15.7
Q ss_pred CCccccCCCCCCCCccccC
Q 027127 196 NSHPCVEGAMHHDCPVCCE 214 (228)
Q Consensus 196 ~~HkCiE~~~~~nCPIC~E 214 (228)
++|+|.+.--.++||-|.+
T Consensus 2 G~H~C~~~CH~G~C~pC~~ 20 (20)
T PF01422_consen 2 GNHTCQQLCHPGPCPPCPQ 20 (20)
T ss_pred CCcccCCcccCCcCCCCCC
Confidence 4799998888899998853
No 105
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=27.75 E-value=33 Score=27.33 Aligned_cols=19 Identities=32% Similarity=0.753 Sum_probs=14.4
Q ss_pred EcCCCCcccccc----ccCCCCC
Q 027127 123 ICSLCGTEQKVQ----QVCVNCG 141 (228)
Q Consensus 123 lCg~C~teQ~v~----~~C~nCg 141 (228)
-|+.|+..++.. +.|+||+
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 688888776653 5899996
No 106
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.62 E-value=62 Score=33.36 Aligned_cols=29 Identities=31% Similarity=0.700 Sum_probs=20.2
Q ss_pred CCCCC-CCeeEcCCCCccccccccCCCCCCccce
Q 027127 114 IPRHE-VNQVICSLCGTEQKVQQVCVNCGVCMGE 146 (228)
Q Consensus 114 ldR~~-vk~VlCg~C~teQ~v~~~C~nCg~~Fa~ 146 (228)
++|.. .+.++|..|+..- .|++|+..+.-
T Consensus 375 lnRrGyap~l~C~~Cg~~~----~C~~C~~~L~~ 404 (665)
T PRK14873 375 VPRRGYVPSLACARCRTPA----RCRHCTGPLGL 404 (665)
T ss_pred ecCCCCCCeeEhhhCcCee----ECCCCCCceeE
Confidence 35543 4678899998753 58999887763
No 107
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=27.19 E-value=70 Score=22.36 Aligned_cols=37 Identities=11% Similarity=0.367 Sum_probs=25.5
Q ss_pred ecCcchhhhhccCcCcCCcCCCCCCCCCCCeeEcCCCCccccc
Q 027127 91 FDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKV 133 (228)
Q Consensus 91 YpCR~CHDE~~~~~~~~~~~~H~ldR~~vk~VlCg~C~teQ~v 133 (228)
-.|..|-+-+. - ..+..+.++....+.||.|.++..+
T Consensus 7 v~C~~C~~lLq-l-----P~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 7 VVCSSCFELLQ-L-----PAKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred eECccHHHHHc-C-----CCccCCCccceeEEeCCCCceeEEE
Confidence 45666665542 1 2356777777889999999987655
No 108
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.14 E-value=42 Score=26.82 Aligned_cols=14 Identities=21% Similarity=0.499 Sum_probs=8.3
Q ss_pred ccccccCCCCCCcc
Q 027127 131 QKVQQVCVNCGVCM 144 (228)
Q Consensus 131 Q~v~~~C~nCg~~F 144 (228)
.|+.-.|..||..|
T Consensus 67 ~p~~~~C~~Cg~~~ 80 (114)
T PRK03681 67 QEAECWCETCQQYV 80 (114)
T ss_pred eCcEEEcccCCCee
Confidence 44555677777544
No 109
>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=26.92 E-value=49 Score=26.41 Aligned_cols=14 Identities=21% Similarity=0.532 Sum_probs=8.3
Q ss_pred ccccccCCCCCCcc
Q 027127 131 QKVQQVCVNCGVCM 144 (228)
Q Consensus 131 Q~v~~~C~nCg~~F 144 (228)
.|+...|.+||..|
T Consensus 67 ~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 67 EPVECECEDCSEEV 80 (115)
T ss_pred eCcEEEcccCCCEE
Confidence 45556676666554
No 110
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=26.34 E-value=73 Score=21.07 Aligned_cols=33 Identities=27% Similarity=0.661 Sum_probs=17.6
Q ss_pred cCCCCCCccceEecCccccc-cCCCCCCeeecCCCC
Q 027127 136 VCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 170 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~-Ddd~~K~~yHC~~CG 170 (228)
.|++||..-+.|| .+ -.. -|++..-.|-|.+||
T Consensus 2 ~Cp~C~~~~a~~~-q~-Q~RsaDE~mT~fy~C~~C~ 35 (40)
T smart00440 2 PCPKCGNREATFF-QL-QTRSADEPMTVFYVCTKCG 35 (40)
T ss_pred cCCCCCCCeEEEE-EE-cccCCCCCCeEEEEeCCCC
Confidence 4788887776665 10 111 223445566666665
No 111
>PLN03086 PRLI-interacting factor K; Provisional
Probab=26.22 E-value=45 Score=34.06 Aligned_cols=85 Identities=22% Similarity=0.536 Sum_probs=44.0
Q ss_pred CCCCeeEcCCCCccccc-------------cccCCC--CCCccceEecCccccccCCCCCCeeecCCCCcceecCC----
Q 027127 117 HEVNQVICSLCGTEQKV-------------QQVCVN--CGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGC---- 177 (228)
Q Consensus 117 ~~vk~VlCg~C~teQ~v-------------~~~C~n--Cg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~---- 177 (228)
..+..|.|..|...-+. ...|++ ||..|.+- .-+..+||+.||- ..+..
T Consensus 403 ~~~~~V~C~NC~~~i~l~~l~lHe~~C~r~~V~Cp~~~Cg~v~~r~-----------el~~H~~C~~Cgk-~f~~s~Lek 470 (567)
T PLN03086 403 MDVDTVECRNCKHYIPSRSIALHEAYCSRHNVVCPHDGCGIVLRVE-----------EAKNHVHCEKCGQ-AFQQGEMEK 470 (567)
T ss_pred CCCCeEECCCCCCccchhHHHHHHhhCCCcceeCCcccccceeecc-----------ccccCccCCCCCC-ccchHHHHH
Confidence 34668889999865332 134664 77766432 1234567777753 11210
Q ss_pred -----CceeeccccCccccccccCCcc---ccCCCCCCCCccccCcc
Q 027127 178 -----DNFFHCNKCRCCYSMLLKNSHP---CVEGAMHHDCPVCCEVI 216 (228)
Q Consensus 178 -----~~ffHC~~C~~C~s~~l~~~Hk---CiE~~~~~nCPIC~E~l 216 (228)
..-+-|. ||.-+.......|. |-++ ...|+.|...+
T Consensus 471 H~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~v 514 (567)
T PLN03086 471 HMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDMV 514 (567)
T ss_pred HHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCcc
Confidence 0123465 66544444445553 5443 24677776443
No 112
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.19 E-value=40 Score=24.88 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=13.2
Q ss_pred EcCCCCccccccccCCCCCCc
Q 027127 123 ICSLCGTEQKVQQVCVNCGVC 143 (228)
Q Consensus 123 lCg~C~teQ~v~~~C~nCg~~ 143 (228)
.|..|...++ .+.||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 5666666663 3468888874
No 113
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.81 E-value=33 Score=27.36 Aligned_cols=9 Identities=33% Similarity=0.634 Sum_probs=3.8
Q ss_pred eeEcCCCCc
Q 027127 121 QVICSLCGT 129 (228)
Q Consensus 121 ~VlCg~C~t 129 (228)
...|..|+.
T Consensus 70 ~~~C~~Cg~ 78 (113)
T PRK12380 70 QAWCWDCSQ 78 (113)
T ss_pred EEEcccCCC
Confidence 344444443
No 114
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=25.50 E-value=67 Score=21.87 Aligned_cols=12 Identities=42% Similarity=0.880 Sum_probs=7.9
Q ss_pred CCCeeecCCCCc
Q 027127 160 SKKQYHCDGCGI 171 (228)
Q Consensus 160 ~K~~yHC~~CGI 171 (228)
.+.+..|+.||-
T Consensus 16 ~~~~irC~~CG~ 27 (44)
T smart00659 16 SKDVVRCRECGY 27 (44)
T ss_pred CCCceECCCCCc
Confidence 356677777773
No 115
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.43 E-value=42 Score=28.23 Aligned_cols=19 Identities=42% Similarity=1.127 Sum_probs=13.0
Q ss_pred ccCCCCCCcc----ceEecCccc
Q 027127 135 QVCVNCGVCM----GEYFCESCK 153 (228)
Q Consensus 135 ~~C~nCg~~F----a~YfC~iCk 153 (228)
..|+.||.++ |+-||++|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 5678887764 566777774
No 116
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=25.25 E-value=54 Score=22.79 Aligned_cols=29 Identities=31% Similarity=0.794 Sum_probs=13.3
Q ss_pred cCCCCCCccceEecCccccccCCCCCCeeecCCCCc
Q 027127 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 136 ~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGI 171 (228)
.|.+|+.... -+|-..+.....-|+.||+
T Consensus 5 ~C~~C~~~~T-------~~WR~g~~g~~~LCnaCgl 33 (52)
T smart00401 5 SCSNCGTTET-------PLWRRGPSGNKTLCNACGL 33 (52)
T ss_pred CcCCCCCCCC-------CccccCCCCCCcEeecccH
Confidence 4566655443 2343333333444555553
No 117
>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=24.81 E-value=62 Score=24.72 Aligned_cols=8 Identities=50% Similarity=1.597 Sum_probs=3.5
Q ss_pred eeeccccC
Q 027127 180 FFHCNKCR 187 (228)
Q Consensus 180 ffHC~~C~ 187 (228)
||.|..||
T Consensus 90 fy~C~~C~ 97 (104)
T TIGR01384 90 FYKCTKCG 97 (104)
T ss_pred EEEeCCCC
Confidence 44444443
No 118
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=24.73 E-value=4.4 Score=29.43 Aligned_cols=46 Identities=17% Similarity=0.551 Sum_probs=26.3
Q ss_pred CccceEecCccccccCCCCCCeeecCCCCcceecC-----CCceeeccccCccccc
Q 027127 142 VCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGG-----CDNFFHCNKCRCCYSM 192 (228)
Q Consensus 142 ~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~-----~~~ffHC~~C~~C~s~ 192 (228)
++|++|.|+.|+-- -+.+..-.|. +|-.++ .+.|+-|..||-=+.+
T Consensus 3 ~SFsry~CDLCn~~--~p~~~LRQCv---lCGRWaC~sCW~deYY~CksC~Gii~l 53 (57)
T PF14445_consen 3 HSFSRYSCDLCNSS--HPISELRQCV---LCGRWACNSCWQDEYYTCKSCNGIINL 53 (57)
T ss_pred hHHhhHhHHhhccc--CcHHHHHHHh---hhchhhhhhhhhhhHhHHHhhhchhhh
Confidence 46888888888732 1222333333 333332 5678888888765444
No 119
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=24.71 E-value=54 Score=23.69 Aligned_cols=34 Identities=29% Similarity=0.506 Sum_probs=19.7
Q ss_pred eeEcCCCCccccc------cccCCCCCCccceEecCcccc
Q 027127 121 QVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKL 154 (228)
Q Consensus 121 ~VlCg~C~teQ~v------~~~C~nCg~~Fa~YfC~iCkl 154 (228)
.|.|..|..+|-+ ...|..||..+++-.=++-+|
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l 46 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARL 46 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEE
Confidence 5778888888766 136888888777665444444
No 120
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=24.62 E-value=47 Score=28.46 Aligned_cols=13 Identities=15% Similarity=0.649 Sum_probs=11.5
Q ss_pred ccCCCCCCccceE
Q 027127 135 QVCVNCGVCMGEY 147 (228)
Q Consensus 135 ~~C~nCg~~Fa~Y 147 (228)
-.|++||..|..|
T Consensus 29 ReC~~C~~RFTTy 41 (147)
T TIGR00244 29 RECLECHERFTTF 41 (147)
T ss_pred ccCCccCCcccee
Confidence 4699999999998
No 121
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=24.01 E-value=30 Score=24.40 Aligned_cols=18 Identities=28% Similarity=0.717 Sum_probs=9.3
Q ss_pred cccCCCCCCeeecCCCCc
Q 027127 154 LFDDDTSKKQYHCDGCGI 171 (228)
Q Consensus 154 l~Ddd~~K~~yHC~~CGI 171 (228)
+|-..+.....-|+.||+
T Consensus 12 ~WR~g~~~~~~LCNaCgl 29 (54)
T cd00202 12 LWRRGPSGGSTLCNACGL 29 (54)
T ss_pred ccccCCCCcchHHHHHHH
Confidence 555544444555555554
No 122
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.95 E-value=31 Score=21.45 Aligned_cols=21 Identities=33% Similarity=0.846 Sum_probs=9.6
Q ss_pred EcCCCCccccc-----cccCCCCCCc
Q 027127 123 ICSLCGTEQKV-----QQVCVNCGVC 143 (228)
Q Consensus 123 lCg~C~teQ~v-----~~~C~nCg~~ 143 (228)
.|+.|+.+... +..|++||..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 57777765332 3467777753
No 123
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=23.90 E-value=52 Score=27.17 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=19.1
Q ss_pred CCCeeEcCCCCccccc---cccCCCCCCcc
Q 027127 118 EVNQVICSLCGTEQKV---QQVCVNCGVCM 144 (228)
Q Consensus 118 ~vk~VlCg~C~teQ~v---~~~C~nCg~~F 144 (228)
....|.|..|+++-.. .+.|.+|+.++
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pL 95 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPL 95 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcC
Confidence 3467888888877443 46888887765
No 124
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=23.80 E-value=62 Score=21.73 Aligned_cols=24 Identities=46% Similarity=1.006 Sum_probs=12.5
Q ss_pred CeeecCCCCcceecCCCceeeccccC
Q 027127 162 KQYHCDGCGICRIGGCDNFFHCNKCR 187 (228)
Q Consensus 162 ~~yHC~~CGICRvG~~~~ffHC~~C~ 187 (228)
..|.|+.||..-+.| ..|||.+|-
T Consensus 3 ~~~~C~~C~~~~i~g--~Ry~C~~C~ 26 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIG--VRYHCLVCP 26 (46)
T ss_dssp SSCE-SSS-SSSEES--SEEEESSSS
T ss_pred CCeECcCCCCCcCcC--CeEECCCCC
Confidence 456777777644333 357777653
No 125
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.68 E-value=38 Score=24.37 Aligned_cols=12 Identities=17% Similarity=0.553 Sum_probs=10.7
Q ss_pred ceecCCCCCeec
Q 027127 81 RIRAPCCNEIFD 92 (228)
Q Consensus 81 kIr~pCC~k~Yp 92 (228)
.|+||-|+++||
T Consensus 53 ~L~Cp~c~r~YP 64 (68)
T PF03966_consen 53 ELICPECGREYP 64 (68)
T ss_dssp EEEETTTTEEEE
T ss_pred EEEcCCCCCEEe
Confidence 489999999997
No 126
>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=23.62 E-value=40 Score=21.44 Aligned_cols=22 Identities=36% Similarity=0.738 Sum_probs=11.4
Q ss_pred eeEcCCCCcccc-ccccCCCCCC
Q 027127 121 QVICSLCGTEQK-VQQVCVNCGV 142 (228)
Q Consensus 121 ~VlCg~C~teQ~-v~~~C~nCg~ 142 (228)
.-.|..|++.+- +...|++||.
T Consensus 11 ~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEE-TTT--EEES--SEETTTT-
T ss_pred EEEcCCCCCEecCCCcCCCCcCc
Confidence 556888887754 4667888864
No 127
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=23.47 E-value=77 Score=20.92 Aligned_cols=23 Identities=30% Similarity=0.691 Sum_probs=17.4
Q ss_pred eeeccccC--ccccccccCCccccC
Q 027127 180 FFHCNKCR--CCYSMLLKNSHPCVE 202 (228)
Q Consensus 180 ffHC~~C~--~C~s~~l~~~HkCiE 202 (228)
-|.|..|+ .|.+-.+.+.|.|..
T Consensus 12 ~f~C~~C~~~FC~~HR~~e~H~C~~ 36 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLPEDHDCPG 36 (39)
T ss_pred CeECCccCCccccccCCccccCCcc
Confidence 46777776 488888889998864
No 128
>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=23.24 E-value=58 Score=22.07 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=6.6
Q ss_pred ccCCCCCCccc
Q 027127 135 QVCVNCGVCMG 145 (228)
Q Consensus 135 ~~C~nCg~~Fa 145 (228)
..|+.||.++-
T Consensus 18 ~~Cp~C~~PL~ 28 (41)
T PF06677_consen 18 EHCPDCGTPLM 28 (41)
T ss_pred CccCCCCCeeE
Confidence 46666766543
No 129
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=23.18 E-value=20 Score=33.87 Aligned_cols=53 Identities=15% Similarity=0.167 Sum_probs=38.6
Q ss_pred ccCCCCCCccceEecCccccccCCCCCCeeecCCCCcceecCCCceeeccccCcccc
Q 027127 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRIGGCDNFFHCNKCRCCYS 191 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~~CGICRvG~~~~ffHC~~C~~C~s 191 (228)
..|+-|....+.-+|.||--+|.. . -|||.|.-||.-.+...-||..|..|..
T Consensus 250 i~C~~~~~~A~~~~C~iC~~~~~~---R-~~C~~~kA~~~~~Q~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 250 IHCSICNHCAVKHGCFICGELDHK---R-STCPNIKAVRKQKQRKSNKMKMETTKGQ 302 (325)
T ss_pred eeeecccchhhhcceeeccccccc---c-ccCccHHHHHHHHhcccchhhhhhhhhh
Confidence 356667777778889999888663 2 7899998888776555667777776654
No 130
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=23.17 E-value=90 Score=21.47 Aligned_cols=7 Identities=43% Similarity=0.933 Sum_probs=4.3
Q ss_pred cCCCCCC
Q 027127 136 VCVNCGV 142 (228)
Q Consensus 136 ~C~nCg~ 142 (228)
.||.||.
T Consensus 3 PCPfCGg 9 (53)
T TIGR03655 3 PCPFCGG 9 (53)
T ss_pred CCCCCCC
Confidence 4666665
No 131
>PLN00209 ribosomal protein S27; Provisional
Probab=23.15 E-value=56 Score=25.78 Aligned_cols=36 Identities=22% Similarity=0.365 Sum_probs=25.0
Q ss_pred eeEcCCCCccccc------cccCCCCCCccceEecCcccccc
Q 027127 121 QVICSLCGTEQKV------QQVCVNCGVCMGEYFCESCKLFD 156 (228)
Q Consensus 121 ~VlCg~C~teQ~v------~~~C~nCg~~Fa~YfC~iCkl~D 156 (228)
.|.|..|..+|.+ ...|..||..+++-.=++.+|-+
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 77 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTE 77 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 6788888888766 13688888887776666655543
No 132
>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=23.07 E-value=1e+02 Score=29.10 Aligned_cols=26 Identities=31% Similarity=0.648 Sum_probs=21.5
Q ss_pred CCeeEcCCCCccccc-cccCCCCCCcc
Q 027127 119 VNQVICSLCGTEQKV-QQVCVNCGVCM 144 (228)
Q Consensus 119 vk~VlCg~C~teQ~v-~~~C~nCg~~F 144 (228)
.+-..|+.|+++=.+ -..|++||..-
T Consensus 208 ~RyL~CslC~teW~~~R~~C~~Cg~~~ 234 (305)
T TIGR01562 208 LRYLSCSLCATEWHYVRVKCSHCEESK 234 (305)
T ss_pred ceEEEcCCCCCcccccCccCCCCCCCC
Confidence 468999999999776 46899999863
No 133
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=22.65 E-value=51 Score=29.33 Aligned_cols=23 Identities=35% Similarity=0.943 Sum_probs=13.7
Q ss_pred cccCCCCCCccceEe--cCcccccc
Q 027127 134 QQVCVNCGVCMGEYF--CESCKLFD 156 (228)
Q Consensus 134 ~~~C~nCg~~Fa~Yf--C~iCkl~D 156 (228)
...|.+||...-.|+ |+.|.=|+
T Consensus 354 ~~~c~~cg~~~~~~~~~c~~c~~~~ 378 (389)
T PRK11788 354 RYRCRNCGFTARTLYWHCPSCKAWE 378 (389)
T ss_pred CEECCCCCCCCccceeECcCCCCcc
Confidence 356777776666554 55555554
No 134
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.63 E-value=59 Score=28.12 Aligned_cols=24 Identities=25% Similarity=0.683 Sum_probs=14.7
Q ss_pred cccCCCCCCcc-ceEecCccccccC
Q 027127 134 QQVCVNCGVCM-GEYFCESCKLFDD 157 (228)
Q Consensus 134 ~~~C~nCg~~F-a~YfC~iCkl~Dd 157 (228)
++.|+.||... ..+.|+.|.+..|
T Consensus 309 S~~C~~cg~~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 309 SKTCPCCGHLSGRLFKCPRCGFVHD 333 (364)
T ss_pred cccccccCCccceeEECCCCCCeeh
Confidence 57888888822 2355666665433
No 135
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.56 E-value=61 Score=26.66 Aligned_cols=8 Identities=50% Similarity=1.294 Sum_probs=3.2
Q ss_pred CccccCcc
Q 027127 209 CPVCCEVI 216 (228)
Q Consensus 209 CPIC~E~l 216 (228)
||.|+..|
T Consensus 126 Cp~Cg~~l 133 (147)
T smart00531 126 CPRCGEEL 133 (147)
T ss_pred CCCCCCEE
Confidence 44444333
No 136
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.18 E-value=67 Score=26.15 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=17.0
Q ss_pred CeeecCCCC-----cceecC--CCceeeccccCc
Q 027127 162 KQYHCDGCG-----ICRIGG--CDNFFHCNKCRC 188 (228)
Q Consensus 162 ~~yHC~~CG-----ICRvG~--~~~ffHC~~C~~ 188 (228)
..|-|+.|| +|.|-. ..-+-+|..||.
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 456666666 566553 345777777775
No 137
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.15 E-value=93 Score=31.84 Aligned_cols=23 Identities=22% Similarity=0.631 Sum_probs=17.8
Q ss_pred CCeeEcCCCCccccccccCCCCCCccc
Q 027127 119 VNQVICSLCGTEQKVQQVCVNCGVCMG 145 (228)
Q Consensus 119 vk~VlCg~C~teQ~v~~~C~nCg~~Fa 145 (228)
.+.+.|..|+... .|++|+..+.
T Consensus 379 ~~~~~C~~Cg~~~----~C~~C~~~l~ 401 (679)
T PRK05580 379 APFLLCRDCGWVA----ECPHCDASLT 401 (679)
T ss_pred CCceEhhhCcCcc----CCCCCCCcee
Confidence 4578899998754 5899998774
No 138
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=21.79 E-value=33 Score=23.23 Aligned_cols=9 Identities=44% Similarity=1.220 Sum_probs=3.5
Q ss_pred CccccCccccC
Q 027127 209 CPVCCEVIHYN 219 (228)
Q Consensus 209 CPIC~E~lFtS 219 (228)
||||.| |++
T Consensus 1 CpIc~e--~~~ 9 (43)
T PF13445_consen 1 CPICKE--FST 9 (43)
T ss_dssp -TTT------T
T ss_pred CCcccc--ccC
Confidence 899999 666
No 139
>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]
Probab=21.73 E-value=41 Score=26.75 Aligned_cols=15 Identities=20% Similarity=0.649 Sum_probs=12.5
Q ss_pred CceeeccccCccccc
Q 027127 178 DNFFHCNKCRCCYSM 192 (228)
Q Consensus 178 ~~ffHC~~C~~C~s~ 192 (228)
.||-+|+.||.|...
T Consensus 63 idYdyCKGCGICa~v 77 (91)
T COG1144 63 IDYDYCKGCGICANV 77 (91)
T ss_pred eEcccccCceechhh
Confidence 588999999999764
No 140
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=21.42 E-value=54 Score=32.75 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=5.9
Q ss_pred eeccccCcccccc
Q 027127 181 FHCNKCRCCYSML 193 (228)
Q Consensus 181 fHC~~C~~C~s~~ 193 (228)
+||..||+=+|++
T Consensus 428 Y~CEDCg~~LS~e 440 (468)
T KOG1701|consen 428 YKCEDCGLLLSSE 440 (468)
T ss_pred eehhhcCcccccc
Confidence 4444444444443
No 141
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=21.32 E-value=47 Score=32.98 Aligned_cols=9 Identities=44% Similarity=1.641 Sum_probs=4.2
Q ss_pred CeeecCCCC
Q 027127 162 KQYHCDGCG 170 (228)
Q Consensus 162 ~~yHC~~CG 170 (228)
..|||..||
T Consensus 152 ~~F~C~~C~ 160 (436)
T KOG2593|consen 152 GEFHCENCG 160 (436)
T ss_pred ceEEEecCC
Confidence 345554443
No 142
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=21.22 E-value=27 Score=27.77 Aligned_cols=40 Identities=25% Similarity=0.762 Sum_probs=22.1
Q ss_pred eEcCCCCccc----cccccCCCCCCccceEecCccccccCCCCCCeeecC
Q 027127 122 VICSLCGTEQ----KVQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCD 167 (228)
Q Consensus 122 VlCg~C~teQ----~v~~~C~nCg~~Fa~YfC~iCkl~Ddd~~K~~yHC~ 167 (228)
-.|..|+++- ..+..|..|+. +.|..|..+ ..++..|.|.
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~~----~VC~~C~~~--~~~~~~WlC~ 98 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCKH----RVCKKCGVY--SKKEPIWLCK 98 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTTE----EEETTSEEE--TSSSCCEEEH
T ss_pred cchhhhCCcccccCCCCCcCCcCCc----cccCccCCc--CCCCCCEECh
Confidence 3677776542 12456777764 467778777 2345566553
No 143
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.17 E-value=28 Score=33.37 Aligned_cols=20 Identities=30% Similarity=0.815 Sum_probs=17.2
Q ss_pred ccCCCCCCccceEecCcccccc
Q 027127 135 QVCVNCGVCMGEYFCESCKLFD 156 (228)
Q Consensus 135 ~~C~nCg~~Fa~YfC~iCkl~D 156 (228)
..|..||+.|+ +|+||+-|-
T Consensus 322 VtCt~CGkrm~--eCPICRqyi 341 (350)
T KOG4275|consen 322 VTCTKCGKRMN--ECPICRQYI 341 (350)
T ss_pred Eeehhhccccc--cCchHHHHH
Confidence 57899999999 999998663
No 144
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.96 E-value=46 Score=19.92 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=9.2
Q ss_pred ccCCCCCCccce
Q 027127 135 QVCVNCGVCMGE 146 (228)
Q Consensus 135 ~~C~nCg~~Fa~ 146 (228)
..|+.||..|+.
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 368899988863
No 145
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.83 E-value=63 Score=26.53 Aligned_cols=8 Identities=38% Similarity=1.074 Sum_probs=4.9
Q ss_pred eeecCCCC
Q 027127 163 QYHCDGCG 170 (228)
Q Consensus 163 ~yHC~~CG 170 (228)
.+.||.||
T Consensus 107 ~~~CP~Cg 114 (135)
T PRK03824 107 FLKCPKCG 114 (135)
T ss_pred CcCCcCCC
Confidence 35566666
No 146
>PRK12496 hypothetical protein; Provisional
Probab=20.78 E-value=45 Score=28.31 Aligned_cols=24 Identities=25% Similarity=0.593 Sum_probs=15.7
Q ss_pred eEcCCCCcccc---ccccCCCCCCccc
Q 027127 122 VICSLCGTEQK---VQQVCVNCGVCMG 145 (228)
Q Consensus 122 VlCg~C~teQ~---v~~~C~nCg~~Fa 145 (228)
..|..|+++-+ ..+.|+.||.+.-
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhh
Confidence 45888887653 3456888887653
No 147
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=20.65 E-value=69 Score=23.22 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=6.4
Q ss_pred CCCeeecCCCCc
Q 027127 160 SKKQYHCDGCGI 171 (228)
Q Consensus 160 ~K~~yHC~~CGI 171 (228)
....|-|++|||
T Consensus 11 ~~v~~~Cp~cGi 22 (55)
T PF13824_consen 11 AHVNFECPDCGI 22 (55)
T ss_pred cccCCcCCCCCC
Confidence 344555555554
No 148
>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=20.52 E-value=89 Score=20.73 Aligned_cols=21 Identities=48% Similarity=1.099 Sum_probs=11.6
Q ss_pred eeecCCCCcceecCCCceeecccc
Q 027127 163 QYHCDGCGICRIGGCDNFFHCNKC 186 (228)
Q Consensus 163 ~yHC~~CGICRvG~~~~ffHC~~C 186 (228)
.+.|+.||. -+.| ..|||..|
T Consensus 4 ~~~C~~C~~-~i~g--~ry~C~~C 24 (44)
T smart00291 4 SYSCDTCGK-PIVG--VRYHCLVC 24 (44)
T ss_pred CcCCCCCCC-CCcC--CEEECCCC
Confidence 456777766 3332 24576665
No 149
>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=20.46 E-value=75 Score=22.05 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=6.6
Q ss_pred eEecCccccc
Q 027127 146 EYFCESCKLF 155 (228)
Q Consensus 146 ~YfC~iCkl~ 155 (228)
+|.|.+|.+.
T Consensus 1 ky~C~~Cgyv 10 (47)
T PF00301_consen 1 KYQCPVCGYV 10 (47)
T ss_dssp EEEETTTSBE
T ss_pred CcCCCCCCEE
Confidence 5777777643
Done!