Query 029670
Match_columns 190
No_of_seqs 123 out of 463
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 16:38:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029670.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029670hhsearch_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 99.9 4.9E-27 1.1E-31 206.8 0.4 108 61-178 23-130 (276)
2 PF05495 zf-CHY: CHY zinc fing 99.9 3.6E-25 7.7E-30 159.4 3.4 70 73-156 1-71 (71)
3 COG4357 Zinc finger domain con 99.8 6.6E-20 1.4E-24 141.3 1.7 77 70-154 12-96 (105)
4 PRK14890 putative Zn-ribbon RN 94.9 0.018 3.8E-07 41.2 2.1 46 120-171 6-56 (59)
5 PF12773 DZR: Double zinc ribb 93.0 0.089 1.9E-06 34.5 2.4 22 124-145 1-23 (50)
6 PF07191 zinc-ribbons_6: zinc- 92.7 0.063 1.4E-06 39.5 1.5 36 120-155 16-59 (70)
7 COG2888 Predicted Zn-ribbon RN 92.7 0.066 1.4E-06 38.6 1.5 45 121-171 9-58 (61)
8 PRK04023 DNA polymerase II lar 92.2 0.12 2.5E-06 53.9 3.1 46 120-171 625-671 (1121)
9 TIGR00595 priA primosomal prot 90.8 0.17 3.7E-06 48.1 2.5 49 82-143 214-262 (505)
10 PF09538 FYDLN_acid: Protein o 90.5 0.15 3.2E-06 40.0 1.6 25 135-171 10-34 (108)
11 PRK14559 putative protein seri 90.0 0.22 4.9E-06 49.2 2.7 46 122-170 2-48 (645)
12 PRK14714 DNA polymerase II lar 88.6 0.45 9.8E-06 50.6 3.8 50 120-171 666-717 (1337)
13 PF10571 UPF0547: Uncharacteri 87.9 0.32 6.9E-06 29.3 1.4 24 123-146 2-26 (26)
14 PF13248 zf-ribbon_3: zinc-rib 87.9 0.23 4.9E-06 29.4 0.7 24 121-144 2-26 (26)
15 PRK14890 putative Zn-ribbon RN 86.2 0.66 1.4E-05 33.3 2.4 35 119-155 23-57 (59)
16 COG1198 PriA Primosomal protei 86.2 0.63 1.4E-05 46.9 3.1 53 82-147 436-488 (730)
17 PHA00626 hypothetical protein 86.1 0.57 1.2E-05 33.6 2.0 6 137-142 3-8 (59)
18 PRK05580 primosome assembly pr 84.9 0.62 1.3E-05 45.8 2.4 49 82-143 382-430 (679)
19 PRK14873 primosome assembly pr 84.7 0.62 1.3E-05 46.2 2.3 48 82-143 384-431 (665)
20 TIGR02300 FYDLN_acid conserved 84.0 0.59 1.3E-05 38.1 1.5 25 135-171 10-34 (129)
21 PF13240 zinc_ribbon_2: zinc-r 83.1 0.6 1.3E-05 27.2 0.9 21 124-144 2-23 (23)
22 PRK14714 DNA polymerase II lar 82.0 0.88 1.9E-05 48.5 2.2 33 135-171 668-700 (1337)
23 PF05191 ADK_lid: Adenylate ki 78.2 0.7 1.5E-05 29.6 0.0 27 136-171 3-29 (36)
24 PF07282 OrfB_Zn_ribbon: Putat 77.5 1.8 4E-05 29.9 2.0 26 135-171 29-54 (69)
25 PF12773 DZR: Double zinc ribb 76.6 1.9 4.2E-05 28.1 1.8 32 121-152 12-49 (50)
26 PRK14559 putative protein seri 75.0 1.7 3.6E-05 43.3 1.7 34 121-155 15-50 (645)
27 KOG1940 Zn-finger protein [Gen 74.7 2.2 4.7E-05 38.6 2.2 50 48-98 150-204 (276)
28 COG2888 Predicted Zn-ribbon RN 71.5 3.1 6.8E-05 30.0 2.0 39 115-155 21-59 (61)
29 COG1198 PriA Primosomal protei 71.4 4.4 9.6E-05 41.0 3.7 46 118-171 432-483 (730)
30 PF04216 FdhE: Protein involve 71.3 2.4 5.3E-05 37.2 1.7 48 119-170 195-245 (290)
31 PF13453 zf-TFIIB: Transcripti 71.1 2.8 6E-05 26.9 1.5 26 136-170 1-26 (41)
32 smart00659 RPOLCX RNA polymera 70.7 2.5 5.5E-05 28.1 1.3 21 123-143 4-28 (44)
33 PF07754 DUF1610: Domain of un 70.1 4.1 8.8E-05 24.4 1.9 9 162-170 15-23 (24)
34 PF14353 CpXC: CpXC protein 68.3 4.4 9.5E-05 31.3 2.4 9 162-170 37-45 (128)
35 PF08271 TF_Zn_Ribbon: TFIIB z 68.1 4.1 9E-05 26.2 1.9 11 160-170 16-26 (43)
36 PRK00398 rpoP DNA-directed RNA 67.8 4.5 9.8E-05 26.4 2.0 8 163-170 21-28 (46)
37 PHA00626 hypothetical protein 67.7 3.7 8E-05 29.5 1.6 33 122-156 1-33 (59)
38 PF01529 zf-DHHC: DHHC palmito 65.8 4.8 0.0001 31.6 2.2 35 138-175 40-74 (174)
39 TIGR00595 priA primosomal prot 65.5 6.6 0.00014 37.5 3.4 47 118-172 210-262 (505)
40 PF03833 PolC_DP2: DNA polymer 65.2 2.1 4.5E-05 44.2 0.0 45 121-171 655-700 (900)
41 PRK00432 30S ribosomal protein 64.2 5 0.00011 27.3 1.7 12 160-171 34-45 (50)
42 TIGR00373 conserved hypothetic 64.2 1.9 4E-05 35.3 -0.4 25 136-170 111-135 (158)
43 smart00661 RPOL9 RNA polymeras 64.1 6.6 0.00014 25.5 2.3 9 162-170 19-27 (52)
44 PRK04023 DNA polymerase II lar 63.4 4.4 9.6E-05 42.7 1.9 36 122-157 639-674 (1121)
45 PF04438 zf-HIT: HIT zinc fing 63.0 3.6 7.9E-05 25.3 0.8 17 136-153 4-20 (30)
46 PF06524 NOA36: NOA36 protein; 62.7 2.9 6.3E-05 38.2 0.5 68 88-171 140-217 (314)
47 smart00778 Prim_Zn_Ribbon Zinc 62.0 8.7 0.00019 24.9 2.5 28 135-171 4-33 (37)
48 PRK06266 transcription initiat 61.9 2.3 5.1E-05 35.5 -0.3 10 136-145 119-128 (178)
49 cd00350 rubredoxin_like Rubred 59.7 7.4 0.00016 24.0 1.8 25 146-171 1-25 (33)
50 PF09723 Zn-ribbon_8: Zinc rib 58.4 5.1 0.00011 26.0 0.9 11 161-171 24-34 (42)
51 PF15616 TerY-C: TerY-C metal 57.6 7.9 0.00017 31.5 2.1 34 135-170 78-112 (131)
52 PF01096 TFIIS_C: Transcriptio 57.5 6.3 0.00014 25.3 1.2 33 136-170 2-35 (39)
53 KOG4317 Predicted Zn-finger pr 56.8 5 0.00011 37.6 0.9 21 135-155 8-28 (383)
54 PF13717 zinc_ribbon_4: zinc-r 55.7 8.6 0.00019 24.3 1.6 10 82-91 3-12 (36)
55 KOG1311 DHHC-type Zn-finger pr 55.5 7.4 0.00016 34.0 1.8 32 141-175 108-139 (299)
56 PF13719 zinc_ribbon_5: zinc-r 55.1 8.8 0.00019 24.3 1.6 9 136-144 27-35 (37)
57 TIGR00100 hypA hydrogenase nic 53.8 6.5 0.00014 30.6 1.0 12 134-145 70-81 (115)
58 KOG2462 C2H2-type Zn-finger pr 53.6 13 0.00028 33.9 2.9 52 119-170 159-250 (279)
59 PRK07219 DNA topoisomerase I; 51.6 18 0.00039 36.7 3.9 22 149-170 672-695 (822)
60 smart00834 CxxC_CXXC_SSSS Puta 51.6 8.3 0.00018 23.8 1.0 9 163-171 26-34 (41)
61 COG5273 Uncharacterized protei 51.2 7.8 0.00017 35.0 1.2 38 135-175 98-135 (309)
62 TIGR01206 lysW lysine biosynth 49.5 16 0.00034 25.5 2.2 26 136-170 4-29 (54)
63 smart00064 FYVE Protein presen 49.3 12 0.00025 25.7 1.6 11 135-145 11-21 (68)
64 PRK00420 hypothetical protein; 48.8 11 0.00023 30.0 1.5 21 135-155 24-49 (112)
65 PF03833 PolC_DP2: DNA polymer 48.1 6 0.00013 41.0 0.0 33 135-171 656-688 (900)
66 PRK00464 nrdR transcriptional 47.8 9.7 0.00021 31.5 1.2 12 136-147 30-41 (154)
67 TIGR02098 MJ0042_CXXC MJ0042 f 47.7 14 0.00029 22.9 1.6 8 136-143 27-34 (38)
68 PF03604 DNA_RNApol_7kD: DNA d 47.6 12 0.00025 23.6 1.2 11 160-170 14-24 (32)
69 COG1996 RPC10 DNA-directed RNA 47.2 12 0.00025 25.9 1.3 29 145-173 5-34 (49)
70 PF01363 FYVE: FYVE zinc finge 46.6 14 0.00031 25.3 1.7 23 135-170 10-32 (69)
71 PF12760 Zn_Tnp_IS1595: Transp 45.4 21 0.00046 23.3 2.3 26 135-170 19-44 (46)
72 PF14803 Nudix_N_2: Nudix N-te 45.2 18 0.00038 23.0 1.8 29 136-171 2-30 (34)
73 PRK00415 rps27e 30S ribosomal 42.7 18 0.0004 25.9 1.8 34 120-153 10-49 (59)
74 PRK03564 formate dehydrogenase 42.6 24 0.00052 32.4 3.0 47 118-170 209-259 (309)
75 COG1327 Predicted transcriptio 42.5 11 0.00025 31.6 0.8 13 135-147 29-41 (156)
76 TIGR00244 transcriptional regu 41.6 15 0.00032 30.6 1.3 14 135-148 29-42 (147)
77 PRK12380 hydrogenase nickel in 40.0 14 0.00031 28.6 1.0 11 135-145 71-81 (113)
78 PRK00564 hypA hydrogenase nick 39.6 19 0.0004 28.1 1.6 14 132-145 69-82 (117)
79 COG1645 Uncharacterized Zn-fin 39.4 16 0.00034 29.9 1.2 19 135-153 29-51 (131)
80 PF08792 A2L_zn_ribbon: A2L zi 39.2 20 0.00043 22.5 1.4 23 122-144 4-31 (33)
81 cd00065 FYVE FYVE domain; Zinc 38.5 20 0.00044 23.5 1.4 10 136-145 4-13 (57)
82 PRK05580 primosome assembly pr 38.5 31 0.00068 34.2 3.3 47 118-172 378-430 (679)
83 TIGR02605 CxxC_CxxC_SSSS putat 38.1 17 0.00037 23.8 1.0 9 163-171 26-34 (52)
84 PF09297 zf-NADH-PPase: NADH p 38.1 14 0.0003 22.5 0.5 21 123-143 5-30 (32)
85 TIGR01384 TFS_arch transcripti 37.8 23 0.00049 26.4 1.8 9 136-144 2-10 (104)
86 PF03107 C1_2: C1 domain; Int 37.2 27 0.00058 21.0 1.7 8 163-170 15-22 (30)
87 PF11023 DUF2614: Protein of u 37.1 22 0.00047 28.6 1.6 29 117-145 65-96 (114)
88 KOG2593 Transcription initiati 36.9 18 0.0004 34.8 1.4 31 136-170 130-160 (436)
89 PF01599 Ribosomal_S27: Riboso 36.9 19 0.00042 24.6 1.1 21 134-154 18-46 (47)
90 PF01155 HypA: Hydrogenase exp 36.9 17 0.00036 28.1 0.9 23 121-143 70-95 (113)
91 PF12675 DUF3795: Protein of u 36.2 20 0.00042 25.9 1.1 36 135-170 35-70 (78)
92 smart00531 TFIIE Transcription 36.0 11 0.00024 30.1 -0.2 11 135-145 100-110 (147)
93 KOG3362 Predicted BBOX Zn-fing 35.3 12 0.00025 31.6 -0.2 19 121-141 118-136 (156)
94 PF08274 PhnA_Zn_Ribbon: PhnA 34.5 19 0.00041 22.4 0.7 23 136-170 4-26 (30)
95 PF11331 DUF3133: Protein of u 34.0 40 0.00087 22.9 2.3 37 92-134 8-44 (46)
96 PF00130 C1_1: Phorbol esters/ 33.2 40 0.00086 21.8 2.2 25 147-171 12-36 (53)
97 smart00440 ZnF_C2C2 C2C2 Zinc 33.2 36 0.00078 21.9 1.9 33 136-170 2-35 (40)
98 KOG1701 Focal adhesion adaptor 33.2 22 0.00048 34.5 1.3 10 162-171 426-435 (468)
99 TIGR01562 FdhE formate dehydro 33.2 47 0.001 30.4 3.3 48 118-170 207-259 (305)
100 PRK12496 hypothetical protein; 32.9 21 0.00045 29.5 0.9 23 122-144 128-153 (164)
101 PF02150 RNA_POL_M_15KD: RNA p 32.9 23 0.00051 22.3 1.0 24 147-171 2-28 (35)
102 PRK01103 formamidopyrimidine/5 32.5 25 0.00054 30.8 1.4 18 83-100 167-184 (274)
103 PF13913 zf-C2HC_2: zinc-finge 32.0 20 0.00044 20.9 0.5 11 136-146 4-14 (25)
104 COG1998 RPS31 Ribosomal protei 31.9 29 0.00063 24.3 1.4 12 160-171 34-45 (51)
105 COG2051 RPS27A Ribosomal prote 31.4 27 0.00059 25.7 1.2 28 120-147 18-51 (67)
106 cd00729 rubredoxin_SM Rubredox 30.9 36 0.00078 21.3 1.6 25 146-171 2-26 (34)
107 PF05502 Dynactin_p62: Dynacti 30.6 27 0.00058 33.6 1.4 49 89-153 4-59 (483)
108 cd07973 Spt4 Transcription elo 30.5 26 0.00056 27.1 1.0 20 123-142 5-28 (98)
109 COG0675 Transposase and inacti 29.9 34 0.00075 28.6 1.8 23 135-157 310-333 (364)
110 PF00643 zf-B_box: B-box zinc 29.3 30 0.00064 21.5 1.0 21 135-155 4-24 (42)
111 PF08273 Prim_Zn_Ribbon: Zinc- 29.3 32 0.00069 22.6 1.1 30 135-170 4-33 (40)
112 PRK11823 DNA repair protein Ra 29.2 28 0.00061 32.8 1.2 22 136-157 9-32 (446)
113 smart00401 ZnF_GATA zinc finge 29.1 40 0.00086 22.8 1.7 29 136-171 5-33 (52)
114 PRK03681 hypA hydrogenase nick 29.0 34 0.00074 26.5 1.5 15 131-145 67-81 (114)
115 TIGR00416 sms DNA repair prote 29.0 28 0.00061 32.9 1.2 23 135-157 8-32 (454)
116 PF10058 DUF2296: Predicted in 28.9 44 0.00095 23.1 1.9 11 120-130 21-31 (54)
117 PRK08351 DNA-directed RNA poly 28.5 30 0.00065 24.8 1.0 20 123-143 5-24 (61)
118 KOG4275 Predicted E3 ubiquitin 28.1 16 0.00034 34.1 -0.6 34 121-156 300-341 (350)
119 PF07649 C1_3: C1-like domain; 27.9 39 0.00085 20.1 1.3 9 162-170 14-22 (30)
120 PRK04136 rpl40e 50S ribosomal 27.8 32 0.00069 23.8 1.0 24 119-142 12-36 (48)
121 PF12172 DUF35_N: Rubredoxin-l 26.7 31 0.00066 21.4 0.7 23 120-142 10-33 (37)
122 PF11405 Inhibitor_I67: Bromel 26.6 24 0.00053 23.3 0.2 16 135-150 16-31 (41)
123 PRK10445 endonuclease VIII; Pr 26.6 35 0.00076 29.9 1.3 17 84-100 164-180 (263)
124 PLN00209 ribosomal protein S27 26.5 49 0.0011 25.4 1.9 38 120-157 35-78 (86)
125 PRK11032 hypothetical protein; 26.2 42 0.00092 28.1 1.7 24 120-143 123-151 (160)
126 PRK05978 hypothetical protein; 26.2 35 0.00077 28.2 1.2 6 135-140 34-39 (148)
127 PRK11788 tetratricopeptide rep 25.8 38 0.00082 29.2 1.4 22 135-156 355-378 (389)
128 smart00067 GHA Glycoprotein ho 25.7 43 0.00092 25.7 1.4 16 159-174 16-31 (87)
129 COG4306 Uncharacterized protei 25.6 22 0.00049 29.6 -0.1 11 177-187 57-67 (160)
130 smart00451 ZnF_U1 U1-like zinc 25.5 37 0.0008 20.0 0.9 11 145-155 2-12 (35)
131 TIGR03655 anti_R_Lar restricti 25.4 67 0.0014 21.5 2.2 33 136-172 3-35 (53)
132 cd02249 ZZ Zinc finger, ZZ typ 25.3 58 0.0013 21.1 1.9 21 147-170 1-21 (46)
133 PF14319 Zn_Tnp_IS91: Transpos 25.1 57 0.0012 25.2 2.1 10 135-144 43-52 (111)
134 PF14446 Prok-RING_1: Prokaryo 25.1 61 0.0013 22.8 2.0 26 120-145 20-52 (54)
135 cd00202 ZnF_GATA Zinc finger D 25.0 26 0.00055 24.1 0.1 18 154-171 12-29 (54)
136 PRK14892 putative transcriptio 24.7 60 0.0013 25.2 2.1 10 136-145 44-53 (99)
137 KOG3507 DNA-directed RNA polym 24.5 58 0.0012 23.7 1.8 28 116-143 15-46 (62)
138 PRK03824 hypA hydrogenase nick 24.4 45 0.00098 26.6 1.5 14 132-145 68-81 (135)
139 PF07295 DUF1451: Protein of u 24.1 49 0.0011 27.1 1.7 24 120-143 111-139 (146)
140 KOG1428 Inhibitor of type V ad 23.9 33 0.00071 38.8 0.7 61 90-152 3602-3662(3738)
141 COG1592 Rubrerythrin [Energy p 23.7 40 0.00087 28.4 1.1 25 121-145 134-160 (166)
142 PF06906 DUF1272: Protein of u 23.1 32 0.0007 24.6 0.4 23 124-146 29-53 (57)
143 PF10122 Mu-like_Com: Mu-like 22.6 39 0.00085 23.6 0.7 9 121-129 4-12 (51)
144 PF00628 PHD: PHD-finger; Int 22.6 94 0.002 19.8 2.5 24 148-173 1-24 (51)
145 PTZ00083 40S ribosomal protein 22.6 64 0.0014 24.7 1.9 37 120-156 34-76 (85)
146 KOG1247 Methionyl-tRNA synthet 22.5 37 0.0008 33.4 0.7 64 118-185 133-201 (567)
147 PF12387 Peptidase_C74: Pestiv 22.5 62 0.0013 28.2 2.0 28 118-145 159-186 (200)
148 COG1545 Predicted nucleic-acid 22.3 55 0.0012 26.3 1.6 28 117-144 25-53 (140)
149 PF09889 DUF2116: Uncharacteri 21.9 27 0.00059 24.8 -0.2 19 135-153 4-25 (59)
150 KOG2824 Glutaredoxin-related p 21.7 72 0.0016 29.2 2.4 48 82-140 230-279 (281)
151 PRK14810 formamidopyrimidine-D 21.0 56 0.0012 28.8 1.5 16 85-100 168-183 (272)
152 TIGR00570 cdk7 CDK-activating 20.9 44 0.00095 30.8 0.8 40 123-170 5-50 (309)
153 TIGR03826 YvyF flagellar opero 20.8 30 0.00066 28.2 -0.2 18 136-153 5-25 (137)
154 PF01667 Ribosomal_S27e: Ribos 20.7 71 0.0015 22.5 1.7 33 121-153 7-45 (55)
155 COG2816 NPY1 NTP pyrophosphohy 20.7 49 0.0011 30.1 1.1 29 117-145 107-140 (279)
156 PF05876 Terminase_GpA: Phage 20.5 78 0.0017 30.8 2.5 34 135-170 201-236 (557)
157 PF01783 Ribosomal_L32p: Ribos 20.2 96 0.0021 21.2 2.2 22 120-141 25-46 (56)
158 PF13824 zf-Mss51: Zinc-finger 20.1 72 0.0016 22.5 1.6 12 160-171 11-22 (55)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=99.92 E-value=4.9e-27 Score=206.82 Aligned_cols=108 Identities=53% Similarity=1.101 Sum_probs=103.8
Q ss_pred chhhccCCCccCccccccCcceecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccccccccc
Q 029670 61 TELLRKGFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNC 140 (190)
Q Consensus 61 ~~~~~~~~~~~gC~HY~R~c~LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nC 140 (190)
.++.+++.++++|.||+|++.+++|||.++|.|++||+++. +|.++|+.+.+|+|+.|+++|++++.|.+|
T Consensus 23 ~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~---------~h~~~r~~v~~~~C~~C~~~q~~~~~c~~c 93 (276)
T KOG1940|consen 23 SDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE---------DHDLDRKTVYELLCMKCRKIQPVGQICSNC 93 (276)
T ss_pred cccccccccccCCchhhhccccccccccceeeeEEecChhh---------hcccchhhhhhhhhhhHHhhhhhhhccccc
Confidence 47889999999999999999999999999999999999986 699999999999999999999999999999
Q ss_pred cccccceecCcccCccCCCCCCeeecCCCCcccccCcc
Q 029670 141 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRFVYVL 178 (190)
Q Consensus 141 g~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGICRvG~~l 178 (190)
+..+++|||.+|+|||++++ .||||+.|||||+|+++
T Consensus 94 ~~~~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~ 130 (276)
T KOG1940|consen 94 HVELGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGL 130 (276)
T ss_pred hhhhhhhcCccccccccccc-ceecccccccccccccc
Confidence 99999999999999999988 99999999999999887
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=3.6e-25 Score=159.41 Aligned_cols=70 Identities=46% Similarity=1.129 Sum_probs=52.7
Q ss_pred ccccccC-cceecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccccccccccccccceecCc
Q 029670 73 CQHYRRR-CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCES 151 (190)
Q Consensus 73 C~HY~R~-c~LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~ 151 (190)
|+||+|+ ++||||||++|||||+||||++ +|+++|+.+++|+||.|+++|++++. +|+ ++|+|++
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 9999999999999999999986 49999999999999999999999876 777 9999999
Q ss_pred ccCcc
Q 029670 152 CKLFD 156 (190)
Q Consensus 152 Ckl~d 156 (190)
|++||
T Consensus 67 C~~~~ 71 (71)
T PF05495_consen 67 CGLYF 71 (71)
T ss_dssp TTEEE
T ss_pred cCCCC
Confidence 99985
No 3
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=99.77 E-value=6.6e-20 Score=141.27 Aligned_cols=77 Identities=23% Similarity=0.604 Sum_probs=68.0
Q ss_pred ccCccccccC---cceecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccc-----ccccccc
Q 029670 70 EYGCQHYRRR---CRIRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQ-----QVCVNCG 141 (190)
Q Consensus 70 ~~gC~HY~R~---c~LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~-----~~C~nCg 141 (190)
+.||.||++. ++|||.||+|||||++||||+++|++ +.|+++....+.||||+|.++.+++ ..||+|.
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 4699999997 67999999999999999999999884 6778887888999999999886653 6899999
Q ss_pred ccccceecCcccC
Q 029670 142 VCMGEYFCESCKL 154 (190)
Q Consensus 142 ~~FnkYfC~~Ckl 154 (190)
++|| |.|+.
T Consensus 88 spFN----p~Ck~ 96 (105)
T COG4357 88 SPFN----PGCKN 96 (105)
T ss_pred CCCC----ccccc
Confidence 9999 88875
No 4
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=94.94 E-value=0.018 Score=41.21 Aligned_cols=46 Identities=37% Similarity=0.918 Sum_probs=30.4
Q ss_pred ceEecCCCCcccc-----cccccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 120 NQVICSLCGTEQK-----VQQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 120 ~~ViCG~C~~eQ~-----~~~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
....|..|+.+.. +.-.|||||... =|-|.+|+-+. ..|.|++||+
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~-I~RC~~CRk~~-----~~Y~CP~CGF 56 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPNCGEVI-IYRCEKCRKQS-----NPYTCPKCGF 56 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCCCCCee-EeechhHHhcC-----CceECCCCCC
Confidence 4456888876532 224788888751 23488887664 3788888885
No 5
>PF12773 DZR: Double zinc ribbon
Probab=92.98 E-value=0.089 Score=34.52 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=10.6
Q ss_pred cCCCCccccc-cccccccccccc
Q 029670 124 CSLCGTEQKV-QQVCVNCGVCMG 145 (190)
Q Consensus 124 CG~C~~eQ~~-~~~C~nCg~~Fn 145 (190)
|..|+++.+. +..|++||+.+.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 3445444333 245555555554
No 6
>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=92.73 E-value=0.063 Score=39.51 Aligned_cols=36 Identities=28% Similarity=0.813 Sum_probs=22.5
Q ss_pred ceEecCCCCcccccccccccccccc--------cceecCcccCc
Q 029670 120 NQVICSLCGTEQKVQQVCVNCGVCM--------GEYFCESCKLF 155 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~~~C~nCg~~F--------nkYfC~~Ckl~ 155 (190)
....|..|...-.....||.|+.++ +.|||..|+=.
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 5778888888766667888888665 57999999744
No 7
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.69 E-value=0.066 Score=38.58 Aligned_cols=45 Identities=33% Similarity=0.883 Sum_probs=33.2
Q ss_pred eEecCCCCccccc-----ccccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 121 QVICSLCGTEQKV-----QQVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 121 ~ViCG~C~~eQ~~-----~~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
...|..|+.+-.+ .-.|||||...= |-|.+|+.+.+ +|-|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I-~Rc~~CRk~g~-----~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEI-YRCAKCRKLGN-----PYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceee-ehhhhHHHcCC-----ceECCCcCc
Confidence 4578899877532 257999995543 56888887744 799999986
No 8
>PRK04023 DNA polymerase II large subunit; Validated
Probab=92.15 E-value=0.12 Score=53.85 Aligned_cols=46 Identities=28% Similarity=0.707 Sum_probs=31.9
Q ss_pred ceEecCCCCccccccccccccccc-ccceecCcccCccCCCCCCeeecCCCCc
Q 029670 120 NQVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~~~C~nCg~~-FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
..-.|..|+++. +...||+||.. -..|||+.|.-- -..|.|++||.
T Consensus 625 g~RfCpsCG~~t-~~frCP~CG~~Te~i~fCP~CG~~-----~~~y~CPKCG~ 671 (1121)
T PRK04023 625 GRRKCPSCGKET-FYRRCPFCGTHTEPVYRCPRCGIE-----VEEDECEKCGR 671 (1121)
T ss_pred cCccCCCCCCcC-CcccCCCCCCCCCcceeCccccCc-----CCCCcCCCCCC
Confidence 345788888875 44688888864 667888888332 22477888885
No 9
>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=90.76 E-value=0.17 Score=48.05 Aligned_cols=49 Identities=20% Similarity=0.611 Sum_probs=42.0
Q ss_pred eecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCccccccccccccccc
Q 029670 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (190)
Q Consensus 82 LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~ 143 (190)
+.|.-||....|..|.-.+.-|. ....+.|-.|+..+++...||+||..
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~-------------~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHK-------------KEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEec-------------CCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 79999999999999988776432 34689999999999999999999864
No 10
>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=90.52 E-value=0.15 Score=39.96 Aligned_cols=25 Identities=32% Similarity=0.765 Sum_probs=19.8
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
..|++||+.|= +++|.+..|++||.
T Consensus 10 R~Cp~CG~kFY------------DLnk~PivCP~CG~ 34 (108)
T PF09538_consen 10 RTCPSCGAKFY------------DLNKDPIVCPKCGT 34 (108)
T ss_pred ccCCCCcchhc------------cCCCCCccCCCCCC
Confidence 36888887664 67899999999994
No 11
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=90.02 E-value=0.22 Score=49.22 Aligned_cols=46 Identities=28% Similarity=0.731 Sum_probs=28.2
Q ss_pred EecCCCCcccccc-cccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 122 VICSLCGTEQKVQ-QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 122 ViCG~C~~eQ~~~-~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
++|..|+.+.+.. ..|++||..+..-.|+.|.--- ....-.|+.||
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~---~~~~~fC~~CG 48 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEV---PVDEAHCPNCG 48 (645)
T ss_pred CcCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCC---CcccccccccC
Confidence 3577777765543 4677777777666677775431 23344677777
No 12
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=88.61 E-value=0.45 Score=50.59 Aligned_cols=50 Identities=30% Similarity=0.725 Sum_probs=36.7
Q ss_pred ceEecCCCCcccccccccccccccc-cceecCcccCc-cCCCCCCeeecCCCCc
Q 029670 120 NQVICSLCGTEQKVQQVCVNCGVCM-GEYFCESCKLF-DDDTSKKQYHCDGCGI 171 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~~~C~nCg~~F-nkYfC~~Ckl~-ddd~~K~~yHC~~CGI 171 (190)
....|..|+++-. ...|+.||... ..|+|+.|+.- ..+++. ...|+.||.
T Consensus 666 ~~rkCPkCG~~t~-~~fCP~CGs~te~vy~CPsCGaev~~des~-a~~CP~CGt 717 (1337)
T PRK14714 666 GRRRCPSCGTETY-ENRCPDCGTHTEPVYVCPDCGAEVPPDESG-RVECPRCDV 717 (1337)
T ss_pred EEEECCCCCCccc-cccCcccCCcCCCceeCccCCCccCCCccc-cccCCCCCC
Confidence 3578999999743 35999999887 46789999764 223333 668999994
No 13
>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=87.95 E-value=0.32 Score=29.28 Aligned_cols=24 Identities=29% Similarity=0.746 Sum_probs=18.1
Q ss_pred ecCCCCccccc-ccccccccccccc
Q 029670 123 ICSLCGTEQKV-QQVCVNCGVCMGE 146 (190)
Q Consensus 123 iCG~C~~eQ~~-~~~C~nCg~~Fnk 146 (190)
.|..|+.+-+. ...||+||..|.+
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~~ 26 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFEA 26 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCcC
Confidence 37788877554 4789999999863
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.90 E-value=0.23 Score=29.41 Aligned_cols=24 Identities=33% Similarity=0.908 Sum_probs=16.3
Q ss_pred eEecCCCCccccc-ccccccccccc
Q 029670 121 QVICSLCGTEQKV-QQVCVNCGVCM 144 (190)
Q Consensus 121 ~ViCG~C~~eQ~~-~~~C~nCg~~F 144 (190)
.+.|..|+++-+. ...|++||+.+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCcccccChhhCCCC
Confidence 3568888886443 36788888764
No 15
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.21 E-value=0.66 Score=33.25 Aligned_cols=35 Identities=23% Similarity=0.579 Sum_probs=29.5
Q ss_pred cceEecCCCCcccccccccccccccccceecCcccCc
Q 029670 119 VNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF 155 (190)
Q Consensus 119 v~~ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~Ckl~ 155 (190)
...-.|..|+.+.-+ +|..|....|.|.|++|.|-
T Consensus 23 ~~~F~CPnCG~~~I~--RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVIIY--RCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCeeEe--echhHHhcCCceECCCCCCc
Confidence 468889999875444 69999999999999999874
No 16
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=86.19 E-value=0.63 Score=46.89 Aligned_cols=53 Identities=23% Similarity=0.526 Sum_probs=44.5
Q ss_pred eecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccccccccccccccce
Q 029670 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEY 147 (190)
Q Consensus 82 LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~FnkY 147 (190)
+.|.-||..+-|..|=.-+.-|. ....+.|-.|+.++++-..||+||...=+|
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~-------------~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~ 488 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHK-------------ATGQLRCHYCGYQEPIPQSCPECGSEHLRA 488 (730)
T ss_pred eecccCCCcccCCCCCcceEEec-------------CCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence 89999999999999987776433 347999999999999999999999874433
No 17
>PHA00626 hypothetical protein
Probab=86.06 E-value=0.57 Score=33.57 Aligned_cols=6 Identities=50% Similarity=1.531 Sum_probs=3.2
Q ss_pred cccccc
Q 029670 137 CVNCGV 142 (190)
Q Consensus 137 C~nCg~ 142 (190)
||+||.
T Consensus 3 CP~CGS 8 (59)
T PHA00626 3 CPKCGS 8 (59)
T ss_pred CCCCCC
Confidence 555554
No 18
>PRK05580 primosome assembly protein PriA; Validated
Probab=84.86 E-value=0.62 Score=45.84 Aligned_cols=49 Identities=22% Similarity=0.635 Sum_probs=41.8
Q ss_pred eecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCccccccccccccccc
Q 029670 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (190)
Q Consensus 82 LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~ 143 (190)
+.|.-||...-|..|.-.+.- |. ..+.+.|-.|+..++....||+||..
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~---------h~----~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTL---------HR----FQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred eEhhhCcCccCCCCCCCceeE---------EC----CCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 899999999999999987764 22 24689999999999988999999875
No 19
>PRK14873 primosome assembly protein PriA; Provisional
Probab=84.74 E-value=0.62 Score=46.18 Aligned_cols=48 Identities=23% Similarity=0.499 Sum_probs=39.3
Q ss_pred eecCCCCCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCccccccccccccccc
Q 029670 82 IRAPCCNEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVC 143 (190)
Q Consensus 82 LrcpCCgk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~ 143 (190)
+.|.-||...-|..|.-.+.- |. ....+.|-.|+..+ ....||+||..
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~---------h~----~~~~l~Ch~CG~~~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGL---------PS----AGGTPRCRWCGRAA-PDWRCPRCGSD 431 (665)
T ss_pred eEhhhCcCeeECCCCCCceeE---------ec----CCCeeECCCCcCCC-cCccCCCCcCC
Confidence 899999999999999988763 21 23588999999876 46799999865
No 20
>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=84.02 E-value=0.59 Score=38.10 Aligned_cols=25 Identities=20% Similarity=0.296 Sum_probs=19.6
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
..||+||+.|= +++|.+..|++||.
T Consensus 10 r~Cp~cg~kFY------------DLnk~p~vcP~cg~ 34 (129)
T TIGR02300 10 RICPNTGSKFY------------DLNRRPAVSPYTGE 34 (129)
T ss_pred ccCCCcCcccc------------ccCCCCccCCCcCC
Confidence 35888877664 67899999999995
No 21
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.12 E-value=0.6 Score=27.20 Aligned_cols=21 Identities=38% Similarity=0.956 Sum_probs=13.8
Q ss_pred cCCCCccccc-ccccccccccc
Q 029670 124 CSLCGTEQKV-QQVCVNCGVCM 144 (190)
Q Consensus 124 CG~C~~eQ~~-~~~C~nCg~~F 144 (190)
|..|+++.+. +..|++||+.+
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 6677776443 46788888754
No 22
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=82.05 E-value=0.88 Score=48.52 Aligned_cols=33 Identities=30% Similarity=0.754 Sum_probs=27.4
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
-.||+||..-...||+.|.-. .+.+|+|+.||.
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 589999988767799999754 356899999997
No 23
>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=78.25 E-value=0.7 Score=29.64 Aligned_cols=27 Identities=33% Similarity=0.725 Sum_probs=18.6
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.|++||+.+|.+| .+.|..--|+.||-
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 4788888888665 44666777888874
No 24
>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=77.53 E-value=1.8 Score=29.90 Aligned_cols=26 Identities=31% Similarity=0.787 Sum_probs=17.8
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
+.|+.||....+ ..+...|.|+.||.
T Consensus 29 q~C~~CG~~~~~-----------~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 29 QTCPRCGHRNKK-----------RRSGRVFTCPNCGF 54 (69)
T ss_pred cCccCccccccc-----------ccccceEEcCCCCC
Confidence 678888877764 23455777777775
No 25
>PF12773 DZR: Double zinc ribbon
Probab=76.62 E-value=1.9 Score=28.08 Aligned_cols=32 Identities=34% Similarity=0.889 Sum_probs=19.3
Q ss_pred eEecCCCCcccc--c--ccccccccccc--cceecCcc
Q 029670 121 QVICSLCGTEQK--V--QQVCVNCGVCM--GEYFCESC 152 (190)
Q Consensus 121 ~ViCG~C~~eQ~--~--~~~C~nCg~~F--nkYfC~~C 152 (190)
...|..|++... . ...|++||... +..||+.|
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccCcc
Confidence 567778877655 2 24688887653 33445544
No 26
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.05 E-value=1.7 Score=43.27 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=19.3
Q ss_pred eEecCCCCccccccccccccccc--ccceecCcccCc
Q 029670 121 QVICSLCGTEQKVQQVCVNCGVC--MGEYFCESCKLF 155 (190)
Q Consensus 121 ~ViCG~C~~eQ~~~~~C~nCg~~--FnkYfC~~Ckl~ 155 (190)
.-.|..|++.... ..|++||+. .+..||+.|...
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcccccccccCCc
Confidence 3456666665432 356777644 555667776543
No 27
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=74.73 E-value=2.2 Score=38.61 Aligned_cols=50 Identities=20% Similarity=0.327 Sum_probs=34.3
Q ss_pred eeeeccccCCCCCc-----hhhccCCCccCccccccCcceecCCCCCcccCchhhh
Q 029670 48 FLVTEESTNHNGST-----ELLRKGFMEYGCQHYRRRCRIRAPCCNEIFDCRHCHN 98 (190)
Q Consensus 48 ~~~~~~~~~~~~~~-----~~~~~~~~~~gC~HY~R~c~LrcpCCgk~YpCr~CHD 98 (190)
+...|+++.-+-++ -+-.+....+.|.||...--++..+|.. |+|..||+
T Consensus 150 H~c~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 150 HKCVERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-YTCPICSK 204 (276)
T ss_pred cchhhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-CCCCcccc
Confidence 44445554444242 1223334457899999955599999999 99999999
No 28
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=71.48 E-value=3.1 Score=30.05 Aligned_cols=39 Identities=23% Similarity=0.561 Sum_probs=31.5
Q ss_pred CccccceEecCCCCcccccccccccccccccceecCcccCc
Q 029670 115 PRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLF 155 (190)
Q Consensus 115 dR~~v~~ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~Ckl~ 155 (190)
.+.....-.|..|+.++-+ +|..|-..=|.|.|++|.|-
T Consensus 21 p~e~~v~F~CPnCGe~~I~--Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 21 PGETAVKFPCPNCGEVEIY--RCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred cCCceeEeeCCCCCceeee--hhhhHHHcCCceECCCcCcc
Confidence 3345567889999987776 78999999999999999874
No 29
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.38 E-value=4.4 Score=41.01 Aligned_cols=46 Identities=26% Similarity=0.628 Sum_probs=35.2
Q ss_pred ccceEecCCCCcccccccccccccccc------cceecCcccCccCCCCCCeeecCCCCc
Q 029670 118 EVNQVICSLCGTEQKVQQVCVNCGVCM------GEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~~~~~C~nCg~~F------nkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
-.+.++|..|+.. ..||+|...+ +...|.-|..= ++.+.+|+.||-
T Consensus 432 ys~~l~C~~Cg~v----~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~----~~~p~~Cp~Cgs 483 (730)
T COG1198 432 YAPLLLCRDCGYI----AECPNCDSPLTLHKATGQLRCHYCGYQ----EPIPQSCPECGS 483 (730)
T ss_pred ccceeecccCCCc----ccCCCCCcceEEecCCCeeEeCCCCCC----CCCCCCCCCCCC
Confidence 4468999999865 3699997554 56778877654 577999999994
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=71.27 E-value=2.4 Score=37.22 Aligned_cols=48 Identities=31% Similarity=0.682 Sum_probs=25.7
Q ss_pred cceEecCCCCcccccc-cccccccccccceecCcccCc--cCCCCCCeeecCCCC
Q 029670 119 VNQVICSLCGTEQKVQ-QVCVNCGVCMGEYFCESCKLF--DDDTSKKQYHCDGCG 170 (190)
Q Consensus 119 v~~ViCG~C~~eQ~~~-~~C~nCg~~FnkYfC~~Ckl~--ddd~~K~~yHC~~CG 170 (190)
.+-+.|+.|+++=.+. ..|++||..-..-+ .+| ++++.-.++-|+.||
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 3688999999996664 78999997755432 233 444556789999998
No 31
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=71.08 E-value=2.8 Score=26.88 Aligned_cols=26 Identities=23% Similarity=0.566 Sum_probs=16.7
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
.||.|+..+..+. + ..-.++.|+.||
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 135677888886
No 32
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=70.72 E-value=2.5 Score=28.12 Aligned_cols=21 Identities=38% Similarity=0.996 Sum_probs=10.0
Q ss_pred ecCCCCcccccc----ccccccccc
Q 029670 123 ICSLCGTEQKVQ----QVCVNCGVC 143 (190)
Q Consensus 123 iCG~C~~eQ~~~----~~C~nCg~~ 143 (190)
+|+.|+++.+.. ..|++||+.
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCce
Confidence 455555543221 356666544
No 33
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=70.12 E-value=4.1 Score=24.36 Aligned_cols=9 Identities=33% Similarity=1.162 Sum_probs=5.9
Q ss_pred CeeecCCCC
Q 029670 162 KQYHCDGCG 170 (190)
Q Consensus 162 ~~yHC~~CG 170 (190)
..|.|+.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 466677666
No 34
>PF14353 CpXC: CpXC protein
Probab=68.31 E-value=4.4 Score=31.26 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=4.9
Q ss_pred CeeecCCCC
Q 029670 162 KQYHCDGCG 170 (190)
Q Consensus 162 ~~yHC~~CG 170 (190)
..|.|+.||
T Consensus 37 ~~~~CP~Cg 45 (128)
T PF14353_consen 37 FSFTCPSCG 45 (128)
T ss_pred CEEECCCCC
Confidence 355555555
No 35
>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=68.11 E-value=4.1 Score=26.25 Aligned_cols=11 Identities=27% Similarity=0.933 Sum_probs=4.9
Q ss_pred CCCeeecCCCC
Q 029670 160 SKKQYHCDGCG 170 (190)
Q Consensus 160 ~K~~yHC~~CG 170 (190)
....+-|..||
T Consensus 16 ~~g~~vC~~CG 26 (43)
T PF08271_consen 16 ERGELVCPNCG 26 (43)
T ss_dssp TTTEEEETTT-
T ss_pred CCCeEECCCCC
Confidence 34444555554
No 36
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=67.82 E-value=4.5 Score=26.36 Aligned_cols=8 Identities=38% Similarity=0.974 Sum_probs=6.3
Q ss_pred eeecCCCC
Q 029670 163 QYHCDGCG 170 (190)
Q Consensus 163 ~yHC~~CG 170 (190)
..+|+.||
T Consensus 21 ~~~Cp~CG 28 (46)
T PRK00398 21 GVRCPYCG 28 (46)
T ss_pred ceECCCCC
Confidence 67888887
No 37
>PHA00626 hypothetical protein
Probab=67.66 E-value=3.7 Score=29.48 Aligned_cols=33 Identities=21% Similarity=0.459 Sum_probs=19.0
Q ss_pred EecCCCCcccccccccccccccccceecCcccCcc
Q 029670 122 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFD 156 (190)
Q Consensus 122 ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~Ckl~d 156 (190)
|.|..|+..+-+ .|.-|...-+.|-|+.|.+..
T Consensus 1 m~CP~CGS~~Iv--rcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceee--eeceecccCcceEcCCCCCee
Confidence 346666655544 455555556666666666553
No 38
>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=65.78 E-value=4.8 Score=31.63 Aligned_cols=35 Identities=20% Similarity=0.510 Sum_probs=25.6
Q ss_pred ccccccccceecCcccCccCCCCCCeeecCCCCccccc
Q 029670 138 VNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRFV 175 (190)
Q Consensus 138 ~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGICRvG 175 (190)
...+......+|.+|+.+. + ....||..||.|..+
T Consensus 40 ~~~~~~~~~~~C~~C~~~k--p-~Rs~HC~~C~~CV~~ 74 (174)
T PF01529_consen 40 PEDDENGELKYCSTCKIIK--P-PRSHHCRVCNRCVLR 74 (174)
T ss_pred hccccCCCCEECcccCCcC--C-Ccceecccccccccc
Confidence 3355777778888888883 2 348899999988765
No 39
>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=65.52 E-value=6.6 Score=37.47 Aligned_cols=47 Identities=28% Similarity=0.676 Sum_probs=33.0
Q ss_pred ccceEecCCCCcccccccccccccccc------cceecCcccCccCCCCCCeeecCCCCcc
Q 029670 118 EVNQVICSLCGTEQKVQQVCVNCGVCM------GEYFCESCKLFDDDTSKKQYHCDGCGIC 172 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~~~~~C~nCg~~F------nkYfC~~Ckl~ddd~~K~~yHC~~CGIC 172 (190)
.++.++|..|+.. ..|++|+..+ +.-.|.-|.+- .+.+..|+.||-=
T Consensus 210 ya~~~~C~~Cg~~----~~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 210 YSKNLLCRSCGYI----LCCPNCDVSLTYHKKEGKLRCHYCGYQ----EPIPKTCPQCGSE 262 (505)
T ss_pred CCCeeEhhhCcCc----cCCCCCCCceEEecCCCeEEcCCCcCc----CCCCCCCCCCCCC
Confidence 3467889999865 3689998665 44568877643 3456789999854
No 40
>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=65.18 E-value=2.1 Score=44.20 Aligned_cols=45 Identities=29% Similarity=0.769 Sum_probs=0.0
Q ss_pred eEecCCCCccccccccccccccc-ccceecCcccCccCCCCCCeeecCCCCc
Q 029670 121 QVICSLCGTEQKVQQVCVNCGVC-MGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 121 ~ViCG~C~~eQ~~~~~C~nCg~~-FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.-.|..|+++ .+...|+.||.. .-.|+|+.|+.--++. +|+.||.
T Consensus 655 ~r~Cp~Cg~~-t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-----~C~~C~~ 700 (900)
T PF03833_consen 655 RRRCPKCGKE-TFYNRCPECGSHTEPVYVCPDCGIEVEED-----ECPKCGR 700 (900)
T ss_dssp ----------------------------------------------------
T ss_pred cccCcccCCc-chhhcCcccCCccccceeccccccccCcc-----ccccccc
Confidence 4567777776 334578888765 4567788886543221 7777773
No 41
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=64.24 E-value=5 Score=27.34 Aligned_cols=12 Identities=33% Similarity=1.046 Sum_probs=9.1
Q ss_pred CCCeeecCCCCc
Q 029670 160 SKKQYHCDGCGI 171 (190)
Q Consensus 160 ~K~~yHC~~CGI 171 (190)
.++.++|..||.
T Consensus 34 ~~~r~~C~~Cgy 45 (50)
T PRK00432 34 HLDRWHCGKCGY 45 (50)
T ss_pred cCCcEECCCcCC
Confidence 346888988885
No 42
>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=64.23 E-value=1.9 Score=35.30 Aligned_cols=25 Identities=28% Similarity=0.772 Sum_probs=13.4
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
.||+|+..|. |++..+ .-|+|+.||
T Consensus 111 ~Cp~c~~r~t---------f~eA~~-~~F~Cp~Cg 135 (158)
T TIGR00373 111 ICPNMCVRFT---------FNEAME-LNFTCPRCG 135 (158)
T ss_pred ECCCCCcEee---------HHHHHH-cCCcCCCCC
Confidence 5677766554 433322 346666665
No 43
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=64.09 E-value=6.6 Score=25.51 Aligned_cols=9 Identities=33% Similarity=1.313 Sum_probs=7.2
Q ss_pred CeeecCCCC
Q 029670 162 KQYHCDGCG 170 (190)
Q Consensus 162 ~~yHC~~CG 170 (190)
..|-|+.||
T Consensus 19 ~~~vC~~Cg 27 (52)
T smart00661 19 RRFVCRKCG 27 (52)
T ss_pred CEEECCcCC
Confidence 478888888
No 44
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.38 E-value=4.4 Score=42.73 Aligned_cols=36 Identities=31% Similarity=0.643 Sum_probs=23.7
Q ss_pred EecCCCCcccccccccccccccccceecCcccCccC
Q 029670 122 VICSLCGTEQKVQQVCVNCGVCMGEYFCESCKLFDD 157 (190)
Q Consensus 122 ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~Ckl~dd 157 (190)
-.|..|+..-.....|+.||...+.|.|++|.+--.
T Consensus 639 frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 639 RRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred ccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCC
Confidence 356666655333347888888888888888875543
No 45
>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=62.97 E-value=3.6 Score=25.35 Aligned_cols=17 Identities=35% Similarity=1.001 Sum_probs=8.7
Q ss_pred ccccccccccceecCccc
Q 029670 136 VCVNCGVCMGEYFCESCK 153 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ck 153 (190)
.|..|+. .++|.|+.|.
T Consensus 4 ~C~vC~~-~~kY~Cp~C~ 20 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCG 20 (30)
T ss_dssp EETSSSS-EESEE-TTT-
T ss_pred CCccCcC-CCEEECCCcC
Confidence 3555555 6666666664
No 46
>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=62.70 E-value=2.9 Score=38.21 Aligned_cols=68 Identities=32% Similarity=0.702 Sum_probs=41.2
Q ss_pred CCcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccccccccccccccceecCcccC-c-cCC-------
Q 029670 88 NEIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESCKL-F-DDD------- 158 (190)
Q Consensus 88 gk~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~Ckl-~-ddd------- 158 (190)
|+.|.|-+|++-+-... +++ |.. .|+....-+..|.+|+ +++.|.|..||. | |+-
T Consensus 140 Grif~CsfC~~flCEDD---QFE-HQA-----------sCQvLe~E~~KC~SCN-rlGq~sCLRCK~cfCddHvrrKg~k 203 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCEDD---QFE-HQA-----------SCQVLESETFKCQSCN-RLGQYSCLRCKICFCDDHVRRKGFK 203 (314)
T ss_pred CeEEEeecCCCeeeccc---hhh-hhh-----------hhhhhhcccccccccc-cccchhhhheeeeehhhhhhhcccc
Confidence 56788888887665321 122 322 3544444445788776 478888888873 2 331
Q ss_pred -CCCCeeecCCCCc
Q 029670 159 -TSKKQYHCDGCGI 171 (190)
Q Consensus 159 -~~K~~yHC~~CGI 171 (190)
...+++-|++||.
T Consensus 204 y~k~k~~PCPKCg~ 217 (314)
T PF06524_consen 204 YEKGKPIPCPKCGY 217 (314)
T ss_pred cccCCCCCCCCCCC
Confidence 1236899999994
No 47
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=62.03 E-value=8.7 Score=24.92 Aligned_cols=28 Identities=36% Similarity=0.866 Sum_probs=20.4
Q ss_pred cccccccc--cccceecCcccCccCCCCCCeeecCCCCc
Q 029670 135 QVCVNCGV--CMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 135 ~~C~nCg~--~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
..||.||. .|. |+|...+..|+|..||.
T Consensus 4 ~pCP~CGG~DrFr---------~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFR---------FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccc---------cccCCCCcCEEeCCCCC
Confidence 46888886 344 46666778999999874
No 48
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=61.93 E-value=2.3 Score=35.53 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=6.1
Q ss_pred cccccccccc
Q 029670 136 VCVNCGVCMG 145 (190)
Q Consensus 136 ~C~nCg~~Fn 145 (190)
.||+|+..|.
T Consensus 119 ~Cp~C~~ryt 128 (178)
T PRK06266 119 FCPNCHIRFT 128 (178)
T ss_pred ECCCCCcEEe
Confidence 5666665554
No 49
>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=59.65 E-value=7.4 Score=23.99 Aligned_cols=25 Identities=28% Similarity=0.787 Sum_probs=17.1
Q ss_pred ceecCcccCccCCCCCCeeecCCCCc
Q 029670 146 EYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 146 kYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.|-|.+|.+.-+ +.++++.|+.||.
T Consensus 1 ~~~C~~CGy~y~-~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYD-GEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEEC-CCcCCCcCcCCCC
Confidence 367888865533 2457888988885
No 50
>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=58.41 E-value=5.1 Score=25.95 Aligned_cols=11 Identities=27% Similarity=0.755 Sum_probs=6.5
Q ss_pred CCeeecCCCCc
Q 029670 161 KKQYHCDGCGI 171 (190)
Q Consensus 161 K~~yHC~~CGI 171 (190)
.+.-.|+.||-
T Consensus 24 ~~~~~CP~Cg~ 34 (42)
T PF09723_consen 24 DDPVPCPECGS 34 (42)
T ss_pred CCCCcCCCCCC
Confidence 34566777763
No 51
>PF15616 TerY-C: TerY-C metal binding domain
Probab=57.64 E-value=7.9 Score=31.51 Aligned_cols=34 Identities=35% Similarity=0.747 Sum_probs=26.0
Q ss_pred cccccccccccceecCcc-cCccCCCCCCeeecCCCC
Q 029670 135 QVCVNCGVCMGEYFCESC-KLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~C-kl~ddd~~K~~yHC~~CG 170 (190)
..||.||..++---| .| ||+-=+ .-....|+-||
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~Ci~-g~~~~~CPwCg 112 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFCID-GEGEVTCPWCG 112 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEEeC-CCCCEECCCCC
Confidence 689999999998889 68 566412 13388999998
No 52
>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=57.47 E-value=6.3 Score=25.31 Aligned_cols=33 Identities=27% Similarity=0.632 Sum_probs=17.6
Q ss_pred ccccccccccceecCcccCc-cCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~-ddd~~K~~yHC~~CG 170 (190)
.||+||+.-+-|+ .+ -.- .|.+..-+|.|-.||
T Consensus 2 ~Cp~Cg~~~a~~~-~~-Q~rsaDE~~T~fy~C~~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-QI-QTRSADEPMTLFYVCCNCG 35 (39)
T ss_dssp --SSS-SSEEEEE-EE-SSSSSSSSSEEEEEESSST
T ss_pred CCcCCCCCeEEEE-Ee-eccCCCCCCeEEEEeCCCC
Confidence 4788887766554 00 000 223456689999887
No 53
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=56.83 E-value=5 Score=37.58 Aligned_cols=21 Identities=43% Similarity=0.934 Sum_probs=16.1
Q ss_pred cccccccccccceecCcccCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLF 155 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ 155 (190)
..|+.|++.+.+|.||-|+|.
T Consensus 8 ~~C~ic~vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 8 LACGICGVQKREYTCPRCNLL 28 (383)
T ss_pred eeccccccccccccCCCCCcc
Confidence 357778888888888888754
No 54
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=55.68 E-value=8.6 Score=24.34 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=4.3
Q ss_pred eecCCCCCcc
Q 029670 82 IRAPCCNEIF 91 (190)
Q Consensus 82 LrcpCCgk~Y 91 (190)
|.||.|+.-|
T Consensus 3 i~Cp~C~~~y 12 (36)
T PF13717_consen 3 ITCPNCQAKY 12 (36)
T ss_pred EECCCCCCEE
Confidence 3444444433
No 55
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=55.53 E-value=7.4 Score=34.01 Aligned_cols=32 Identities=25% Similarity=0.816 Sum_probs=23.6
Q ss_pred cccccceecCcccCccCCCCCCeeecCCCCccccc
Q 029670 141 GVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRFV 175 (190)
Q Consensus 141 g~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGICRvG 175 (190)
|......||..|+++- .+...||.-|+.|-.+
T Consensus 108 ~~~~~~~~C~~C~~~r---PpRs~HCsvC~~CV~r 139 (299)
T KOG1311|consen 108 GIQVEWKYCDTCQLYR---PPRSSHCSVCNNCVLR 139 (299)
T ss_pred CcccceEEcCcCcccC---CCCcccchhhcccccc
Confidence 4555678888888883 3457899999988654
No 56
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=55.05 E-value=8.8 Score=24.30 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=4.2
Q ss_pred ccccccccc
Q 029670 136 VCVNCGVCM 144 (190)
Q Consensus 136 ~C~nCg~~F 144 (190)
.|++|++.|
T Consensus 27 rC~~C~~~f 35 (37)
T PF13719_consen 27 RCPKCGHVF 35 (37)
T ss_pred ECCCCCcEe
Confidence 444444444
No 57
>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=53.81 E-value=6.5 Score=30.56 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=6.7
Q ss_pred cccccccccccc
Q 029670 134 QQVCVNCGVCMG 145 (190)
Q Consensus 134 ~~~C~nCg~~Fn 145 (190)
...|.+||..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (115)
T TIGR00100 70 ECECEDCSEEVS 81 (115)
T ss_pred EEEcccCCCEEe
Confidence 345666665554
No 58
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=53.62 E-value=13 Score=33.95 Aligned_cols=52 Identities=29% Similarity=0.703 Sum_probs=30.9
Q ss_pred cceEecCCCCccccc-------------cccccccccccc----------------ceecCcc-cCccCC----------
Q 029670 119 VNQVICSLCGTEQKV-------------QQVCVNCGVCMG----------------EYFCESC-KLFDDD---------- 158 (190)
Q Consensus 119 v~~ViCG~C~~eQ~~-------------~~~C~nCg~~Fn----------------kYfC~~C-kl~ddd---------- 158 (190)
.+.-.|-.|.++..- .-.|+-||..|. -|-|+.| |=|.|+
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTH 238 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTH 238 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhh
Confidence 456677777765221 125777777776 2447777 444441
Q ss_pred CCCCeeecCCCC
Q 029670 159 TSKKQYHCDGCG 170 (190)
Q Consensus 159 ~~K~~yHC~~CG 170 (190)
-..+.|-|..||
T Consensus 239 S~~K~~qC~~C~ 250 (279)
T KOG2462|consen 239 SDVKKHQCPRCG 250 (279)
T ss_pred cCCccccCcchh
Confidence 122389999988
No 59
>PRK07219 DNA topoisomerase I; Validated
Probab=51.64 E-value=18 Score=36.75 Aligned_cols=22 Identities=23% Similarity=0.693 Sum_probs=13.2
Q ss_pred cCcccCccCCC--CCCeeecCCCC
Q 029670 149 CESCKLFDDDT--SKKQYHCDGCG 170 (190)
Q Consensus 149 C~~Ckl~ddd~--~K~~yHC~~CG 170 (190)
|+.|+...... ......|+.||
T Consensus 672 CP~C~~~~~~~~~~~~~~~CP~Cg 695 (822)
T PRK07219 672 CPDCEAEKEEEDPDEVIGPCPKCG 695 (822)
T ss_pred CCCCCCCccccccccccccCCCCC
Confidence 77776654321 22357888887
No 60
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=51.58 E-value=8.3 Score=23.81 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=4.9
Q ss_pred eeecCCCCc
Q 029670 163 QYHCDGCGI 171 (190)
Q Consensus 163 ~yHC~~CGI 171 (190)
.-.|+.||.
T Consensus 26 ~~~CP~Cg~ 34 (41)
T smart00834 26 LATCPECGG 34 (41)
T ss_pred CCCCCCCCC
Confidence 444666654
No 61
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=51.15 E-value=7.8 Score=35.04 Aligned_cols=38 Identities=24% Similarity=0.634 Sum_probs=30.7
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCCccccc
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGICRFV 175 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGICRvG 175 (190)
..+...+....+-||.+|+.|--+ ...||..||.|-..
T Consensus 98 ~~~~~~~~~~~~~~C~~C~~~KP~---RS~HC~~Cn~CV~k 135 (309)
T COG5273 98 SRLLDDGKFGTENFCSTCNIYKPP---RSHHCSICNRCVLK 135 (309)
T ss_pred hhhhhcCccccceeccccccccCC---CCccchhhcchhhc
Confidence 567778899999999999999432 36799999999754
No 62
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=49.52 E-value=16 Score=25.53 Aligned_cols=26 Identities=27% Similarity=0.764 Sum_probs=18.3
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
.||.||..+. +.++..-.+.-|+.||
T Consensus 4 ~CP~CG~~ie---------v~~~~~GeiV~Cp~CG 29 (54)
T TIGR01206 4 ECPDCGAEIE---------LENPELGELVICDECG 29 (54)
T ss_pred CCCCCCCEEe---------cCCCccCCEEeCCCCC
Confidence 6888888775 4444345688888888
No 63
>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 PRK00420 hypothetical protein; Validated
Probab=48.83 E-value=11 Score=29.98 Aligned_cols=21 Identities=24% Similarity=0.471 Sum_probs=13.7
Q ss_pred ccccccccccc-----ceecCcccCc
Q 029670 135 QVCVNCGVCMG-----EYFCESCKLF 155 (190)
Q Consensus 135 ~~C~nCg~~Fn-----kYfC~~Ckl~ 155 (190)
..||.||.++- +.||+.|.-.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 57888887644 4677777543
No 65
>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=48.12 E-value=6 Score=41.00 Aligned_cols=33 Identities=30% Similarity=0.698 Sum_probs=0.0
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
-.|++||..--...|+.|.-. +.+.|.|+.||+
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~----T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSH----TEPVYVCPDCGI 688 (900)
T ss_dssp -------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCc----cccceecccccc
Confidence 479999988777789988755 567899999986
No 66
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=47.78 E-value=9.7 Score=31.52 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=6.6
Q ss_pred ccccccccccce
Q 029670 136 VCVNCGVCMGEY 147 (190)
Q Consensus 136 ~C~nCg~~FnkY 147 (190)
.|++||..|+.|
T Consensus 30 ~c~~c~~~f~~~ 41 (154)
T PRK00464 30 ECLACGKRFTTF 41 (154)
T ss_pred eccccCCcceEe
Confidence 455555555544
No 67
>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=47.69 E-value=14 Score=22.89 Aligned_cols=8 Identities=38% Similarity=0.962 Sum_probs=3.4
Q ss_pred cccccccc
Q 029670 136 VCVNCGVC 143 (190)
Q Consensus 136 ~C~nCg~~ 143 (190)
.|++||..
T Consensus 27 ~C~~C~~~ 34 (38)
T TIGR02098 27 RCGKCGHV 34 (38)
T ss_pred ECCCCCCE
Confidence 34444443
No 68
>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=47.64 E-value=12 Score=23.58 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=6.5
Q ss_pred CCCeeecCCCC
Q 029670 160 SKKQYHCDGCG 170 (190)
Q Consensus 160 ~K~~yHC~~CG 170 (190)
..++..|..||
T Consensus 14 ~~~~irC~~CG 24 (32)
T PF03604_consen 14 PGDPIRCPECG 24 (32)
T ss_dssp TSSTSSBSSSS
T ss_pred CCCcEECCcCC
Confidence 34455666666
No 69
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.21 E-value=12 Score=25.93 Aligned_cols=29 Identities=28% Similarity=0.589 Sum_probs=18.3
Q ss_pred cceecCcc-cCccCCCCCCeeecCCCCccc
Q 029670 145 GEYFCESC-KLFDDDTSKKQYHCDGCGICR 173 (190)
Q Consensus 145 nkYfC~~C-kl~ddd~~K~~yHC~~CGICR 173 (190)
..|-|..| +.++.+....-..|+.||.=.
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 34556666 344545567788899988643
No 70
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=46.62 E-value=14 Score=25.30 Aligned_cols=23 Identities=30% Similarity=0.850 Sum_probs=10.0
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
..|..|+..|+- -+..+||-.||
T Consensus 10 ~~C~~C~~~F~~-------------~~rrhhCr~CG 32 (69)
T PF01363_consen 10 SNCMICGKKFSL-------------FRRRHHCRNCG 32 (69)
T ss_dssp SB-TTT--B-BS-------------SS-EEE-TTT-
T ss_pred CcCcCcCCcCCC-------------ceeeEccCCCC
Confidence 467777777751 25567777777
No 71
>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=45.39 E-value=21 Score=23.27 Aligned_cols=26 Identities=31% Similarity=0.901 Sum_probs=15.0
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
..||.||.. .-|. + .....|.|..|+
T Consensus 19 ~~CP~Cg~~-~~~~------~---~~~~~~~C~~C~ 44 (46)
T PF12760_consen 19 FVCPHCGST-KHYR------L---KTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCe-eeEE------e---CCCCeEECCCCC
Confidence 358888876 2221 1 125677777775
No 72
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.20 E-value=18 Score=23.01 Aligned_cols=29 Identities=21% Similarity=0.677 Sum_probs=13.4
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.|++||.++..- +-++ +++.-+-|+.||.
T Consensus 2 fC~~CG~~l~~~------ip~g-d~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERR------IPEG-DDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--------TT--SS-EEEETTTTE
T ss_pred ccccccChhhhh------cCCC-CCccceECCCCCC
Confidence 467777665532 2233 3677888888873
No 73
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=42.68 E-value=18 Score=25.86 Aligned_cols=34 Identities=35% Similarity=0.567 Sum_probs=24.7
Q ss_pred ceEecCCCCcccccc------cccccccccccceecCccc
Q 029670 120 NQVICSLCGTEQKVQ------QVCVNCGVCMGEYFCESCK 153 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~------~~C~nCg~~FnkYfC~~Ck 153 (190)
-.|.|..|..+|.+- -.|..||..+++-.=.+.+
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~ 49 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAK 49 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCccee
Confidence 478999999998651 4799999888865433333
No 74
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.59 E-value=24 Score=32.38 Aligned_cols=47 Identities=28% Similarity=0.633 Sum_probs=31.7
Q ss_pred ccceEecCCCCccccc-ccccccccccccceecCcccCc--cCC-CCCCeeecCCCC
Q 029670 118 EVNQVICSLCGTEQKV-QQVCVNCGVCMGEYFCESCKLF--DDD-TSKKQYHCDGCG 170 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~~-~~~C~nCg~~FnkYfC~~Ckl~--ddd-~~K~~yHC~~CG 170 (190)
..+-..|+.|.++=.+ ...|++||..-.- .+| +++ ..-.+.-|+.|+
T Consensus 209 G~RyL~CslC~teW~~~R~~C~~Cg~~~~l------~y~~~~~~~~~~r~e~C~~C~ 259 (309)
T PRK03564 209 GLRYLHCNLCESEWHVVRVKCSNCEQSGKL------HYWSLDSEQAAVKAESCGDCG 259 (309)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCCCce------eeeeecCCCcceEeeeccccc
Confidence 3468899999999665 4789999964221 223 332 234578888887
No 75
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=42.53 E-value=11 Score=31.64 Aligned_cols=13 Identities=23% Similarity=0.853 Sum_probs=11.3
Q ss_pred cccccccccccce
Q 029670 135 QVCVNCGVCMGEY 147 (190)
Q Consensus 135 ~~C~nCg~~FnkY 147 (190)
-.|++||..|..|
T Consensus 29 ReC~~C~~RFTTf 41 (156)
T COG1327 29 RECLECGERFTTF 41 (156)
T ss_pred hcccccccccchh
Confidence 3799999999976
No 76
>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=41.59 E-value=15 Score=30.63 Aligned_cols=14 Identities=14% Similarity=0.510 Sum_probs=11.9
Q ss_pred ccccccccccccee
Q 029670 135 QVCVNCGVCMGEYF 148 (190)
Q Consensus 135 ~~C~nCg~~FnkYf 148 (190)
-.|++||..|..|=
T Consensus 29 ReC~~C~~RFTTyE 42 (147)
T TIGR00244 29 RECLECHERFTTFE 42 (147)
T ss_pred ccCCccCCccceee
Confidence 37999999999883
No 77
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=40.01 E-value=14 Score=28.63 Aligned_cols=11 Identities=18% Similarity=0.592 Sum_probs=5.7
Q ss_pred ccccccccccc
Q 029670 135 QVCVNCGVCMG 145 (190)
Q Consensus 135 ~~C~nCg~~Fn 145 (190)
..|..||..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45555555443
No 78
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.63 E-value=19 Score=28.15 Aligned_cols=14 Identities=29% Similarity=0.648 Sum_probs=8.3
Q ss_pred cccccccccccccc
Q 029670 132 KVQQVCVNCGVCMG 145 (190)
Q Consensus 132 ~~~~~C~nCg~~Fn 145 (190)
+....|..||..|.
T Consensus 69 p~~~~C~~Cg~~~~ 82 (117)
T PRK00564 69 KVELECKDCSHVFK 82 (117)
T ss_pred CCEEEhhhCCCccc
Confidence 33456777775554
No 79
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.41 E-value=16 Score=29.93 Aligned_cols=19 Identities=42% Similarity=1.127 Sum_probs=14.1
Q ss_pred cccccccccc----cceecCccc
Q 029670 135 QVCVNCGVCM----GEYFCESCK 153 (190)
Q Consensus 135 ~~C~nCg~~F----nkYfC~~Ck 153 (190)
..||.||.++ ++-|||+|-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCC
Confidence 4788888774 566788885
No 80
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=39.15 E-value=20 Score=22.54 Aligned_cols=23 Identities=39% Similarity=0.911 Sum_probs=12.1
Q ss_pred EecCCCCccccc-c----cccccccccc
Q 029670 122 VICSLCGTEQKV-Q----QVCVNCGVCM 144 (190)
Q Consensus 122 ViCG~C~~eQ~~-~----~~C~nCg~~F 144 (190)
.+|..|+....+ + ..|+.||..|
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 456666655443 1 3566666544
No 81
>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=38.53 E-value=20 Score=23.46 Aligned_cols=10 Identities=30% Similarity=0.876 Sum_probs=5.8
Q ss_pred cccccccccc
Q 029670 136 VCVNCGVCMG 145 (190)
Q Consensus 136 ~C~nCg~~Fn 145 (190)
.|..|+..|+
T Consensus 4 ~C~~C~~~F~ 13 (57)
T cd00065 4 SCMGCGKPFT 13 (57)
T ss_pred cCcccCcccc
Confidence 4555665555
No 82
>PRK05580 primosome assembly protein PriA; Validated
Probab=38.49 E-value=31 Score=34.16 Aligned_cols=47 Identities=21% Similarity=0.552 Sum_probs=31.4
Q ss_pred ccceEecCCCCccccccccccccccccc------ceecCcccCccCCCCCCeeecCCCCcc
Q 029670 118 EVNQVICSLCGTEQKVQQVCVNCGVCMG------EYFCESCKLFDDDTSKKQYHCDGCGIC 172 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~~~~~C~nCg~~Fn------kYfC~~Ckl~ddd~~K~~yHC~~CGIC 172 (190)
..+.+.|..|+... .|++|+..+. .-.|.-|..- ...+..|+.||-=
T Consensus 378 y~~~~~C~~Cg~~~----~C~~C~~~l~~h~~~~~l~Ch~Cg~~----~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 378 YAPFLLCRDCGWVA----ECPHCDASLTLHRFQRRLRCHHCGYQ----EPIPKACPECGST 430 (679)
T ss_pred CCCceEhhhCcCcc----CCCCCCCceeEECCCCeEECCCCcCC----CCCCCCCCCCcCC
Confidence 44678888887653 6888986653 3457777644 2345678888743
No 83
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=38.14 E-value=17 Score=23.78 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=5.1
Q ss_pred eeecCCCCc
Q 029670 163 QYHCDGCGI 171 (190)
Q Consensus 163 ~yHC~~CGI 171 (190)
.-.|+.||-
T Consensus 26 ~~~CP~Cg~ 34 (52)
T TIGR02605 26 LATCPECGG 34 (52)
T ss_pred CCCCCCCCC
Confidence 344666664
No 84
>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=38.11 E-value=14 Score=22.47 Aligned_cols=21 Identities=33% Similarity=0.846 Sum_probs=10.2
Q ss_pred ecCCCCccccc-----cccccccccc
Q 029670 123 ICSLCGTEQKV-----QQVCVNCGVC 143 (190)
Q Consensus 123 iCG~C~~eQ~~-----~~~C~nCg~~ 143 (190)
.|+.|+.+... +..|++||..
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 57788766332 2478888754
No 85
>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=37.79 E-value=23 Score=26.35 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=4.7
Q ss_pred ccccccccc
Q 029670 136 VCVNCGVCM 144 (190)
Q Consensus 136 ~C~nCg~~F 144 (190)
.|++||..|
T Consensus 2 fC~~Cg~~l 10 (104)
T TIGR01384 2 FCPKCGSLM 10 (104)
T ss_pred CCcccCccc
Confidence 355555554
No 86
>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=37.18 E-value=27 Score=21.01 Aligned_cols=8 Identities=50% Similarity=1.327 Sum_probs=6.5
Q ss_pred eeecCCCC
Q 029670 163 QYHCDGCG 170 (190)
Q Consensus 163 ~yHC~~CG 170 (190)
.|+|..|+
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 88888876
No 87
>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=37.15 E-value=22 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.652 Sum_probs=21.9
Q ss_pred cccceEecCCCCccccc---cccccccccccc
Q 029670 117 HEVNQVICSLCGTEQKV---QQVCVNCGVCMG 145 (190)
Q Consensus 117 ~~v~~ViCG~C~~eQ~~---~~~C~nCg~~Fn 145 (190)
..+..|.|..|+++... .+.|++|+.+..
T Consensus 65 tkav~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred ccceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 35578899999987543 268999988876
No 88
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.92 E-value=18 Score=34.80 Aligned_cols=31 Identities=35% Similarity=0.904 Sum_probs=19.0
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
.||+|+..|+.- ..=.|+++ ....|||..||
T Consensus 130 ~Cp~C~kkyt~L--ea~~L~~~--~~~~F~C~~C~ 160 (436)
T KOG2593|consen 130 VCPNCQKKYTSL--EALQLLDN--ETGEFHCENCG 160 (436)
T ss_pred cCCccccchhhh--HHHHhhcc--cCceEEEecCC
Confidence 577777666532 11124443 46789999998
No 89
>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=36.88 E-value=19 Score=24.60 Aligned_cols=21 Identities=24% Similarity=0.812 Sum_probs=12.3
Q ss_pred ccccc--cccc------cccceecCcccC
Q 029670 134 QQVCV--NCGV------CMGEYFCESCKL 154 (190)
Q Consensus 134 ~~~C~--nCg~------~FnkYfC~~Ckl 154 (190)
...|| .||. -+++++|.+|.+
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 35688 7875 256666776654
No 90
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=36.86 E-value=17 Score=28.10 Aligned_cols=23 Identities=30% Similarity=0.667 Sum_probs=9.2
Q ss_pred eEecCCCCcccccc---ccccccccc
Q 029670 121 QVICSLCGTEQKVQ---QVCVNCGVC 143 (190)
Q Consensus 121 ~ViCG~C~~eQ~~~---~~C~nCg~~ 143 (190)
+..|..|+.+-++. ..||+||..
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred cEECCCCCCEEecCCCCCCCcCCcCC
Confidence 44555555443221 245555543
No 91
>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=36.21 E-value=20 Score=25.94 Aligned_cols=36 Identities=28% Similarity=0.575 Sum_probs=24.7
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
..|+.|...=.+..+..|.+.+=-.+|.+-||-.|.
T Consensus 35 ~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~ 70 (78)
T PF12675_consen 35 IRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECP 70 (78)
T ss_pred CcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCC
Confidence 357777655444677788877665677788887775
No 92
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=36.01 E-value=11 Score=30.11 Aligned_cols=11 Identities=27% Similarity=0.471 Sum_probs=7.6
Q ss_pred ccccccccccc
Q 029670 135 QVCVNCGVCMG 145 (190)
Q Consensus 135 ~~C~nCg~~Fn 145 (190)
-.||+||..|.
T Consensus 100 Y~Cp~C~~~y~ 110 (147)
T smart00531 100 YKCPNCQSKYT 110 (147)
T ss_pred EECcCCCCEee
Confidence 36888876665
No 93
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=35.33 E-value=12 Score=31.56 Aligned_cols=19 Identities=47% Similarity=1.265 Sum_probs=8.8
Q ss_pred eEecCCCCccccccccccccc
Q 029670 121 QVICSLCGTEQKVQQVCVNCG 141 (190)
Q Consensus 121 ~ViCG~C~~eQ~~~~~C~nCg 141 (190)
+-.|.+|+-...| .|.+||
T Consensus 118 r~fCaVCG~~S~y--sC~~CG 136 (156)
T KOG3362|consen 118 RKFCAVCGYDSKY--SCVNCG 136 (156)
T ss_pred chhhhhcCCCchh--HHHhcC
Confidence 4445555533333 355555
No 94
>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=34.55 E-value=19 Score=22.39 Aligned_cols=23 Identities=30% Similarity=0.678 Sum_probs=9.1
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
.||.|+..++ | . +..+|-|+.||
T Consensus 4 ~Cp~C~se~~-y-------~----D~~~~vCp~C~ 26 (30)
T PF08274_consen 4 KCPLCGSEYT-Y-------E----DGELLVCPECG 26 (30)
T ss_dssp --TTT------E-------E-----SSSEEETTTT
T ss_pred CCCCCCCcce-e-------c----cCCEEeCCccc
Confidence 5666766666 1 1 24467777776
No 95
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=34.00 E-value=40 Score=22.95 Aligned_cols=37 Identities=11% Similarity=0.350 Sum_probs=24.2
Q ss_pred cCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccc
Q 029670 92 DCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQ 134 (190)
Q Consensus 92 pCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~ 134 (190)
.|..|=+-+.- | ....+.++...++.||.|+....++
T Consensus 8 ~C~~C~~lLql-P-----~~~~~~~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 8 VCSSCFELLQL-P-----AKFSLSKKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred ECccHHHHHcC-C-----CccCCCccceeEEeCCCCceeEEEe
Confidence 46666555432 2 3455666668899999999876553
No 96
>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=33.23 E-value=40 Score=21.85 Aligned_cols=25 Identities=32% Similarity=0.838 Sum_probs=13.6
Q ss_pred eecCcccCccCCCCCCeeecCCCCc
Q 029670 147 YFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 147 YfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.+|..|+-+--...++-|+|..|++
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGL 36 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-
T ss_pred CCCcccCcccCCCCCCeEEECCCCC
Confidence 3455553222125678888888885
No 97
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=33.21 E-value=36 Score=21.90 Aligned_cols=33 Identities=27% Similarity=0.661 Sum_probs=19.3
Q ss_pred ccccccccccceecCcccCc-cCCCCCCeeecCCCC
Q 029670 136 VCVNCGVCMGEYFCESCKLF-DDDTSKKQYHCDGCG 170 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~-ddd~~K~~yHC~~CG 170 (190)
.||+||+.-+-|+ .. -.. -|.+..-+|-|..||
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 4788877666554 10 111 223455688998887
No 98
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=33.20 E-value=22 Score=34.47 Aligned_cols=10 Identities=40% Similarity=1.398 Sum_probs=8.4
Q ss_pred CeeecCCCCc
Q 029670 162 KQYHCDGCGI 171 (190)
Q Consensus 162 ~~yHC~~CGI 171 (190)
+-|||++||+
T Consensus 426 ~CY~CEDCg~ 435 (468)
T KOG1701|consen 426 NCYKCEDCGL 435 (468)
T ss_pred cceehhhcCc
Confidence 5799999986
No 99
>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=33.16 E-value=47 Score=30.38 Aligned_cols=48 Identities=29% Similarity=0.609 Sum_probs=30.7
Q ss_pred ccceEecCCCCccccc-ccccccccccccc-eecCcccCccCC---CCCCeeecCCCC
Q 029670 118 EVNQVICSLCGTEQKV-QQVCVNCGVCMGE-YFCESCKLFDDD---TSKKQYHCDGCG 170 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~~-~~~C~nCg~~Fnk-YfC~~Ckl~ddd---~~K~~yHC~~CG 170 (190)
..+-..|+.|.++=.+ ...|++||..-.- |+ -++++ ..-...-|+.|+
T Consensus 207 G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~-----~~e~~~~~~~~r~e~C~~C~ 259 (305)
T TIGR01562 207 GLRYLSCSLCATEWHYVRVKCSHCEESKHLAYL-----SLEHDAEKAVLKAETCDSCQ 259 (305)
T ss_pred CceEEEcCCCCCcccccCccCCCCCCCCceeeE-----eecCCCCCcceEEeeccccc
Confidence 3468899999999665 4789999975321 21 11332 123566777777
No 100
>PRK12496 hypothetical protein; Provisional
Probab=32.91 E-value=21 Score=29.47 Aligned_cols=23 Identities=26% Similarity=0.635 Sum_probs=11.1
Q ss_pred EecCCCCcccc---cccccccccccc
Q 029670 122 VICSLCGTEQK---VQQVCVNCGVCM 144 (190)
Q Consensus 122 ViCG~C~~eQ~---~~~~C~nCg~~F 144 (190)
.+|..|+++-+ ....||.||++.
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChh
Confidence 34555655432 124455555543
No 101
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=32.86 E-value=23 Score=22.29 Aligned_cols=24 Identities=38% Similarity=1.000 Sum_probs=12.6
Q ss_pred eecCccc-Cc--cCCCCCCeeecCCCCc
Q 029670 147 YFCESCK-LF--DDDTSKKQYHCDGCGI 171 (190)
Q Consensus 147 YfC~~Ck-l~--ddd~~K~~yHC~~CGI 171 (190)
-||+.|+ |+ ..+..+.+ .|..||.
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~-~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRV-ACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTE-EESSSS-
T ss_pred eeCCCCCccceEcCCCccCc-CCCCCCC
Confidence 3788884 33 22223444 7888874
No 102
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=32.50 E-value=25 Score=30.84 Aligned_cols=18 Identities=6% Similarity=0.003 Sum_probs=13.3
Q ss_pred ecCCCCCcccCchhhhhc
Q 029670 83 RAPCCNEIFDCRHCHNEA 100 (190)
Q Consensus 83 rcpCCgk~YpCr~CHDE~ 100 (190)
+.+=-|.+|+--.+..+-
T Consensus 167 ~iaGiGNiya~EiLf~a~ 184 (274)
T PRK01103 167 VVVGVGNIYADEALFRAG 184 (274)
T ss_pred eEecccHhHHHHHHHHcC
Confidence 456678888888888753
No 103
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.04 E-value=20 Score=20.89 Aligned_cols=11 Identities=27% Similarity=0.604 Sum_probs=9.2
Q ss_pred ccccccccccc
Q 029670 136 VCVNCGVCMGE 146 (190)
Q Consensus 136 ~C~nCg~~Fnk 146 (190)
.|+.||..|+.
T Consensus 4 ~C~~CgR~F~~ 14 (25)
T PF13913_consen 4 PCPICGRKFNP 14 (25)
T ss_pred cCCCCCCEECH
Confidence 69999999873
No 104
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=31.93 E-value=29 Score=24.32 Aligned_cols=12 Identities=33% Similarity=1.005 Sum_probs=7.1
Q ss_pred CCCeeecCCCCc
Q 029670 160 SKKQYHCDGCGI 171 (190)
Q Consensus 160 ~K~~yHC~~CGI 171 (190)
-++.|+|-.||.
T Consensus 34 H~dR~~CGkCgy 45 (51)
T COG1998 34 HKDRWACGKCGY 45 (51)
T ss_pred cCceeEeccccc
Confidence 345666666663
No 105
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=31.43 E-value=27 Score=25.67 Aligned_cols=28 Identities=39% Similarity=0.739 Sum_probs=21.3
Q ss_pred ceEecCCCCcccccc------cccccccccccce
Q 029670 120 NQVICSLCGTEQKVQ------QVCVNCGVCMGEY 147 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~------~~C~nCg~~FnkY 147 (190)
-.|.|.-|..+|.+- -.|..||..+++-
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 478999999988752 4788888877743
No 106
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=30.89 E-value=36 Score=21.26 Aligned_cols=25 Identities=20% Similarity=0.656 Sum_probs=13.7
Q ss_pred ceecCcccCccCCCCCCeeecCCCCc
Q 029670 146 EYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 146 kYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.|-|.+|.+.-+. .+++..|+-||.
T Consensus 2 ~~~C~~CG~i~~g-~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEG-EEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeEC-CcCCCcCcCCCC
Confidence 3567777654221 235566766663
No 107
>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=30.59 E-value=27 Score=33.61 Aligned_cols=49 Identities=29% Similarity=0.689 Sum_probs=26.8
Q ss_pred CcccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCccccc------ccccc-cccccccceecCccc
Q 029670 89 EIFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKV------QQVCV-NCGVCMGEYFCESCK 153 (190)
Q Consensus 89 k~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~------~~~C~-nCg~~FnkYfC~~Ck 153 (190)
+.|-|+.||.=-... ....++..-.|..|..+.+. +.+|. || |-||+|.
T Consensus 4 ~L~fC~~C~~irc~~----------c~~~Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~C------f~CP~C~ 59 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPR----------CVSEEIDSYYCPNCLFEVPSSEARSEKNRCSRNC------FDCPICF 59 (483)
T ss_pred cceecccccccCChh----------hcccccceeECccccccCChhhheeccceecccc------ccCCCCC
Confidence 356788888643310 11134456677777766443 24555 54 3377774
No 108
>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=30.54 E-value=26 Score=27.14 Aligned_cols=20 Identities=30% Similarity=0.660 Sum_probs=14.4
Q ss_pred ecCCCCcccccc----cccccccc
Q 029670 123 ICSLCGTEQKVQ----QVCVNCGV 142 (190)
Q Consensus 123 iCG~C~~eQ~~~----~~C~nCg~ 142 (190)
-|..|+..++.. ..||||+.
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~ 28 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEG 28 (98)
T ss_pred hhccCCcccccccccCCCCCCCcc
Confidence 588888776543 58999963
No 109
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.94 E-value=34 Score=28.62 Aligned_cols=23 Identities=30% Similarity=0.820 Sum_probs=14.0
Q ss_pred ccccccccccc-ceecCcccCccC
Q 029670 135 QVCVNCGVCMG-EYFCESCKLFDD 157 (190)
Q Consensus 135 ~~C~nCg~~Fn-kYfC~~Ckl~dd 157 (190)
..|+.||.... .+.|+.|.+..|
T Consensus 310 ~~C~~cg~~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 310 KTCPCCGHLSGRLFKCPRCGFVHD 333 (364)
T ss_pred ccccccCCccceeEECCCCCCeeh
Confidence 68888888222 245666665433
No 110
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=29.33 E-value=30 Score=21.48 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=14.5
Q ss_pred cccccccccccceecCcccCc
Q 029670 135 QVCVNCGVCMGEYFCESCKLF 155 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ 155 (190)
..|..++.....|||..|+.+
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 357777777788888887654
No 111
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=29.31 E-value=32 Score=22.64 Aligned_cols=30 Identities=30% Similarity=0.732 Sum_probs=14.8
Q ss_pred cccccccccccceecCcccCccCCCCCCeeecCCCC
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
..||.||-.=. =++|+|...+..|+|..|+
T Consensus 4 ~pCP~CGG~Dr------Fri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 4 GPCPICGGKDR------FRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp E--TTTT-TTT------EEEETT----S-EEETTTT
T ss_pred CCCCCCcCccc------cccCcCcccCCCEECCCCC
Confidence 46788875311 1367887778899999994
No 112
>PRK11823 DNA repair protein RadA; Provisional
Probab=29.23 E-value=28 Score=32.76 Aligned_cols=22 Identities=27% Similarity=0.909 Sum_probs=13.4
Q ss_pred cccccccccccee--cCcccCccC
Q 029670 136 VCVNCGVCMGEYF--CESCKLFDD 157 (190)
Q Consensus 136 ~C~nCg~~FnkYf--C~~Ckl~dd 157 (190)
.|.+||....+++ ||.|+-|+.
T Consensus 9 ~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (446)
T PRK11823 9 VCQECGAESPKWLGRCPECGAWNT 32 (446)
T ss_pred ECCcCCCCCcccCeeCcCCCCccc
Confidence 4666666666655 666666643
No 113
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=29.07 E-value=40 Score=22.82 Aligned_cols=29 Identities=31% Similarity=0.794 Sum_probs=15.3
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCCc
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGI 171 (190)
.|.+|+.... .+|...+.....-|+.||+
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 4666665444 2354433444566666665
No 114
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=29.04 E-value=34 Score=26.54 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=9.9
Q ss_pred ccccccccccccccc
Q 029670 131 QKVQQVCVNCGVCMG 145 (190)
Q Consensus 131 Q~~~~~C~nCg~~Fn 145 (190)
.+....|..||..|.
T Consensus 67 ~p~~~~C~~Cg~~~~ 81 (114)
T PRK03681 67 QEAECWCETCQQYVT 81 (114)
T ss_pred eCcEEEcccCCCeee
Confidence 344467888887664
No 115
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=28.97 E-value=28 Score=32.91 Aligned_cols=23 Identities=26% Similarity=0.804 Sum_probs=17.5
Q ss_pred ccccccccccccee--cCcccCccC
Q 029670 135 QVCVNCGVCMGEYF--CESCKLFDD 157 (190)
Q Consensus 135 ~~C~nCg~~FnkYf--C~~Ckl~dd 157 (190)
-.|.+||....+++ ||.|+-|+.
T Consensus 8 y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 8 FVCQHCGADSPKWQGKCPACHAWNT 32 (454)
T ss_pred EECCcCCCCCccccEECcCCCCccc
Confidence 36888888877776 888888854
No 116
>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=28.90 E-value=44 Score=23.09 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=6.7
Q ss_pred ceEecCCCCcc
Q 029670 120 NQVICSLCGTE 130 (190)
Q Consensus 120 ~~ViCG~C~~e 130 (190)
.++||..|...
T Consensus 21 ~aLIC~~C~~h 31 (54)
T PF10058_consen 21 YALICSKCFSH 31 (54)
T ss_pred eeEECcccchh
Confidence 46667777543
No 117
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=28.49 E-value=30 Score=24.83 Aligned_cols=20 Identities=25% Similarity=0.620 Sum_probs=11.9
Q ss_pred ecCCCCccccccccccccccc
Q 029670 123 ICSLCGTEQKVQQVCVNCGVC 143 (190)
Q Consensus 123 iCG~C~~eQ~~~~~C~nCg~~ 143 (190)
.|..|...++ ...||+||..
T Consensus 5 AC~~C~~i~~-~~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT-EDRCPVCGSR 24 (61)
T ss_pred hhhhCCcccC-CCcCCCCcCC
Confidence 4666666553 2368888764
No 118
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.10 E-value=16 Score=34.13 Aligned_cols=34 Identities=24% Similarity=0.718 Sum_probs=24.4
Q ss_pred eEecCCCCcc------ccc--ccccccccccccceecCcccCcc
Q 029670 121 QVICSLCGTE------QKV--QQVCVNCGVCMGEYFCESCKLFD 156 (190)
Q Consensus 121 ~ViCG~C~~e------Q~~--~~~C~nCg~~FnkYfC~~Ckl~d 156 (190)
+-+|.+|... .+- ...|..||..+| +||||+-+-
T Consensus 300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm~--eCPICRqyi 341 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKRMN--ECPICRQYI 341 (350)
T ss_pred HHHHHHHhcCCcceEEeecCcEEeehhhccccc--cCchHHHHH
Confidence 6677777543 111 147999999999 999998663
No 119
>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=27.89 E-value=39 Score=20.06 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=2.9
Q ss_pred CeeecCCCC
Q 029670 162 KQYHCDGCG 170 (190)
Q Consensus 162 ~~yHC~~CG 170 (190)
..|+|..|.
T Consensus 14 ~~Y~C~~Cd 22 (30)
T PF07649_consen 14 WFYRCSECD 22 (30)
T ss_dssp -EEE-TTT-
T ss_pred ceEECccCC
Confidence 344444443
No 120
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=27.83 E-value=32 Score=23.83 Aligned_cols=24 Identities=29% Similarity=0.738 Sum_probs=19.8
Q ss_pred cceEecCCCCcccccc-cccccccc
Q 029670 119 VNQVICSLCGTEQKVQ-QVCVNCGV 142 (190)
Q Consensus 119 v~~ViCG~C~~eQ~~~-~~C~nCg~ 142 (190)
...+||..|+...++. ..|..||+
T Consensus 12 ~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 12 FNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hcccchhcccCCCCccccccccCCC
Confidence 3578999999998875 68988886
No 121
>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=26.71 E-value=31 Score=21.36 Aligned_cols=23 Identities=35% Similarity=0.663 Sum_probs=11.1
Q ss_pred ceEecCCCCcccc-cccccccccc
Q 029670 120 NQVICSLCGTEQK-VQQVCVNCGV 142 (190)
Q Consensus 120 ~~ViCG~C~~eQ~-~~~~C~nCg~ 142 (190)
..-.|..|++.+- ....|++|+.
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEcCCCCCEecCCCcCCCCcCc
Confidence 3556777777644 3467777764
No 122
>PF11405 Inhibitor_I67: Bromelain inhibitor VI; InterPro: IPR022713 Bromelain inhibitor VI is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain. ; PDB: 2BI6_H 1BI6_H.
Probab=26.63 E-value=24 Score=23.27 Aligned_cols=16 Identities=31% Similarity=0.912 Sum_probs=12.3
Q ss_pred cccccccccccceecC
Q 029670 135 QVCVNCGVCMGEYFCE 150 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~ 150 (190)
..|..|.+.|++|.|.
T Consensus 16 gfcktckaefgkyicl 31 (41)
T PF11405_consen 16 GFCKTCKAEFGKYICL 31 (41)
T ss_dssp TT-SSEEEETTEEEE-
T ss_pred hHHHHHHHHhcceEEE
Confidence 5688899999999874
No 123
>PRK10445 endonuclease VIII; Provisional
Probab=26.60 E-value=35 Score=29.89 Aligned_cols=17 Identities=0% Similarity=-0.095 Sum_probs=11.5
Q ss_pred cCCCCCcccCchhhhhc
Q 029670 84 APCCNEIFDCRHCHNEA 100 (190)
Q Consensus 84 cpCCgk~YpCr~CHDE~ 100 (190)
.+=-|.+|+.-..+.+-
T Consensus 164 vaGIGNiyadEiLf~A~ 180 (263)
T PRK10445 164 LAGLGNYLRVEILWQAG 180 (263)
T ss_pred cccccHHHHHHHHHHcC
Confidence 34557788887777653
No 124
>PLN00209 ribosomal protein S27; Provisional
Probab=26.51 E-value=49 Score=25.42 Aligned_cols=38 Identities=21% Similarity=0.318 Sum_probs=25.7
Q ss_pred ceEecCCCCcccccc------cccccccccccceecCcccCccC
Q 029670 120 NQVICSLCGTEQKVQ------QVCVNCGVCMGEYFCESCKLFDD 157 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~------~~C~nCg~~FnkYfC~~Ckl~dd 157 (190)
-.|.|..|..+|.+- -.|..||..+++-.=.+.+|-++
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~g 78 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTEG 78 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecCC
Confidence 367888888887651 36888888877666555555543
No 125
>PRK11032 hypothetical protein; Provisional
Probab=26.23 E-value=42 Score=28.09 Aligned_cols=24 Identities=21% Similarity=0.656 Sum_probs=16.2
Q ss_pred ceEecCCCCcccccc-----ccccccccc
Q 029670 120 NQVICSLCGTEQKVQ-----QVCVNCGVC 143 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~-----~~C~nCg~~ 143 (190)
-.++|-.|+++..+. ..||.||+.
T Consensus 123 G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 123 GNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred ceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 467788887764442 578888753
No 126
>PRK05978 hypothetical protein; Provisional
Probab=26.20 E-value=35 Score=28.21 Aligned_cols=6 Identities=33% Similarity=0.994 Sum_probs=3.0
Q ss_pred cccccc
Q 029670 135 QVCVNC 140 (190)
Q Consensus 135 ~~C~nC 140 (190)
..||+|
T Consensus 34 grCP~C 39 (148)
T PRK05978 34 GRCPAC 39 (148)
T ss_pred CcCCCC
Confidence 345555
No 127
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=25.81 E-value=38 Score=29.17 Aligned_cols=22 Identities=36% Similarity=0.963 Sum_probs=13.9
Q ss_pred ccccccccccccee--cCcccCcc
Q 029670 135 QVCVNCGVCMGEYF--CESCKLFD 156 (190)
Q Consensus 135 ~~C~nCg~~FnkYf--C~~Ckl~d 156 (190)
..|.+||...-+|+ ||.|+=|+
T Consensus 355 ~~c~~cg~~~~~~~~~c~~c~~~~ 378 (389)
T PRK11788 355 YRCRNCGFTARTLYWHCPSCKAWE 378 (389)
T ss_pred EECCCCCCCCccceeECcCCCCcc
Confidence 45777776666655 66666664
No 128
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=25.71 E-value=43 Score=25.72 Aligned_cols=16 Identities=31% Similarity=0.723 Sum_probs=12.8
Q ss_pred CCCCeeecCCCCcccc
Q 029670 159 TSKKQYHCDGCGICRF 174 (190)
Q Consensus 159 ~~K~~yHC~~CGICRv 174 (190)
+.+++|.|-+|=+=|.
T Consensus 16 ~~~PiyQC~GCCFSrA 31 (87)
T smart00067 16 PGAPIYQCMGCCFSRA 31 (87)
T ss_pred CCCceeEecceecccc
Confidence 4679999999976654
No 129
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.60 E-value=22 Score=29.56 Aligned_cols=11 Identities=36% Similarity=0.543 Sum_probs=6.2
Q ss_pred cccccccccCC
Q 029670 177 VLLLLAHHFEP 187 (190)
Q Consensus 177 ~l~~~~~~~~~ 187 (190)
|.++|||++||
T Consensus 57 gvlglg~dye~ 67 (160)
T COG4306 57 GVLGLGGDYEP 67 (160)
T ss_pred eeeccCCCCCC
Confidence 44556666665
No 130
>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=25.46 E-value=37 Score=20.00 Aligned_cols=11 Identities=27% Similarity=1.165 Sum_probs=7.9
Q ss_pred cceecCcccCc
Q 029670 145 GEYFCESCKLF 155 (190)
Q Consensus 145 nkYfC~~Ckl~ 155 (190)
+.|+|..|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 46788888655
No 131
>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=25.39 E-value=67 Score=21.50 Aligned_cols=33 Identities=24% Similarity=0.444 Sum_probs=17.0
Q ss_pred ccccccccccceecCcccCccCCCCCCeeecCCCCcc
Q 029670 136 VCVNCGVCMGEYFCESCKLFDDDTSKKQYHCDGCGIC 172 (190)
Q Consensus 136 ~C~nCg~~FnkYfC~~Ckl~ddd~~K~~yHC~~CGIC 172 (190)
.||.||..=-... .-+++....-.|+|..||--
T Consensus 3 PCPfCGg~~~~~~----~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 3 PCPFCGGADVYLR----RGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCcceeeE----eccCCCCCEEEEECCCCCCC
Confidence 5888875322110 01233334457788888853
No 132
>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=25.28 E-value=58 Score=21.11 Aligned_cols=21 Identities=33% Similarity=0.825 Sum_probs=12.2
Q ss_pred eecCcccCccCCCCCCeeecCCCC
Q 029670 147 YFCESCKLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 147 YfC~~Ckl~ddd~~K~~yHC~~CG 170 (190)
|.|++|+. + ..-..|||..|-
T Consensus 1 ~~C~~C~~-~--i~g~r~~C~~C~ 21 (46)
T cd02249 1 YSCDGCLK-P--IVGVRYHCLVCE 21 (46)
T ss_pred CCCcCCCC-C--CcCCEEECCCCC
Confidence 45666665 1 122577777776
No 133
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=25.10 E-value=57 Score=25.22 Aligned_cols=10 Identities=30% Similarity=0.660 Sum_probs=6.1
Q ss_pred cccccccccc
Q 029670 135 QVCVNCGVCM 144 (190)
Q Consensus 135 ~~C~nCg~~F 144 (190)
..|++||+..
T Consensus 43 ~~C~~Cg~~~ 52 (111)
T PF14319_consen 43 YRCEDCGHEK 52 (111)
T ss_pred eecCCCCceE
Confidence 4666666554
No 134
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=25.08 E-value=61 Score=22.80 Aligned_cols=26 Identities=31% Similarity=0.791 Sum_probs=17.7
Q ss_pred ceEecCCCCcc-----ccccccccc--cccccc
Q 029670 120 NQVICSLCGTE-----QKVQQVCVN--CGVCMG 145 (190)
Q Consensus 120 ~~ViCG~C~~e-----Q~~~~~C~n--Cg~~Fn 145 (190)
..|+|..|++. -.+...|+. |+..|+
T Consensus 20 DiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~~ 52 (54)
T PF14446_consen 20 DIVVCPECGAPYHRDCWEKAGGCINYSCGTGFE 52 (54)
T ss_pred CEEECCCCCCcccHHHHhhCCceEeccCCCCcc
Confidence 57888888876 223467777 777665
No 135
>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=25.01 E-value=26 Score=24.09 Aligned_cols=18 Identities=28% Similarity=0.717 Sum_probs=9.3
Q ss_pred CccCCCCCCeeecCCCCc
Q 029670 154 LFDDDTSKKQYHCDGCGI 171 (190)
Q Consensus 154 l~ddd~~K~~yHC~~CGI 171 (190)
+|...+.....-|+.||+
T Consensus 12 ~WR~g~~~~~~LCNaCgl 29 (54)
T cd00202 12 LWRRGPSGGSTLCNACGL 29 (54)
T ss_pred ccccCCCCcchHHHHHHH
Confidence 454444444555666654
No 136
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.69 E-value=60 Score=25.16 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=4.3
Q ss_pred cccccccccc
Q 029670 136 VCVNCGVCMG 145 (190)
Q Consensus 136 ~C~nCg~~Fn 145 (190)
.|++||.-++
T Consensus 44 ~C~~CG~y~~ 53 (99)
T PRK14892 44 TCGNCGLYTE 53 (99)
T ss_pred ECCCCCCccC
Confidence 3444444433
No 137
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=24.50 E-value=58 Score=23.66 Aligned_cols=28 Identities=32% Similarity=0.693 Sum_probs=18.8
Q ss_pred ccccceEecCCCCcccccc----ccccccccc
Q 029670 116 RHEVNQVICSLCGTEQKVQ----QVCVNCGVC 143 (190)
Q Consensus 116 R~~v~~ViCG~C~~eQ~~~----~~C~nCg~~ 143 (190)
|.+.-.-+||.|+.+.... -.|.-||.+
T Consensus 15 r~~~miYiCgdC~~en~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLKRGDVIRCRECGYR 46 (62)
T ss_pred CcccEEEEeccccccccccCCCcEehhhcchH
Confidence 4455567888888886653 367777654
No 138
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.40 E-value=45 Score=26.62 Aligned_cols=14 Identities=29% Similarity=0.527 Sum_probs=8.7
Q ss_pred cccccccccccccc
Q 029670 132 KVQQVCVNCGVCMG 145 (190)
Q Consensus 132 ~~~~~C~nCg~~Fn 145 (190)
+....|++||..|.
T Consensus 68 p~~~~C~~CG~~~~ 81 (135)
T PRK03824 68 EAVLKCRNCGNEWS 81 (135)
T ss_pred ceEEECCCCCCEEe
Confidence 34456777776665
No 139
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=24.13 E-value=49 Score=27.15 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=14.9
Q ss_pred ceEecCCCCcccccc-----ccccccccc
Q 029670 120 NQVICSLCGTEQKVQ-----QVCVNCGVC 143 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~-----~~C~nCg~~ 143 (190)
-..+|..|+++..+. ..||.||+.
T Consensus 111 G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 111 GTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred ceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 356677777664432 578888753
No 140
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=23.90 E-value=33 Score=38.80 Aligned_cols=61 Identities=20% Similarity=0.450 Sum_probs=33.0
Q ss_pred cccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccccccccccccccceecCcc
Q 029670 90 IFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNCGVCMGEYFCESC 152 (190)
Q Consensus 90 ~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nCg~~FnkYfC~~C 152 (190)
||-|++|-.+--.....=..+ -.-+.+...+.+||.|+....+ +.||.=|..|=+|.|.-|
T Consensus 3602 Y~vC~KCrKAYFGGEaRCdAe-~~~ddydP~ELiCG~CSDvS~a-QmCPkHGtdfLEYKCRyC 3662 (3738)
T KOG1428|consen 3602 YYVCYKCRKAYFGGEARCDAE-AGGDDYDPRELICGACSDVSRA-QMCPKHGTDFLEYKCRYC 3662 (3738)
T ss_pred hhhhhhhhhhhcCchhhcchh-cCCCCCCHHHhhhccccccccc-eecccccchhhhhhhhee
Confidence 677777765543221100000 0013356679999999876444 356666666655554444
No 141
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.73 E-value=40 Score=28.44 Aligned_cols=25 Identities=28% Similarity=0.717 Sum_probs=17.5
Q ss_pred eEecCCCCcc--ccccccccccccccc
Q 029670 121 QVICSLCGTE--QKVQQVCVNCGVCMG 145 (190)
Q Consensus 121 ~ViCG~C~~e--Q~~~~~C~nCg~~Fn 145 (190)
.-+|.+|+.. .+.-..||.||++-.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k~ 160 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPKE 160 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChHH
Confidence 6788888764 433468999987644
No 142
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=23.12 E-value=32 Score=24.58 Aligned_cols=23 Identities=35% Similarity=0.859 Sum_probs=14.5
Q ss_pred cCCCCc--ccccccccccccccccc
Q 029670 124 CSLCGT--EQKVQQVCVNCGVCMGE 146 (190)
Q Consensus 124 CG~C~~--eQ~~~~~C~nCg~~Fnk 146 (190)
|.+|.. +......|||||-.|.+
T Consensus 29 CTFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 29 CTFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred CcccHHHHHHHhcCcCcCCCCcccc
Confidence 345543 23336789999987764
No 143
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=22.62 E-value=39 Score=23.63 Aligned_cols=9 Identities=22% Similarity=0.903 Sum_probs=4.5
Q ss_pred eEecCCCCc
Q 029670 121 QVICSLCGT 129 (190)
Q Consensus 121 ~ViCG~C~~ 129 (190)
++.|+.|++
T Consensus 4 eiRC~~Cnk 12 (51)
T PF10122_consen 4 EIRCGHCNK 12 (51)
T ss_pred ceeccchhH
Confidence 455555544
No 144
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=22.59 E-value=94 Score=19.81 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=15.2
Q ss_pred ecCcccCccCCCCCCeeecCCCCccc
Q 029670 148 FCESCKLFDDDTSKKQYHCDGCGICR 173 (190)
Q Consensus 148 fC~~Ckl~ddd~~K~~yHC~~CGICR 173 (190)
+|.+|+-. +......-|+.|+.-.
T Consensus 1 ~C~vC~~~--~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQS--DDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTSS--CTTSSEEEBSTTSCEE
T ss_pred eCcCCCCc--CCCCCeEEcCCCChhh
Confidence 46777662 3356777888877433
No 145
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=22.58 E-value=64 Score=24.74 Aligned_cols=37 Identities=22% Similarity=0.341 Sum_probs=24.5
Q ss_pred ceEecCCCCcccccc------cccccccccccceecCcccCcc
Q 029670 120 NQVICSLCGTEQKVQ------QVCVNCGVCMGEYFCESCKLFD 156 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~------~~C~nCg~~FnkYfC~~Ckl~d 156 (190)
-.|.|.-|..+|.+- -.|..||..+++-.=.+.+|-+
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~ 76 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLTE 76 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecC
Confidence 367788888877651 3688888777766555555543
No 146
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=22.48 E-value=37 Score=33.38 Aligned_cols=64 Identities=31% Similarity=0.555 Sum_probs=41.6
Q ss_pred ccceEecCCCCcccc---cccccccccccccc-eecCcc-cCccCCCCCCeeecCCCCcccccCccccccccc
Q 029670 118 EVNQVICSLCGTEQK---VQQVCVNCGVCMGE-YFCESC-KLFDDDTSKKQYHCDGCGICRFVYVLLLLAHHF 185 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~---~~~~C~nCg~~Fnk-YfC~~C-kl~ddd~~K~~yHC~~CGICRvG~~l~~~~~~~ 185 (190)
.+++..|-.|.+-.+ +...|+.||-.=++ -+|++| +++.--+.+. ++|.||+++..-+-..|-|
T Consensus 133 tv~qLyC~vc~~fladr~veg~cp~C~yd~ARGDqcd~cG~l~N~~el~~----pkc~ic~~~p~~~~t~h~F 201 (567)
T KOG1247|consen 133 TVKQLYCEVCDTFLADRFVEGKCPFCGYDDARGDQCDKCGKLVNAAELKI----PKCKICQAGPVVRQTQHLF 201 (567)
T ss_pred eeeeEEehhhcccccchhhhccCCCCCCccccchhhhhhhhhcCHHHhcC----cchheeccCCeeeeeeEEE
Confidence 567888888887633 45788888765554 357777 4443322222 4789999998766666654
No 147
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=22.45 E-value=62 Score=28.16 Aligned_cols=28 Identities=18% Similarity=0.489 Sum_probs=21.8
Q ss_pred ccceEecCCCCccccccccccccccccc
Q 029670 118 EVNQVICSLCGTEQKVQQVCVNCGVCMG 145 (190)
Q Consensus 118 ~v~~ViCG~C~~eQ~~~~~C~nCg~~Fn 145 (190)
.-..|+|.+|...+--...||.||..=-
T Consensus 159 ~~hcilCtvCe~r~w~g~~CPKCGr~G~ 186 (200)
T PF12387_consen 159 SKHCILCTVCEGREWKGGNCPKCGRHGK 186 (200)
T ss_pred CCceEEEeeeecCccCCCCCCcccCCCC
Confidence 3468999999988777778999986433
No 148
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=22.26 E-value=55 Score=26.30 Aligned_cols=28 Identities=21% Similarity=0.479 Sum_probs=21.6
Q ss_pred cccceEecCCCCcc-cccccccccccccc
Q 029670 117 HEVNQVICSLCGTE-QKVQQVCVNCGVCM 144 (190)
Q Consensus 117 ~~v~~ViCG~C~~e-Q~~~~~C~nCg~~F 144 (190)
...-...|..|++. -|....|++|+..-
T Consensus 25 ~kl~g~kC~~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 25 GKLLGTKCKKCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred CcEEEEEcCCCCeEEcCCcccCCCCCCCC
Confidence 45567889999987 45678899998774
No 149
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=21.88 E-value=27 Score=24.80 Aligned_cols=19 Identities=37% Similarity=0.924 Sum_probs=12.9
Q ss_pred ccccccccc--ccceecC-ccc
Q 029670 135 QVCVNCGVC--MGEYFCE-SCK 153 (190)
Q Consensus 135 ~~C~nCg~~--FnkYfC~-~Ck 153 (190)
..|++||.+ .++-||+ .|+
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~ 25 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCR 25 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHH
Confidence 368888865 5677774 664
No 150
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=72 Score=29.22 Aligned_cols=48 Identities=21% Similarity=0.522 Sum_probs=30.0
Q ss_pred eecCCCCC--cccCchhhhhccCCCCcCCcCcccCCccccceEecCCCCcccccccccccc
Q 029670 82 IRAPCCNE--IFDCRHCHNEAMNNINVDQKLRHDIPRHEVNQVICSLCGTEQKVQQVCVNC 140 (190)
Q Consensus 82 LrcpCCgk--~YpCr~CHDE~~~h~~~~~~~~H~ldR~~v~~ViCG~C~~eQ~~~~~C~nC 140 (190)
..|..||. |-||.-||..-+- |.-.-.....+.|..|+.-..+ .|+.|
T Consensus 230 ~~C~~CGg~rFlpC~~C~GS~kv---------~~~~~~~~~~~rC~~CNENGLv--rCp~C 279 (281)
T KOG2824|consen 230 GVCESCGGARFLPCSNCHGSCKV---------HEEEEDDGGVLRCLECNENGLV--RCPVC 279 (281)
T ss_pred CcCCCcCCcceEecCCCCCceee---------eeeccCCCcEEECcccCCCCce--eCCcc
Confidence 78899975 8999999987653 2211123346667777654444 45554
No 151
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.04 E-value=56 Score=28.77 Aligned_cols=16 Identities=6% Similarity=0.061 Sum_probs=11.3
Q ss_pred CCCCCcccCchhhhhc
Q 029670 85 PCCNEIFDCRHCHNEA 100 (190)
Q Consensus 85 pCCgk~YpCr~CHDE~ 100 (190)
.=-|.+|+.-.+..+-
T Consensus 168 aGiGNiya~EiLf~a~ 183 (272)
T PRK14810 168 RGVGNIYADEALFRAG 183 (272)
T ss_pred ccccHhHHHHHHHHcC
Confidence 4557788888887753
No 152
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.92 E-value=44 Score=30.85 Aligned_cols=40 Identities=35% Similarity=0.742 Sum_probs=20.7
Q ss_pred ecCCCCcccccc---cccc-cccccccceecCcc--cCccCCCCCCeeecCCCC
Q 029670 123 ICSLCGTEQKVQ---QVCV-NCGVCMGEYFCESC--KLFDDDTSKKQYHCDGCG 170 (190)
Q Consensus 123 iCG~C~~eQ~~~---~~C~-nCg~~FnkYfC~~C--kl~ddd~~K~~yHC~~CG 170 (190)
+|..|.+..... ..=+ .|||.| |..| ++|.. ....|+.|+
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~----C~sCv~~l~~~----~~~~CP~C~ 50 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTL----CESCVDLLFVR----GSGSCPECD 50 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcc----cHHHHHHHhcC----CCCCCCCCC
Confidence 466666642221 0011 377764 6677 46632 345787665
No 153
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.83 E-value=30 Score=28.19 Aligned_cols=18 Identities=33% Similarity=0.783 Sum_probs=13.4
Q ss_pred ccccccccccc---eecCccc
Q 029670 136 VCVNCGVCMGE---YFCESCK 153 (190)
Q Consensus 136 ~C~nCg~~Fnk---YfC~~Ck 153 (190)
.|+.||..|+. ..|+.|.
T Consensus 5 nC~~CgklF~~~~~~iCp~C~ 25 (137)
T TIGR03826 5 NCPKCGRLFVKTGRDVCPSCY 25 (137)
T ss_pred cccccchhhhhcCCccCHHHh
Confidence 68888888873 4688885
No 154
>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=20.75 E-value=71 Score=22.47 Aligned_cols=33 Identities=27% Similarity=0.470 Sum_probs=18.0
Q ss_pred eEecCCCCcccccc------cccccccccccceecCccc
Q 029670 121 QVICSLCGTEQKVQ------QVCVNCGVCMGEYFCESCK 153 (190)
Q Consensus 121 ~ViCG~C~~eQ~~~------~~C~nCg~~FnkYfC~~Ck 153 (190)
.|.|..|..+|.+- -.|..||..+++-.=.+-+
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~ 45 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKAR 45 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeE
Confidence 57777787776651 3677777777655434333
No 155
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.69 E-value=49 Score=30.12 Aligned_cols=29 Identities=28% Similarity=0.518 Sum_probs=19.0
Q ss_pred cccceEecCCCCccccc-----cccccccccccc
Q 029670 117 HEVNQVICSLCGTEQKV-----QQVCVNCGVCMG 145 (190)
Q Consensus 117 ~~v~~ViCG~C~~eQ~~-----~~~C~nCg~~Fn 145 (190)
+..+-=.||.|+++... ...|++||+.+=
T Consensus 107 w~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 107 WYRSHRFCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred HHhhCcCCCCCCCcCccccCceeeeCCCCCCccC
Confidence 34455678899876333 357888887643
No 156
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=20.51 E-value=78 Score=30.79 Aligned_cols=34 Identities=24% Similarity=0.507 Sum_probs=19.5
Q ss_pred cccccccccccceecCcccCccC--CCCCCeeecCCCC
Q 029670 135 QVCVNCGVCMGEYFCESCKLFDD--DTSKKQYHCDGCG 170 (190)
Q Consensus 135 ~~C~nCg~~FnkYfC~~Ckl~dd--d~~K~~yHC~~CG 170 (190)
-.||+||+.+---|=. -.|+. .+....|.|+.||
T Consensus 201 vpCPhCg~~~~l~~~~--l~w~~~~~~~~a~y~C~~Cg 236 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWEN--LKWDKGEAPETARYVCPHCG 236 (557)
T ss_pred ccCCCCCCCccccccc--eeecCCCCccceEEECCCCc
Confidence 4677776655433200 22343 3456789999998
No 157
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=20.21 E-value=96 Score=21.25 Aligned_cols=22 Identities=41% Similarity=0.943 Sum_probs=12.4
Q ss_pred ceEecCCCCccccccccccccc
Q 029670 120 NQVICSLCGTEQKVQQVCVNCG 141 (190)
Q Consensus 120 ~~ViCG~C~~eQ~~~~~C~nCg 141 (190)
..+.|..|+......-.|++||
T Consensus 25 ~l~~c~~cg~~~~~H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHRVCPSCG 46 (56)
T ss_dssp SEEESSSSSSEESTTSBCTTTB
T ss_pred ceeeeccCCCEecccEeeCCCC
Confidence 4566666665544445566655
No 158
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=20.05 E-value=72 Score=22.53 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=8.0
Q ss_pred CCCeeecCCCCc
Q 029670 160 SKKQYHCDGCGI 171 (190)
Q Consensus 160 ~K~~yHC~~CGI 171 (190)
....|-|+.|||
T Consensus 11 ~~v~~~Cp~cGi 22 (55)
T PF13824_consen 11 AHVNFECPDCGI 22 (55)
T ss_pred cccCCcCCCCCC
Confidence 445677777775
Done!